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Overdispersion is a common phenomenon in genetic data, such as gene expression count data. In genetic association studies, it is important to investigate the association between a gene expression and a set of genetic variants from a pathway. However, existing approaches for pathway analysis are primarily designed for continuous and binary outcomes and are not applicable to overdispersed count data. In this paper, we propose a hierarchical approach to analyze the association between an overdispersed count response and a set of low-frequency genetic variants in negative binomial regression. We derive score-type test statistics for both fixed and random effects of genetic variants, and further introduce a novel procedure for efficiently combining these two statistics for global testing. Through simulation studies, we demonstrate that the proposed method tends to be more powerful than existing methods under a wide range of scenarios. Additionally, we apply the proposed method to a colorectal cancer study, demonstrating its power in identifying associations between gene expression and somatic mutations. [ABSTRACT FROM AUTHOR]

Background: Pacific Biosciences (PacBio) circular consensus sequencing (CCS), also known as high fidelity (HiFi) technology, has revolutionized modern genomics by producing long (10 + kb) and highly accurate reads. This is achieved by sequencing circularized DNA molecules multiple times and combining them into a consensus sequence. Currently, the accuracy and quality value estimation provided by HiFi technology are more than sufficient for applications such as genome assembly and germline variant calling. However, there are limitations in the accuracy of the estimated quality scores when it comes to somatic variant calling on single reads. Results: To address the challenge of inaccurate quality scores for somatic variant calling, we introduce TopoQual, a novel tool designed to enhance the accuracy of base quality predictions. TopoQual leverages techniques including partial order alignments (POA), topologically parallel bases, and deep learning algorithms to polish consensus sequences. Our results demonstrate that TopoQual corrects approximately 31.9% of errors in PacBio consensus sequences. Additionally, it validates base qualities up to q59, which corresponds to one error in 0.9 million bases. These improvements will significantly enhance the reliability of somatic variant calling using HiFi data. Conclusion: TopoQual represents a significant advancement in genomics by improving the accuracy of base quality predictions for PacBio HiFi sequencing data. By correcting a substantial proportion of errors and achieving high base quality validation, TopoQual enables confident and accurate somatic variant calling. This tool not only addresses a critical limitation of current HiFi technology but also opens new possibilities for precise genomic analysis in various research and clinical applications. [ABSTRACT FROM AUTHOR]

Simple Summary: This study explores the structural and stability impacts of rare genetic and somatic mutations in two glutathione peroxidase proteins, GPx7 and GPx8, which play crucial roles in cellular stress responses. This study aims to identify how these mutations affect protein stability, as these changes are often associated with cancers and other complex diseases. Using advanced computational methods, this research analyzed thousands of potential mutations to predict their effects on protein function. The findings reveal that destabilizing mutations are more likely to be associated with diseases, providing insights into the molecular mechanisms of cancer development. By focusing on high-impact mutations, this study provides a foundation for developing targeted therapies and better understanding the molecular basis of diseases associated with these proteins. Background/Objectives: Somatic and genetic mutations in glutathione peroxidases (GPxs), including GPx7 and GPx8, have been linked to intellectual disability, microcephaly, and various tumors. GPx7 and GPx8 evolved the latest among the GPx enzymes and are present in the endoplasmic reticulum. Although lacking a glutathione binding domain, GPx7 and GPx8 possess peroxidase activity that helps the body respond to cellular stress. However, the protein mutations in these peroxidases remain relatively understudied. Methods: By elucidating the structural and stability consequences of missense mutations, this study aims to provide insights into the pathogenic mechanisms involved in different cancers, thereby aiding clinical diagnosis, treatment strategies, and the development of targeted therapies. We performed saturated computational mutagenesis to analyze 2926 and 3971 missense mutations of GPx7 and GPx8, respectively. Results: The results indicate that G153H and G153F in GPx7 are highly destabilizing, while E93M and W142F are stabilizing. In GPx8, N74W and G173W caused the most instability while S70I and S119P increased stability. Our analysis shows that highly destabilizing somatic and genetic mutations are more likely pathogenic compared to stabilizing mutations. Conclusions: This comprehensive analysis of missense mutations in GPx7 and GPx8 provides critical insights into their impact on protein structure and stability, contributing to a deeper understanding of the roles of somatic mutations in cancer development and progression. These findings can inform more precise clinical diagnostics and targeted treatment approaches for cancers. [ABSTRACT FROM AUTHOR]

Somatic mutation and fusion detection in acute myeloid leukemia to determine disease subtype and treatment regime is a common practice, but it's not yet employed in chronic myeloid leukemia (CML). CML is still monitored by routine quantitative determination of the BCR-ABL fusion transcript and treated with tyrosine kinase inhibitors (TKIs). Despite the availability of the three generations of TKIs, resistance and progression in CML pathogenesis suggest a strong role for somatic mutations. The present study aimed to identify the role of somatic mutation profiling in CML patients in disease management. 196 CML patient samples were used in this investigation, comprising 26 CML-BP, 8 CML-AP, and 162 CML-CP samples. Following cytogenetic analysis for confirmation, each sample was sequenced utilizing the Ion Torrent platform by a targeted panel. Of the 196 CML samples, 81 (41.33%) had 125 variations affecting 27 genes, while 115 (58.67%) harboured no mutations. The study revealed that ASXL1 (31.2%), ABL1 (14.4%), and TET2 (8.8%) were the most frequently altered genes. These genes are recognized indicators of CML disease. Few samples found with mutated GATA2, IDH1, NRAS, SETBP1, WT1, PHF6, KIT, etc. and fusions like RUNX1(5)-MECOM (2) and CBFB- MYH11 are indicative of disease progression. The outcome of this study suggests that mutational profiling of CML patients can help in the prognostication of disease. Based on the results of the study, the authors have also provided possible future risk stratification and diagnosis workflow for CML disease. [ABSTRACT FROM AUTHOR]

Background/Aim: Bile tract cancer (BTC) is a malignant tumor with a poor prognosis. Recent studies have reported the heterogeneity of the genomic background and gene alterations in BTC, but its genetic heterogeneity and molecular profiles remain poorly understood. Whole-genome sequencing may enable the identification of novel actionable gene mutations involved in BTC carcinogenesis, malignant progression, and treatment resistance. Patients and Methods: We performed whole-genome sequencing of six BTC samples to elucidate its genetic heterogeneity and identify novel actionable gene mutations. Somatic mutations, structural variations, copy number alterations, and their associations with clinical factors were analyzed. Results: The average number of somatic mutations detected in each case was 53,705, with SNVs accounting for most of these mutations (85.02%). None of the 331 mutations related to BTC in The Cancer Genome Atlas (TCGA) database were found in the mutations identified in our study. A higher prevalence of gene mutations was observed in samples without vascular invasion than in those with vascular invasion. Several genes with differences in mutation accumulation between groups were identified, including ADAMTS7, AHNAK2, and CAPN10. Conclusion: Our study provides novel insights into the genomic landscape of BTC and highlights the potential of whole-genome sequencing analysis to identify actionable gene mutations and understand the molecular mechanisms underlying this malignancy. The high mutational burden, structural variations, and copy number alterations observed in BTC samples in this study underscore the genetic complexity and heterogeneity of this disease. [ABSTRACT FROM AUTHOR]

