Search

Objective: To assess whether women with a genetic predisposition to medical conditions known to increase pre‐eclampsia risk have an increased risk of pre‐eclampsia in pregnancy. Design: Case–control study. Setting and population: Pre‐eclampsia cases (n = 498) and controls (n = 1864) in women of European ancestry from five US sites genotyped on a cardiovascular gene‐centric array. Methods: Significant single‐nucleotide polymorphisms (SNPs) from 21 traits in seven disease categories (cardiovascular, inflammatory/autoimmune, insulin resistance, liver, obesity, renal and thrombophilia) with published genome‐wide association studies (GWAS) were used to create a genetic instrument for each trait. Multivariable logistic regression was used to test the association of each continuous scaled genetic instrument with pre‐eclampsia. Odds of pre‐eclampsia were compared across quartiles of the genetic instrument and evaluated for significance. Main outcome measures: Genetic predisposition to medical conditions and relationship with pre‐eclampsia. Results: An increasing burden of risk alleles for elevated diastolic blood pressure (DBP) and increased body mass index (BMI) were associated with an increased risk of pre‐eclampsia (DBP, overall OR 1.11, 95% CI 1.01–1.21, P = 0.025; BMI, OR 1.10, 95% CI 1.00–1.20, P = 0.042), whereas alleles associated with elevated alkaline phosphatase (ALP) were protective (OR 0.89, 95% CI 0.82–0.97, P = 0.008), driven primarily by pleiotropic effects of variants in the FADS gene region. The effect of DBP genetic loci was even greater in early‐onset pre‐eclampsia cases (at <34 weeks of gestation, OR 1.30, 95% CI 1.08–1.56, P = 0.005). For other traits, there was no evidence of an association. Conclusions: These results suggest that the underlying genetic architecture of pre‐eclampsia may be shared with other disorders, specifically hypertension and obesity. A genetic predisposition to increased diastolic blood pressure and obesity increases the risk of pre‐eclampsia. A genetic predisposition to increased diastolic blood pressure and obesity increases the risk of pre‐eclampsia. [ABSTRACT FROM AUTHOR]

Objectives: Nonsyndromic orofacial clefts (OFCs) etiology involves multiple genetic and environmental factors with over 60 identified risk loci; however, they account for only a minority of the estimated risk. Epigenetic factors such as differential DNA methylation (DNAm) are also associated with OFCs risk and can alter risk for different cleft types and modify OFCs penetrance. DNAm is a covalent addition of a methyl (CH3) group to the nucleotide cytosine that can lead to changes in expression of the targeted gene. DNAm can be affected by environmental influences and genetic variation via methylation quantitative loci (meQTLs). We hypothesize that aberrant DNAm and the resulting alterations in gene expression play a key role in the etiology of OFCs, and that certain common genetic variants that affect OFCs risk do so by influencing DNAm., Methods: We used genotype from 10 cleft-associated SNPs and genome-wide DNA methylation data (Illumina 450K array) for 409 cases with OFCs and 456 controls and identified 23 cleft-associated meQTLs. We then used an independent cohort of 362 cleft-discordant sib pairs for replication. We used methylation-specific qPCR to measure methylation levels of each CpG site and combined genotypic and methylation data for an interaction analysis of each SNP-CpG pair using the R package MatrixeQTL in a linear model. We also performed a Paired T-test to analyze differences in DNA methylation between each member of the sibling pairs., Results: We replicated 9 meQTLs, showing interactions between rs13041247 ( MAFB ) - cg18347630 ( PLCG1 ) (P=0.04); rs227731 ( NOG ) - cg08592707 (PPM1E) (P=0.01); rs227731 ( NOG ) - cg10303698 ( CUEDC1 ) (P=0.001); rs3758249 ( FOXE1 ) - cg20308679 ( FRZB ) (P=0.04); rs8001641 ( SPRY2 ) - cg19191560 ( LGR4 ) (P=0.04); rs987525(8q24) - cg16561172( MYC ) (P=0.00000963); rs7590268( THADA ) - cg06873343 ( TTYH3 ) (P=0.04); rs7078160 ( VAX1 ) - cg09487139 (P=0.05); rs560426 ( ABCA4/ARHGAP29 ) - cg25196715 ( ABCA4/ARHGAP29 ) (P=0,03). Paired T-test showed significant differences for cg06873343 ( TTYH3 ) (P=0.04); cg17103269 ( LPIN3 ) (P=0.002), and cg19191560 ( LGR4 ) (P=0.05)., Conclusions: Our results confirm previous evidence that some of the common non-coding variants detected through GWAS studies can influence the risk of OFCs via epigenetic mechanisms, such as DNAm, which can ultimately affect and regulate gene expression. Given the large prevalence of non-coding SNPs in most OFCs genome wide association studies, our findings can potentially address major knowledge gaps, like missing heritability, reduced penetrance, and variable expressivity associated with OFCs phenotypes.

Background: The use of real-world data is increasing to examine immune-related adverse event (irAE) incidence and risk factors in immune checkpoint inhibitor (ICI) users. We aimed to validate five case definition algorithms for irAE in a Johns Hopkins lung cancer registry., Methods: We conducted a retrospective cohort study using linked electronic health record (EHR) and cancer registry data from a large academic healthcare system. The Lung Immunotherapy irAE Monitoring Registry assesses irAEs in a group of patients treated for lung cancer at Johns Hopkins Medicine from 2013 to 2020. We used data from inpatient, outpatient, and emergency department encounters, including International Classification of Disease (ICD)-10 codes and medication administration records to classify the presence or absence of irAEs using five distinct algorithms. These algorithms included three that used both diagnosis (Dx) and medication (Rx) codes, one that used Rx codes only, and one that used Dx codes only, ranging from most numerous criteria (most stringent) to least numerous criteria (least stringent). We compared all five algorithms' performances against chart review-ascertained irAE status and reported sensitivity (Se), specificity (Sp), positive predictive value (PPV), negative predictive value (NPV), and C-statistic (C-stat), with 95% confidence intervals (CI). We also explored algorithm performance by specific organ system toxicities and by Common Terminology Criteria for Adverse Events (CTCAE) severity., Results: The study cohort included 354 patients with ICI exposure for whom chart review-ascertained irAE status was available. A total of 89 (25.1%) experienced at least one irAE (38 pneumonitis, 12 arthritis, 12 colitis, 7 thyroiditis, and others). Across algorithm versions, Se ranged from 59.3% to 93.2% in descending order of algorithm stringency; Sp ranged from 21.0% to 77.6% in ascending order of algorithm stringency, and PPV ranged from 19.1% to 34.7%. The C-stat ranged from 0.57 (95% CI, 0.53-0.61) (Dx codes only) to 0.71 (0.64-0.77) (Rx codes only). For severe irAE (CTCAE Grade 3-5), all algorithms performed better than in the primary analysis, and four exceeded the threshold for usefulness as a measurement tool (maximum C-stat: 0.78 [0.71-0.85] [Rx codes only]). For severe tissue-specific toxicities, algorithmic detection of irAE pneumonitis, colitis, and hepatitis performed better than for the overall group of severe toxicities. Generally, the algorithm versions depicted a Se-Sp tradeoff depending on algorithm stringency., Conclusion: In this validation study of five irAE case definition algorithms, a combination of ICD-10 codes and medication administration codes generally perform well to identify more severe irAE (CTCAE Grade 3-5), and severe pneumonitis, hepatitis, and colitis (common irAEs) among all possible irAE severity levels and sites. Medication codes alone perform well at identifying severe irAE, while the most stringent algorithm (mirroring guideline-recommended irAE treatment) has the highest Sp and PPV. Algorithms have utility for comparing the relative risk of irAE between regimens or patient subgroups., (© 2025 John Wiley & Sons Ltd.)

Objective: Oculoauriculovertebral spectrum (OAVS) encompasses abnormalities on derivatives from the first and second pharyngeal arches including macrostomia, hemifacial microsomia, micrognathia, preauricular tags, ocular, and vertebral anomalies. We present genetic findings on a 3-generation family affected with macrostomia, preauricular tags and ptosis following an autosomal dominant pattern., Design: We generated whole-genome sequencing data for the proband, affected father, and unaffected paternal grandmother followed by Sanger sequencing on 23 family members for the top candidate gene mutations. We performed parent and sibling-based transmission disequilibrium tests (TDTs) and burden analysis via a penalized linear mixed model, for segregation and mutation burden, respectively. Next, via bioinformatic tools we predicted protein function, mutation pathogenicity, and pathway enrichment to investigate the biological relevance of mutations identified., Results: Rare missense mutations in SIX1 , KDR/VEGFR2 , and PDGFRA showed the best segregation with the OAVS phenotypes in this family. When considering any of the 3 OAVS phenotypes as an outcome, SIX1 had the strongest associations in parent-TDTs and sib-TDTs ( P  = 0.025, P  = 0.052) (unadjusted P -values). Burden analysis identified SIX1 (RC = 0.87) and PDGFRA (RC = 0.98) strongly associated with OAVS severity. Using phenotype-specific outcomes, sib-TDTs identified SIX1 with uni- or bilateral ptosis ( P  = 0.049) and ear tags ( P  = 0.01), and PDGFRA and KDR/VEGFR2 with ear tags (both P  < 0.01)., Conclusion: SIX1 , PDGFRA , and KDR/VEGFR2 are strongly associated to OAVS phenotypes. SIX1 has been previously associated with OAVS ear malformations and is co-expressed with EYA1 during ear development. Efforts to strengthen the genotype-phenotype co-relation underlying the OAVS are key to discover etiology, family counseling, and prevention., Competing Interests: Declaration of Conflicting InterestsThe authors declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

Van der Woude syndrome (VWS) is an autosomal dominant disorder characterized by lower lip pits and orofacial clefts (OFCs). With a prevalence of approximately 1 in 35,000 live births, it is the most common form of syndromic clefting and may account for ~2% of all OFCs. The majority of VWS is attributed to genetic variants in IRF6 (~70%) or GRHL3 (~5%), leaving up to 25% of individuals with VWS without a molecular diagnosis. Both IRF6 and GRHL3 function in a transcriptional regulatory network governing differentiation of periderm, a single layer of epithelial cells that prevents pathological adhesions during palatogenesis. Disruption of this layer results in a spectrum of phenotypes ranging from lip pits and OFCs to severe pterygia and other congenital anomalies that can be incompatible with life. Understanding the mechanisms of peridermopathies is vital in improving health outcomes for affected individuals. We reasoned that genes encoding additional members of the periderm gene regulatory network, including kinases acting upstream of IRF6 (i.e., atypical protein kinase C family members, RIPK4, and CHUK), are candidates to harbor variants resulting in VWS. Consistent with this prediction, we identified 6 de novo variants (DNs) and 11 rare variants in PRKCI , an atypical protein kinase C, in 17 individuals with clinical features consistent with syndromic OFCs and peridermopathies. Of the identified DNs, 4 were identical p.(Asn383Ser) variants in unrelated individuals with syndromic OFCs, indicating a likely hotspot mutation. We also performed functional validation of 12 variants using the enveloping layer in zebrafish embryos, a structure analogous to the periderm. Three patient-specific alleles (p.Arg130His, p.(Asn383Ser), and p.Leu385Phe) were confirmed to be loss-of-function variants. In summary, we identified PRKCI as a novel causal gene for VWS and syndromic OFC with other features of peridermopathies., Competing Interests: Declaration of interests The authors declare no competing interests.

Background: Prenatally transmitted viruses can cause severe damage to the developing brain. There is unexplained variability in prenatal brain injury and postnatal neurodevelopmental outcomes, suggesting disease modifiers. Of note, prenatal Zika infection can cause a spectrum of neurodevelopmental disorders, including congenital Zika syndrome. Currently, there is no preventative treatment or cure. The Prenatal Infection and Neurodevelopmental Genetics (PING) Consortium aims to identify modulators of brain injury and adverse neurodevelopmental outcomes for Zika and other prenatal viral infections., Methods: The Consortium pools information from eight multi-site studies conducted at 23 research centers in six countries to build a growing clinical and genomic repository, which is being mined for modifiers of virally induced brain injury. Partners include Children's National Hospital (USA), Instituto Nacional de Salud (Colombia), the Natural History of Zika Virus Infection in Gestation program (Brazil), Zika Instituto Fernandes Figueira (Brazil), the Centers for Disease Control and Prevention, and the National Institutes of Health., Results: We have enrolled 4102 mothers and 3877 infants with 3063 biological samples and clinical data covering over 80 phenotypic fields and 5000 variables. Thus far, we have performed whole exome sequencing on 1226 participants., Conclusion: Here, we present the Consortium's formation and overarching study design., Impact: The PING Consortium brings together investigators and institutions to determine the causes of virally induced brain injury and neurological deficits. The clinical and genomic repository, with data from over 8000 patients, will serve as a foundation for a variety of basic and clinical studies., Competing Interests: Competing interests: The authors declare no competing interests. Ethics approval and consent statement: Samples and associated data collected through the Prenatal Infection and Neurodevelopmental Genetics Consortium were IRB approved by participating institutions and by Children’s National Hospital (IRB reference number 8259). Any changes to the protocol or materials are submitted for approval by the IRB/CEP before being implemented, through amendments to the project. The research team notifies the IRB/CEP of deviations from the protocol or any adverse events that might be related to the present study. Brazilian studies were also approved by CONEP (approval numbers of the original related projects: CAAEs: 61936216.9.0000.5404; 56673616.3.2002.5440; 61936216.9.0000.5404). The researchers ensured that this study was conducted in full compliance with the principles set out in the Belmont Report: Ethical Principles and Guidelines for the Protection of Human Subjects in Research by the US National Commission for the Protection of Human Subjects in Biomedical and Behavioral Research (18 April 1979) and encoded in 45 CFR Section 46 or the ICH E6; 62 Federal Regulations 25691 (1997). The Investigators’ institution must maintain an up-to-date, federal-level policy (FWA) issued by the Office of Human Protection in Research for US government-funded research. Both multi-center and site-specific IRB approvals were obtained in one of in two ways. A majority of the studies obtained informed consent for genetic testing prospectively. In some cases, informed consent was obtained retrospectively., (© 2025. The Author(s).)

