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Summary: Next Generation Sequencing (NGS) technologies offer affordable ways to study craniofacial growth and development patterns in orthodontic patients, including patients with rare congenital disorders, to learn more about the gene regulatory networks that govern various aspects of craniofacial complex [Display omitted] With the development of Sanger DNA Sequencing in the 1970's, the scientific community gained a new tool to understand relationships between phenotype and genotype. This methodology allowed one to sequence small regions of DNA in the human genome, but was expensive, time consuming and used radioactive labels; making it impractical to use to study an entire human genome. As technologies improved, DNA amplification by polymerase chain reaction (PCR) in the 1980's allowed scientists to selectively amplify a targeted DNA sequence. This advancement, along with the utilization of fluorescently–labeled nucleotides significantly influenced the automation of sequencing technology. Today, Next–Generation Sequencing (NGS) can affordably sequence millions of DNA fragments simultaneously and is being used to examine the entire code of the human genome. This capability is revolutionary and offers new hope in identifying key genes involved in numerous craniofacial anomalies. [ABSTRACT FROM AUTHOR]

• Genetic defects play a vital role in the pathogenesis of Primary ovarian insufficiency (POI) • TWNK mutation impaired the ovarian function by dysfunctional mitochondria. • Specific variants localizing in different locus of TWNK might induce heterogeneous phenotypes. • The genetic screening of patients with POI would be useful for early recognition of other disease or other phenotypes of syndromic POI. Primary ovarian insufficiency (POI) is defined as cessation of ovarian function before the age of 40 years, which is characterized by amenorrhoea, infertility, elevated gonadotrophin level and sex-steroid deficiency. The phenotypes of POI are heterogeneous, including isolated and syndromic forms. Perrault syndrome (PS), characterized by sensorineural hearing loss (SNHL) and ovarian dysfunction before 40 years in females, is one type of syndromic POI. Genetic defects play a vital role in the pathogenesis of POI. To illustrate the genetic causation of Perrault syndrome, we performed whole exome sequencing (WES) in one pedigree with the disease, and identified a novel homozygous mutation in TWNK (c.1388G > A, p.R463Q). TWNK encodes a hexameric DNA helicase in mitochondria and plays a critical role in mtDNA replication. In order to determine the effect of the novel mutation on the mitochondrial function, we generated immortalized cell lines by infecting lymphocytes from the family members with EB virus in vitro. Functional studies found that TWNK p.R463Q impaired mtDNA replication and the respiration potential of mitochondria, while the ROS level remains unaffected. Our study provided evidence that TWNK mutation impaired the ovarian function by dysfunctional mitochondria. Moreover, considering the patients here presented POI onset earlier than SNHL, specific variants localizing in different locus of TWNK might induce heterogeneous phenotypes, indicating that the genetic screening of patients with POI would be useful for early recognition of other disease or other phenotypes of syndromic POI. [ABSTRACT FROM AUTHOR]

• This study demonstrates for the first time that LGI1 may be a candidate pathogenic gene of FMTLE. • This study reports two novel variants of LGI1 in patients with FMTLE. • Focal to bilateral tonic-clonic seizures were a common seizure type in FMTLE. To expand the clinical phenotype and mutation spectrum of familial mesial temporal lobe epilepsy (FMTLE) and provide a new perspective for exploring the pathological mechanisms of epilepsy caused by leucine-rich glioma inactivated 1 (LGI1) variants. We reported clinical data from two families with FMTLE and screened patients for variants in the LGI1 gene using Whole-exome sequencing and Sanger sequencing. The clinical features of FMTLE were analysed. The pathogenicity of the causative loci was assessed according to the American College of Medical Genetics and Genomics guidelines, and potential pathogenic mechanisms were predicted through multiple bioinformatics and molecular dynamics software. We identified two novel LGI1 truncating variants within two large families with FMTLE: LGI1 (c.1174C>T, p.Q392X) and LGI1 (c.703C>T, p.Q235X). Compared to previous reports, we found that focal to bilateral tonic-clonic seizures are a common type of seizure in FMTLE. The clinical phenotypes of patients with FMTLE caused by LGI1 variants were relatively mild, and all patients responded well to valproic acid. Bioinformatics analyses and molecular dynamics simulations showed that protein structure and interactions were considerably weakened or damaged as a result of both variants. This study presents the first report identifying LGI1 as a potential novel pathogenic gene within FMTLE families, thereby broadening the mutation spectrum associated with FMTLE. The findings of this study offer novel insights and avenues for understanding the intricate molecular mechanisms underlying LGI1 variants and their correlations with patient phenotypes. This study proposes the possibility of familial focal epilepsy syndromes overlapping. [ABSTRACT FROM AUTHOR]

This study aimed to explore the genetic causes of agenesis of the corpus callosum (ACC) and assess the utility of karyotype analysis, copy number variation sequencing (CNV-seq), and whole-exome sequencing (WES) to genetically diagnose fetal ACC. We retrospectively examined 40 fetuses diagnosed with ACC who underwent prenatal ultrasonography or magnetic resonance imaging between January 2019 and October 2023. Genetic tests were conducted on the fetuses using karyotype analysis or CNV-seq as the first-line diagnosis. WES was performed if aneuploid and pathogenic CNVs were excluded. Among the 40 fetuses, 29 (72 %) had non-isolated ACC and 11 (28 %) had isolated ACC. Cerebellar dysplasia and hydrocephalus were the most common abnormal developments in the central nervous system. Twenty-eight patients underwent karyotype analysis, with a detection rate of 14 % (4/28). Twenty-six patients underwent CNV-seq; three patients were found to have pathogenic CNVs, with a detection rate of 12 % (3/26). Thirty-three fetuses with no findings of karyotype analysis or CNV-seq were subsequently tested using WES, with a detection rate of 36 % (12/33). Overall, the total diagnostic yield was 48 % (19/40), and monogenic etiology accounted for 30 % (12/40). The genetic detection rate of fetal non-isolated ACC (62 %, 18/29) was higher than that of isolated ACC (9 %, 1/11). Prenatal genetic analysis of fetuses with ACC is clinically significant, with monogenic disorders being the main cause. WES may enhance the detection rate of fetuses with ACC with negative karyotype analysis or CNV-seq results. [ABSTRACT FROM AUTHOR]

VATER/VACTERL-like association is associated with adverse pregnancy outcomes. Genetic evidence of this disorder is sporadic. In this study, we aimed to provide genetic insights to improve the diagnosis of VACTERL. We have described a Chinese family in which four members were affected by renal defects or agenesis, anal atresia, and anovaginal fistula, which is consistent with the diagnosis of a VACTERL-like association. Pedigree and genetic analyses were conducted using genome and exome sequencing. Segregation analysis revealed the presence of a recessive X-linked microdeletion in two living affected individuals, harboring a 196–380 kb microdeletion on Xq27.1, which was identified by familial exome sequencing. Genome sequencing was performed on the affected male, confirming a -196 kb microdeletion in Xq27.1, which included a 28% loss of the CDR-1 gene. Four family members were included in the co-segregation analysis, and only VACTERL-like cases with microdeletions were reported in X27.1. These results suggest that the 196–380 kb microdeletion in Xq27.1 could be a possible cause of the VATER/VACTERL-like association. However, further genetic and functional analyses are required to confirm or rule out genetic background as the definitive cause of the VACTERL association. [ABSTRACT FROM AUTHOR]