Background/Aim: The Kaplan-Meier curves for patients treated with immune checkpoint inhibitors (ICIs) display a small group of potentially-cured patients with longterm survival, creating a 'kangaroo-tail' shape of the survival curve. However, the mechanistic basis of this phenomenon and what occurs in patients whose cancer is resistant to ICIs remain unclear. The present study aimed to answer these questions. Materials and Methods: We analyzed mutations in mouse 4T1 mammary-gland-derived cancer cells expressing the hemagglutinin antigen (4T1-HA), which were grown in either wild-type mice or cytotoxic T-lymphocyte (CTL)-loaded immunocompromised mice (RAG-/- + ACT) under immune stress. These mutations were compared to those in 4T1-HA cells grown in RAG-/- mice without immune stress as a control. Results: The number of gene mutations, the tumor mutation burden (TMB) and microsatellite instability (MSI) scores were increased in the cancer cells under immune stress. The mutations in the antigen protein were such that the protein retained its immunogenicity and could still function as a neoantigen. Repeated immune recognition of additional neoantigens may lead to the kangaroo-tail survival phenomenon. The common genetic mutations of the analyzed 4T1-HA cells under immune stress included genes related to immune response. Analysis of alternative splicing of genes showed that are accumulated gene alterations under immune stress related to cancer-cell proliferation. Copy-number variation (CNV) analysis indicated that normal-antigen presentation and immune responses may be impaired under immune stress. Conclusion: Cancer cells, under immune stress, may acquire both immune escape capabilities and increased immunogenicity. This dual effect could lead to either resistance or response to ICIs, respectively. [ABSTRACT FROM AUTHOR]

Abstract Glaucoma is a sight threatening neurodegenerative condition of the optic nerve head associated with ageing and marked by the loss of retinal ganglion cells. Mitochondrial dysfunction plays a crucial role in the pathogenesis of neurodegeneration in the most prevalent type of glaucoma: primary open angle glaucoma (POAG). All previous mitochondrial genome sequencing studies in POAG analyzed mitochondrial DNA (mtDNA) isolated from peripheral blood leukocytes and have not evaluated cells derived from ocular tissue, which better represent the glaucomatous disease context. In this study, we evaluated mitochondrial genome variation and heteroplasmy using massively parallel sequencing of mtDNA in a cohort of patients with POAG, and in a subset assess the role of somatic mitochondrial genome mutations in disease pathogenesis using paired samples of peripheral blood leukocytes and ocular tissue (Tenon’s ocular fibroblasts). An enrichment of potentially pathogenic nonsynonymous mtDNA variants was identified in Tenon’s ocular fibroblasts from participants with POAG. The absence of oxidative DNA damage and predominance of transition variants support the concept that errors in mtDNA replication represent the predominant mutation mechanism in Tenon’s ocular fibroblasts from patients with POAG. Pathogenic somatic mitochondrial genome mutations were observed in people with POAG. This supports the role of somatic mitochondrial genome variants in the etiology of glaucoma.

Abstract Background Understanding the molecular basis of sport mutations in fruit trees has the potential to accelerate generation of improved cultivars. Results For this, we analyzed the genome of the apple tree that developed the RubyMac phenotype through a sport mutation that led to the characteristic fruit coloring of this variety. Overall, we found 46 somatic mutations that distinguished the mutant and wild-type branches of the tree. In addition, we found 54 somatic gene conversions (i.e., loss-of-heterozygosity mutations) that also distinguished the two parts of the tree. Approximately 20% of the mutations were specific to individual cell lineages, suggesting that they originated from the corresponding meristematic layers. Interestingly, the de novo mutations were enriched for GC = > AT transitions while the gene conversions showed the opposite bias for AT = > GC transitions, suggesting that GC-biased gene conversions have the potential to counteract the AT-bias of de novo mutations. By comparing the gene expression patterns in fruit skins from mutant and wild-type branches, we found 56 differentially expressed genes including 18 involved in anthocyanin biosynthesis. While none of the differently expressed genes harbored a somatic mutation, we found that some of them in regions of the genome that were recently associated with natural variation in fruit coloration. Conclusion Our analysis revealed insights in the characteristics of somatic change, which not only included de novo mutations but also gene conversions. Some of these somatic changes displayed strong candidate mutations for the change in fruit coloration in RubyMac.

Background: The immune response against tumors relies on distinguishing between self and non-self, the basis of cancer immunotherapy. Neoantigens from somatic mutations are central to many immunotherapeutic strategies and understanding their landscape in breast cancer is crucial for targeted interventions. We aimed to profile neoantigens in Kenyan breast cancer patients using genomic DNA and total RNA from paired tumor and adjacent non-cancerous tissue samples of 23 patients. Methods: We sequenced the genome-wide exome (WES) and RNA, from which somatic mutations were identified and their expression quantified, respectively. Neoantigen prediction focused on human leukocyte antigens (HLA) crucial to cancer, HLA type I. HLA alleles were predicted from WES data covering the adjacent non-cancerous tissue samples, identifying four alleles that were present in at least 50% of the patients. Neoantigens were deemed potentially immunogenic if their predicted median IC50 (half-maximal inhibitory concentration) binding scores were ≤500nM and were expressed [transcripts per million (TPM) >1] in tumor samples. Results: An average of 1465 neoantigens covering 10260 genes had ≤500nM median IC50 binding score and >1 TPM in the 23 patients and their presence significantly correlated with the somatic mutations (R 2 = 0.570, P =0.001). Assessing 58 genes reported in the catalog of somatic mutations in cancer (COSMIC, v99) to be commonly mutated in breast cancer, 44 (76%) produced >2 neoantigens among the 23 patients, with a mean of 10.5 ranging from 2 to 93. For the 44 genes, a total of 477 putative neoantigens were identified, predominantly derived from missense mutations (88%), indels (6%), and frameshift mutations (6%). Notably, 78% of the putative breast cancer neoantigens were patient-specific. HLA-C*06:01 allele was associated with the majority of neoantigens (194), followed by HLA-A*30:01 (131), HLA-A*02:01 (103), and HLA-B*58:01 (49). Among the genes of interest that produced putative neoantigens were MUC17 , TTN , MUC16 , AKAP9 , NEB , RP1L1 , CDH23 , PCDHB10 , BRCA2 , TP53 , TG , and RB1. Conclusions: The unique neoantigen profiles in our patient group highlight the potential of immunotherapy in personalized breast cancer treatment as well as potential biomarkers for prognosis. The unique mutations producing these neoantigens, compared to other populations, provide an opportunity for validation in a much larger sample cohort. [ABSTRACT FROM AUTHOR]

Background: The majority of patients with bladder cancer suffer from tumour recurrence. Identifying prognostic factors for tumour recurrence is crucial for treatment and follow-up in affected patients. The study aimed to assess the impact of somatic mutations in bladder cancer on patient outcomes and tumour recurrence. Methods: The study group comprised 46 patients with urothelial bladder cancers referred for transurethral resection of the tumour. A molecular study on tumour-derived DNA was performed using next-generation sequencing. Somatic mutations were screened in 50 genes involved in carcinogenesis. Results: We identified 81 variants in 23 genes, including 54 pathogenic mutations, 18 likely pathogenic variants, and 9 variants of unknown significance. The most frequently mutated genes were FGFR3, PIK3CA, and TP53 in 52%, 35%, and 24% of tumours, respectively. The average tumour-free survival was significantly longer in cases with mutations in the PIK3CA gene (p = 0.02), and mutations in the PIK3CA gene were associated with a decreased risk of tumour recurrence (Hazard Ratio = 0.26; 95% CI: 0.11–0.62; p = 0.018). Conclusions: The PIK3CA gene was shown to be a predictive marker of a low risk of bladder tumour recurrence. Molecular screening of bladder cancers supported predictive biomarkers of tumour recurrence and showed that tumour-free survival is molecularly determined. [ABSTRACT FROM AUTHOR]