Folliculitis decalvans (FD) is a chronic inflammatory alopecia characterized by painful, scarring lesions and recurrent flares, often complicated by secondary bacterial infections. Despite the use of topical and systemic anti-inflammatory or antimicrobial therapies, FD remains challenging to manage, with limited therapeutic advancements. We report a case of recalcitrant FD in a man in his 40s who experienced significant symptom improvement and hair regrowth following the initiation of tirzepatide for weight management. This case highlights a previously unreported therapeutic benefit of tirzepatide in FD, potentially mediated through its anti-inflammatory and immunomodulatory effects. As glucagon-like peptide 1 (GLP-1) receptor agonists gain recognition for their efficacy in other inflammatory skin conditions, such as psoriasis and hidradenitis suppurativa, this case supports further exploration of their role in managing FD and other refractory dermatologic diseases., Competing Interests: Human subjects: Consent for treatment and open access publication was obtained or waived by all participants in this study. Conflicts of interest: In compliance with the ICMJE uniform disclosure form, all authors declare the following: Payment/services info: All authors have declared that no financial support was received from any organization for the submitted work. Financial relationships: All authors have declared that they have no financial relationships at present or within the previous three years with any organizations that might have an interest in the submitted work. Other relationships: All authors have declared that there are no other relationships or activities that could appear to have influenced the submitted work., (Copyright © 2024, Morrissette et al.)

Maternal exposures are known to influence the risk of isolated cleft lip with or without cleft palate (CL/P) - a common and highly heritable birth defect with a multifactorial etiology. To identify new CL/P risk loci, we conducted a genome-wide gene-environment interaction (GEI) analysis of CL/P on a sample of 540 cases and 260 controls recruited from the Philippines, incorporating the interaction effects of genetic variants with maternal smoking and vitamin use. As GEI analyses are typically low in power and the results can be difficult to interpret, we used multiple testing frameworks to evaluate potential GEI effects: 1 degree-of-freedom (1df) GxE test, the 3df joint test, and the two-step EDGE approach. While we did not detect any genome-wide significant interactions, we detected 12 suggestive GEI with smoking and 25 suggestive GEI with vitamin use between all testing frameworks. Several of these loci showed biological plausibility. Notable interactions with smoking include loci near FEZF1 , TWIST2, and NET1. While FEZF1 is involved in early neuronal development, TWIST2 and NET1 regulate epithelial-mesenchymal transition which is required for proper lip and palate fusion. Interactions with vitamins encompass CECR2 - a chromatin remodeling protein required for neural tube closure-and FURIN, a critical protease during early embryogenesis that activates various growth factor and extracellular-matrix protein. The activity of both proteins is influenced by folic acid. Our findings highlight the critical role of maternal exposures in identifying genes associated with structural birth defects such as CL/P and provide new paths to explore for CL/P genetics.

Non-syndromic orofacial clefts (NSOC) are common craniofacial birth defects, and result from both genetic and environmental factors. NSOC include three major sub-phenotypes: non-syndromic cleft lip with palate (NSCLP), non-syndromic cleft lip only (NSCLO) and non-syndromic cleft palate only (NSCPO), NSCLP and NSCLO are also sometimes grouped as non-syndromic cleft lip with or without cleft palate (NSCL/P) based on epidemiology. Currently known loci only explain a limited proportion of the heritability of NSOC. Further, differences in genetic susceptibility among the sub-phenotypes are poorly characterized. We performed a multi-ancestry GWAS meta-analysis on 44,094 individuals (9,381 cases, 28,510 controls, 2042 case-parent trios and 18 multiplex pedigrees) of East Asian, European, Latin and South American, and African ancestry for both NSOC and subtypes. We identified 50 loci, including 11 novel loci: four loci ( CALD1 , SHH , NRG1 and LINC00320 ) associated with both NSOC and NSCL/P, two loci ( NTRK1 and RUNX1 ) only associated with NSOC, four loci ( HMGCR , PRICKLE1 , SOX9 and MYH9 ) only associated with NSCL/P and one locus ( ALX1 ) specifically associated with NSCLO. Five of the novel loci are located in regions containing genes associated with syndromic orofacial clefts ( SHH , NTRK1, CALD1, ALX1 and SOX9 ); seven of the novel loci are located in regions containing genes-implicated in craniofacial development ( HMGCR, SHH, PRICKLE1, ALX1, SOX9, RUNX1, MYH9 ). Genetic correlation and colocalization analyses revealed an overlap between signals associated with NSCLO, NSCPO and NSCLP, but there were also notable differences, emphasizing the complexity of common and distinct genetic processes affecting lip and palate development.

Background and Objectives: Immune checkpoint inhibitors (ICIs) are increasingly used against various cancers but are associated with immune-related adverse events (irAEs). Risk of irAEs may be higher in patients with certain preexisting autoimmune diseases, and these patients may also experience exacerbation of the underlying autoimmune disease following ICI initiation. People with multiple sclerosis (MS) have mostly been excluded from clinical trials of ICIs, so data on the safety of ICIs in MS are limited. This study aims to assess the rate of MS activity, as well as neurologic and nonneurologic irAEs in persons with MS treated with ICIs for cancer., Methods: Participating sites were invited to this retrospective observational study through the Medical Partnership 4 MS+ listserv. Seven large academic centers participated in the study, each conducting a systematic search of their electronic medical record system for patients with MS and history of ICI treatment. The participating neurologist reviewed each chart individually to ensure the inclusion criteria were met. Demographics and data on MS and cancer history, treatments, and outcomes were abstracted from patient charts using a structured instrument., Results: We identified 66 people with MS (median age 66 years, 73% female, 68% not on disease-modifying therapy for MS) who were treated with ICIs for lung cancer (35%), melanoma (21%), or another oncologic indication. During post-ICI follow-up (median: 11.7 months, range 0.2-106.3 months), 2 patients (3%) had relapse or MRI activity, 3 (5%) had neurologic irAEs, and 21 (32%) had nonneurologic irAEs. At the last follow-up, 25 (38%) participants had partial or complete remission of their cancer, while 35 (53%) were deceased., Discussion: In this multi-institutional systematic retrospective study of predominantly older patients with MS, most of whom were not on disease-modifying therapy, MS activity and neurologic irAEs following ICI treatment were rare. These data suggest that preexisting MS should not preclude the use of ICIs for cancer in older patients, but the results may not be generalizable to younger patients with active MS. Prospective studies of ICI safety that enroll younger patients with MS are needed.