Unresectable locally advanced head and neck cancer (LAHNSCC) presents high heterogeneity1, which has yet to be elucidated at the molecular level. Consequently, it hampers the guidance of standard chemoradiotherapy (ChRT) and the implementation of precision medicine. Our study aims at assessing intratumor heterogeneity (ITH) and tumor evolution by examining the mutation profiles from WES in paired tissue and plasma both at baseline and relapse. Primary tumor (PT) biopsies from 61 unresectable LAHNSCC patients at baseline, along with parallel biopsies at relapse and paired plasma samples (baseline and relapse) from the INCLIVA Biobank's Head and Neck Cancer Collection were obtained. Patients provided informed consent, and the study received ethical approval from our Institutional review board. WES of the collected samples was performed on a HiSeq 3000 (Illumina) using the KAPA HyperExome (Roche) panel. UMI barcodes were added to correct background noise. Samples were selected based on a minimum average coverage (50x for WBC, 100x for FFPE and 250x for plasma samples). Only patients with White Blood Cells (WBCs) and plasma samples were included. Single-Nucleotide Variants (SNV), Copy Number Variants (CNVs) and small insertions and deletions (Indel) were called with an in-house bioinformatics pipeline. Minimum Variant allele frequencies (VAF) were set to 0.1% and 10% for plasma and tissue samples, respectively. Oncogenic somatic variants and related treatments were identified and annotated with OncoKB and Ensembl v107. Functional enrichment was performed using the cluster Profiler 4.6.2 R package and databases org.Hs.eg.db 3.16.0 and MSigDB 2023.1. A total of 37 unresectable LAHNSCC cases meeting quality criteria were included in our analysis (Figure 1). Clinicopathologic characteristics and treatment details are given in Table 1. [Display omitted] In Figure 2, we've employed an oncoprint to depict the WES results, showing the genomic status of the 58 most frequently mutated genes (CNVs and In/Del) in paired samples. [Display omitted] To discern the baseline genomic heterogeneity, we compared the WES results between a single biopsy of the PT and the paired baseline ctDNA from 30 patients. Among all the SNVs and In/Del mutations, an average of 88.2% of events displayed discrepancies between PT and ctDNA. Significantly, up to 67% of oncogenic mutations were exclusively identified in ctDNA. To assess ITH at relapse, we analyzed WES results from paired relapsed tissue biopsies and ctDNA (n=13). Our observations revealed a median concordance of 12.50%, with up to 58% of oncogenic mutations exclusively detected in plasma. To elucidate tumor evolution, we compared WES results of PT vs. relapsed tissue biopsies (n=10) and WES results of baseline ctDNA vs. ctDNA at relapse (n=37). When focusing on tissue analysis, a median concordance of 40% was observed, with up to 38% of oncogenic mutations exclusively identified in the relapsed tissue biopsy. In contrast, focusing on plasma results, discordance was higher, with only a 10.34% median concordance and up to 50% of oncogenic mutations found only in plasma at relapse. In our WES analysis of WBC, we identified pathogenic germline variants in 43.2% (16/37) of cases, highlighting mutations in BRCA2, CHEK2 and KIT as potentially actionable. No enrichment of APOBEC signatures or apoptosis pathways were detected. However, further analysis of defective DNA mismatch repair signatures and treatment-related signatures is currently underway. Our findings confirm the significant ITH in LAHNSCC, characterized by limited concordance between tissue and plasma mutational profiles. WES of ctDNA proves more effective at capturing this ITH, uncovering mutations absent in tissue profiles. Additionally, ctDNA-based WES enhances mutation detection during LAHNSCC relapse, offering valuable insights into resistance mechanisms to ChRT and enabling the potential use of targeted therapies to address these challenges. [ABSTRACT FROM AUTHOR]

• Androgen receptor mutations were identified in women with Müllerian duct anomalies. • In silico analysis and ACMG guidelines classified the variants' pathogenicity. • Androgen receptor mutations resulted in conformational changes of the native protein. Müllerian duct anomalies (MDAs) are congenital developmental disorders exhibiting as a variety of malformations of female reproductive tract. The identified etiology of MDAs is limited. The present study aimed to unravel the underlying genetic causes of MDAs. Rare variants in androgen receptor (AR) were called from the cohort consists of patients with MDAs and underwent whole exome sequencing (WES) at Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China. Sanger sequencing was used to confirm the causative genetic mutations. In silico analysis were used to classify the pathogenicity of each variant. Molecular modeling and simulations were conducted to investigate the conformational changes between the wild-type (WT) and mutant proteins. A total of 3 rare heterozygous variants in AR from the MDAs cohort in our institution were identified, with unknown effects. All variants were missense mutations, including c.173A > T, c.558C > A and c.1208C > T, and were absent or rare in East Asian populations in Genome Aggregation Database and the Exome Aggregation Consortium Database. According to the American College of Medical Genetics and Genomics guidelines, c.1208C > T variant was classified as likely pathogenic, while the other two were variants of uncertain significance. During molecular dynamics simulations, WT and mutant proteins all reached stable status according to root-mean-square variance. Values of radius of gyration showed that Q58L and S186R protein would be more compact than WT, while the structure of A403V became looser. Despite, in comparison with WT, the number of hydrogen bonds increased in Q58L, while decreased in the other two variants. Furthermore, the solvent-accessible surface area diminished in Q58L and A403V while enlarged in S186R proteins, when compared with WT. To our knowledge, this is the first report regarding the association of AR mutation and MDAs. The identification of these variants, predicted to damage the structure and function of AR protein, not only expanded the mutational spectrum of causative genes of MDAs, but provide novel molecular genetic reference for future studies. [ABSTRACT FROM AUTHOR]

• Whole-Exome sequencing is an excellent tool for genetic screening in individuals with suspected epilepsy. • Seizures in epilepsy suspected patients might be directly caused, or influenced by hypoglycemia due to pathogenic variants in the GYS2 gene. • Loss of phosphorylation site in glycogen synthase enzyme due to deletions can have disastrous effects on its normal functioning. Adequate glucose supply is essential for brain function, therefore hypoglycemic states may lead to seizures. Since blood glucose supply for brain is buffered by liver glycogen, an impairment of liver glycogen synthesis by mutations in the liver glycogen synthase gene (GYS2) might result in a substantial neurological involvement. Here, we describe the phenotypes of affected siblings of two families harboring biallelic mutations in GYS2. Two suspected families - a multiplex Pakistani family (family A) with three affected siblings and a family of Moroccan origin (family B) with a single affected child who presented with seizures and reduced fasting blood glucose levels were genetically characterized. Whole exome sequencing (WES) was performed on the index patients, followed by Sanger sequencing-based segregation analyses on all available members of both families. The variant prioritization of WES and later Sanger sequencing confirmed three mutations in the GYS2 gene (12p12.1) consistent with an autosomal recessive pattern of inheritance. A homozygous splice acceptor site variant (NM_021957.3, c. 1646 -2A>G) segregated in family A. Two novel compound heterozygous variants (NM_021957.3: c.343G>A; p.Val115Met and NM_021957.3: c.875A>T; p.Glu292Val) were detected in family B, suggesting glycogen storage disorder. A special diet designed to avoid hypoglycemia, in addition to change of the anti-seizure medication led to reduction in seizure frequency. This study suggests that the seizures in patients initially diagnosed with epilepsy might be directly caused, or influenced by hypoglycemia due to pathogenic variants in the GYS2 gene. [ABSTRACT FROM AUTHOR]