CRISPR/Cas9 is the most popular genome editing platform for investigating gene function or improving traits in plants. The specificity of gene editing has yet to be evaluated at a genome-wide scale in seed-propagated Camelina sativa (L.) Crantz (camelina) or clonally propagated Solanum tuberosum L. (potato). In this study, seven potato and nine camelina stable transgenic Cas9-edited plants were evaluated for on and off-target editing outcomes using 55x and 60x coverage whole genome shotgun sequencing data, respectively. For both potato and camelina, a prevalence of mosaic somatic edits from constitutive Cas9 expression was discovered as well as evidence of transgenerational editing in camelina. CRISPR/Cas9 editing provided negligible off-target activity compared to background variation in both species. The results from this study guide deployment and risk assessment of genome editing in commercially relevant traits in food crops. [ABSTRACT FROM AUTHOR]

Background: Thyroidectomy is increasingly performed for suspected malignancy. This cohort study aimed to identify genetic markers associated with malignancy and determine the molecular landscape of papillary thyroid carcinoma (PTC) through next‐generation sequencing (NGS) in patients undergoing total thyroidectomy. Patients and Methods: Among 116 surgical candidates, 103 patients (age = 42.9 ± 13.7 years; Male: Female = 14:89) with benign or malignant thyroid nodules were eligible. Live thyroid tissue samples harvested intraoperatively with adequate DNA and RNA yield were subjected to NGS on the Illumina NovaSeq 6000 platform for genomic and transcriptomic analysis, respectively. Results: Histopathology comprised 20 malignant (19.4%) and 83 benign (80.6%) cases, including 16 PTC (15.5%) cases. On NGS, single nucleotide polymorphisms (SNPs) in NTRK1 at NC_000001.11:156879016 on chromosome 1 and ALK at NC_000002.12:29717663 on chromosome 2 were frequent in malignant lesions (p < 0.05). A SNP in ALK at NC_000002.12:29193706 was consistently a homozygous alternate allele across the cohort. DNA‐sequencing of PTC lesions identified recurrent somatic mutations in BRAF (100%), ALK (56.3%), RET (18.8%), PIK3CA (12.5%), NTRK1 (12.5%), NTRK2 (87.5%), NTRK3 (12.5%), NRAS (6.3%), and PTCH1 (31.3%) genes. RNA sequencing revealed novel fusion genes, including MKRN1‐BRAF, RN7SL1‐CDH1, IRF2BPL‐MED12, MED12‐IRF2BPL, CPM‐MDM2, and AC005895.3‐PDGFRB. In receiver operative characteristics analysis, the AUCs of ALK mutation predicting recurrence and metastases were 0.818 and 0.783. Conclusion: This Indian study identified novel somatic mutations and fusion genes in PTC, revealing a distinct genomic landscape with implications in precision diagnostics and personalized therapies. NGS with intraoperative live sampling shows promise in prognostication and therapeutic optimization of advanced/metastatic PTC cases. Trial Registration No: CTRI/2020/09/027607 dt 04/09/2020; REF/2020/08/036119. [ABSTRACT FROM AUTHOR]

Introduction: Retinoblastoma is initiated by inactivation of RB1 gene, but additional alterations may be required for tumor progression. Substitution and INDEL variants in different genes, aside RB1, are infrequent, while large copy number variants (CNVs) like gains on 1q, 2p, 6p and loss on 16q are common, they include oncogenes or tumor suppressors and are typical of retinoblastoma. Aim: To provide the molecular profile that is useful for prognosis and understanding of retinoblastoma development. Methods: To identify genomic variants in six retinoblastoma tumors whole exome sequencing and informatic analysis were performed. Results: RB1 was the only gene with nonsense or frameshift mutations. SNVs in other 11 genes were missense and at non-canonical splice-sites, all nonpathogenic. CNVs, similar to those reported, were identified in all retinoblastoma tumors. The most frequent were 1q gain and 16q loss. Additionally, deletions were identified on 13q, including RB1 gene, and on the X chromosome, including BCOR gene, the most frequently mutated, after RB1, in retinoblastoma. The number of CNVs detected in each tumor was between 1 and 7, depending on the age at diagnosis. Conclusion: The analysis of genomic alterations in retinoblastoma is useful to understand the severity of tumor progression and to apply appropriate treatments. [ABSTRACT FROM AUTHOR]

Background: Colorectal cancer (CRC) is the leading cancer among Saudis, and mutations in BRAF , KRAS , and NRAS genes are therapeutically significant due to their association with pathways critical for cell cycle regulation. This study evaluates the prevalence and frequency of somatic mutations in these actionable genes in Saudi CRC patients and assesses their pathogenicity with bioinformatics methods. Methodology: The study employed the TruSight Tumor 15 next-generation sequencing (NGS) panel on 86 colorectal cancer (CRC) samples to detect somatic mutations in BRAF , KRAS , and NRAS genes. Bioinformatic analyses of NGS sequences included variant annotation with ANNOVAR, pathogenicity prediction, variant reclassification with CancerVar, and extensive structural analysis. Additionally, molecular docking assessed the binding of Encorafenib to wild-type and mutant BRAF proteins, providing insights into the therapeutic relevance of pathogenic variants. Results: Out of 86 tumor samples, 40 (46.5%) harbored somatic mutations within actionable genes (BRAF : 2.3%, KRAS : 43%, NRAS : 2.3%). Fourteen missense variants were identified (BRAF : n = 1, KRAS : n = 11, NRAS : n = 2). Variants with strong clinical significance included BRAF V600E (2.32%) and KRAS G12D (18.60%). Variants with potential clinical significance included several KRAS and an NRAS mutation, while variants of unknown significance included KRAS E49K and NRAS R102Q. One variant was novel: NRAS R102Q, and two were rare: KRAS E49K and G138E. We further extended the CancerVar prediction capability by adding new pathogenicity prediction tools. Molecular docking demonstrated that Encorafenib inhibits the V600E variant BRAF protein less effectively compared to its wild-type counterpart. Conclusion: Overall, this study highlights the importance of comprehensive molecular screening and bioinformatics in understanding the mutational landscape of CRC in the Saudi population, ultimately improving targeted drug treatments. [ABSTRACT FROM AUTHOR]

The increased sensitivity of novel DNA sequencing techniques has made it possible to identify somatic mutations in small circulating clones of haematopoietic stem cells. When the mutation affects a 'driver' gene, the mutant clone gains a competitive advantage and has the potential to expand over time, a phenomenon referred to as clonal haematopoiesis (CH), which is emerging as a new risk factor for various non-haematological conditions, most notably cardiovascular disease (e.g. heart failure). Dilated cardiomyopathy (DCM) is a form of non-ischaemic heart failure that is characterized by a heterogeneous aetiology. The first evidence is arising that CH plays an important role in the disease course in patients with DCM, and a strong association of CH with multiple aetiologies of DCM has been described (e.g. inflammation, chemotherapy, and atrial fibrillation). The myocardial inflammation induced by CH may be an important trigger for DCM development for an already susceptible heart, e.g. in the presence of genetic variants, environmental triggers, and comorbidities. Studies investigating the role of CH in the pathogenesis of DCM are expected to increase rapidly. To move the field forward, it will be important to report the methodology and results in a standardized manner, so results can be combined and compared. The accurate measurement of CH in patients with DCM can provide guidance of specific (anti-inflammatory) therapies, as mutations in the CH driver genes prime the inflammasome pathway. [ABSTRACT FROM AUTHOR]