For patients with advanced non-small-cell lung cancer (NSCLC), dual immune checkpoint blockade (ICB) with CTLA4 inhibitors and PD-1 or PD-L1 inhibitors (hereafter, PD-(L)1 inhibitors) is associated with higher rates of anti-tumour activity and immune-related toxicities, when compared with treatment with PD-(L)1 inhibitors alone. However, there are currently no validated biomarkers to identify which patients will benefit from dual ICB 1,2 . Here we show that patients with NSCLC who have mutations in the STK11 and/or KEAP1 tumour suppressor genes derived clinical benefit from dual ICB with the PD-L1 inhibitor durvalumab and the CTLA4 inhibitor tremelimumab, but not from durvalumab alone, when added to chemotherapy in the randomized phase III POSEIDON trial 3 . Unbiased genetic screens identified loss of both of these tumour suppressor genes as independent drivers of resistance to PD-(L)1 inhibition, and showed that loss of Keap1 was the strongest genomic predictor of dual ICB efficacy-a finding that was confirmed in several mouse models of Kras-driven NSCLC. In both mouse models and patients, KEAP1 and STK11 alterations were associated with an adverse tumour microenvironment, which was characterized by a preponderance of suppressive myeloid cells and the depletion of CD8 + cytotoxic T cells, but relative sparing of CD4 + effector subsets. Dual ICB potently engaged CD4 + effector cells and reprogrammed the tumour myeloid cell compartment towards inducible nitric oxide synthase (iNOS)-expressing tumoricidal phenotypes that-together with CD4 + and CD8 + T cells-contributed to anti-tumour efficacy. These data support the use of chemo-immunotherapy with dual ICB to mitigate resistance to PD-(L)1 inhibition in patients with NSCLC who have STK11 and/or KEAP1 alterations., Competing Interests: Competing interests F.S. reports consulting for AstraZeneca, Amgen, Revolution Medicines, Novartis, BridgeBio, Beigene, BergenBio, Guardant Health, Calithera Biosciences, Tango Therapeutics, Hookipa Pharma, Novocure, Merck Sharp & Dohme, Roche; grant or research support from Amgen, Mirati Therapeutics, Revolution Medicines, Pfizer, Novartis, Merck & Co; stockholder in BioNTech, Moderna; and honoraria from ESMO, Japanese Lung Cancer Society, Medscape, Intellisphere, VSPO McGill Universite de Montreal, RV Mais Promocao Eventos, MJH Life Sciences, IDEOlogy Health, MI&T, PER, CURIO, DAVA Oncology, the American Association for Cancer Research and the International Association for the Study of Lung Cancer. M.M. reports stockholder in Roche Holdings. N.J. reports shareholder and former employee of Pionyr Immunotherapeutics. J.M.J. reports stock of D2G Oncology. C.M., Y.Y., X.P. and A.H. report employee of Tango Therapeutics. K.C.A. reports personal fees from Sanofi Genzyme and other support from Revolution Medicines, Genentech, and Mirati outside the submitted work. N.V. receives consulting fees from Sanofi Genzyme, Oncocyte, Eli Lilly, Regeneron, and research funding to the institution from Mirati, Oncocyte, and Circulogene, outside the submitted work. P.D.P. reports advisory fees from AstraZeneca and Jazz Pharmaceuticals. M.E.M. reports research funding from Eli Lilly (Inst), AstraZeneca (Inst), Merck (Inst), Genentech (Inst); consulting role with AstraZeneca, Novocure, Boehringer Ingelheim, Janssen, Takeda, Blueprint Pharmaceuticals, Bayer, Bristol Myers Squibb, Ikena; honorarium from Thermo Fisher Scientific; and stock in Merck, Johnson & Johnson. M.M.A. reports grants and personal fees from Genentech, Bristol Myers Squibb and AstraZeneca; grants from Lilly; and personal fees from Maverick, Blueprint Medicine, Syndax, Nektar, Gritstone, ArcherDX, Mirati, NextCure, Novartis, EMD Serono and Panvaxal/NovaRX, outside of the submitted work. J.C.M. reports consulting or honoraria: MJH Life Sciences, Johnson & Johnson and Doximity; and research funding (to institution): Merck via the Conquer Cancer Foundation. J.F.G. reports served as a compensated consultant or received honoraria from Bristol Myers Squibb, Genentech (Roche), Takeda, Loxo (Lilly), Blueprint Medicine, Gilead, Moderna, AstraZeneca, Mariana Therapeutics, Mirati, Jounce, Merus Pharmacueticals, Nuvalent, Pfizer, Novocure, AI Proteins, Novartis, Merck, iTeos, Karyopharm and Silverback Therapeutics; research support from Novartis, Genentech (Roche) and Takeda; institutional research support from Bristol Myers Squibb, Palleon, Tesaro, Moderna, Blueprint, Jounce, Array Biopharma, Merck, Adaptimmune, Novartis and Alexo; has equity in AI Proteins; and has an immediate family member who is an employee with equity at Ironwood Pharmaceuticals. A.D. reports honoraria: Intellisphere, Roche (Genentech); ad board: TP Therapeutics, Guardant Health, AnHeart Therapeutics, ChromaCode; clinical trial support: Syntrix Pharmaceuticals, Novartis, Merck, AnHeart Therapeutics, Sorrento Therapeutics, Guardant Health and Philogen. C. M. Bestvina reports consulting or advisory role: AstraZeneca, Genentech, AbbVie, Curio Science, OncLive Clinical Congress Consultants, Seagen, Creative Educational Concepts, Takeda, Janssen, CVS, Bristol Myers Squibb (Celgene), Jazz Pharmaceuticals, Novartis, Sanofi–Regeneron and Novocure; speakers’ bureau: Merck; research funding: Bristol Myers Squibb and AstraZeneca. C.A.S. reports advisory boards to AstraZeneca, Gilead, Janssen, Genentech, Mirati, Takeda and Arcus Biosciences. J.W.R. reports honoraria or consulting (self): Boehringer Ingelheim, BMS, Turning Point Roche (Genentech), Biodesix, EMD Serono, Daiichi Sankyo, Blueprint, Novartis, Regeneron, Sanofi, Janssen, Jazz Pharmaceuticals, Bayer, Beigene, Merus and Seagen; research support (to institution): ArriVent, Merck, Novartis, AstraZeneca, Spectrum, Revolution Medicines, IO Biotech and Kinnate. C. M. Blakely reports research funding: AstraZeneca, Novartis, Mirati, Spectrum, Takeda, Puma and Pfizer; and consulting: Janssen and Bayer. C.V.P. reports a founder and equity and intellectual property in EnFuego Therapeutics. F.T. reports speaker bureau or honoraria: Roche, AstraZeneca, Novartis and Takeda. M.S. reports institutional support: Dracen Pharmaceuticals; advisory board: Amgen, AstraZeneca, Boehringer Ingelheim, Janssen Pharmaceuticals, Novartis, Pfizer, Roche, Sanofi-Aventis, Siemens Healthineers, Takeda Pharmaceuticals and Bristol Myers Squibb; leadership or fiduciary role: ESMO and EORTC. S.D. reports independent image analysis for hospital-contracted clinical research trials programs for Merck, Pfizer, Bristol Myers Squibb, Novartis, Roche, Polaris, Cascadian, Abbvie, Gradalis, Bayer, Zai laboratories, Biengen, Resonance and Analise; research grants from Lunit, GE, Qure AI; and an honorarium from Siemens. M.J.M. reports AstraZeneca, Bristol Myers Squibb and Istari Oncology & Regeneron. A.G.S. reports AstraZeneca, Genentech (Roche) and Bristol Myers Squibb. A.N.S. reports serving as a consultant and/or advisory board member for Eli Lilly, Daiichi Sankyo and Zymeworks; and research funding from Eli Lilly, Novartis, Daiichi Sankyo, Genentech, AstraZeneca, Memgen, Mersana, Turning Point Therapeutics, BioAtla and Genmab to his institution. J.R. reports consulting fees or honoraria from AstraZeneca, Takeda, Sanofi Genzyme, Genentech, Guardant Health, Summit, G1 Therapeutics, BioAtla, Jazz, Amgen, and Janssen; contracted for research (institutional) with AstraZeneca, BioAtla, Blueprint Medicines, EpimAb Biotherapeutics, LOXO Oncology, Enliven, Redcloud and ORIC. T.S. reports advisory board or consulting fees for Seagen, Astellas and AstraZeneca; and research grant GRAIL. S.B.G. reports research funding from AstraZeneca, Boehringer Ingelheim and Mirati; and consulting or advisory board member for AstraZeneca, Boehringer Ingelheim, Bristol Myers Squibb, Genentech, Amgen, Blueprint Medicine, Sanofi Genzyme, Daiichi Sankyo, Takeda, Janssen, Summit Therapeutics, Merck and Regeneron. J.K. reports for Arterys. K.S. reports consultant, advisor or speaker for Clinica Alemana Santiago, Shattuck Labs, AstraZeneca, EMD Serono, Takeda, Torque/Repertoire Therapeutics, CSRlife, Agenus, Genmab, OnCusp, Parthenon Therapeutics, Bristol Myers Squibb, Roche, Molecular Templates, Abbvie, Sanofi, Merck, PeerView, PER and Forefront Collaborative; research funding from Navigate BP, Tesaro/GSK, Moderna, Takeda, Surface Oncology, Pierre-Fabre, Merck, Bristol Myers Squibb, AstraZeneca, Ribon Therapeutics, Eli Lilly, Boehringer Ingelheim, Genentech (Roche) and Akoya Biosciences. K.D.D. reports consulting fees or other remuneration from Rain Therapeutics. V.A. reports research funding to Johns Hopkins University from AstraZeneca and Personal Genome Diagnostics, has received research funding to Johns Hopkins University from Bristol Myers Squibb and Delfi Diagnostics in the past five years and is an advisory board member for Neogenomics and AstraZeneca. V.A. is an inventor on patent applications (63/276,525, 17/779,936, 16/312,152, 16/341,862, 17/047,006 and 17/598,690) submitted by Johns Hopkins University related to cancer genomic analyses, ctDNA therapeutic response monitoring and immunogenomic features of response to immunotherapy that have been licensed to one or more entities. Under the terms of these license agreements, the University and inventors are entitled to fees and royalty distributions. K.A.M. reports consulting or advisory fees from AstraZeneca, Amgen, Janssen, Mirati Therapeutics, Daiichi Sankyo (Lilly) and Puma Biotechnology, as well as honoraria from AstraZeneca. K.A.M. receives research funding to Johns Hopkins University from Bristol Myers Squibb and Mirati Therapeutics. P.M.F. reports consulting fee (for example, advisory board): Ascendis, AstraZeneca, BMS, Curevac, Novartis, Regeneron, G1, Genelux, Genentech, Gritstone, Merck, Janssen, F-Star, Sanofi, Amgen, Fosun, Teva, Synthekine, Flame, Iteos, Tavotek and Teva; contracted research: AstraZeneca, BMS, Novartis, Regeneron and BioNTech. B.R. reports advisory board or consultant: Regeneron, AstraZeneca, Amgen; honoraria: Targeted Oncology. E.M.V.A reports advisory or consulting: Tango Therapeutics, Genome Medical, Genomic Life, Enara Bio, Manifold Bio, Monte Rosa, Novartis Institute for Biomedical Research, Riva Therapeutics and Serinus Bio; research support: Novartis, BMS and Sanofi; equity: Tango Therapeutics, Genome Medical, Genomic Life, Syapse, Enara Bio, Manifold Bio, Microsoft, Monte Rosa, Riva Therapeutics and Serinus Bio; patents: institutional patents filed on chromatin mutations and immunotherapy response, and methods for clinical interpretation; intermittent legal consulting on patents for Foaley & Hoag; editorial boards: JCO Precision Oncology and Science Advances. A.L.C. reports consulting for AstraZeneca, Merus and Tempus; research funds from AstraZeneca, Genentech (Roche), Merck and Novartis. J.W.G. reports research grants: AstraZeneca, BMS, Eli Lilly, Genentech, Merck and Pfizer; consulting fees: AstraZeneca, BMS, Genentech, Gilead, Gritstone, Eli Lilly, Pfizer and Regeneron. C.A. reports consulting or advisory role: Genentech, Lilly, Celgene, Merck, AstraZeneca, Blueprint Genetics, Shionogi, Daiichi Sankyo–AstraZeneca, Sanofi/Regeneron, Eisai, BeiGene, Turning Point Therapeutics, Pfizer, Janssen, Boehringer Ingelheim; research funding: Genentech/Roche (Inst), Incyte (Inst), Macrogenics (Inst), Merck Sharp & Dohme (Inst) and AstraZeneca–MedImmune (Inst). L.R. reports honoraria: Merck, AstraZeneca, Genzyme, EMD Serono and Astellas Pharmas; consulting or advisory role: Amgen. J.W.N. reports honoraria: CME Matters, Clinical Care Options CME, Research to Practice CME, Medscape CME, Biomedical Learning Institute CME, MLI Peerview CME, Prime Oncology CME, Projects in Knowledge CME, Rockpointe CME, MJH Life Sciences CME, Medical Educator Consortium, HMP education consulting or advisory role: AstraZeneca, Genentech (Roche), Exelixis, Takeda Pharmaceuticals, Eli Lilly, Amgen, Iovance Biotherapeutics, Blueprint Pharmaceuticals, Regeneron Pharmaceuticals, Natera, Sanofi, D2G Oncology, Surface Oncology, Turning Point Therapeutics, Mirati Therapeutics, Gilead Sciences, Abbive, Summit Therapeutics, Novartis, Novocure, Janssen Oncology, Anheart Therapeutics Research Funding: Genentech (Roche), Merck, Novartis, Boehringer Ingelheim, Exelixis, Nektart Therapeutics, Takeda Pharmaceuticals, Adaptimmune, GlaxoSmithKline, Janssen Pharmaceuticals, Abbvie Pharmaceuticals and Novocure. Y.Y.E. reports honoraria: CME Matters, Clinical Care Options CME, Research to Practice CME, Medscape CME, Biomedical Learning Institute CME, MLI Peerview CME, Prime Oncology CME, Projects in Knowledge CME, Rockpointe CME, MJH Life Sciences CME, Medical Educator Consortium, HMP education consulting or advisory role: AstraZeneca, Genentech (Roche), Exelixis, Takeda Pharmaceuticals, Eli Lilly, Amgen, Iovance Biotherapeutics, Blueprint Pharmaceuticals, Regeneron Pharmaceuticals, Natera, Sanofi, D2G Oncology, Surface Oncology, Turning Point Therapeutics, Mirati Therapeutics, Gilead Sciences, Abbive, Summit Therapeutics, Novartis, Novocure, Janssen Oncology, Anheart Therapeutics Reserach Funding: Genentech/Roche, Merck, Novartis, Boehringer Ingelheim, Exelixis, Nektart Therapeutics, Takeda Pharmaceuticals, Adaptimmune, GlaxoSmithKline, Janssen Pharmaceuticals, Abbvie Pharmaceuticals and Novocure. M.V.N. reports research funding to institution: Mirati, Novartis, Checkmate (ended), Alaunos, AstraZeneca, Pfizer, Genentech, Navire; consultant or advisory board: Mirati, Merck/MSD, Novartis and Genentech. X.L. reports receiving consulting or advisory fees from EMD Serono (Merck KGaA), AstraZeneca, Spectrum Pharmaceutics, Novartis, Eli Lilly, Boehringer Ingelheim, Hengrui Therapeutics, Janssen, Blueprint Medicines, Regeneron, Sensei Biotherapeutics, Abion and Abbvie, and research funding from Eli Lilly, EMD Serono, Janssen, ArriVent, Teligene, BlackDiamond, Regeneron and Boehringer Ingelheim. V.K.L. reports consultant or advisory role for Takeda, Seattle Genetics, BMS, AstraZeneca, Guardant Health and AnHeart Therapeutics and has received research funding from GSK, BMS, AstraZeneca, Merck and Seattle Genetics. W.E.L. reports advisory boards: Eisai and Takeda, Grand Rounds and BMS for repotrectinib. J.A.R. reports consultancy, stock, Genprex; patents issued and pending. T.C. reports speaker fees or honoraria from the Society for Immunotherapy of Cancer (SITC), Mark Foundation for Cancer Research, Bristol Myers Squibb, Roche, Medscape, IDEOlogy Health, Physicians’ Education Resource (PER), OncLive and PeerView; travel and/or food/beverage expenses from SITC, International Association for the Study of Lung Cancer, Parker Institute for Cancer Immunotherapy, PER, Dava Oncology, IDEOlogy Health, AstraZeneca and Bristol Myers Squibb; advisory role or consulting fees from MedImmune–AstraZeneca, Bristol Myers Squibb, Merck, Genentech, Arrowhead Pharmaceuticals, Pfizer and Regeneron; and institutional research funding from MedImmune–AstraZeneca, Bristol Myers Squibb and EMD Serono. J.Z. reports grants from Merck, grants and personal fees from Johnson & Johnson and Novartis, personal fees from Bristol Myers Squibb, AstraZeneca, GenePlus, Innovent and Hengrui outside the submitted work. G.R.B. reports grant or contract for clinical trial from MacroGenics; grants from Amgen, Bayer, Adaptimmune, Exelixis, Daiichi Sankyo, GlaxoSmithKline, Immatics, Immunocore, Incyte, Kite Pharma, MacroGenics, Torque, AstraZeneca, Bristol Myers Squibb, Celgene, Genentech, MedImmune, Merck, Novartis, Roche, Sanofi, Xcovery, Tmunity Therapeutics, Regeneron, BeiGene, Repertoire Immune Medicines, Verastem, CytomX Therapeutics and Duality Biologics; consulting fees from AbbVie, Adicet, Amgen, Ariad, Bayer, Clovis Oncology, AstraZeneca, Bristol Myers Squibb, Celgene, Daiichi Sankyo, Instil Bio, Genentech, Genzyme, Gilead, Eli Lilly, Janssen, MedImmune, Merck, Novartis, Roche, Sanofi, Tyme Oncology, Xcovery, Virogin Biotech, Maverick Therapeutics, BeiGene, Regeneron, Cytomx Therapeutics, Intervenn Biosciences and Onconova Therapeutics; participation in advisory boards at Virogin Biotech and Maverick Therapeutics; stock in Virogin Biotech; and employment of family member at Johnson & Johnson/Janssen. C.G. reports member of the advisory board at Jazz Pharmaceuticals, AstraZeneca and Bristol Myers Squibb and served as speaker for AstraZeneca and BeiGene. L.A.B. reports consulting fees and research funding from AstraZeneca, GenMab and Sierra Oncology and research funding from Tolero Pharmaceuticals and served as advisor or consultant for PharmaMar, AbbVie, Bristol Myers Squibb, Alethia, Merck, Pfizer, Jazz Pharmaceuticals, Genentech and Debiopharm Group. D.L.G. reports AstraZeneca, Eli Lilly, Menarini Richerche, 4D Pharma, Onconova Therapeutics and Sanofi. A.T. reports Ariad, AstraZeneca, Bristol Myers Squibb, Boehringer Ingelheim, Eli Lilly, EMD Serono, Genentech, GlaxoSmithKline, Merck, Novartis, Pfizer, Roche, Seattle Genetics, Gilead Sciences and Summit Therapeutics. T.G.B. reports Chan-Zuckerberg Biohub. D.R.C. reports CoI Company sponsored trials at institution (PI roles): AZ, Roche (Genentech) advisory role: ad hoc advisory boards or consultations 2023: Abbvie (steering committee), Anheart, Beigene (IDMC), Eli Lilly (IDMC), Imagene, Immunocore, Janssen, Mirati (IDMC), Prelude, Seattle Genetics, Valencee; 2022: Abbvie, Anheart, Appolomics (SRC), AstraZeneca–Daiichi (ILD adjudication committee), Beigene (DSMB) Dizal, EMD Serono, Elevation, Hengrui, (DSMB), Hummingbird, Janssen, Medtronic, Mersana (ILD adjudication committee), Mirati, Nalo Therapeutics, Onkure, Regeneron, Roche, Sanofi, Takeda, Theseus, Xcovery; 2021: Abbvie, Amgen, Anheart, Apollomics (SRC), AstraZeneca (SRC/SC), Beigene (DSMC), Bio-Thera (DSMB), Blueprint, Daiichi Sankyo (ILD adjudication committee), Elevation (SRC), Eli Lilly (DSMB and NCCN), EMD Serono, Helsinn (DSMB), Hengrui (DSMC), Janssen, Kestrel (SAB, Shares), Mersana, Nuvalent (SAB), Puma (NCCN), Ribon, Roche (Genentech), Sanofi, Seattle Genetics, Takeda and Turning Point. J.E.G. reports honoraria: Jazz Pharmaceuticals, Merck and OncoCyte; consulting or advisory role: AstraZeneca, Blueprint Medicines, Bristol Myers Squibb, EMD Serono, Lilly, Sanofi, Merck Sharp & Dohme, Loxo, Jazz Pharmaceuticals, Novartis, AstraZeneca–MedImmune, Janssen Scientific Affairs, National Comprehensive Cancer Network, AbbVie and Regeneron; research funding: Merck (Inst), AstraZeneca (Inst), Bristol Myers Squibb (Inst), Boehringer Ingelheim (Inst), Genentech (Roche) (Inst), G1 Therapeutics (Inst), Novartis (Inst), Pfizer (Inst), Ludwig Institute for Cancer Research (Inst), SWOG (Inst), Array BioPharma (Inst) and ECOG-ACRIN (Inst). N.L. reports CME and research funding: AstraZeneca. B.L. reports Genentech (Roche), Eli Lilly, Merck, Pfizer, Janssen, Daiichi Sankyo, Takeda, Mirati, Novartis and Guardant 360. J.R.B. reports grant funding: AstraZeneca; advisory board: AstraZeneca, Amgen, Novartis, Incyte, Bristol Myers Squibb, Genentech, Janssen, Sanofi, Regeneron, Merck, GlaxoSmithKline; DSMB: Sanofi, Janssen and GlaxoSmithKline. M.C.G. reports AstraZeneca, Abion, MSD International, Bayer, BMS, Boehringer Ingelheim Italia S.p.A, Celgene, Eli Lilly, Incyte, Novartis, Pfizer, Roche, Takeda, Seattle Genetics, Mirati, Daiichi Sankyo, Regeneron, Merck, Blueprint, Janssen, Sanofi, AbbVie, BeiGenius, Oncohost and Medscape. D.R.G. reports institutional research grants from Amgen, AstraZeneca, Genentech and Merck; consultant or advisory board for Adagene, AstraZeneca, Roche (Genentech), Guardant, IO Biotech, Oncocyte, OncoHost, Lilly, Merck and Novartis. E.B.G. reports consulting or advisory role: Novartis, GlaxoSmithKline, Merck, Boehringer Ingelheim, Shionogi, Eisai, Bristol Myers Squibb, ABL Bio, Xilio Therapeutics, Natera, Sanofi–Regeneron, Lilly, Personalis, Gilead Sciences, AstraZeneca, AbbVie–Abbott, Arcus Biosciences, Seagan and Summit Therapeutics; research funding: Merck (Inst), Genentech (Inst), AstraZeneca (Inst), Novartis (Inst), Lilly (Inst), Bristol Myers Squibb (Inst), Mirati Therapeutics (Inst), Dynavax Technologies (Inst), Iovance Biotherapeutics (Inst), Neon Therapeutics (Inst), EMD Serono (Inst), ABL Bio (Inst) and Daiichi Sankyo–UCB Japan (Inst); patents, royalties, other intellectual property: diagnosistic and therapeutic use of ‘Motif Neoepitopes’ as defined by Cummings et al.76. N.A.R. reports an employee at Synthekine and holds equity at Synthekine and Gritstone. G.V.S. reports honoraria, research funding and personal fees from AstraZeneca, Bayer, BeiGene Switzerland, F. Hoffman–La Roche, Merck Sharpe & Dohme, Eli Lilly, Johnson & Johnson, Pfizer, Takeda Oncology, Tesaro and Verastem outside the submitted work. J.W. reports advisory boards and lecture fees: Amgen, AstraZeneca, Bayer, Blueprint, BMS, Boehringer Ingelheim, Chugai, Daiichi Sankyo, Ignyta, Janssen, Lilly, Loxo, Merck, Mirati, MSD (Merck Sharp & Dohme), Novartis, Nuvalent, Pfizer, Roche, Seattle Genetics, Takeda and Turning Point; research support (to institution): BMS, Janssen, Novartis, Pfizer and AstraZeneca. B.B. reports receiving grants from AbbVie, Amgen, AstraZeneca, Chugai, Daiichi Sankyo, Ellipse, EISAI, Genmab, Genzyme Corporation, Hedera Dx, Inivata, IPSEN, Janssen, MSD, PharmaMar, Roche (Genentech), Sanofi, Socar Research, Tahio Oncology and Turning Point Therapeutics. R.S.H. reports consulting roles with AbbVie Pharmaceuticals, ARMO Biosciences, AstraZeneca, Biodesix, Bolt Biotherapeutics, Bristol Myers Squibb, Cybrexa Therapeutics, eFFECTOR Therapeutics, Eli Lilly, EMD Serono, Genentech (Roche), Genmab, Halozyme Therapeutics, Heat Biologics, I-Mab Biopharma, Immunocore, Infinity Pharmaceuticals, Loxo Oncology, Merck, Mirati Therapeutics, Nektar, Neon Therapeutics, NextCure, Novartis, Oncternal Therapeutics, Pfizer, Sanofi, Seattle Genetics, Shire, Spectrum Pharmaceuticals, STCube Pharmaceuticals, Symphogen, Takeda, Tesaro, Tocagen and WindMIL Therapeutics; advisory board roles with AstraZeneca, Bolt Biotherapeutics, Cybrexa Therapeutics, EMD Serono, I-Mab Biopharma, Immunocore, Infinity Pharmaceuticals, Neon Therapeutics, Novartis and STCube Pharmaceuticals; research support from AstraZeneca, Eli Lilly, Genentech (Roche) and Merck; and non-executive board membership for Junshi Pharmaceuticals and Immunocore. H.A.W. reports grants or contracts from any entity: Bayer, Arrys Therapeutics, AstraZeneca–Medimmune, BMS, Clovis Oncology, Genentech (Roche), Merck, Novartis, Seagen, Xcovery and Helsinn; advisory board: Mirati, Merck and Genentech (Roche); leadership: International Association for the Study of Lung Cancer (IASLC), President; ECOG-ACRIN, executive committee. N.A.P. reports an employee at Synthekine and holds equity at Synthekine and Gritstone. A.T.S. is currently an employee of Novartis. P.A.J. reports stock and other ownership interests: Gatekeeper Pharmaceuticals and Loxo; consulting or advisory role: Pfizer, Boehringer Ingelheim, AstraZeneca, Merrimack, Chugai, Roche (Genentech), Loxo, Mirati Therapeutics, Araxes Pharma, Ignyta, Lilly, Takeda, Novartis, Biocartis, Voronoi Health Analytics, SFJ Pharmaceuticals Group, Sanofi, Daiichi Sankyo, Silicon Therapeutics, Nuvalent, Eisai, Bayer, Syndax, AbbVie, Allorion Therapeutics, Accutar Biotech, Transcenta, Monte Rosa Therapeutics, Scorpion Therapeutics, Merus, Frontier Medicines, Hongyun Biotech and Duality Biologics; research funding: AstraZeneca (Inst), Astellas Pharma (Inst), Daiichi Sankyo (Inst), Lilly (Inst), Boehringer Ingelheim (Inst), Puma Biotechnology (Inst), Takeda (Inst) and Revolution Medicines (Inst); patents, royalties, other intellectual property: I am a co-inventor on a DFCI owned patent on EGFR mutations licensed to Lab Corp. I receive post-marketing royalties from this invention. D.P.C. reports advisory boards or consulting: Abbvie, Arcus Biosciences, AstraZeneca, BMS Israel, G1 Therapeutics, Genentech, GlaxoSmithKline, InThought, Iovance Biotherapeutics, Janssen, Jazz, JNJ, Merck–EMD Serono, Merck KGaA, Mirati, MSD, Novartis, Novocure, OncoHost, Pfizer Egypt, Regeneron, Roche and Sanofi; KOL/presentation/education/forum: AstraZeneca, Curio Science, Intellisphere, Merck US, OncLive, Pfizer, PPD Development and Roche Taiwan. M.D.H. is an employee of and stockholder in AstraZeneca. C.M.R. reports consulted regarding oncology drug development with AbbVie, Amgen, AstraZeneca, D2G, Daiichi Sankyo, Epizyme, Genentech (Roche), Ipsen, Jazz, Kowa, Lilly, Merck and Syros. He serves on the scientific advisory boards of Auron, Bridge Medicines, DISCO, Earli and Harpoon Therapeutics. L.A. is an employee of Foundation Medicine and a stockholder of Roche Holding AG. H.M. reports full-time employee of AstraZeneca and stock/shares. Z.Z. reports employee of AstraZeneca as well as stockholder of AstraZeneca and Pfizer. Z.L. reports full-time employee and stock owner of AstraZeneca. R.S. reports other support from AstraZeneca during the conduct of the study, as well as other support from Pfizer outside the submitted work. S.P. reports consultation or advisory role: AbbVie, Amgen, Arcus, AstraZeneca, Bayer, Beigene, BerGenBio, Biocartis, BioInvent, Blueprint Medicines, Boehringer Ingelheim, Bristol Myers Squibb, Clovis, Daiichi Sankyo, Debiopharm, Eli Lilly, F-Star, Fishawack, Foundation Medicine, Genzyme, Gilead, GSK, Hutchmed, Illumina, Incyte, Ipsen, iTeos, Janssen, Merck Sharp and Dohme, Merck Serono, Merrimack, Mirati, Nykode Therapeutics, Novartis, Novocure, PharmaMar, Promontory Therapeutics, Pfizer, Regeneron, Roche (Genentech), Sanofi, Seattle Genetics and Takeda; Board of Directors position: Galenica; talk in a company’s organized public event: AstraZeneca, Boehringer Ingelheim, Bristol Myers Squibb, Eli Lilly, Foundation Medicine, GSK, Illumina, Ipsen, Merck Sharp and Dohme, Mirati, Novartis, Pfizer, Roche (Genentech), Sanofi and Takeda; receipt of grants or research support: principal investigator in trials (institutional financial support for clinical trials) sponsored by Amgen, Arcus, AstraZeneca, Beigene, Bristol Myers Squibb, GSK, iTeos, Merck Sharp and Dohme, Mirati, PharmaMar, Promontory Therapeutics, Roche (Genentech) and Seattle Genetics. J.M.J. and M.J.R. are employees and shareholders of D2G Oncology. I.P.W. is a co-founder, employee and shareholder of D2G Oncology. M.M.W. is a co-founder, shareholder, member of the board of directors and compensated scientific advisor of D2G Oncology. I.P.W. and M.M.W. are co-inventors of patents relating to technologies for an autochthonous mouse model of human cancer, which D2G Oncology has exclusively licensed from Stanford University. V.A.P. reports Pfizer employee and stockholder. K.K.W. is a founder and equity holder of G1 Therapeutics and has sponsored research agreements with Takeda, TargImmune, Bristol Myers Squibb, Mirati, Merus and Alkermes, and consulting and sponsored research agreements with AstraZeneca, Janssen, Pfizer, Novartis, Merck, Zentalis, BridgeBio and Blueprint. P.J. reports employee and stock or stock options of AstraZeneca. I.I.W. reports honoraria from Genentech (Roche), Bayer, Bristol Myers Squibb, AstraZeneca, Pfizer, Merck, Guardant Health, Flame, Novartis, Sanofi, Daiichi Sankyo, Amgen, Janssen, Merus, G1 Therapeutics, Abbvie, Catalyst Therapeutics, Regeneron, Oncocyte, Medscape, Platform Health and Physicians’ Education Resources; research support from Genentech, Merck, Bristol Myers Squibb, Medimmune, Adaptive, Adaptimmune, EMD Serono, Pfizer, Takeda, Amgen, Karus, Johnson & Johnson, Bayer, Iovance, 4D, Novartis and Akoya. A.G.P. reports Pfizer. J.V.H. reports Advisory Committees: Genentech, Mirati Therapeutics, Eli Lilly, Janssen, Boehringer Ingelheim, Regeneron, Takeda, BerGenBio, Jazz, Curio Science, Novartis, AstraZeneca, BioAlta, Sanofi, Spectrum, GlaxoSmithKline, EMD Serono, BluePrint Medicine and Chugai; research support: AstraZeneca, Boehringer Ingelheim, Spectrum, Mirati, Bristol Myers Squibb and Takeda; licensing or royalties: Spectrum. H.A.A., M.T.D., A.G.C., Y.Q., R.P., D.M., D.H.O., R.M., J.A.H., L.M., S.C.M.L., R.P.J., C.L., Z.W., M.G.W., D.V., H.S., M.K., S.K., Y.N., J.T.A., J.S., L.L., H.N.K., B.C., S.S., R.L., T.Z., J.J.L., D.P., M.L.J. T.T., A.P., Y.K. and J.L.: no disclosures were reported by these authors., (© 2024. The Author(s).)