• This study reports five novel missense variants of FRMPD4 in patients with epilepsy. • This study demonstrates that FRMPD4 gene is potentially a candidate pathogenic gene of epilepsy. • This study suggests a quantitative correlation between FRMPD4 impairment and phenotypic variation. The etiology of unexplained epilepsy in most patients remains unclear. Variants of FRMPD4 are suggested to be associated with neurodevelopmental disorders. Therefore, we screened for disease-causing FRMPD4 variants in patients with epilepsy. Trios-based whole-exome sequencing was conducted on a cohort of 85 patients with unexplained epilepsy, their parents, and extended family members. Additional cases with FRMPD4 variants were identified from the China Epilepsy Gene Matching Platform V.1.0. The frequency of variants was analyzed, and their subregional effects were predicted using in silico tools. The genotype–phenotype correlation of the newly defined causative genes and protein stability were analyzed using I-Mutant V.3.0 and Grantham scores. Two novel missense variants of FRMPD4 were identified in two families. Using the gene matching platform, we identified three additional novel missense variants. These variants presented at low or no allele frequencies in the gnomAD database. All the variants were located outside the three FRMPD4 main domains (WW, PDZ, and FERM). In silico analyses revealed that the variants were damaging and were predicted to be the least stable. All patients eventually became seizure-free. Eight of the 21 patients with FRMPD4 variants had epilepsy, of which five (63%) had missense variants located outside the domains, two had deletions involving exon 2, and one had a frameshift variant located outside the domains. Patients with epilepsy caused by missense variants were often free of intellectual disabilities (4/5), whereas patients with epilepsy caused by truncated variants had intellectual disabilities and structural brain abnormalities (3/3). The FRMPD4 gene is potentially associated with epilepsy. The genotype–phenotype correlation of FRMPD4 variants indicated that differences in variant types and locations of FRMPD4 may explain their phenotypic variation. [ABSTRACT FROM AUTHOR]

• Small fetal HC that are less than −3 SD is associated with genetic variants, especially those with intracranial anomalies. • Fetuses with small head that do not reach the diagnosis criteria of microcephalycan't be simply explained as part of FGR. • Genetic variants, mainly CNV and SNV, can explain a substantial proportion of small fetal HC and most them are de novo. • CMA is practical for testing fetuses with small HC, and WES is more effective for genetic testing. • The novel findings about microcephaly-associated genes add value to the clinical use of exome sequencing in this population. • These findings help with the prenatal diagnosis of suspected fetal microcephaly and distribute to our clinical counselling. Objectives: To comprehensively evaluate the contributions of numerical chromosomal abnormality, copy number variant (CNV), and sequence variant (SV) to fetuses with small head circumference in a Chinese cohort using chromosome microarray analysis and whole exome sequencing. Methods: A total of 157 fetuses with small heads defined as head circumference < − 2 standard deviation (SD) were recruited between October 2014 and March 2023. We used the ultrasonic measurement parameter Z-score to define small head as possible microcephaly (3 < Z ≤ -2), microcephaly (-5 < Z ≤ -3), or pathologic microcephaly (Z ≤ -5). Ultrasound findings and genetic results were analyzed. Results: The overall diagnostic yield of chromosomal abnormalities by microarray analysis was 13 %. Whole exome sequencing revealed eight novel variants and two interesting candidate genes and provided a 25.4 % incremental yield compared with microarray analysis. Of the detected SVs, 56 % were de novo and the most common inheritance pattern was autosomal dominant inheritance presented in 11/16 fetuses. Compared with isolated small heads, non-isolated small heads had a significantly higher detection rate of chromosomal abnormalities (16 % vs. 3.0 %, P = 0.049) but not SVs (24 % vs. 5.5 %, P = 0.126). Subgroup analysis showed that intracranial anomalies had a similar high detection rate of SVs in fetuses with all small heads subgroups while no chromosomal abnormalities and causative SVs were found in fetuses with isolated possible microcephaly. Conclusions: Ultrasound findings of small fetal head circumference < 3 SD below the mean, especially those with intracranial structural abnormalities, indicate the need for genetic counseling. Genetic variants, mainly copy number variants and SV, may be responsible for the substantial proportion of small fetal head circumference, while most are de novo. Whole exome sequencing and microarray analysis are effective diagnostic approaches for this population. [ABSTRACT FROM AUTHOR]

Familial cases, twin studies, and associated Mendelian syndromes all suggest that genetic factors play important roles in the pathogenesis of Chiari malformation type 1 (CM1). Genes regulating transcription, genes related to bone or collagen, and genes encoding early developmental signaling pathways have been implicated in CM1 pathogenesis. Clinical and radiographic heterogeneity has hindered genomic investigation of CM1. Whole-exome sequencing (WES) of large patient cohorts has begun to identify new candidate genes. Chiari malformation type 1 (CM1) is the most common structural brain disorder involving the craniocervical junction, characterized by caudal displacement of the cerebellar tonsils below the foramen magnum into the spinal canal. Despite the heterogeneity of CM1, its poorly understood patho-etiology has led to a 'one-size-fits-all' surgical approach, with predictably high rates of morbidity and treatment failure. In this review we present multiplex CM1 families, associated Mendelian syndromes, and candidate genes from recent whole exome sequencing (WES) and other genetic studies that suggest a significant genetic contribution from inherited and de novo germline variants impacting transcription regulation, craniovertebral osteogenesis, and embryonic developmental signaling. We suggest that more extensive WES may identify clinically relevant, genetically defined CM1 subtypes distinguished by unique neuroradiographic and neurophysiological endophenotypes. [ABSTRACT FROM AUTHOR]

Polyhydramnios can be caused by genetic defects at times. However, to establish an accurate diagnosis and provide a precise prenatal consultation in a given case is still a great challenge toward obstetricians. To uncover the genetic cause of polyhydramnios in the two consecutive pregnancies, we performed whole-exome sequencing of DNA for the second suffering fetuses, their parents, and targeted sanger sequencing of other members of this family. We discovered a hemizygous truncating variant in MTM1 gene, c.438_439 del (p. H146Q fs*10) in this Chinese family. In the light of the molecular discoveries, the fetus's clinical phenotype was considered to be a good fit for X-linked myotubular myopathy (XLMTM). There is no related research to the prenatal manifestations of MTM1-related XLMTM among Chinese population, and this is the first one to present. Though the etiology of polyhydramnios is complicated, WES may provide us with a creative avenue in prenatal diagnosis. [ABSTRACT FROM AUTHOR]