Summary: This study compared decitabine exposure when administered IV (DEC‐IV) at a dose of 20 mg/m2 for 5‐days with orally administered decitabine with cedazuridine (DEC‐C), as well as the clinical efficacy and safety of DEC‐C in patients with acute myeloid leukaemia (AML) who were ineligible for intensive induction chemotherapy. In all, 89 patients were randomised 1:1 to DEC‐IV or oral DEC‐C (days 1–5 in a 28‐day treatment cycle), followed by 5 days of the other formulation in the next treatment cycle. All patients received oral DEC‐C for subsequent treatment cycles until treatment discontinuation. Equivalent systemic decitabine exposures were demonstrated (5‐day area under the curve ratio between the two decitabine formulations of 99.64 [90% confidence interval 91.23%, 108.80%]). Demethylation rates also were similar (≤1.1% difference). Median overall survival (OS), clinical response and safety profile with oral DEC‐C were consistent with those previously observed with DEC‐IV. Next‐generation sequencing was performed to identify molecular abnormalities that impact OS and TP53 mutations were associated with a poor outcome. These findings support the use of oral DEC‐C in patients with AML. [ABSTRACT FROM AUTHOR]

Background: Brain arteriovenous malformation (bAVM) is an abnormal vascular mass with disordered arteriovenous connection. Endothelial KRAS mutation is common in bAVM. In vivo studies have demonstrated that mutations of KRAS in somatic cells can induce bAVM-like angiogenesis, suggesting that KRAS gene may play a key role in the development and progression of bAVM. Summary: In this article, we will provide a comprehensive review of action mechanisms of KRAS mutations in the development of bAVM and summarize potential targeting drugs for KRAS mutations in bAVM somatic cells. Key Message: KRAS mutation in human brain endothelial cells is a key driver in the pathogenesis of sporadic cerebral arteriovenous malformations. It is of great clinical importance to explore and summarize the changes in the signaling pathway induced by KRAS mutation, which may provide additional targets for the treatment of sporadic bAVM development. [ABSTRACT FROM AUTHOR]

Background/Objectives: Metastatic colorectal cancer remains a fatal disease, with a 5-year survival rate lower than 15%. The most common metastatic sites are the lungs and the liver, while skin metastases are very rare and often indicate a poor prognosis with a lower survival rate. Methods. Herein, we present the clinical case of a 62-year-old female patient with rectal cancer metastases to the skin of the anogenital and abdominal regions, diagnosed 2 years after completion of treatment of the underlying disease. Results: Histological examination of the skin lesions revealed adenocarcinoma, and expression of the same immunohistochemical markers was also found in the primary tumor and in the cutaneous metastases. However, next-generation sequencing demonstrated differences in the mutational profiles of the primary tumor and metastasis to the skin. Somatic mutations in the APC, TP53, and PTPN11 genes were revealed in primary rectal adenocarcinoma, but another pathogenic TP53 mutation and a frameshift variant in the DYNC1I1 gene were found in cutaneous metastases. The patient underwent several courses of FOLFOX6 chemotherapy in combination with bevacizumab, but the treatment was unsuccessful. An analysis of 50 clinical cases from the literature concerning various manifestations of cutaneous metastases of rectal cancer showed a median survival of 8.5 months from the time of detection of the skin lesions. Conclusions: In this regard, careful skin examination of patients with rectal cancer and timely detection of cutaneous metastases are essential steps in the follow-up of patients who have undergone treatment of the primary tumor. [ABSTRACT FROM AUTHOR]

Les maladies auto-inflammatoires (MAI) sont des maladies liées à des dérégulations de l'immunité innée au cours desquelles les patients présentent classiquement des manifestations inflammatoires systémiques, en particulier de la fièvre, des éruptions cutanéomuqueuses, des arthromyalgies et des douleurs abdominales avec une élévation des biomarqueurs sanguins d'inflammation. Lors de leur découverte, ces maladies ont été associées à des mutations constitutionnelles dans des gènes codant pour des protéines intervenant dans l'immunité innée et il était considéré que ces maladies devaient donc débuter dans l'enfance. Ce dogme des mutations constitutionnelles dans les MAI n'est plus aussi incontestable puisque depuis 2005, plusieurs cas de mosaïcismes ont été rapportés dans la littérature, initialement dans les cryopyrinopathies, mais également dans d'autres MAI chez des patients avec des phénotypes cliniques évidents et un début tardif d'expression de la maladie, en particulier dans le syndrome VEXAS (Vacuoles, E1 enzyme, X-linked, Autoinflammatory, Somatic syndrome) et très récemment dans le gène MEFV. Les techniques de séquençage de nouvelle génération sont plus sensibles que le Sanger pour détecter les mosaïcismes. Ainsi, lorsqu'un diagnostic clinique semble évident mais qu'aucune mutation constitutionnelle n'est retrouvée par les analyses génétiques avec faible profondeur, il est utile de discuter avec les généticiens experts afin d'envisager une autre approche génétique que ce soit chez un enfant ou un adulte. Cela modifie les situations devant lesquelles les cliniciens peuvent évoquer ces maladies. Cette revue fait le point sur les cas de mosaïcisme décrits dans les MAI à ce jour. Systemic auto-inflammatory diseases (SAIDs) are disorders associated with deregulation of innate immunity in which patients present classically with systemic inflammatory manifestations, in particular fever, skin-mucosal rashes, arthromyalgia and abdominal pain, with an increase in blood biomarkers of inflammation. At the time of their discovery, these diseases were associated with constitutional mutations in genes encoding proteins involved in innate immunity, and it was then considered that they had to begin in childhood. This dogma of constitutional mutations in SAIDs is no longer so unquestionable, since 2005 several cases of mosaicism have been reported in the literature, initially in cryopyrinopathies, but also in other SAIDs in patients with obvious clinical phenotypes and late onset of disease expression, in particular in the VEXAS syndrome (Vacuoles, E1 enzyme, X-linked, Autoinflammatory, Somatic Syndrome) and very recently in MEVF gene. Next-generation sequencing techniques are more sensitive than Sanger for detecting mosaicisms. So, when a clinical diagnosis seems obvious but no constitutional mutation is found by low-depth genetic analysis, it is useful to discuss with expert geneticists whether to consider another genetic approach in a child or an adult. This modifies the situations in which clinicians can evoke these diseases. This review provides an update on mosaicism in SAIDs. [ABSTRACT FROM AUTHOR]

Understanding the functional impact of genetic mutations on protein structures is essential for advancing cancer research and developing targeted therapies. The main challenge lies in accurately mapping these mutations to protein structures and analysing their effects on protein function. To address this, Mut-Map (https://genemutation.org/) is a comprehensive computational pipeline designed to integrate mutation data from the Catalogue Of Somatic Mutations In Cancer database with protein structural data from the Protein Data Bank and AlphaFold models. The pipeline begins by taking a UniProt ID and proceeds through mapping corresponding Protein Data Bank structures, renumbering residues, and assessing disorder percentages. It then overlays mutation data, categorizes mutations based on structural context, and visualizes them using advanced tools like MolStar. This approach allows for a detailed analysis of how mutations may disrupt protein function by affecting key regions such as DNA interfaces, ligand-binding sites, and dimer interactions. To validate the pipeline, a case study on the TP53 gene, a critical tumour suppressor often mutated in cancers, was conducted. The analysis highlighted the most frequent mutations occurring at the DNA-binding interface, providing insights into their potential role in cancer progression. Mut-Map offers a powerful resource for elucidating the structural implications of cancer-associated mutations, paving the way for more targeted therapeutic strategies and advancing our understanding of protein structure–function relationships. [ABSTRACT FROM AUTHOR]