Structural birth defects affect 3-4% of all live births and, depending on the type, tend to manifest in a sex-biased manner. Orofacial clefts (OFCs) are the most common craniofacial structural birth defects and are often divided into cleft lip with or without cleft palate (CL/P) and cleft palate only (CP). Previous studies have found sex-specific risks for CL/P, but these risks have yet to be evaluated in CP. CL/P is more common in males and CP is more frequently observed in females, so we hypothesized there would also be sex-specific differences for CP. Using a trio-based cohort, we performed sex-stratified genome-wide association studies (GWAS) based on proband sex followed by a genome-wide gene-by-sex (G × S) interaction testing. There were 13 loci significant for G × S interactions, with the top finding in LTBP1 (RR = 3.37 [2.04-5.56], p = 1.93 × 10 -6 ). LTBP1 plays a role in regulating TGF-β bioavailability, and knockdown in both mice and zebrafish lead to craniofacial anomalies. Further, there is evidence for differential expression of LTBP1 between males and females in both mice and humans. Therefore, we tested the association between the imputed genetically regulated gene expression of genes with significant G × S interactions and the CP phenotype. We found significant association for LTBP1 in cell cultured fibroblasts in female probands (p = 0.0013) but not in males. Taken altogether, we show there are sex-specific risks for CP that are otherwise undetectable in a combined sex cohort, and LTBP1 is a candidate risk gene, particularly in females., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Nonsyndromic orofacial clefts (NSOFCs) represent a large proportion (70%-80%) of all OFCs. They can be broadly categorized into nonsyndromic cleft lip with or without cleft palate (NSCL/P) and nonsyndromic cleft palate only (NSCPO). Although NSCL/P and NSCPO are considered etiologically distinct, recent evidence suggests the presence of shared genetic risks. Thus, we investigated the genetic overlap between NSCL/P and NSCPO using African genome-wide association study (GWAS) data on NSOFCs. These data consist of 814 NSCL/P, 205 NSCPO cases, and 2159 unrelated controls. We generated common single-nucleotide variants (SNVs) association summary statistics separately for each phenotype (NSCL/P and NSCPO) under an additive genetic model. Subsequently, we employed the pleiotropic analysis under the composite null (PLACO) method to test for genetic overlap. Our analysis identified two loci with genome-wide significance (rs181737795 [p = 2.58E-08] and rs2221169 [p = 4.5E-08]) and one locus with marginal significance (rs187523265 [p = 5.22E-08]). Using mouse transcriptomics data and information from genetic phenotype databases, we identified MDN1, MAP3k7, KMT2A, ARCN1, and VADC2 as top candidate genes for the associated SNVs. These findings enhance our understanding of genetic variants associated with NSOFCs and identify potential candidate genes for further exploration., (© 2024 The Authors. Genetic Epidemiology published by Wiley Periodicals LLC.)