Autism spectrum disorder (ASD) is a neurodevelopmental disorder that causes impairments in social communication and stereotypical behaviors, often accompanied by developmental delay or intellectual disability. A growing body of evidence suggests that ASD is highly heritable, and genetic studies have defined numerous risk genes. However, most studies have been conducted with individuals of European and Hispanic ancestry, and there is a lack of genetic analyses of ASD in the East Asian population. We performed whole-exome sequencing on 772 Chinese ASD trios and combined the data with a previous study of 369 Chinese ASD trios, identifying de novo variants in 1141 ASD trios. We used single-cell RNA sequencing analysis to identify the cell types in which ASD-related genes were enriched. In addition, we validated the function of a candidate high-functioning autism gene in mouse models using genetic approaches. Our findings showed that ASD without developmental delay or intellectual disability carried fewer disruptive de novo variants than ASD with developmental delay or intellectual disability. Moreover, we identified 9 novel ASD candidate genes that were not present in the current ASD gene database. We further validated one such novel ASD candidate gene, SLC35G1 , by showing that mice harboring a heterozygous deletion of Slc35g1 exhibited defects in interactive social behaviors. Our work nominates novel ASD candidate genes and emphasizes the importance of genome-wide genetic studies with ASD cohorts of different ancestries to reveal the comprehensive genetic architecture of ASD. [ABSTRACT FROM AUTHOR]

Kabuki syndrome (KS) and spinocerebellar ataxia (SCA) are both rare conditions with neurodevelopmental abnormalities. Approaching a patient with complex phenotypes and differentiating the role of mutations may be beneficial but challenging in predicting the disease prognosis. A boy presented with progressive ataxia, developmental regression, and myoclonus since 4 years of age. Additional features included growth hormone deficiency, excessive body hair, dysmorphic facies, hypoparathyroidism, and bilateral sensorineural hearing impairment. Brain magnetic resonance imaging depicted T2-weighted hyperintensities over bilateral globus pallidus, thalamus, subcortical white matter, and brainstem. The results of tandem mass spectrometry, mitochondrial deletion, and mitochondrial DNA sequencing were inconclusive. Whole-exome sequencing (WES) on genomic DNA obtained from peripheral blood cells revealed a known pathogenic variant at KMT2D gene (c.5993A > G, p.Tyr1998Cys) related to KS and two compound heterozygous, likely pathogenic variants at VPS13D gene (c.908G > A, p.Arg303Gln and c.8561T > G, p.Leu2854Arg) related to autosomal recessive SCA type 4 (SCAR4). SCAR4 is mainly adult-onset, but a few pediatric cases have recently been reported with progressive gait instability and developmental delay. The VPS13D gene has been suggested to play a role in mitochondrial size, autophagy, and clearance, thus explaining the clinical and imaging phenotypes. Our case showed a rare co-existence of KS and SCAR4, highlighting the utility of WES in atypical cases that a single-gene disease cannot fully explain. [ABSTRACT FROM AUTHOR]

Multiple idiopathic cervical root resorption (MICRR) is a disease with an unknown etiology that causes invasive cervical root resorption in multiple teeth. Although previous MICRR genomic studies have identified candidate gene variants, the etiology of the condition remains poorly understood. In the present study, we investigated the genetic causality of MICRR to explore candidate variants. Saliva samples from a family containing 2 affected and two unaffected subjects with the dominant transmission of MICRR were subjected to whole-exome sequencing. As a result, we identified novel candidate variants of 10 genes. Each variant was confirmed by Sanger sequencing. Among them, the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) guidelines classified doublecortin domain containing 1 (c.1099 C > T) and β-defensin 114 (c.189 T > G) as "pathogenic," and solute carrier family 45 member 2 (c.152_153del) as "likely pathogenic." These results provide new insight to help clarify the pathogenesis of MICRR, and the variants could be applied for further investigation to understand invasive cervical root resorption. [ABSTRACT FROM AUTHOR]

In the last decade, the utility of whole-exome sequencing in uncovering genetic aetiologies of a variety of liver diseases has been demonstrated. These new diagnoses have guided the management, treatment, and prognostication of previously undiagnosed patients, largely thanks to improved insight into the underlying pathogenesis of their conditions. Despite its clear benefits, the uptake of genetic testing by hepatologists has been limited, in part due to limited prior genetic training and/or opportunities for continuing education. Herein, we show that Hepatology Genome Rounds, an interdisciplinary forum highlighting hepatology cases of clinical interest and educational value, are an important venue for integrating genotypic and phenotypic information to enable accurate diagnosis and appropriate management, dissemination of genomic knowledge within the field of hepatology, and ongoing education to providers and trainees in genomic medicine. We describe our single-centre experience and discuss practical considerations for clinicians interested in launching such a series. We foresee that this format will be adopted at other institutions and by additional specialties, with the aim of further incorporating genomic information into clinical medicine. [ABSTRACT FROM AUTHOR]

• There is a lack consensus on whether thrombophilia should be included in the diagnostic criteria for TAO. • 27.3% of TAO patients had potential thrombophilic gene mutations in PROC, PROS1, F9, F5, THBD and SERPIND1. • 66.7% of TAO patients with thrombophilia had PROC genetic mutations combined with other thrombophilic genetic mutations • Other variants in ADAMTS13, F5, F9, F11, F12, PLAT, PLG, SERPINA10 and HABP2 were identified in TAO patients but not controls. [ABSTRACT FROM AUTHOR]

Data on the frequency of colorectal neoplasia in sporadic ampullary tumors remains scarce. We retrospectively reviewed 135 patients undergoing endoscopic ampullectomy from January 2018 to July 2021, and identified 95 patients with sporadic ampullary adenoma who underwent total colonoscopy. Colonoscopy findings were compared with 380 asymptomatic controls using the chi-squared test. Whole-exome sequencing (WES) was performed on one patient with synchronous adenomas of the ampulla of Vater and ascending colon. Colorectal polyps were present in 60% of Cases vs. 34.7% of Controls (P = 0.001), advanced adenoma in 20% vs. 5.5%, and adenocarcinoma in 4.2% vs. 0.8%. Cases tended to have larger polyps than Controls (P <0.001), while there was no difference in polyp location and histology between the two groups. The odds ratio of all the colorectal lesions, advanced colorectal adenoma and adenocarcinoma in C ases was 1.7, 4.2, and 4, respectively. WES in one patient revealed that both of ampullary adenoma and colonic adenoma shared somatic ABCB1 mutation. The frequency of colorectal polyps or neoplasia was significantly higher in Cases than Controls. We proposed that ampullary neoplasia is analogous to colon lesions and warrants total colonoscopy screening in patients diagnosed with ampullary tumors. [ABSTRACT FROM AUTHOR]