Purpose: To perform a molecular profiling of the metastases from papillary thyroid carcinomas (PTCs) and poorly differentiated thyroid carcinomas (PDTCs). Methods: We retrieved and analyzed the molecular and clinical features of 136 metastases from PTCs and 35 metastases from PDTCs subjected to targeted DNA sequencing, from cBioPortal. The clinicopathological data included the number and location of the metastases, and genomic data included mutations, translocations, copy number alterations and fraction of the genome altered (FGA). Results: Bone metastases from PTCs had a lower frequency of BRAF mutations than the lymph node metastases (LNMs) (43% vs 88%, p < 0.01), and a higher frequency of RBM10 and NRAS mutations than the LNMs (21% vs 3% for both, p < 0.05). The FGA of the bone metastases was higher than the FGA of the lung metastases (5.6% vs 1.3%, p < 0.05). The frequency of RET translocations was higher in the lung metastases from PTCs than the LNMs (15% vs 3%, p < 0.05). The LNMs from PTC patients harboring 4 or more distant metastases (DMs) had a higher frequency of TERT promoter mutations than the LNMs from patients harboring less than 4 DMs (96% vs 65%, p < 0.001). SDHA gene amplifications were enriched in the bone metastases from PDTCs and absent in the LNMs (38% vs 0%, p < 0.05). Conclusion: Metastases from PTCs and PDTCs harbor clinically relevant alterations affecting distinct body locations, such as NRAS and RBM10 mutations, RET translocations and SDHA amplifications that may be explored therapeutically. [ABSTRACT FROM AUTHOR]

Glaucoma is a sight threatening neurodegenerative condition of the optic nerve head associated with ageing and marked by the loss of retinal ganglion cells. Mitochondrial dysfunction plays a crucial role in the pathogenesis of neurodegeneration in the most prevalent type of glaucoma: primary open angle glaucoma (POAG). All previous mitochondrial genome sequencing studies in POAG analyzed mitochondrial DNA (mtDNA) isolated from peripheral blood leukocytes and have not evaluated cells derived from ocular tissue, which better represent the glaucomatous disease context. In this study, we evaluated mitochondrial genome variation and heteroplasmy using massively parallel sequencing of mtDNA in a cohort of patients with POAG, and in a subset assess the role of somatic mitochondrial genome mutations in disease pathogenesis using paired samples of peripheral blood leukocytes and ocular tissue (Tenon's ocular fibroblasts). An enrichment of potentially pathogenic nonsynonymous mtDNA variants was identified in Tenon's ocular fibroblasts from participants with POAG. The absence of oxidative DNA damage and predominance of transition variants support the concept that errors in mtDNA replication represent the predominant mutation mechanism in Tenon's ocular fibroblasts from patients with POAG. Pathogenic somatic mitochondrial genome mutations were observed in people with POAG. This supports the role of somatic mitochondrial genome variants in the etiology of glaucoma. [ABSTRACT FROM AUTHOR]

Objective: Identification of driver mutations in tumors is an extremely important task in oncology for the choice of treatment strategy and assessment of therapy efficacy. In many cases, especially in disease monitoring, there is a need to detect a small number of copies of the mutant allele against the background of excessive content of wild-type DNA. Methods: Genomic DNA was isolated from tumor tissue in paraffine blocks and amplified using polymerase-chain reaction (PCR) with blocking of wild-type DNA amplification via addition of locked-nucleic acid (LNA) oligonucleotides. Fluorescently labelled PCR-product enriched by IDH-mutant alleles was hybridized on a biochip with immobilized oligonucleotide probes which was able to determine 5 mutations in the IDH1 gene and 2 mutations in the IDH2 gene. Results and Discussion: The method was developed and tested on a collection of 26 samples of paraffinized tumor tissue (glioma, glioblastoma, chondrosarcoma). In three cases, R132C, R132L, and R132H mutations in the IDH1 gene were detected in tumor samples with low representation of the mutant allele. The limit of detection of mutant DNA was determined to be 0.1% in the wild-type DNA background. The advantages of the method are simultaneous analysis of multiple targets, simplicity, reliability, and cost-effectiveness. Conclusions: A highly sensitive method for detecting somatic mutations in the IDH1/2 genes by LNA-mediated blocking of amplification of wild-type alleles and hybridization in a biological microchip was developed. We believe that the method may be useful for detecting low-abundance mutations in tumor samples, as well as in circular tumor DNA. [ABSTRACT FROM AUTHOR]

Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is a potential cure for myelodysplastic neoplasms (MDSs) and other hematologic malignancies. This study investigates post-transplantation genetic evolution and telomere dynamics in hematopoietic cells, with a focus on clonal hematopoiesis (CH). We conducted a longitudinal analysis of 21 MDS patients who underwent allo-HSCT between September 2009 and February 2015. Genetic profiles of hematopoietic cells from both recipients and donors were compared at equivalent pre- and post-transplantation time points. Targeted sequencing identified CH-associated mutations, and real-time quantitative PCR measured telomere length. Furthermore, we compared CH incidence between recipients and age-matched controls from the GENIE cohort from routine health checkups. Post-allo-HSCT, 38% of recipients developed somatic mutations not detected before transplantation, indicating de novo CH originating from donor cells. Compared to age-matched healthy controls, recipients showed a significantly higher incidence of CH, suggesting increased susceptibility to genetic changes post-transplant. Telomere length analysis also revealed accelerated shortening in transplanted cells, highlighting the heightened stress and proliferation demands in the new microenvironment. Our findings reveal a notable incidence of donor-derived CH in allo-HSCT recipients, alongside significant telomere attrition. This suggests the potential influence of the marrow microenvironment on genetic and molecular changes in hematopoietic cells. [ABSTRACT FROM AUTHOR]

Background: Understanding the molecular basis of sport mutations in fruit trees has the potential to accelerate generation of improved cultivars. Results: For this, we analyzed the genome of the apple tree that developed the RubyMac phenotype through a sport mutation that led to the characteristic fruit coloring of this variety. Overall, we found 46 somatic mutations that distinguished the mutant and wild-type branches of the tree. In addition, we found 54 somatic gene conversions (i.e., loss-of-heterozygosity mutations) that also distinguished the two parts of the tree. Approximately 20% of the mutations were specific to individual cell lineages, suggesting that they originated from the corresponding meristematic layers. Interestingly, the de novo mutations were enriched for GC = > AT transitions while the gene conversions showed the opposite bias for AT = > GC transitions, suggesting that GC-biased gene conversions have the potential to counteract the AT-bias of de novo mutations. By comparing the gene expression patterns in fruit skins from mutant and wild-type branches, we found 56 differentially expressed genes including 18 involved in anthocyanin biosynthesis. While none of the differently expressed genes harbored a somatic mutation, we found that some of them in regions of the genome that were recently associated with natural variation in fruit coloration. Conclusion: Our analysis revealed insights in the characteristics of somatic change, which not only included de novo mutations but also gene conversions. Some of these somatic changes displayed strong candidate mutations for the change in fruit coloration in RubyMac. [ABSTRACT FROM AUTHOR]

ABSTRACT Background In the 8th edition of the TNM classification, extracapsular spread (ECS) became a factor in classifying the UICC stage of oropharyngeal carcinomas (OPSCC). We aimed to find genetic markers for ECS and to identify differences between HPV/p16‐positive and HPV/p16‐negative cases. Methods We performed targeted next‐generation sequencing on 99 samples of operable OPSCC and a retrospective analysis of clinical data. Results We included 55 HPV/p16‐positive and 44 HPV/p16‐negative patients. We found a significant difference between both groups, particularly in TP53 mutation (p