Non-syndromic orofacial clefts (NSOFCs) are common birth defects with a complex etiology. While over 60 common risk loci have been identified, they explain only a small proportion of the heritability for NSOFCs. Rare variants have been implicated in the missing heritability. Thus, our study aimed to identify genes enriched with nonsynonymous rare coding variants associated with NSOFCs. Our sample included 814 non-syndromic cleft lip with or without palate (NSCL/P), 205 non-syndromic cleft palate only (NSCPO), and 2150 unrelated control children from Nigeria, Ghana, and Ethiopia. We conducted a gene-based analysis separately for each phenotype using three rare-variants collapsing models: (1) protein-altering (PA), (2) missense variants only (MO); and (3) loss of function variants only (LOFO). Subsequently, we utilized relevant transcriptomics data to evaluate associated gene expression and examined their mutation constraint using the gnomeAD database. In total, 13 genes showed suggestive associations (p = E-04). Among them, eight genes (ABCB1, ALKBH8, CENPF, CSAD, EXPH5, PDZD8, SLC16A9, and TTC28) were consistently expressed in relevant mouse and human craniofacial tissues during the formation of the face, and three genes (ABCB1, TTC28, and PDZD8) showed statistically significant mutation constraint. These findings underscore the role of rare variants in identifying candidate genes for NSOFCs., (© 2024. The Author(s).)

Background: Prenatally transmitted viruses can cause severe damage to the developing brain. There is unexplained variability in prenatal brain injury and postnatal neurodevelopmental outcomes, suggesting disease modifiers. Discordant outcomes among dizygotic twins could be explained by genetic susceptibly or protection. Among several well-recognized threats to the developing brain, Zika is a mosquito-borne, positive-stranded RNA virus that was originally isolated in Uganda and spread to cause epidemics in Africa, Asia, and the Americas. In the Americas, the virus caused congenital Zika syndrome and a multitude of neurodevelopmental disorders. As of now, there is no preventative treatment or cure for the adverse outcomes caused by prenatal Zika infection. The Prenatal Infection and Neurodevelopmental Genetics (PING) Consortium was initiated in 2016 to identify factors modulating prenatal brain injury and postnatal neurodevelopmental outcomes for Zika and other prenatal viral infections., Methods: The Consortium has pooled information from eight multi-site studies conducted at 23 research centers in six countries to build a growing clinical and genomic data repository. This repository is being mined to search for modifiers of virally induced brain injury and developmental outcomes. Multilateral partnerships include commitments with Children's National Hospital (USA), Instituto Nacional de Salud (Colombia), the Natural History of Zika Virus Infection in Gestation program (Brazil), and Zika Instituto Fernandes Figueira (Brazil), in addition to the Centers for Disease Control and Prevention and the National Institutes of Health., Discussion: Our goal in bringing together these sets of patient data was to test the hypothesis that personal and populational genetic differences affect the severity of brain injury after a prenatal viral infection and modify neurodevelopmental outcomes. We have enrolled 4,102 mothers and 3,877 infants with 3,063 biological samples and clinical data covering over 80 phenotypic fields and 5,000 variables. There were several notable challenges in bringing together cohorts enrolled in different studies, including variability in the timepoints evaluated and the collected clinical data and biospecimens. Thus far, we have performed whole exome sequencing on 1,226 participants. Here, we present the Consortium's formation and the overarching study design. We began our investigation with prenatal Zika infection with the goal of applying this knowledge to other prenatal infections and exposures that can affect brain development.

Introduction: Up to 20% of EGFR-mutated NSCLC cases harbor uncommon EGFR mutations, including atypical exon 19 and compound mutations. Relatively little is known about the efficacy of osimertinib in these cases., Methods: Patients treated with first-line osimertinib for NSCLC with rare EGFR exon 19 (non E746&#95;A750del) or compound mutations were included. Response assessment and time to progression were determined using Response Evaluation Criteria in Solid Tumors version 1.1 criteria. Kaplan-Meier analyses were used to estimate progression-free survival (PFS), time to treatment discontinuation (TTD), and overall survival (OS)., Results: Thirty-seven patients with NSCLC harboring an atypical EGFR exon 19 mutation or compound mutation were treated with first-line osimertinib at Johns Hopkins from 2016 to 2021. Overall response rate (ORR) was 76% and median PFS, TTD, and OS were 13 months (95% confidence interval [CI]: 10-15), 22 months (95% CI: 17-32) and 36 months (95% CI, 29-48), respectively. Among atypical exon 19 mutations (n = 25), ORR was 80%, median PFS was 12 months (95% CI: 10-15), median TTD was 19 months (95% CI: 17-38), and median OS was 48 months (95% CI: 25-not reached). Compound mutations (n = 12) had an ORR of 67%, median PFS of 14 months (95% CI: 5-22), median TTD of 26 months (95% CI: 5-36), and median OS of 36 months (95% CI: 20-46). Twelve patients (32%) continued first-line osimertinib after local therapy for oligoprogression., Conclusions: Osimertinib exhibited favorable outcomes for rare EGFR exon 19 and compound mutations. The heterogeneity in outcomes among these groups of tumors with similar mutations underscores the need for continued reporting and further study of outcomes among rare variants to optimize management for each patient., Competing Interests: Dr. Houseknecht has been consulting for AstraZeneca, Aptar Pharma, and has stock ownership with Pfizer. Dr. Feliciano has received research funding direct to the institution from 10.13039/100004325AstraZeneca, 10.13039/100004319Pfizer, 10.13039/100002491Bristol Myers Squibb and was consulting for Regeneron, AstraZeneca, Coherus, Eli Lilly, Genentech, Takeda, Jansen, Daiichi Sankyo. Dr. Hann has received research funding direct to the institution from AstraZeneca, Amgen, Daiichi, Bristol Meyers Squibb, AbbVie; and personal fees from AstraZeneca, Puma BioTechnology, Daiichi, Janssen and Bristol Meyers Squibb. Dr. Lam was consulting for Iovance Biotherapeutics, Anheart Therapeutics, Takeda, Seattle Genetics, Bristol Myers Squibb, AstraZeneca, and Guardant Health; and has received research funding direct to the institution from GlaxoSmithKline, Bristol Myers Squibb, AstraZeneca, Merck and Seattle Genetics. Dr. Levy has received personal fees from AstraZeneca, Novartis, Eli Lilly, Genentech, Pfizer, Guardant 360, Takeda, Bristol Meyers Squibb, Novocure, Janssen, Daiichi Sankyo, Merck. Dr. Murray has received personal fees from Regeneron, Johnson & Johnson. Dr. Brahmer has received personal fees from 10.13039/100004337Roche, grants and personal fees from Bristol Meyers Squibb, grants from 10.13039/100004334Merck, personal fees from 10.13039/100009857Regeneron, grants and personal fees from AstraZeneca, personal fees from 10.13039/100002429Amgen, personal fees from Summit, personal fees from Mestag, grants and personal fees from RAPT therapeutics, personal fees from 10.13039/100004330GlaxoSmithKline, and personal fees from Sanofi.Dr.Forde has received research funding direct to the institution from AstraZeneca, BMS, Novartis, Regeneron, BioNTech; consulting fees from Ascendis, AstraZeneca, BMS, Curevac, Novartis, Regeneron, G1, Genelux, Genentech, Gritstone, Merck, Janssen, F Star, Sanofi, Amgen, Fosun, Teva, Synthekine, Flame, Iteos, Tavotek, Teva; and has DSMB membership for Polaris. Dr. Marrone has been consulting for AstraZeneca, Amgen, Janssen, Mirati Therapeutics, Daiichi Sankyo/Lilly and Puma Biotechnology; and has received honoraria from AstraZeneca, research funding direct to the institution from Bristol-Myers Squibb and Mirati Therapeutics. Dr. Scott has received research funding direct to the institution from Mirati and Janssen; and has been consulting for AstraZeneca, Foundation Medicine, Genentech, Regeneron, and Tempus. The remaining authors declare no conflict of interest., (© 2024 The Authors.)

Novel or rare damaging mutations have been implicated in the developmental pathogenesis of nonsyndromic cleft lip with or without cleft palate (nsCL ± P). Thus, we investigated the human genome for high-impact mutations that could explain the risk of nsCL ± P in our cohorts., We conducted next-generation sequencing (NGS) analysis of 130 nsCL ± P case-parent African trios to identify pathogenic variants that contribute to the risk of clefting. We replicated this analysis using whole-exome sequence data from a Brazilian nsCL ± P cohort. Computational analyses were then used to predict the mechanism by which these variants could result in increased risks for nsCL ± P., We discovered damaging mutations within the AFDN gene, a cell adhesion molecule (CAMs) that was previously shown to contribute to cleft palate in mice. These mutations include p.Met1164Ile, p.Thr453Asn, p.Pro1638Ala, p.Arg669Gln, p.Ala1717Val, and p.Arg1596His. We also discovered a novel splicing p.Leu1588Leu mutation in this protein. Computational analysis suggests that these amino acid changes affect the interactions with other cleft-associated genes including nectins (PVRL1, PVRL2, PVRL3, and PVRL4) CDH1, CTNNA1, and CTNND1., This is the first report on the contribution of AFDN to the risk for nsCL ± P in humans. AFDN encodes AFADIN, an important CAM that forms calcium-independent complexes with nectins 1 and 4 (encoded by the genes PVRL1 and PVRL4 ). This discovery shows the power of NGS analysis of multiethnic cleft samples in combination with a computational approach in the understanding of the pathogenesis of nsCL ± P., Competing Interests: Declaration of Conflicting InterestsThe author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

Background: Inadequate knowledge among health care providers (HCPs) and parents of affected children limits the understanding and utility of secondary genetic findings (SFs) in under-represented populations in genomics research. SFs arise from deep DNA sequencing done for research or diagnostic purposes and may burden patients and their families despite their potential health importance. This study aims to evaluate the perspective of both groups regarding SFs and their choices in the return of results from genetic testing in the context of orofacial clefts., Methods: Using an online survey, we evaluated the experiences of 252 HCPs and 197 parents across participating cleft clinics in Ghana and Nigeria toward the return of SFs across several domains., Results: Only 1.6% of the HCPs felt they had an expert understanding of when and how to incorporate genomic medicine into practice, while 50.0% agreed that all SFs should be returned to patients. About 95.4% of parents were willing to receive all the information from genetic testing (including SFs), while the majority cited physicians as their primary information source (64%)., Conclusions: Overall, parents and providers were aware that genetic testing could help in the clinical management of diseases. However, they cited a lack of knowledge about genomic medicine, uncertain clinical utility, and lack of available learning resources as barriers. The knowledge gained from this study will assist with developing guidelines and policies to guide providers on the return of SFs in sub-Saharan Africa and across the continent.

While tyrosine kinase inhibitors (TKI) have shown remarkable efficacy in anaplastic lymphoma kinase (ALK) fusion-positive advanced non-small cell lung cancer (NSCLC), clinical outcomes vary and acquired resistance remains a significant challenge. We conducted a retrospective study of patients with ALK-positive NSCLC who had clinico-genomic data independently collected from two academic institutions (n = 309). This was paired with a large-scale genomic cohort of patients with ALK-positive NSCLC who underwent liquid biopsies (n = 1,118). Somatic co-mutations in TP53 and loss-of-function alterations in CDKN2A/B were most commonly identified (24.1% and 22.5%, respectively in the clinical cohort), each of which was independently associated with inferior overall survival (HR: 2.58; 95% confidence interval, CI: 1.62-4.09 and HR: 1.93; 95% CI: 1.17-3.17, respectively). Tumors harboring EML4-ALK variant 3 (v3) were not associated with specific co-alterations but were more likely to develop ALK resistance mutations, particularly G1202R and I1171N (OR: 4.11; P < 0.001 and OR: 2.94; P = 0.026, respectively), and had inferior progression-free survival on first-line TKI (HR: 1.52; 95% CI: 1.03-2.25). Non-v3 tumors were associated with L1196M resistance mutation (OR: 4.63; P < 0.001). EML4-ALK v3 and somatic co-alterations in TP53 and CDKN2A/B are associated with inferior clinical outcomes. v3 status is also associated with specific patterns of clinically important ALK resistance mutations. These tumor-intrinsic features may inform rational selection and optimization of first-line and consolidative therapy., Significance: In a large-scale, contemporary cohort of patients with advanced ALK-positive NSCLC, we evaluated molecular characteristics and their impact on acquired resistance mutations and clinical outcomes. Our findings that certain ALK variants and co-mutations are associated with differential survival and specific TKI-relevant resistance patterns highlight potential molecular underpinnings of the heterogenous response to ALK TKIs and nominate biomarkers that may inform patient selection for first-line and consolidative therapies., (© 2024 The Authors; Published by the American Association for Cancer Research.)