N -methyl- d -aspartate receptors (NMDARs) are ligand-gated ion channels that mediate excitatory synaptic transmission and brain development in the central nervous system. Mutations in GRIN2D encoding the NMDAR subunit GluN2D are associated with a wide spectrum of neurodevelopmental disorders. We report a novel de novo GRIN2D variant (NM_000836.2: c.2024C > T, p.Ala675Val) in an infant with severe developmental and epileptic encephalopathy. Clinical characteristics and treatment outcomes of patients with GRIN2D -related developmental and epileptic encephalopathy were summarized by reviewing the literature. In silico analysis suggested this p.Ala675Val variant residing in the highly conserved M3 helix of GluN2D would interfere with channel gating. Therapeutic options including multiple anticonvulsants, oral corticosteroid therapy, and ketogenic diet failed to achieve seizure control. Eventually, adjunctive therapy with perampanel led to marked electroclinical improvement. Perampanel can be beneficial adjuvant therapy for patients with GRIN2D -related intractable epilepsy. Mechanistic understanding and case- per -se analysis are required to enable more individualized treatment for the patients. [ABSTRACT FROM AUTHOR]

A dysregulated immune response is a hallmark of autoimmune disorders. Evidence suggests that systemic autoimmune diseases and primary immunodeficiency disorders (PIDs) may be similar diseases with different clinical phenotypes. This study aimed to investigate the burden of PID-associated genetic variants in patients with childhood-onset systemic lupus erythematosus (cSLE). We enrolled 118 cSLE patients regularly followed at Chang Gung Memorial Hospital. Targeted next-generation sequencing identified PID genetic variants in patients versus 1475 unrelated healthy individuals, which were further filtered by allelic frequency and various functional scores. Customized immune assays tested the functions of the identified variants. On filtration, 36 patients (30.5%) harbored rare variants in PID-associated genes predicted to be damaging. One homozygous TREX1 (c.294dupA) mutation and 4 heterozygous variants with possible dominant PID traits, including BCL11B (c.G1040T), NFKB1 (c.T695G), and NFKB2 (c.G1210A, c.G1651A), were discovered. With recessive traits, variants were found across all PID types; one fifth involved phagocyte number or function defects. Predicted pathogenic PID variants were more predominant in those with a family history of lupus, regardless of infection susceptibility. Moreover, mutation loads were greater among cSLE patients than controls despite sex or age at disease onset. While greater mutation loads were observed among cSLE patients with peripubertal disease onset, no significant differences in sex or phenotype were noted among cSLE patients. cSLE is mostly not monogenic. Gene-specific analysis and mutation load investigations suggested that rare and predicted damaging variants in PID-related genes can potentially contribute to cSLE susceptibility. [ABSTRACT FROM AUTHOR]

Twin studies suggest that additive genetic effects account for about a quarter of the variance in handedness. Recently, Schijven et al. used exome-wide sequencing to provide evidence for a role of rare protein-coding variants in handedness. These included the gene encoding beta-tubulin, TUBB4B , suggesting that microtubules are relevant for handedness ontogenesis. [ABSTRACT FROM AUTHOR]

• Empty follicle syndrome is failure to retrieve oocytes after ovarian stimulation. • Genuine EFS is caused by mutations in genes encoding zona pellucida (ZP) proteins. • We report on genuine EFS caused by a ZP1 mutation. • Genuine EFS should prompt the sequencing of genes encoding ZP proteins. Genuine empty follicle syndrome (gEFS) is a rare cause of female infertility; it is defined as the presence of cumulus-oocyte complexes (COCs) in follicular fluid but the absence of oocytes after denudation in an in vitro fertilization (IVF) programme. Mutations in one of the four genes encoding zona pellucida (ZP) proteins have been implicated in gEFS. The objectives of the present study were to explore the molecular basis of idiopathic infertility in a 35-year-old woman with gEFS (observed after four ovarian retrievals), compare her phenotype and genotype with those of other patients described in the literature, and discuss therapeutic approaches that could be adopted by reproductive health centres in this situation. Sequencing of the ZP genes revealed a new homozygous missense variant in ZP1 : c.1097G > A;p.(Arg366Gln). The variant is located in the ZP-N domain, which is essential for ZP protein polymerization. An immunohistochemical assessment of an ovarian biopsy confirmed the absence of ZP1 protein. The novel variant appears to prevent ZP assembly, which would explain the absence of normal oocytes after denudation in our patient (and despite the retrieval of COCs). ZP gene sequencing should be considered for patients with a phenotype suggestive of gEFS. An etiological genetic diagnosis enables appropriate genetic counselling and a switch to an IVF programme (with a suitable denudation technique) or an oocyte donation programme. [ABSTRACT FROM AUTHOR]

Next-generation sequencing (NGS) is one of the most promising technologies that have truly revolutionized many aspects of clinical practice in recent years. It has been and is increasingly applied in many disciplines of medicine; however, it seems that pediatric neurosurgery despite its great potential has not truly embraced this new technology and is hesitant to use it in routine practice and guidelines. In this review, we summarize the developments that led to the establishment of NGS technology, review the applications and potentials of NGS in the disorders treated by pediatric neurosurgeons, and discuss the steps that we need to be taken to better harness NGS in pediatric neurosurgery. [ABSTRACT FROM AUTHOR]

Breast cancer has a significant heritable basis, of which ∼60% remains unexplained. Testing for BRCA1 / BRCA2 offers useful discrimination of breast cancer risk within families, and identification of additional breast cancer susceptibility genes could offer clinical utility. We included 2135 invasive breast cancer cases recruited via the Breast and Ovarian Cancer Susceptibility study, a retrospective UK study of familial breast cancer. Eligibility criteria: female, BRCA -negative, white European ethnicity, and one of: (i) breast cancer family history, (ii) bilateral disease, (iii) young age of onset (<30 years), and (iv) concomitant ovarian cancer. We undertook exome sequencing of cases and carried out gene-level burden testing of rare damaging variants against those from 51 377 ethnicity-matched population controls from gnomAD. 159/2135 (7.4%) cases had a qualifying variant in an established breast cancer susceptibility gene, with minimal evidence of signal in other cancer susceptibility genes. Known breast cancer susceptibility genes PALB2 , CHEK2, and ATM were the only genes to retain statistical significance after correcting for multiple testing. Due to the enrichment of hereditary cases in the series, we had good power (>80%) to detect a gene of BRCA1 -like risk [odds ratio (OR) = 10.6] down to a population minor allele frequency of 4.6 × 10−5 (1 in 10 799, less than one-tenth that of BRCA1)and of PALB2 -like risk (OR = 5.0) down to a population minor allele frequency of 2.8 × 10−4 (1 in 1779, less than half that of PALB2). Power was lower for identification of novel moderate penetrance genes (OR = 2-3) like CHEK2 and ATM. This is the largest case-control whole-exome analysis of enriched breast cancer published to date. Whilst additional breast cancer susceptibility genes likely exist, those of high penetrance are likely to be of very low mutational frequency. Contention exists regarding the clinical utility of such genes. • We report the largest exome sequencing study of hereditary breast cancer to date, comparing 2135 cases to 51 377 controls. • We demonstrate that a novel breast cancer gene (OR ≥ 5) is unlikely to exist at any appreciable population frequency. • We had good power (> 80%) to detect any PALB2 -like breast cancer gene (odds ratio = 5) at population frequency of 1 in 1779 (< half that of PALB2). • Our insights into the architecture of breast cancer susceptibility give context to the negative findings of the last decade. [ABSTRACT FROM AUTHOR]