Peutz-Jeghers syndrome (PJS) is characterized by an increased risk of gynecologic tumors. Gastric-type endocervical adenocarcinoma (GEA) is a rare non-human papillomavirus (HPV)-related tumor. We reported an uncommon case of a 39-year-old woman with PJS who developed GEA, superficial cervical vaginal myofibroblastoma, sex cord-stromal tumors with annular tubules of the ovaries, and cervical and vaginal high-grade squamous interepithelial neoplasia (HSIL). Before being verified GEA, the patient had been experiencing suspicious symptoms for over 9 years, with nabothian cysts and vaginitis being misdiagnosed. HSIL displayed widespread p16 immunostaining, and HPV DNA screening confirmed HPV-18 infection, although GEA was negative. Further, we verified TP53 mutation and HER2 amplification of GEA by fluorescence in situ hybridization (FISH). TP53 was the most commonly mutated gene. The therapy with the anti-HER2 antibody trastuzumab was suggested based on HER2 amplification. We also analyzed the somatic mutations of GEA by whole genome sequencing (WES). There were 157 single nucleotide variations (SNVs) and 215 indels, with all of them being heterozygotes. Nonsynonymous and frameshift insertions were the most common kinds of mutations. The germine STK11 gene mutation was found, which may play an important role in tumor development. According to gene function enrichment analyses, the genomic changes primarily implicated general transcription or expression pathways and cell cycle pathways. In addition, the JAK2/STAT3 pathway could be a major focus of targeted therapy for GEA patients with PJS. Our findings show that the patient with PJS can have a variety of unusual gynecologic tumors. Patients with PJS must have routine gynecological, ultrasonographic, and cytological examinations to detect precursor or early-stage lesions. The patient’s abnormal symptoms must be treated early with caution. A comprehensive genomic study reveals the potential causative genetic factors, therapeutic targets, and chemotherapy resistance of GEA. Further research will focus on the main driving genes, molecular mechanisms, and molecular target therapy in more patients.

BACKGROUND: Cancer genome sequencing enables accurate classification of tumours and tumour subtypes. However, prediction performance is still limited using exome-only sequencing and for tumour types with low somatic mutation burden such as many paediatric tumours. Moreover, the ability to leverage deep representation learning in discovery of tumour entities remains unknown. METHODS: We introduce here Mutation-Attention (MuAt), a deep neural network to learn representations of simple and complex somatic alterations for prediction of tumour types and subtypes. In contrast to many previous methods, MuAt utilizes the attention mechanism on individual mutations instead of aggregated mutation counts. RESULTS: We trained MuAt models on 2587 whole cancer genomes (24 tumour types) from the Pan-Cancer Analysis of Whole Genomes (PCAWG) and 7352 cancer exomes (20 types) from the Cancer Genome Atlas (TCGA). MuAt achieved prediction accuracy of 89% for whole genomes and 64% for whole exomes, and a top-5 accuracy of 97% and 90%, respectively. MuAt models were found to be well-calibrated and perform well in three independent whole cancer genome cohorts with 10,361 tumours in total. We show MuAt to be able to learn clinically and biologically relevant tumour entities including acral melanoma, SHH-activated medulloblastoma, SPOP-associated prostate cancer, microsatellite instability, POLE proofreading deficiency, and MUTYH-associated pancreatic endocrine tumours without these tumour subtypes and subgroups being provided as training labels. Finally, scrunity of MuAt attention matrices revealed both ubiquitous and tumour-type specific patterns of simple and complex somatic mutations. CONCLUSIONS: Integrated representations of somatic alterations learnt by MuAt were able to accurately identify histological tumour types and identify tumour entities, with potential to impact precision cancer medicine.

Background: For effective screening of breast cancer patients for candidates for target therapy with alpelisib, it is necessary to identify activating somatic mutations in the PIK3CA gene by allele specific polymerase chain reaction (PCR); this requires that an optimal list of mutations should be compiled. Aim: To determine the spectrum of somatic mutations in the PIK3CA gene in breast cancer tumors by means of high performance sequencing (next generation sequencing, NGS) and to identify their minimal set for clinical diagnostic testing by allele specific PCR. Methods: Targeted NGS was used to identify mutations in the PIK3CA gene in DNA obtained from paraffin blocks with tumor material from 431 patients with HR+HER2- breast cancer. A set of the most common somatic mutations was also detected by allele specific PCR. Results: We have developed a set of reagents and a protocol for targeted NGS of frequently mutating regions of the PIK3CA and ESR1 genes, which was used to analyze samples from 451 HR+/HER2- breast cancer patients. Clinically significant activating mutations in the PIK3CA gene were found in 32.7% of the samples (141/431). The frequency of the mutant allele ranged from 0.15 to 0.65. Six mutations were most common: c.3140AG p.His1047Arg (69), c.1633GA p.Glu545Lys (32), c.1035TA p.Asn345Lys (12), c.1624GA p.Glu542Lys (9), c.3140AT p.His1047Leu (8), Cys420Arg c.1258TC (3). In total, these mutations amounted to 94.3% (133/141). In 3.5% of the samples (15/431), there were clinically significant somatic mutations in the ESR1 gene: c.1613AG p, Asp538Gly (7), c.1610AC p.Tyr537Ser (6), c.1609TA p.Tyr537Asn (1), c.1610AG p.Tyr537Cys (1), causing resistance to hormone therapy in patients with breast cancer. While rare mutations comprised only 5.7% of our sample, we validated a set of reagents to identify the six mutations described above by allele specific PCR. NGS and PCR were completely concordant. Conclusion: PCR testing of activating somatic mutations of the PIK3CA gene meets the requirements for sensitivity ( 90%) and specificity (100%) for a clinical test and can be used in the selection of patients for targeted therapy with PIK3CA inhibitors.

Aim: to study the relationship between clinical and morphological parameters of skin melanoma and the BRAF status of the tumor in patients with stage I of the disease. Materials and methods. The study was retrospective and included 200 patients with stage I skin melanoma (pT1-2aN0M0), of which BRAF status was assessed in 88 patients. All patients underwent clinical data analysis, an extended morphological study and a molecular genetic study to determine the BRAF V600E mutation in the primary tumor. Results. The median age of patients in the total sample was 61.5 years. Mutation in the BRAF V600E gene was detected in 25 patients (28.4%). Patient age, tumor location and Breslow thickness were recognized as independent predictors of BRAF status of stage I skin melanoma. With an increase in the patient's age by 1 year, the chance of having a BRAF V600E mutation decreased by 3.4% or 1.04 times (OR = 0.966; 95% CI = 0.935–0.999; p = 0.045). When melanoma was localized in the lumbar region, the chance of having a BRAF V600E mutation increased by 15.311 times (95% CI = 1.239–189.142; p = 0.033). With a tumor thickness according to Breslow of more than 0.7 mm, the chance of having a BRAF V600E mutation increased by 2.939 times (95% CI = 1.031-8.376; p = 0.044). With a threshold value of the logistic function of 50%, the sensitivity and specificity of the proposed model were 28.0% and 93.7%, respectively. When the threshold function value is reduced to 25.3%, the sensitivity of the model increases to 68% with a simultaneous drop in specificity to 61.9%. Conclusion. Younger age, greater tumor thickness according to Breslow, and tumor localization in the lumbar region in patients with stage I skin melanoma increase the chance of having a BRAF V600E mutation, while other morphological parameters of the tumor are not associated with BRAF status. However, moderate sensitivity does not allow for a sufficiently accurate determination of the presence of a mutation, thereby strengthening the belief in the need for molecular genetic testing.