Purpose: To compare objective and subjective clinical outcomes between suture-augmented anterior cruciate ligament (ACL) repair (SAACLR) and conventional ACL reconstruction (CACLR) with minimum 2-year follow-up., Methods: In this nonrandomized, prospective study, 30 patients underwent SAACLR for proximal ACL avulsion or high-grade partial ACL tear (Sherman grade 1 or 2) and 30 patients underwent CACLR for proximal one-third/distal two-thirds junction tears and mid-substance tears (Sherman grade 3 or 4) tear types by 1 surgeon between 2018 and 2020. Failure was defined as ACL reinjury. Outcome measures were KT-1000 for side-to-side knee laxity evaluation, Visual Analog Scale for pain, International Knee Documentation Committee (IKDC) Subjective Knee Evaluation Form, Knee Injury and Osteoarthritis Severity Score (KOOS), Tegner Activity Scale, Western Ontario and McMaster Universities Osteoarthritis Index, Lysholm Knee Scoring Scale, and Single Assessment Numeric Evaluation. Minimal clinically important difference (MCID) was calculated for IKDC and KOOS subscores., Results: Three failures (10%) occurred in the SAACLR group, with no failures in the CACLR group (P = .24). A total of 23 (85%) SAACLR patients and 27 (90%) CACLR patients had patient-reported outcomes and physical examination at minimum 2 years. Two-year KT-1000 testing with 20 lbs showed less than 1 mm side-to-side difference between the groups. No significant differences in the percentage of patients meeting the MCID were found between the SAACLR and CACLR groups at 2 years: IKDC, 10.81 (82%) versus 10.54 (93%) (P = .48); KOOS Pain, 11.55 (73%) versus 10.58 (78%) (P = .94); KOOS Symptoms, 8.15 (77%) versus 10.32 (74%) (P = 1.0); KOOS Activities of Daily Living, 12.19 (59%) versus 12.28 (70%) (P = .60); 18.99 (71%) versus 16.77 (86%) (P = .42). Significantly higher IKDC scores were observed with SAACLR versus CACLR at 3 months (P = .01) and 6 months (P = .02), and significantly higher Lysholm scale, Tegner Activity Scale, and all KOOS subscale scores were observed at 6 months., Conclusions: At 2 years after surgery, KT-1000 testing showed less than 1 mm side-to-side difference and no differences were observed between the groups in the percentage of patients who met or exceeded the MCID. Significantly higher early patient-reported outcome scores were found with SAACLR versus CACLR. The rerupture rate between the groups was not significantly different., Level of Evidence: Level II, Prospective cohort study., (Copyright © 2023 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.)

Objectives: Understand from a real-world cohort the unique clinical and genomic determinants of a durable response to immune checkpoint inhibitors (ICIs)., Materials and Methods: This is a retrospective study of patients with NSCLC who received any ICI-based regimen as first or second line therapy. Long-term responders (LTR) achieved an overall survival (OS) ≥ 3 years from time of treatment start, while nonresponders (NR) were patients who had an OS of 6 to 12 months from time of treatment start. Clinical and demographic covariables were collected from electronic medical records. Fisher's exact test and Mann-Whitney test were used to analyze the association of a long-term response to ICI in relation to clinical and genomic variables. All P-values were considered significant at P-value < .05., Results: A total of 72 patients were included in this study (LTR n = 37, NR n = 35). There were no significant differences in age, sex, race, and BMI between groups. The presence of liver metastases at the time of ICI initiation and PD-L1 status were not associated with LTR to ICIs. Patients in the LTR were more likely to experience irAEs at 3-,6- and 12-months. KRAS mutant tumors were numerically more common in the LTR group (n = 13 vs. 8)., Conclusion: We observe no strong clinical and biomarkers of a prolonged response to ICIs. Additional large prospective cohort studies are needed to investigate the genomic footprint of long-term responders., Competing Interests: Disclosure PG has no disclosures. JCM is a consultant for Regeneron, Johnson & Johnson and Doximity. JM receives research funding to the institution from Merck. MH is a consultant for Regeneron and MJH Life Sciences. MZG has no disclosures. DSE has no disclosures. JF receives research funding to the institution from AstraZeneca, Bristol Myers and Pfizer. JF is a consultant for Regeneron, Coherus, AstraZeneca, Bristol Myers, Merck, Takeda and Eli Lilly. PF received research funding to the institution from AstraZeneca, BMS, Corvus, Kyowa, Novartis and Regeneron. PF is a consultant for Amgen, AstraZeneca, BMS, Daiichi, F-Star, G1, Genentech, Janssen, Iteos, Merck, Sanofi, Novartis and Surface. CH is a consultant for Amgen and AstraZeneca. CH receives research funding to the institution form AbbVie, Amgen, AstraZeneca, and BMS. VL is a consultant for Seattle Genetics, Bristol-Myers Squibb, AstraZeneca, Guardant Health, Takeda and Anheart Therapeutics. VL receives funding to the institution from BMS, Merck, Seattle Genetics and AstraZeneca. BL is a consultant for Genentech, Eli Lilly, Astra Zeneca, Pfizer, Daiichi Sankyo, Janssen, Mirati, Amgen, Merck and Sanofi. VA receives research funding to Johns Hopkins University from Astra Zeneca, Personal Genome Diagnostics and Delfi Diagnostics and has received research funding to Johns Hopkins University from Bristol-Myers Squibb in the past 5 years. V.A. is an advisory board member for Neogenomics and V.A. is an inventor on patent applications (63/276,525, 17/779,936, 16/312,152, 16/341,862, 17/047,006, and 17/598,690) submitted by Johns Hopkins University related to cancer genomic analyses, ctDNA therapeutic response monitoring and immunogenomic features of response to immunotherapy that have been licensed to 1 or more entities. Under the terms of these license agreements, the University and inventors are entitled to fees and royalty distributions. JRB is an advisor for Amgen, AstraZeneca, BMS, Genentech/Roche, GlaxoSmithKline, Merck, Sanofi, Regeneron, Janssen and Johnson & Johnson. JRB also receives to the institution research funding from AstraZeneca and BMS. JRB is also part of the Data and Safety monitory board of Janssen. KM receives honoraria from AstraZeneca. KM is a consultant for AstraZeneca, Amgen, Puma Biotechnology, Janssen, Mirati Therapeutics, Mirati Therapeutics and Regeneron. KM receives research funding to the institution from Mirati, BMS, AstraZeneca., (Copyright © 2023 Elsevier Inc. All rights reserved.)

Background: A fundamental ethical issue in African genomics research is how socio-cultural factors impact perspectives, acceptance, and utility of genomic information, especially in stigmatizing conditions like orofacial clefts (OFCs). Previous research has shown that gatekeepers (e.g., religious, political, family or community leaders) wield considerable influence on the decision-making capabilities of their members, including health issues. Thus, their perspectives can inform the design of engagement strategies and increase exposure to the benefits of genomics testing/research. This is especially important for Africans underrepresented in genomic research. Our study aims to investigate the perspectives of gatekeepers concerning genomic risk information (GRI) in the presence of OFCs in a sub-Saharan African cohort., Methods: Twenty-five focus group discussions (FGDs) consisting of 214 gatekeepers (religious, community, ethnic leaders, and traditional birth attendants) in Lagos, Nigeria, explored the opinions of participants on genomic risk information (GRI), OFC experience, and the possibility of involvement in collaborative decision-making in Lagos, Nigeria. Transcripts generated from audio recordings were coded and analyzed in NVivo using thematic analysis., Results: Three main themes-knowledge, beliefs, and willingness to act-emerged from exploring the perspective of gatekeepers about GRI in this group. We observed mixed opinions regarding the acceptance of GRI. Many participants believed their role is to guide and support members when they receive results; this is based on the level of trust their members have in them. However, participants felt they would need to be trained by medical experts to do this. Also, religious and cultural beliefs were crucial to determining participants' understanding of OFCs and the acceptance and utilization of GRI., Conclusions: Incorporating cultural sensitivity into public engagement could help develop appropriate strategies to manage conflicting ideologies surrounding genomic information in African communities. This will allow for more widespread access to the advances in genomics research in underrepresented populations. We also recommend a synergistic relationship between community health specialists/scientists, and community leaders, including spiritual providers to better understand and utilize GRI., (© 2024. The Author(s).)

Purpose: Although immunotherapy is the mainstay of therapy for advanced non-small cell lung cancer (NSCLC), robust biomarkers of clinical response are lacking. The heterogeneity of clinical responses together with the limited value of radiographic response assessments to timely and accurately predict therapeutic effect-especially in the setting of stable disease-calls for the development of molecularly informed real-time minimally invasive approaches. In addition to capturing tumor regression, liquid biopsies may be informative in capturing immune-related adverse events (irAE)., Experimental Design: We investigated longitudinal changes in circulating tumor DNA (ctDNA) in patients with metastatic NSCLC who received immunotherapy-based regimens. Using ctDNA targeted error-correction sequencing together with matched sequencing of white blood cells and tumor tissue, we tracked serial changes in cell-free tumor load (cfTL) and determined molecular response. Peripheral T-cell repertoire dynamics were serially assessed and evaluated together with plasma protein expression profiles., Results: Molecular response, defined as complete clearance of cfTL, was significantly associated with progression-free (log-rank P = 0.0003) and overall survival (log-rank P = 0.01) and was particularly informative in capturing differential survival outcomes among patients with radiographically stable disease. For patients who developed irAEs, on-treatment peripheral blood T-cell repertoire reshaping, assessed by significant T-cell receptor (TCR) clonotypic expansions and regressions, was identified on average 5 months prior to clinical diagnosis of an irAE., Conclusions: Molecular responses assist with the interpretation of heterogeneous clinical responses, especially for patients with stable disease. Our complementary assessment of the peripheral tumor and immune compartments provides an approach for monitoring of clinical benefits and irAEs during immunotherapy., (©2023 The Authors; Published by the American Association for Cancer Research.)

Background: Social media use has grown across healthcare delivery and practice, with dramatic changes occurring in response to the coronavirus (COVID-19) pandemic. The purpose of this study was to conduct a comprehensive systematic review to determine the current landscape of social media use by (1) orthopaedic surgery residencies/fellowship training programs and (2) individual orthopaedic surgeons and the change in use over time., Methods: We searched 3 electronic databases (PubMed, MEDLINE, and Embase) from their inception to April 2022 for all studies that analyzed the use of social media in orthopaedic surgery. Two reviewers independently determined study eligibility, rated study quality, and extracted data. Methodology was in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines., Results: Twenty-eight studies were included, of which 11 analyzed social media use by orthopaedic surgery residency and fellowship training programs and 17 examined its use by individual orthopaedic surgeons. Among residency and fellowship programs, Instagram was identified as the most common platform used, with 42% to 88% of programs reporting program-specific Instagram accounts, followed by Twitter/X (20%-52%) and Facebook (10%-38%). Social media was most commonly used by programs for recruitment and information dissemination to prospective residency applicants (82% and 73% of included studies, respectively). After the start of the COVID-19 pandemic, there was a 620% and 177% increase in the number of training programs with Instagram and Twitter/X accounts, respectively. Individual use of social media ranged from 1.7% to 76% (Twitter/X), 10% to 73% (Facebook), 0% to 61% (Instagram), 22% to 61% (LinkedIn), and 6.5% to 56% (YouTube)., Conclusions: Instagram, Twitter/X, and Facebook are the premier platforms that patients, residency applicants, and institutions frequent. With the continued growth of social media use anticipated, it will be critical for institutions and individuals to create and abide by guidelines outlining respectful and professional integration of social media into practice., Level of Evidence: Level IV., Competing Interests: Disclosure: The Disclosure of Potential Conflicts of Interest forms are provided with the online version of the article (http://links.lww.com/JBJSOA/A585)., (Copyright © 2024 The Authors. Published by The Journal of Bone and Joint Surgery, Incorporated. All rights reserved.)

Background: Copper (Cu), an essential trace mineral regulating multiple actions of inflammation and oxidative stress, has been implicated in risk for preterm birth (PTB)., Objectives: This study aimed to determine the association of maternal Cu concentration during pregnancy with PTB risk and gestational duration in a large multicohort study including diverse populations., Methods: Maternal plasma or serum samples of 10,449 singleton live births were obtained from 18 geographically diverse study cohorts. Maternal Cu concentrations were determined using inductively coupled plasma mass spectrometry. The associations of maternal Cu with PTB and gestational duration were analyzed using logistic and linear regressions for each cohort. The estimates were then combined using meta-analysis. Associations between maternal Cu and acute-phase reactants (APRs) and infection status were analyzed in 1239 samples from the Malawi cohort., Results: The maternal prenatal Cu concentration in our study samples followed normal distribution with mean of 1.92 μg/mL and standard deviation of 0.43 μg/mL, and Cu concentrations increased with gestational age up to 20 wk. The random-effect meta-analysis across 18 cohorts revealed that 1 μg/mL increase in maternal Cu concentration was associated with higher risk of PTB with odds ratio of 1.30 (95% confidence interval [CI]: 1.08, 1.57) and shorter gestational duration of 1.64 d (95% CI: 0.56, 2.73). In the Malawi cohort, higher maternal Cu concentration, concentrations of multiple APRs, and infections (malaria and HIV) were correlated and associated with greater risk of PTB and shorter gestational duration., Conclusions: Our study supports robust negative association between maternal Cu and gestational duration and positive association with risk for PTB. Cu concentration was strongly correlated with APRs and infection status suggesting its potential role in inflammation, a pathway implicated in the mechanisms of PTB. Therefore, maternal Cu could be used as potential marker of integrated inflammatory pathways during pregnancy and risk for PTB., (Copyright © 2023. Published by Elsevier Inc.)