Ameloblastic fibrosarcoma (AFS) is the most common odontogenic sarcoma, but the incidence is relatively low, and its molecular biology is poorly understood. We experienced a young female patient with a rapidly growing soft tissue tumor of the left maxilla, which eventually occupied the left side of the oral cavity. Histologically, the tumor mainly consisted of a proliferation of atypical spindle to polygonal cells without any specific differentiation, but a small number of benign odontogenic epithelial foci mainly in the tumor periphery were also noted; thus, a diagnosis of AFS was made. We performed whole-exome sequencing (WES) on the tumor to investigate its molecular features and identify therapeutic options. We found that the tumor harbored EGFR exon 20 insertions and MDM2 amplification; the former may be a target for newly developed tyrosine kinase inhibitors in case of recurrence. To the best of our knowledge, this is the first case of AFS for which WES was performed and with EGFR mutation. Our case provides new genetic information on AFS and suggests that comprehensive genetic analysis can clarify the molecular biology in rare cancers, potentially leading to the proposal of therapeutic strategies. [ABSTRACT FROM AUTHOR]

A rare case of extensive multiple idiopathic cervical root resorption with potential genetic predisposition was presented. A heathy 19-year-old Chinese male with no contributory medical or family/social history complained of pain during mastication that lasted for several months. Oral examination identified 7 missing teeth and external cervical root resorption involving 9 teeth. Comparison of orthopantomograms taken in May 2021 and February 2022 identified that cervical root resorption occurred in 22 teeth. Resorption commenced at the cementoenamel junction and progressed rapidly over the 9-month period. Laboratory test results were within normal limits. Trio-based whole-exome sequencing showed a missense mutation c.5630 C > T in the filamin A (FLNA) gene at chromosome X of the subject. This is suggestive of the possibility of sex-linked recessive inheritance. This is the first study to report FLNA mutation in human subjects with cervical root resorption involving multiple teeth. [ABSTRACT FROM AUTHOR]

• MFRP emerges as the predominant disease-causing gene in a large Chinese microphthalmia cohort. • Variant p.E496K exhibits the highest frequency among nine novel and seven known variants. • The association of p.E496K with a short axial length represents a novel genotype-phenotype correlation. Microphthalmia is a severe congenital ocular disease featured by abnormal ocular development. The aim of this study was to detail the genetic and clinical characteristics of a large cohort of Chinese patients with microphthalmia related to MFRP variants, focusing on uncovering genotype-phenotype correlations. Fifty microphthalmia patients from 44 unrelated Chinese families were recruited. Whole-exome sequencing (WES) was conducted to analyze the coding regions and adjacent intronic regions of MFRP. Axial lengths (AL) were measured for all probands and available family members. Protein structures of mutations with high frequency in our cohort were predicted. The genotype-phenotype correlations were explored by statistical analysis. Sixteen MFRP variants were detected in 17 families, accounting for 38.64 % of all microphthalmia families. There were 9 novel mutations (c.427+1G>C, c.428-2A>C, c.561_575del:p.A188_E192del, c.836G>A:p.C279Y, c.1010_1021del:p.H337_E340del:p.Y479*, c.1516_1517del:p.S506Pfs*66, c.1561T>G:p.C521G, c.1616G>A:p.R539H, and c.1735C>T:p.P579S) and six previously reported variants in MFRP , with p.E496K and p.H337_E340del being highly frequent, found in eight (47.06 %) and two families (11.76 %), respectively. Seven variants (43.75 %) were located in the C-terminal cysteine-rich frizzled-related domain (CRD) (7/16, 43.75 %). Protein prediction implicated p.E496K and p.H337_E340del mutations might lead to a destabilization of the MFRP protein. The average AL of all 42 eyes was 16.02 ± 1.05 mm, and 78.36 % of eyes with AL < 16 mm harbored p.E496K variant. Twenty-six eyes with variant variant had shorter AL than that of the other 16 eyes without this variant (p = 0.006), highlighting a novel genotype-phenotype correlation. In this largest cohort of Chinese patients with microphthalmia, the 9 novel variants, high frequency of p.E496W, and mutation hotspots in CRD reveals unique insights into the MFRP mutation spectrum among Chinese patients, indicating ethnic variability. A new genotype-phenotype correlation that p.E496K variant associated with a shorter AL is unveiled. Our findings enhance the current knowledge of MFRP -associated microphthalmia and provide valuable information for prenatal diagnosis as well as future therapy. [ABSTRACT FROM AUTHOR]

Keshan disease is an endemic fatal dilated cardiomyopathy that can cause heart enlargement, heart failure, and cardiogenic death. Selenium deficiency is considered to be the main cause of Keshan disease. However, the molecular mechanism underlying Keshan disease remains unclear. Our whole-exome sequencing from 68 patients with Keshan disease and 100 controls found 199 candidate genes by gene-level burden tests. Interestingly, using multiomics data, the selenium-related gene ALAD (δ-aminolevulinic acid dehydratase) was the only candidate causative gene identified by three different analysis approaches. Based on single-cell transcriptome data, ALAD was highly expressed in cardiomyocytes and double mutations of human ALAD dramatically reduced its enzyme activity in vitro compared to negative control. Functional analysis of ALAD inhibition in mice resulted in a Keshan phenotype with left ventricular enlargement and cardiac dysfunction, whereas administration of sodium selenite markedly reversed the changes caused by ALAD inhibition. In addition, sodium selenite reversed Keshan phenotypes by affecting energy metabolism and mitochondrial function in mice as shown by the transcriptomic and proteomic data and the ultrastructure of cardiac myocytes. Our findings are the first to demonstrate that the selenium-related gene ALAD is essential for cardiac function by maintaining normal mitochondrial activity, providing strong molecular evidence supporting the hypothesis of selenium deficiency in Keshan disease. These results identified ALAD as a novel target for therapeutic intervention in Keshan disease and Keshan disease-related dilated cardiomyopathy. Blood samples were collected and analyzed with whole-exome sequencing from 68 patients with Keshan disease and 100 healthy individuals, and the selenium-related gene ALAD is the only candidate pathogenic gene identified by three different analysis approaches. The inhibition of ALAD in mice promoted left ventricular enlargement and cardiac dysfunction, but the addition of sodium selenite remarkably reserved the changes caused by inhibition of ALAD. Our data showed that a large number of proteins associated with energy metabolism were upregulated and mitochondrial function was impaired by ALAD inhibition, while widespread upregulated proteins were returned to normal expression with the addition of sodium selenite. [Display omitted] • Selenium-related gene ALAD is a novel target for therapeutic intervention in Keshan disease. • ALAD inhibition in mice resulted in left ventricular enlargement and cardiac dysfunction, and sodium selenite reversed KD phenotypes. [ABSTRACT FROM AUTHOR]