Abstract Clonal haematopoiesis of indeterminate potential (CHIP) has been associated with many adverse health outcomes. However, further research is required to understand the critical genes and pathways relevant to CHIP subtypes, evaluate how CHIP clones evolve with time, and further advance functional characterisation and therapeutic studies. Large epidemiological studies are well placed to address these questions but often collect saliva rather than blood from participants. Paired saliva- and blood-derived DNA samples from 94 study participants were sequenced using a targeted CHIP-gene panel. The ten genes most frequently identified to carry CHIP-associated variants were analysed. Fourteen unique variants associated with CHIP, ten in DNMT3A, two in TP53 and two in TET2, were identified with a variant allele fraction (VAF) between 0.02 and 0.2 and variant depth ≥ 5 reads. Eleven of these CHIP-associated variants were detected in both the blood- and saliva-derived DNA sample. Three variants were detected in blood with a VAF > 0.02 but fell below this threshold in the paired saliva sample (VAF 0.008—0.013). Saliva-derived DNA is suitable for detecting CHIP-associated variants. Saliva can offer a cost-effective biospecimen that could both advance CHIP research and facilitate clinical translation into settings such as risk prediction, precision prevention, and treatment monitoring.

Abstract Background Somatic mutations have been observed to induce aldosterone-producing adenomas (APAs). These may be accelerated during pregnancy. Somatic PRKACA mutations are common in cortisol-producing adenomas (CPAs). However, their role in APAs, particularly aldosterone- and cortisol-producing adenomas (A/CPAs), is not well understood. This study aims to investigate the association between PRKACA mutations and the accelerated development of A/CPAs during pregnancy. Case presentation A patient with primary aldosteronism (PA) associated with severe Cushing’s syndrome (CS) underwent surgical resection of an adrenal tumor one year after delivery. Pathologic examination revealed an adrenocortical adenoma characterized primarily by zona glomerulosa hyperplasia. Somatic mutation analysis revealed the presence of the somatic PRKACA mutation, which was validated as a deleterious mutation by various computational databases. Immunohistochemical results showed positive staining for cytochrome P450 family 11 subfamily B member 1 (CYP11B1), cytochrome P450 family 11 subfamily B member 2 (CYP11B2), and luteinizing hormone/chorionic gonadotropin receptor (LHCGR). Our study included a review of 20 previously documented cases of aldosterone- and cortisol-producing adenomas (A/CPAs), two of which were concurrently positive for both CYP11B1 and CYP11B2, consistent with our findings. Conclusion Somatic mutations in PRKACA may correlate with the upregulation of LHCGR, which synergistically drives the accelerated growth of co-secretion tumors during pregnancy, thereby exacerbating disease progression.

Abstract Background Plant meristems are structured organs consisting of distinct layers of stem cells, which differentiate into new plant tissue. Mutations in meristematic layers can propagate into large sectors of the plant. However, the characteristics of meristematic mutations remain unclear, limiting our understanding of the genetic basis of somaclonal phenotypic variation. Results Here, we analyse the frequency and distribution of somatic mutations in an apricot tree. We separately sequence the epidermis (developing from meristem layer 1) and the flesh (developing from meristem layer 2) of several fruits sampled across the entire tree. We find that most somatic mutations (> 90%) are specific to individual layers. Interestingly, layer 1 shows a higher mutation load than layer 2, implying different mutational dynamics between the layers. The distribution of somatic mutations follows the branching of the tree. This suggests that somatic mutations are propagated to developing branches through axillary meristems. In turn, this leads us to the unexpected observation that the genomes of layer 1 of distant branches are more similar to each other than to the genomes of layer 2 of the same branches. Finally, using single-cell RNA sequencing, we demonstrate that layer-specific mutations were only transcribed in the cells of the respective layers and can form the genetic basis of somaclonal phenotypic variation. Conclusions Here, we analyse the frequency and distribution of somatic mutations with meristematic origin. Our observations on the layer specificity of somatic mutations outline how they are distributed, how they propagate, and how they can impact clonally propagated crops.

Simple Summary: The diagnosis and treatment of ovarian cancer still pose many problems; so, it is important to search for effective biomarkers that will allow for the detection of changes in the early stages of the disease. There is more and more talk about the use of circulating tumor DNA in oncology as a promising biomarker and an aid in tailoring individual therapy to patients. We describe what changes we can observe in ctDNA in patients with ovarian cancer and how we can use this information in diagnosis and therapy. Ovarian cancer is the deadliest of all gynecological diseases because its diagnosis and treatment still pose many problems. Surgical excision, hormone therapy, radiation, chemotherapy, or targeted therapy for eradicating the main tumor and halting the spread of metastases are among the treatment options available to individuals with ovarian cancer, depending on the disease's stage. Tumor DNA that circulates in a patient's bodily fluids has been studied recently as a possible novel biomarker for a number of cancers, as well as a means of quantifying tumor size and evaluating the efficacy of cancer therapy. The most significant alterations that we could find in the ctDNA of ovarian cancer patients—such as chromosomal instability, somatic mutations, and methylation—are discussed in this review. Additionally, we talk about the utility of ctDNA in diagnosis, prognosis, and therapy response prediction for these patients. [ABSTRACT FROM AUTHOR]

Tumor‐informed mutation‐based approaches are frequently used for detection of circulating tumor DNA (ctDNA). Not all mutations make equally effective ctDNA markers. The objective was to explore if prioritizing mutations using mutational features—such as cancer cell fraction (CCF), multiplicity, and error rate—would improve the success rate of tumor‐informed ctDNA analysis. Additionally, we aimed to develop a practical and easily implementable analysis pipeline for identifying and prioritizing candidate mutations from whole‐exome sequencing (WES) data. We analyzed WES and ctDNA data from three tumor‐informed ctDNA studies, one on bladder cancer (Cohort A) and two on colorectal cancer (Cohorts I and N). The studies included 390 patients. For each patient, a unique set of mutations (median mutations/patient: 6, interquartile 13, range: 1–46, total n = 4023) were used as markers of ctDNA. The tool PureCN was used to assess the CCF and multiplicity of each mutation. High‐CCF mutations were detected more frequently than low‐CCF mutations (Cohort A: odds ratio [OR] 20.6, 95% confidence interval [CI] 5.72–173, p = 1.73e−12; Cohort I: OR 2.24, 95% CI 1.44–3.52, p = 1.66e−04; and Cohort N: OR 1.78, 95% CI 1.14–2.79, p = 7.86e−03). The detection‐likelihood was additionally improved by selecting mutations with multiplicity of two or above (Cohort A: OR 1.55, 95% CI 1. 14–2.11, p = 3.85e−03; Cohort I: OR 1.78, 95% CI 1.23–2.56, p = 1.34e−03; and Cohort N: OR 1.94, 95% CI 1.63–2.31, p = 2.83e−14). Furthermore, selecting the mutations for which the ctDNA detection method had the lowest error rates, additionally improved the detection‐likelihood, particularly evident when plasma cell‐free DNA tumor fractions were below 0.1% (p = 2.1e−07). Selecting mutational markers with high CCF, high multiplicity, and low error rate significantly improve ctDNA detection likelihood. We provide free access to the analysis pipeline enabling others to perform qualified prioritization of mutations for tumor‐informed ctDNA analysis. [ABSTRACT FROM AUTHOR]

Idiopathic granulomatous mastitis (IGM) is a rare condition characterised by chronic inflammation and granuloma formation in the breast. The aetiology of IGM is unclear. By focusing on the protein-coding regions of the genome, where most disease-related mutations often occur, whole-exome sequencing (WES) is a powerful approach for investigating rare and complex conditions, like IGM. We report WES results on paired blood and tissue samples from eight IGM patients. Samples were processed using standard genomic protocols. Somatic variants were called with two analytical pipelines: nf-core/sarek with Strelka2 and GATK4 with Mutect2. Our WES study of eight patients did not find evidence supporting a clear genetic component. The discrepancies between variant calling algorithms, along with the considerable genetic heterogeneity observed amongst the eight IGM cases, indicate that common genetic drivers are not readily identifiable. With only three genes, CHIT1, CEP170, and CTR9, recurrently altering in multiple cases, the genetic basis of IGM remains uncertain. The absence of validation for somatic variants by Sanger sequencing raises further questions about the role of genetic mutations in the disease. Other potential contributors to the disease should be explored. [ABSTRACT FROM AUTHOR]