Background: Brain metastasis (BRM) is uncommon in gastroesophageal cancer. As such, clinicopathologic and molecular determinants of BRM and impact on clinical outcome remain incompletely understood., Methods: We retrospectively analyzed clinicopathologic data from advanced esophageal/gastroesophageal junction (E/GEJ) patients at Johns Hopkins from 2003 to 2021. We investigated the association between several clinical and molecular features and the occurrence of BRM, with particular focus on human epidermal growth factor receptor 2 (HER2) overexpression. Survival outcomes and time to BRM onset were also evaluated., Results: We included 515 patients with advanced E/GEJ cancer. Tumors were 78.3% esophageal primary, 82.9% adenocarcinoma, 31.0% HER2 positive. Cumulative incidence of BRM in the overall cohort and within HER2+ subgroup was 13.8% and 24.3%, respectively. HER2 overexpression was associated with increased risk of BRM [odds ratio 2.45; 95% confidence interval (CI) 1.10-5.46]. On initial presentation with BRM, 50.7% had a solitary brain lesion and 11.3% were asymptomatic. HER2+ status was associated with longer median time to onset of BRM (14.0 versus 6.3 months, P < 0.01), improved median progression free survival on first-line systemic therapy (hazard ratio 0.35, 95% CI 0.16-0.80), and improved median overall survival (hazard ratio 0.20, 95% CI 0.08-0.54) in patients with BRM., Conclusion: HER2 overexpression identifies a gastroesophageal cancer molecular subtype that is significantly associated with increased risk of BRM, though with later onset of BRM and improved survival likely reflecting the impact of central nervous system-penetrant HER2-directed therapy. The prevalence of asymptomatic and solitary brain lesions suggests that brain surveillance for HER2+ patients warrants prospective investigation., (Copyright © 2023 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Purpose: To perform a descriptive epidemiologic analysis of National Basketball Association (NBA) injuries from 2016 to 2021, to evaluate the impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (coronavirus disease 2019, or COVID-19) on injury patterns and performance statistics, and to determine the effect of infection with SARS-CoV-2 on individual performance statistics., Methods: Injury epidemiology in the NBA from the 2016 to 2021 seasons was collected using a comprehensive online search. Injuries and time missed were categorized by injury location and type. Player positions and timing of injury were recorded. Performance statistics were collected including traditional game statistics and Second Spectrum (speed, distance) statistics. Comparisons were made over seasons and comparing the pre-COVID-19 pandemic seasons to the pandemic era seasons. Players diagnosed with COVID-19 were analyzed for changes in performance in the short or long term., Results: Of the 3,040 injuries captured, 1,880 (61.84%) were in the lower extremity. Guards (77.44%) and forwards (75.88%) had a greater proportion of soft-tissue injuries ( P < .001) than centers. Guards had the highest proportion of groin (3.27%, P  = .001) and hamstring (6.21%, P < .001) injuries. Despite minor differences on a per-season basis, there were no differences in injury patterns identified between pre-COVID-19 and COVID-19 eras. Of players diagnosed with COVID-19 during the NBA Bubble, there were no detriments in short- or long-term performance identified, including traditional game statistics and speed and distance traveled., Conclusions: In the NBA seasons from 2016 to 2021, most injuries were to the lower extremity. The SARS-CoV-2 pandemic did not substantially impact injury patterns in the NBA, including locations of injury and type of injury (bony or soft tissue). Furthermore, infection with SARS-CoV-2 does not appear to have a significant impact on performance in basketball-specific or speed and distance measures., Level of Evidence: Level IV, prognostic case series., Competing Interests: The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: N.K.P. reports consultant for OrthoPediatrics and educational support from Evolution Surgical, Inc. All other authors (Sachin A., A.R.G., N.C., N.T., A.P.G., J.C.M., Sameer A.) declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. Full ICMJE author disclosure forms are available for this article online, as supplementary material., (© 2023 The Authors.)

Introduction: Immune checkpoint inhibitors (ICI) are standard treatment for nonsmall cell lung cancer (NSCLC). However, the burden of infectious complications during ICI therapy is poorly described., Materials and Methods: We conducted a retrospective study of patients with NSCLC treated with ICIs between 2007 and 2020 at a tertiary academic center. The incidence, characteristics, and healthcare utilization outcomes of infections during ICI therapy and within 3 months of ICI discontinuation are presented using descriptive statistics. Cox proportional hazard models are used to examine infection-free survival by demographic and treatment factors. Associations between patient or treatment characteristics and hospitalization or ICU admission are analyzed by logistic regression, presented as odds ratios (OR)., Results: Of 298 patients, infections occurred in 54.4% (n = 162). Of these patients, 59.3% (n = 96) required hospitalization and 15.4% (n = 25) required ICU admission. The most common infection was bacterial pneumonia. Fungal infections occurred in 12 patients (7.4%). Patients with chronic obstructive pulmonary disease (COPD) (OR 2.15, 95% CI, 1.01-4.58), corticosteroid treatment within 1 month prior to infection onset (OR 3.04, 95% CI, 1.47-6.30), and concomitant irAE and infection (OR 5.48, 95% CI, 2.15-14.00) had higher odds of hospitalization. Corticosteroid use was associated with higher odds of ICU admission (OR 3.09, 95% CI, 1.29-7.38)., Conclusion: In this large single-institution study we identify that more than half of patients with ICI-treated NSCLC develop infectious complications. We identify that patients with COPD, recent corticosteroid use, and concomitant irAE and infection have higher odds of hospitalization, and that unusual infections (eg, fungal) can occur. This highlights clinical awareness of infections as important complications during ICI therapy in patients with NSCLC., (Copyright © 2023 Elsevier Inc. All rights reserved.)

Purpose: Concomitant autoimmune rheumatic diseases (ARD) can add morbidity and complicate treatment decisions for patients with lung cancer. We evaluated the tumour characteristics at diagnosis and clinical outcomes in lung cancer patients with or without ARD., Methods: This retrospective cohort study included 10 963 patients with lung cancer, treated at Johns Hopkins. Clinical data including tumour characteristics and outcomes were extracted from the cancer registry. Data on patients' history of 20 ARD were extracted from the electronic medical record. Logistic regression was used to compare tumour characteristics between those with and without ARD; Kaplan-Meier curves and Cox proportional hazards models were performed to compare survival outcomes., Results: ARD was present in 3.6% of patients (n=454). The mean age at diagnosis was 69 (SD 10) and 68 (SD 12) in patients with and without ARD (p=0.02). Female sex and smoking history were significantly associated with a history of ARD (OR: 1.75, OR: 1.46, p<0.05). Patients with ARD were more likely to be diagnosed with stage 1 lung cancer (36.8% vs 26.9%, p<0.001) and with smaller tumour size (OR: 0.76, p=0.01), controlling for sex, race and histology. Notably, lung cancer patients with ARD had a significantly prolonged median overall survival (OS) (7.11 years vs 1.7 years, p<0.001), independent of stage., Conclusion: Patients with ARD and lung cancer had better OS compared with their counterparts, independent of cancer stage and treatments and were less likely to have advanced stage lung cancer at diagnosis. Additional studies are needed to investigate the differential immunological anti-tumour immune activity and genomic variations in patients with and without ARD., Competing Interests: Competing interests: PG has no disclosures. JCM is a consultant/advisory: Regeneron, Johnson & Johnson, Doximity. JCM receives research funding to Merck. KAM has research funding from AstraZeneca, Bristol-Myers Squibb, Mirati and is a consultant and serves on the advisory boards for Amgen, AstraZeneca, Bristol-Myers Squibb, Janssen, Regeneron. SCS is a consultant for Amgen, Genentech, Foundation Medicine. JLF is a consultant to Eli Lilly, Astra Zeneca, Genentech, Takeda, Regeneron, Coherus, Jansen, Merck and Bristol-Myers Squibb. JLF receives research funding from Bristol-Myers Squibb, Astra Zeneca, Pfizer. VKL is a consultant to Seattle Genetics, Bristol-Myers Squibb, AstraZeneca, Guardant Health, Takeda and Anheart Therapeutics. VKL receives funding from Bristol-Myers Squibb, Merck, Seattle Genetics and Astra Zeneca. CLH is a consultant to Amgen and AstraZeneca. CLH receives research funding from AbbVie, Amgen, AstraZeneca and Bristol-Myers Squibb. DSE is an advisor to Beyond Spring and Chair of the NCCN NSCLC Guideline. BPL is a consultant and on the advisory board for AstraZeneca, Daiichi Sankyo, Janssen, Bristol-Myers Squibb, Novartis, Genentech, Eli Lilly, Pfizer, Guardant 360, Mirati, Amgen, Foundation one. PMF receives research funding from AstraZeneca, Bristol-Myers Squibb, Corvus, Kyowa, Novartis, Regeneron. PMF is a consultant to Amgen, AstraZeneca, Bristol-Myers Squibb, Daiichi, F-Star, G1, Genentech, Janssen, Iteos, Merck, Sanofi, Novartis, Surface. PMF is a DSMB member for Polaris. AAS obtains research funding from Arena Pharmaceuticals, Medpace, Eicos Sciences, Kadmon Corporation. CM is a consultant for Boehringer Ingelheim and Department of Justice Vaccine Injury Compensation Program. JB has research funding from AstraZeneca and Bristol-Myers Squibb, consulting for AstraZeneca, Bristol-Myers Squibb, Merck, Genentech/Roche, Eli Lilly, Amgen, Bluprint, Janssen, Johnson & Johnson, Regneron and Sanofi, and honoraria from Janssen. LCC has research funding from Bristol-Myers Squibb., (© Author(s) (or their employer(s)) 2023. Re-use permitted under CC BY. Published by BMJ.)

Purpose: Orofacial clefts (OFCs) are common birth defects including cleft lip, cleft lip and palate, and cleft palate. OFCs have heterogeneous etiologies, complicating clinical diagnostics because it is not always apparent if the cause is Mendelian, environmental, or multifactorial. Sequencing is not currently performed for isolated or sporadic OFCs; therefore, we estimated the diagnostic yield for 418 genes in 841 cases and 294 controls., Methods: We evaluated 418 genes using genome sequencing and curated variants to assess their pathogenicity using American College of Medical Genetics criteria., Results: 9.04% of cases and 1.02% of controls had "likely pathogenic" variants (P < .0001), which was almost exclusively driven by heterozygous variants in autosomal genes. Cleft palate (17.6%) and cleft lip and palate (9.09%) cases had the highest yield, whereas cleft lip cases had a 2.80% yield. Out of 39 genes with likely pathogenic variants, 9 genes, including CTNND1 and IRF6, accounted for more than half of the yield (4.64% of cases). Most variants (61.8%) were "variants of uncertain significance", occurring more frequently in cases (P = .004), but no individual gene showed a significant excess of variants of uncertain significance., Conclusion: These results underscore the etiological heterogeneity of OFCs and suggest sequencing could reduce the diagnostic gap in OFCs., Competing Interests: Conflict of Interest The authors declare no conflicts of interests., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Exome sequencing (ES) is now a relatively straightforward process to identify causal variants in Mendelian disorders. However, the same is not true for ES in families where the inheritance patterns are less clear, and a complex etiology is suspected. Orofacial clefts (OFCs) are highly heritable birth defects with both Mendelian and complex etiologies. The phenotypic spectrum of OFCs may include overt clefts and several subclinical phenotypes, such as discontinuities in the orbicularis oris muscle (OOM) in the upper lip, velopharyngeal insufficiency (VPI), microform clefts or bifid uvulas. We hypothesize that expanding the OFC phenotype to include these phenotypes can clarify inheritance patterns in multiplex families, making them appear more Mendelian. We performed exome sequencing to find rare, likely causal genetic variants in 31 multiplex OFC families, which included families with multiple individuals with OFCs and individuals with subclinical phenotypes. We identified likely causal variants in COL11A2, IRF6, SHROOM3, SMC3, TBX3, and TP63 in six families. Although we did not find clear evidence supporting the subclinical phenotype hypothesis, our findings support a role for rare variants in the etiology of OFCs., (© 2023 Wiley Periodicals LLC.)

As one of the most common structural birth defects, orofacial clefts (OFCs) have been studied for decades, and recent studies have demonstrated that there are genetic differences between the different phenotypic presentations of OFCs. However, the contribution of rare genetic variation genome-wide to different subtypes of OFCs has been understudied, with most studies focusing on common genetic variation or rare variation within targeted regions of the genome. Therefore, we used whole-genome sequencing data from the Gabriella Miller Kids First Pediatric Research Program to conduct a gene-based burden analysis to test for genetic modifiers of cleft lip (CL) vs cleft lip and palate (CLP). We found that there was a significantly increased burden of rare variants in SEC24D in CL cases compared to CLP cases (p = 6.86 [Formula: see text] 10 -7 ). Of the 15 variants within SEC24D, 53.3% were synonymous, but overlapped a known craniofacial enhancer. We then tested whether these variants could alter predicted transcription factor binding sites (TFBS), and found that the rare alleles destroyed binding sites for 9 transcription factors (TFs), including Pax1 (p = 0.0009), and created binding sites for 23 TFs, including Pax6 (p = 6.12 [Formula: see text] 10 -5 ) and Pax9 (p = 0.0001), which are known to be involved in normal craniofacial development, suggesting a potential mechanism by which these synonymous variants could have a functional impact. Overall, this study indicates that rare genetic variation may contribute to the phenotypic heterogeneity of OFCs and suggests that regulatory variation may also contribute and warrant further investigation in future studies of genetic variants controlling risk to OFC., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Introduction: The frequency and implications of secondary findings (SFs) from genomic testing data have been extensively researched. However, little is known about the frequency or reporting of SFs in Africans, who are underrepresented in large-scale population genomic studies. The availability of data from the first whole-genome sequencing for orofacial clefts in an African population motivated this investigation., Methods: In total, 130 case-parent trios were analyzed for SFs within the ACMG SFv.3.0 list genes. Additionally, we filtered for four more genes (HBB, HSD32B, G6PD and ACADM)., Results: We identified 246 unique variants in 55 genes; five variants in four genes were classified as pathogenic or likely pathogenic (P/LP). The P/LP variants were seen in 2.3% (9/390) of the subjects, a frequency higher than ~1% reported for diverse ethnicities. On the ACMG list, pathogenic variants were observed in PRKAG (p. Glu183Lys). Variants in the PALB2 (p. Glu159Ter), RYR1 (p. Arg2163Leu) and LDLR (p. Asn564Ser) genes were predicted to be LP., Conclusion: This study provides information on the frequency and pathogenicity of SFs in an African cohort. Early risk detection will help reduce disease burden and contribute to efforts to increase knowledge of the distribution and impact of actionable genomic variants in diverse populations., (© 2023 The Authors. Molecular Genetics & Genomic Medicine published by Wiley Periodicals LLC.)

Cleft palate (CP) is one of the most common craniofacial birth defects; however, there are relatively few established genetic risk factors associated with its occurrence despite high heritability. Historically, CP has been studied as a single phenotype, although it manifests across a spectrum of defects involving the hard and/or soft palate. We performed a genome-wide association study using transmission disequilibrium tests of 435 case-parent trios to evaluate broad risks for any cleft palate (ACP) (n = 435), and subtype-specific risks for any cleft soft palate (CSP), (n = 259) and any cleft hard palate (CHP) (n = 125). We identified a single genome-wide significant locus at 9q33.3 (lead SNP rs7035976, p = 4.24 × 10 -8 ) associated with CHP. One gene at this locus, angiopoietin-like 2 ( ANGPTL2 ), plays a role in osteoblast differentiation. It is expressed both in craniofacial tissue of human embryos and developing mouse palatal shelves. We found 19 additional loci reaching suggestive significance (p < 5 × 10 -6 ), of which only one overlapped between groups (chromosome 17q24.2, ACP and CSP). Odds ratios for the 20 loci were most similar across all 3 groups for SNPs associated with the ACP group, but more distinct when comparing SNPs associated with either subtype. We also found nominal evidence of replication (p < 0.05) for 22 SNPs previously associated with orofacial clefts. Our study to evaluate CP risks in the context of its subtypes and we provide newly reported associations affecting the broad risk for CP as well as evidence of subtype-specific risks., Competing Interests: M.P.E. is a member of the Human Genetics and Genomics Advances Editorial Board., (© 2023 The Authors.)