[Display omitted] Teratozoospermia is usually associated with defective spermiogenesis and is a disorder with considerable genetic heterogeneity. Although previous studies have identified several teratozoospermia-associated genes, the etiology remains unknown for a majority of affected men. Here, we identified a homozygous missense mutation and a compound heterozygous mutation of CCIN in patients suffering from teratozoospermia. CCIN encodes the cytoskeletal protein Calicin that is involved in the formation and maintenance of the highly regular organization of the calyx of mammalian spermatozoa, and has been proposed to play a role in sperm head structure remodeling during the process of spermiogenesis. Our morphological and ultrastructural analyses of the spermatozoa obtained from all three men harboring deleterious CCIN mutants reveal severe head malformation. Further immunofluorescence assays unveil markedly reduced levels of Calicin in spermatozoa. These patient phenotypes are successfully recapitulated in mouse models expressing the disease-associated variants, confirming the role of Calicin in male fertility. Notably, all mutant spermatozoa from mice and human patients fail to adhere to the zona mass, which likely is the major mechanistic reason for CCIN -mutant sperm-derived infertility. Finally, the use of intra-cytoplasmic sperm injections (ICSI) successfully makes mutated mice and two couples with CCIN variants have healthy offspring. Taken together, our findings identify the role of Calicin in sperm head shaping and male fertility, providing important guidance for genetic counseling and assisted reproduction treatments. [ABSTRACT FROM AUTHOR]

• The use of NGS is an efficient technique to diagnose cerebral creatine deficiency syndrome precisely. • A combined mass spectrometry with gene mutation analysis is helpful in CCDS diagnosis. • Genetic diagnosis determined that all seven patients were positive for SLC6A8 or GAMT variation. • A total of 12 variants were identified in this cohort, including six novel ones. Cerebral creatine deficiency syndromes (CCDSs) are a group of rare mendelian disorders mainly characterized by intellectual disability, movement anomaly, behavior disorder and seizures. SLC6A8 , GAMT , and GATM are known genes responsible for CCDS. In this study, seven pediatric patients with developmental delay were recruited and submitted to a series of clinical evaluation, laboratory testing, and genetic analysis. The clinical manifestations and core biochemical indications of each child were basically consistent with the diagnosis of CCDS. Genetic diagnosis determined that all patients were positive for SLC6A8 or GAMT variation. A total of 12 variants were identified in this cohort, including six novel ones. The frequency of these variants, the Revel scores and the conservatism of the affected amino acids support their pathogenicity. Our findings expanded the mutation spectrum of CCDS disorders, and provided solid evidence for the counseling to affected families. [ABSTRACT FROM AUTHOR]

Mutations in RET have been found in multiple diseases including isolated and associated congenital anomalies. Here, we report a case presented with disparate phenotypes in each pregnancy but caused by the same novel mutation. Whole-exome sequencing (WES) was performed on the proband/abortion product-parental trio and a novel missense variant in RET (chr10:43615610C > G; c.2689C > G; p.Arg897Gly) was identified. The mother was a low-level somatic carrier of this new mutation, with 17.3% in blood, 19.1% in oral mucous membrane, and 15.7% in urine by droplet digital polymerase chain reaction (dd PCR). Our finding not only broadens the mutation spectrum of RET but also gives supportive genetic counseling and timely guidance on fertility choices. [ABSTRACT FROM AUTHOR]

• The WES successfully identified several common exonic variants (e.g., MUC6) and depicted the feature of mutations and evolution. • Several immune-related pathways were significantly enriched, and Foxd4, differing from the other four mutated genes, was inversely correlated with the GSVA-enriched pathway. • This is the first time to identify 16 SCID-related mutant exon genes, including MUC6, RP11-683L23.1, CNN4, and SCGB1C1, using WES analysis, suggesting that these genes may be useful as biomarkers for the early diagnosis and treatment of SCID, as well as gain new insight into the mechanisms of disease development. Severe combined immunodeficiency (SCID) is the most fatal form of inherited primary immunodeficiency disease. Known molecular defect mutations occur in most children with SCID. Herein, we report Adenosine Deaminase-SCID (ADA-SCID) using whole-exome sequencing (WES), explore exome mutational landscape and significance for 17 SCID samples, and verify the mutated exon genes using the Gene Expression Omnibus (GEO) datasets. A total of 250 patients, who were hospitalized at the Neonatal Intensive Care Unit (NICU) of The Seventh Medical Center of the PLA General Hospital for 3 years (from 2017 to 2020), were screened for SCID. We collected mutated genes from the WES data of 17 SCID children. GSE609 and GSE99176 cohorts were used to identify the expressions of mutated exon genes and molecular features in SCID. Gene set variation analyses (GSVA) and correlation analyses were performed. The detection rate with approximately 6.8 % (17/250) of SCID is high in the NICU. A total of 16 genes were identified among 17 SCID samples, of which the Top 2 genes (MUC6 and RP11-683L23.1) might be crucial in the progression of SCID with 94 % mutation frequency. Furthermore, CNN2 and SCGB1C1 had significant co-mutations and may cooperate to affect SCID development. Importantly, the phylogenetic tree classification results of 17 SCID samples are more correlated to MUC6 with the most significant mutations. Expression profiles of seven mutated genes and five mutated genes were documented in GSE609 and GSE99176 cohorts based on microarray, respectively. Several immune-related pathways were significantly enriched, and Foxd4, differing from the other four mutated genes, was inversely correlated with the GSVA-enriched pathway. Due to its high detection rate (6.8%) and fatality rate (100%), the inclusion of SCID in newborn screening (NBS) is urgent for children in China. The WES successfully identified several common exonic variants (e.g., MUC6) and depicted the feature of mutations and evolution, which will help develop new diagnostic methods for SCID. [ABSTRACT FROM AUTHOR]

Early prediction and prevention of recurring illness is critical for improving the survival rates of patients with non-small cell lung cancer (NSCLC). Previously, we demonstrated that the presence of premalignant epithelial changes in the small bronchi distant to the primary tumor is associated with NSCLC progression: isolated basal cell hyperplasia (iBCH) indicates a high risk of distant metastasis, BCH combined with squamous metaplasia (BCHSM) – a high risk of locoregional recurrence. Here, we aimed to identify germline single nucleotide variants (SNVs) and insertions and deletions (InDels) associated with distant metastasis and locoregional recurrence in cases with iBCH and BCHSM using whole-exome sequencing of 172 NSCLC patients. The rs112065068 of the TGOLN2 gene was identified only in iBCH patients and was associated with a high risk of distant metastasis (P <.001) and worse metastasis-free survival (HR = 4.19 (95 %CI 1.97–8.93); P <.001). This variant was validated in a group of 109 NSCLC patients using real-time PCR and Sanger sequencing analyses. To our knowledge, this study is the first to identify a germline variant associated with NSCLC distant metastasis. [ABSTRACT FROM AUTHOR]