Simple Summary: Cancer develops through a complex process involving genetic changes that can lead to uncontrolled cell growth and tumor formation. This research focuses on developing an advanced approach to classify tumors into meaningful subgroups based on somatic mutations. Using machine learning techniques, specifically a deep neural network, and integrating genetic data with known gene interaction networks, we propose a framework for tumor stratification, called D3NS (deep neural network integrated into network-based stratification). This framework identifies patient subtypes predictive for survival and significantly associated with several clinical outcomes (tumor stage, grade and treatment response). We applied D3NS to real-world data from the Cancer Genome Atlas for bladder, ovarian, and kidney cancers. The results demonstrate the potential of this approach to improve cancer stratification, positioning it as a useful base model for cancer research and a promising tool in clinical settings. (1) Background: The identification of tumor subtypes is fundamental in precision medicine for accurate diagnoses and personalized therapies. Cancer development is often driven by the accumulation of somatic mutations that can cause alterations in tissue functions and morphologies. In this work, a method based on a deep neural network integrated into a network-based stratification framework (D3NS) is proposed to stratify tumors according to somatic mutations. (2) Methods: This approach leverages the power of deep neural networks to detect hidden information in the data by combining the knowledge contained in a network of gene interactions, as typical of network-based stratification methods. D3NS was applied using real-world data from The Cancer Genome Atlas for bladder, ovarian, and kidney cancers. (3) Results: This technique allows for the identification of tumor subtypes characterized by different survival rates and significant associations with several clinical outcomes (tumor stage, grade or response to therapy). (4) Conclusion: D3NS can provide a base model in cancer research and could be considered as a useful tool for tumor stratification, offering potential support in clinical settings. [ABSTRACT FROM AUTHOR]

Clonal haematopoiesis of indeterminate potential (CHIP) has been associated with many adverse health outcomes. However, further research is required to understand the critical genes and pathways relevant to CHIP subtypes, evaluate how CHIP clones evolve with time, and further advance functional characterisation and therapeutic studies. Large epidemiological studies are well placed to address these questions but often collect saliva rather than blood from participants. Paired saliva- and blood-derived DNA samples from 94 study participants were sequenced using a targeted CHIP-gene panel. The ten genes most frequently identified to carry CHIP-associated variants were analysed. Fourteen unique variants associated with CHIP, ten in DNMT3A, two in TP53 and two in TET2, were identified with a variant allele fraction (VAF) between 0.02 and 0.2 and variant depth ≥ 5 reads. Eleven of these CHIP-associated variants were detected in both the blood- and saliva-derived DNA sample. Three variants were detected in blood with a VAF > 0.02 but fell below this threshold in the paired saliva sample (VAF 0.008—0.013). Saliva-derived DNA is suitable for detecting CHIP-associated variants. Saliva can offer a cost-effective biospecimen that could both advance CHIP research and facilitate clinical translation into settings such as risk prediction, precision prevention, and treatment monitoring. [ABSTRACT FROM AUTHOR]

Accurate detection and analysis of somatic variants in cancer involve multiple third-party tools with complex dependencies and configurations, leading to laborious, error-prone, and time-consuming data conversions. This approach lacks accuracy, reproducibility, and portability, limiting clinical application. Musta was developed to address these issues as an end-to-end pipeline for detecting, classifying, and interpreting cancer mutations. Musta is based on a Python command-line tool designed to manage tumor-normal samples for precise somatic mutation analysis. The core is a Snakemake-based workflow that covers all key cancer genomics steps, including variant calling, mutational signature deconvolution, variant annotation, driver gene detection, pathway analysis, and tumor heterogeneity estimation. Musta is easy to install on any system via Docker, with a Makefile handling installation, configuration, and execution, allowing for full or partial pipeline runs. Musta has been validated at the CRS4-NGS Core facility and tested on large datasets from The Cancer Genome Atlas and the Beijing Institute of Genomics. Musta has proven robust and flexible for somatic variant analysis in cancer. It is user-friendly, requiring no specialized programming skills, and enables data processing with a single command line. Its reproducibility ensures consistent results across users following the same protocol. [ABSTRACT FROM AUTHOR]

Plant architecture is shaped by the production of new organs, most of which emerge postembryonically. This process includes the formation of new lateral branches along existing shoots. Current evidence supports a detached-meristem model as the cellular basis of lateral shoot initiation. In this model, a small number of undifferentiated cells are sampled from the periphery of the shoot apical meristem (SAM) to act as precursors for axillary buds, which eventually develop into new shoots. Repeated branching thus creates cellular bottlenecks (i.e. somatic drift) that affect how de novo (epi)genetic mutations propagate through the plant body during development. Somatic drift could be particularly relevant for stochastic DNA methylation gains and losses (i.e. spontaneous epimutations), as they have been shown to arise rapidly with each cell division. Here, we formalize a special case of the detached-meristem model, where precursor cells are randomly sampled from the SAM periphery in a way that maximizes cell lineage independence. We show that somatic drift during repeated branching gives rise to a mixture of cellular phylogenies within the SAM over time. This process is dependent on the number of branch points, the strength of drift as well as the epimutation rate. Our model predicts that cell-to-cell DNA methylation heterogeneity in the SAM converges to nonzero states during development, suggesting that epigenetic variation is an inherent property of the SAM cell population. Our insights have direct implications for empirical studies of somatic (epi)genomic diversity in long-lived perennial and clonal species using bulk or single-cell sequencing approaches. [ABSTRACT FROM AUTHOR]

Advancements in micropropagation techniques have made it easier to produce large numbers of cannabis clones, but these methods may also introduce genetic instability over successive generations. This instability often manifests as somaclonal variation, characterized by the progressive accumulation of genetic mutations or epigenetic alterations with each subculture. In this study, we examined how mutations accumulate in cannabis clones subjected to 6–11 subcultures. Using genotyping-by-sequencing, we identified 9405 polymorphic variants across 70 clones. The analysis revealed a correlation between the number of subcultures and the frequency of these mutations, revealing that genetic changes accumulate over successive subcultures despite clones sharing the same chronological age. Furthermore, we evaluated the functional impacts of accumulated mutations, with particular attention to implications on gene function and overall plant health. While rare, 14 high-impact variants were identified in genes that are important for plant development. Notably, six variants were also found in genes related to cannabinoid and terpene synthesis pathways, potentially affecting the plant's biochemical composition. These findings highlight the need for genetic assessments in micropropagation protocols, impacting plant breeding and conservation. Understanding genetic variations in clonally propagated plants optimizes practices for stability. Crucial for cannabis and horticultural plants, it emphasizes techniques to prevent genetic decay and ensure viability. [ABSTRACT FROM AUTHOR]

The mutation rate is a pivotal biological characteristic, intricately governed by natural selection and historically garnering considerable attention. Recent advances in high-throughput sequencing and analytical methodologies have profoundly transformed our understanding in this domain, ushering in an unprecedented era of mutation rate research. This paper aims to provide a comprehensive overview of the key concepts and methodologies frequently employed in the study of mutation rates. It examines various types of mutations, explores the evolutionary dynamics and associated theories, and synthesizes both classical and contemporary hypotheses. Furthermore, this review comprehensively explores recent advances in understanding germline and somatic mutations in animals and offers an overview of experimental methodologies, mutational patterns, molecular mechanisms, and driving forces influencing variations in mutation rates across species and tissues. Finally, it proposes several potential research directions and pressing questions for future investigations. [ABSTRACT FROM AUTHOR]