Purpose: Although immunotherapy is the mainstay of therapy for advanced non-small cell lung cancer (NSCLC), robust biomarkers of clinical response are lacking. The heterogeneity of clinical responses together with the limited value of radiographic response assessments to timely and accurately predict therapeutic effect -especially in the setting of stable disease-call for the development of molecularly-informed real-time minimally invasive predictive biomarkers. In addition to capturing tumor regression, liquid biopsies may be informative in evaluating immune-related adverse events (irAEs)., Experimental Design: We investigated longitudinal changes in circulating tumor DNA (ctDNA) in patients with metastatic NSCLC who received immunotherapy-based regimens. Using ctDNA targeted error-correction sequencing together with matched sequencing of white blood cells and tumor tissue, we tracked serial changes in cell-free tumor load (cfTL) and determined molecular response for each patient. Peripheral T-cell repertoire dynamics were serially assessed and evaluated together with plasma protein expression profiles., Results: Molecular response, defined as complete clearance of cfTL, was significantly associated with progression-free (log-rank p=0.0003) and overall survival (log-rank p=0.01) and was particularly informative in capturing differential survival outcomes among patients with radiographically stable disease. For patients who developed irAEs, peripheral blood T-cell repertoire reshaping, assessed by significant TCR clonotypic expansions and regressions were noted on-treatment., Conclusions: Molecular responses assist with interpretation of heterogeneous clinical responses especially for patients with stable disease. Our complementary assessment of the tumor and immune compartments by liquid biopsies provides an approach for monitoring of clinical benefit and immune-related toxicities for patients with NSCLC receiving immunotherapy., Statement of Translational Relevance: Longitudinal dynamic changes in cell-free tumor load and reshaping of the peripheral T-cell repertoire capture clinical outcomes and immune-related toxicities during immunotherapy for patients with non-small cell lung cancer.

Preterm birth (PTB) is the leading cause of death in children under five, yet comprehensive studies are hindered by its multiple complex etiologies. Epidemiological associations between PTB and maternal characteristics have been previously described. This work used multiomic profiling and multivariate modeling to investigate the biological signatures of these characteristics. Maternal covariates were collected during pregnancy from 13,841 pregnant women across five sites. Plasma samples from 231 participants were analyzed to generate proteomic, metabolomic, and lipidomic datasets. Machine learning models showed robust performance for the prediction of PTB (AUROC = 0.70), time-to-delivery ( r = 0.65), maternal age ( r = 0.59), gravidity ( r = 0.56), and BMI ( r = 0.81). Time-to-delivery biological correlates included fetal-associated proteins (e.g., ALPP, AFP, and PGF) and immune proteins (e.g., PD-L1, CCL28, and LIFR). Maternal age negatively correlated with collagen COL9A1, gravidity with endothelial NOS and inflammatory chemokine CXCL13, and BMI with leptin and structural protein FABP4. These results provide an integrated view of epidemiological factors associated with PTB and identify biological signatures of clinical covariates affecting this disease.

Antibody Drug Conjugates (ADCs) are a novel class of therapeutic that structurally comprise an antibody directed at a tumor epitope connected via a linker to a cytotoxic payload that have shown significant antitumor activity across a range of malignancies including lung cancer. In this article we review the pharmacology of ADCs, describe results of trials with ADCs directed at targets in lung cancer including Trophoblast cell-surface antigen 2(TROP2), HER3, MET, Carcinoembryonic antigen-related cell adhesion molecular 5(CECAM-5) and HER2. Trastuzumab Deruxtecan (also known as DS-8201a or T-DXd) an ADC directed at HER2 recently became the first ADC to receive FDA approval in lung cancer, on the basis of its activity in tumors with HER2 mutations, demonstrated in the Destiny-Lung01 and Lung02 trials.

AMOTL1 encodes angiomotin-like protein 1, an actin-binding protein that regulates cell polarity, adhesion, and migration. The role of AMOTL1 in human disease is equivocal. We report a large cohort of individuals harboring heterozygous AMOTL1 variants and define a core phenotype of orofacial clefting, congenital heart disease, tall stature, auricular anomalies, and gastrointestinal manifestations in individuals with variants in AMOTL1 affecting amino acids 157-161, a functionally undefined but highly conserved region. Three individuals with AMOTL1 variants outside this region are also described who had variable presentations with orofacial clefting and multi-organ disease. Our case cohort suggests that heterozygous missense variants in AMOTL1, most commonly affecting amino acid residues 157-161, define a new orofacial clefting syndrome, and indicates an important functional role for this undefined region., (© 2023 Wiley Periodicals LLC.)

Eccrine angiomatous hamartoma is an uncommon, benign clinical entity constituting a nodular proliferation of eccrine glands and vascular structures localized to the dermis that typically present as unilateral, flesh-colored, erythematous, or violaceous papules on the extremities. These hamartomas may be associated with pain, hyperhidrosis, joint deformity, or functional impairment depending on the severity of the disease process. We present a case of bilaterally symmetric, asymptomatic eccrine angiomatous hamartomas involving all proximal interphalangeal joints of both hands. To date, there are only four prior cases of bilaterally symmetric eccrine angiomatous hamartomas reported in the literature, suggesting that the distribution experienced by our patient may represent a previously undescribed syndrome.

Purpose: Infant and young childhood medulloblastoma (iMB) is usually treated without craniospinal irradiation (CSI) to avoid neurocognitive late effects. Unfortunately, many children relapse. The purpose of this study was to assess salvage strategies and prognostic features of patients with iMB who relapse after CSI-sparing therapy., Methods: We assembled a large international cohort of 380 patients with relapsed iMB, age younger than 6 years, and initially treated without CSI. Univariable and multivariable Cox models of postrelapse survival (PRS) were conducted for those treated with curative intent using propensity score analyses to account for confounding factors., Results: The 3-year PRS, for 294 patients treated with curative intent, was 52.4% (95% CI, 46.4 to 58.3) with a median time to relapse from diagnosis of 11 months. Molecular subgrouping was available for 150 patients treated with curative intent, and 3-year PRS for sonic hedgehog (SHH), group 4, and group 3 were 60%, 84%, and 18% ( P = .0187), respectively. In multivariable analysis, localized relapse ( P = .0073), SHH molecular subgroup ( P = .0103), CSI use after relapse ( P = .0161), and age ≥ 36 months at initial diagnosis ( P = .0494) were associated with improved survival. Most patients (73%) received salvage CSI, and although salvage chemotherapy was not significant in multivariable analysis, its use might be beneficial for a subset of children receiving salvage CSI < 35 Gy ( P = .007)., Conclusion: A substantial proportion of patients with relapsed iMB are salvaged after initial CSI-sparing approaches. Patients with SHH subgroup, localized relapse, older age at initial diagnosis, and those receiving salvage CSI show improved PRS. Future prospective studies should investigate optimal CSI doses and the role of salvage chemotherapy in this population., Competing Interests: Craig ErkerConsulting or Advisory Role: Novartis Canada Pharmaceuticals Inc Martin MynarekEmployment: Novartis, BioNTech SE Maura MassiminoConsulting or Advisory Role: Oncoscience, Novartis Juliette HukinStock and Other Ownership Interests: AbbVieConsulting or Advisory Role: AstraZeneca, Novartis Vijay RamaswamyHonoraria: AstraZenecaConsulting or Advisory Role: AstraZeneca Canada Alvaro LassalettaStock and Other Ownership Interests: Gilead SciencesConsulting or Advisory Role: Jazz Pharmaceuticals, Servier, Alexion Pharmaceuticals Sébastien PerreaultLeadership: BayerStock and Other Ownership Interests: NovocureHonoraria: BayerConsulting or Advisory Role: BayerSpeakers' Bureau: BayerExpert Testimony: Bayer Cassie N. KlineResearch Funding: Regeneron (Inst), Curis (Inst), Midatech Pharma (Inst), Ipsen (Inst), Day One Therapeutics (Inst), Bristol Myers Squibb (Inst), Kazia Therapeutics (Inst), Chimerix (Inst) Eric S. SandlerConsulting or Advisory Role: Protara Therapeutics Lindsey M. HoffmanHonoraria: AstraZeneca Kathleen DorrisStock and Other Ownership Interests: Amgen, Gilead SciencesConsulting or Advisory Role: Day One Biopharmaceuticals Helen ToledanoConsulting or Advisory Role: AstraZeneca, Novartis Derek S. TsangTravel, Accommodations, Expenses: Mevion Medical Systems Jeffrey KnipsteinEmployment: PRA Health Sciences, ServierConsulting or Advisory Role: Atheneum Zhihong J. WangHonoraria: AstraZenecaConsulting or Advisory Role: AstraZenecaSpeakers' Bureau: AstraZeneca Kenneth J. CohenConsulting or Advisory Role: Novartis, Bristol Myers Squibb, DNAtrixResearch Funding: Novartis, Bristol Myers Squibb Jordan R. HansfordStock and Other Ownership Interests: AnteotechConsulting or Advisory Role: Bayer Sabine MuellerResearch Funding: Regeneron (Inst), DayOne Pharmaceuticals (Inst), Curis Pharamceuticals (Inst), Curis Pharamceuticals (Inst), Bristol Myers Squibb (Inst) Amar GajjarConsulting or Advisory Role: Roche/Genentech, QED Therapeutics, Day One Therapeutics, Geanno BioResearch Funding: Genentech (Inst), Kazia Therapeutics (Inst) Stefan RutkowskiConsulting or Advisory Role: Bristol Myers Squibb GmbH & Co. KGaA, Germany, Celgene, Roche Pharma AG, Grenzach-Wyhlen, Bayer Germany Giles RobinsonResearch Funding: Novartis (Inst), Genentech/Roche (Inst), Novartis (Inst), SpringWorks Therapeutics (Inst) Eric BouffetConsulting or Advisory Role: NovartisResearch Funding: Roche (Inst) Lucie Lafay-CousinHonoraria: Servier, Innomar StrategiesNo other potential conflicts of interest were reported.

Purpose: Precision oncology mandates developing standardized common data models (CDMs) to facilitate analyses and enable clinical decision making. Expert-opinion-based precision oncology initiatives are epitomized in Molecular Tumor Boards (MTBs), which process large volumes of clinical-genomic data to match genotypes with molecularly guided therapies., Methods: We used the Johns Hopkins University MTB as a use case and developed a precision oncology core data model (Precision-DM) to capture key clinical-genomic data elements. We leveraged existing CDMs, building upon the Minimal Common Oncology Data Elements model (mCODE). Our model was defined as a set of profiles with multiple data elements, focusing on next-generation sequencing and variant annotations. Most elements were mapped to terminologies or code sets and the Fast Healthcare Interoperability Resources (FHIR). We subsequently compared our Precision-DM with existing CDMs, including the National Cancer Institute's Genomic Data Commons (NCI GDC), mCODE, OSIRIS, the clinical Genome Data Model (cGDM), and the genomic CDM (gCDM)., Results: Precision-DM contained 16 profiles and 355 data elements. 39% of the elements derived values from selected terminologies or code sets, and 61% were mapped to FHIR. Although we used most elements contained in mCODE, we significantly expanded the profiles to include genomic annotations, resulting in a partial overlap of 50.7% between our core model and mCODE. Limited overlap was noted between Precision-DM and OSIRIS (33.2%), NCI GDC (21.4%), cGDM (9.3%), and gCDM (7.9%). Precision-DM covered most of the mCODE elements (87.7%), with less coverage for OSIRIS (35.8%), NCI GDC (11%), cGDM (26%) and gCDM (33.3%)., Conclusion: Precision-DM supports clinical-genomic data standardization to support the MTB use case and may allow for harmonized data pulls across health care systems, academic institutions, and community medical centers.

Background: Axenfeld-Rieger syndrome (ARS) is characterised by typical anterior segment anomalies, with or without systemic features. The discovery of causative genes identified ARS subtypes with distinct phenotypes, but our understanding is incomplete, complicated by the rarity of the condition., Methods: Genetic and phenotypic characterisation of the largest reported ARS cohort through comprehensive genetic and clinical data analyses., Results: 128 individuals with causative variants in PITX2 or FOXC1 , including 81 new cases, were investigated. Ocular anomalies showed significant overlap but with broader variability and earlier onset of glaucoma for FOXC1 -related ARS. Systemic anomalies were seen in all individuals with PITX2 -related ARS and the majority of those with FOXC1 -related ARS. PITX2 -related ARS demonstrated typical umbilical anomalies and dental microdontia/hypodontia/oligodontia, along with a novel high rate of Meckel diverticulum. FOXC1 -related ARS exhibited characteristic hearing loss and congenital heart defects as well as previously unrecognised phenotypes of dental enamel hypoplasia and/or crowding, a range of skeletal and joint anomalies, hypotonia/early delay and feeding disorders with structural oesophageal anomalies in some. Brain imaging revealed highly penetrant white matter hyperintensities, colpocephaly/ventriculomegaly and frequent arachnoid cysts. The expanded phenotype of FOXC1 -related ARS identified here was found to fully overlap features of De Hauwere syndrome. The results were used to generate gene-specific management plans for the two types of ARS., Conclusion: Since clinical features of ARS vary significantly based on the affected gene, it is critical that families are provided with a gene-specific diagnosis, PITX2 -related ARS or FOXC1 -related ARS. De Hauwere syndrome is proposed to be a FOXC1opathy., Competing Interests: Competing interests: BW and GR are employees of GeneDx, Inc., (© Author(s) (or their employer(s)) 2023. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)