In invasive lung adenocarcinoma (LUAD), patients with micropapillary (MIP) or solid (SOL) components had a significantly poorer prognosis than those with only lepidic (LEP), acinar (ACI) or papillary (PAP) components. It is interesting to explore the genetic features of different histologic subtypes, especially the highly aggressive components. Based on a cohort of 5,933 patients, this study observed that in different tumor size groups, LUAD with MIP/SOL components showed a different prevalence, and patients with ALK alteration or TP53 mutations had a higher probability of developing MIP/SOL components. To control individual differences, this research used spatial whole-exome sequencing (WES) via laser-capture microdissection of five patients harboring these five coexistent components and identified genetic features among different histologic components of the same tumor. In tracing the evolution of components, we found that titin (TTN) mutation might serve as a crucial intratumor potential driver for MIP/SOL components, which was validated by a cohort of 146 LUAD patients undergoing bulk WES. Functional analysis revealed that TTN mutations enriched the complement and coagulation cascades, which correlated with the pathway of cell adhesion, migration, and proliferation. Collectively, the histologic subtypes of invasive LUAD were genetically different, and certain trunk genotypes might synergize with branching TTN mutation to develop highly aggressive components. [ABSTRACT FROM AUTHOR]

• A novel EIF4ENIF1 variant c.623G > A;p.R208H was identified in a sporadic POI case. • EIF4ENIF1 208H and Q842P exhibited reduced translation inhibition ability in vitro. • T&T-seq as a sensitive method to evaluate variants of translation regulator genes. Various genetic variants have been found to be associated with the clinical onset of premature ovarian insufficiency (POI). However, when measured in vitro , the functional influence of the variants can be difficult to determine. By whole-exome sequencing (WES) of 93 patients with sporadic POI, we found a missense variant c.623G > A;p.R208H in the EIF4ENIF1 gene. In silico prediction of the variant using different algorithms suggested it might be a damaging variant. We compared the property of EIF4ENIF1 R208H and Q842P, a POI-related mutant that we reported previously, with wildtype (WT) protein using 293FT cells in vitro. Surprisingly, a change in subcellular distribution and granule forming ability (Q842P) and nuclear import capacity (R208H) was not observed, despite domain prediction evidences. Since EIF4ENIF1 was reported to inhibit translation, we employed T&T-seq, a translation-transcription dual-omics sequencing method, to profile gene expression upon overexpression of EIF4ENIF1 WT and mutants. EIF4ENIF1 WT overexpression group exhibited significantly (P < 0.0001) lower translation efficiency (TE) than empty vector or GFP overexpression control group. Surprisingly, EIF4ENIF1 Q842P overexpression failed to repress global translation, showing an overall TE significantly higher than WT group. Overexpression R208H significantly (P < 0.0001) lowered the overall TE, whereas exhibiting a reduced translation inhibitory effect on high-TE genes (TE > 2 in GFP control group). Several fertility-associated genes, such as AMH in Q842P group and SERPINE1 and THBS1 in R208H group, was translationally up-regulated in mutant groups versus WT control, suggesting a potential mechanism of mutated EIF4ENIF1 causing POI via impaired translation repression. It is further proposed that T&T-seq can be a sensitive evaluation tool for the measurement of functional alteration by variants in many other translational regulator genes, not only EIF4ENIF1 , helping to eliminate misinterpretation of clinical significance of genetic variants. [ABSTRACT FROM AUTHOR]

• Identifying high-confidence risk genes of tic disorder (TD) has been challenging due to poor replication across studies; • Fourteen variants were identified as potential susceptibility variants of TD; • Ten variants were identified as potential disease-causing variants of TD; • Several genes enriched in the PI3K-Akt signaling, sphingolipid metabolism and serotonergic synaptic pathways were considered potential new candidate genes. Tic disorder (TD) is a polygenic neurodevelopmental disorder with high susceptibility. However, identifying high-confidence risk genes has been challenging due to poor replication across multiple studies. Whole-exome sequencing was performed on 390 TD patients and 372 unaffected individuals in a Chinese Han population. Analysis of variance, burden analysis and in silico prediction were used to identify candidate genes for TD. To facilitate data analysis and to focus on high-confidence genes, we defined a panel of 160 genes as known causal or candidate TD genes from previous studies. Gene enrichment and protein–protein interaction analysis were utilized to detect potential novel TD risk genes. Totally, 14 variants across 12 known TD candidate genes were considered potential susceptibility variants. Ten variants across 10 known TD candidate genes were identified as potential disease-causing variants. Burden analysis identified variants of 28 known genes were significantly excess in TD patients. In addition, 354 previously unproven TD genes are over-represented in patients. Genes enriched in the PI3K-Akt signaling, sphingolipid metabolism and serotonergic synaptic pathways, as well as those interacting with FN1 , were considered potential new candidate genes for TD. This is the largest WES study focusing on TD patients in a Chinese Han population. Several variants recurring in our cohort were identified as high-confidence risk loci for TD. Moreover, we provided potential new risk genes that may be prioritized for further investigation. [ABSTRACT FROM AUTHOR]

Rare and low-frequency variants contribute to schizophrenia (SCZ), and may influence its age-at-onset (AAO). We examined the association of rare or low-frequency deleterious coding variants in Chinese patients with SCZ. We collected DNA samples in 197 patients with SCZ spectrum disorder and 82 healthy controls (HC), and performed exome sequencing. The AAO variable was ascertained in the majority of SCZ participants for identify the early-onset (EOS, AAO<=18) and adult-onset (AOS, AAO>18) subgroups. We examined the overall association of rare/low-frequency, damaging variants in SCZ versus HC, EOS versus HC, and AOS versus HC at the gene and gene-set levels using Sequence Kernel Association Test. The quantitative rare-variant association test of AAO was conducted. Resampling was used to obtain empirical p -values and to control for family-wise error rate (FWER). In binary-trait association tests, we identified 5 potential candidate risk genes and 10 gene ontology biological processes (GOBP) terms, among which PADI2 reached FWER-adjusted significance. In quantitative rare-variant association tests, we found marginally significant correlations of AAO with alterations in 4 candidate risk genes, and 5 GOBP pathways. Together, the biological and functional profiles of these genes and gene sets supported the involvement of perturbations of neural systems in SCZ, and altered immune functions in EOS. [ABSTRACT FROM AUTHOR]

Cutaneous squamous cell carcinoma (cSCC) is the second most common nonmelanoma skin cancer worldwide. Recent studies have reported several genetic mutations in development of cSCC such as TP53 , HRAS , and NOTCH1. Whole-exome sequencing (WES) of cSCC has not been reported in East Asian populations. We aimed to investigate genetic mutations of cSCCs in Korean patients by WES. cSCCs and paired peripheral blood samples were obtained from 19 Korean patients who underwent wide excision on the cheek from 2016 to 2020 and divided into moderate to poor-differentiated (MP-D) cSCCs (n = 9) and well-differentiated (W-D) cSCCs (n = 10) according to the histopathological evaluation. WES was performed for analysis of genomic mutations of cSCCs. The mean total mutation burden of MP-D cSCCs was higher than W-D cSCCs. Also, we observed proportionately more driver mutations in MP-D cSCC than W-D cSCC groups. CSMD3 , COL22A1 , FMN2 , and ASXL3 mutations are highly frequent than the results of previous reports in cSCC of Caucasians. These results may aid in further our understanding of the complex process underlying tumorigenesis of cSCC in non-Caucasian populations. • The mean total mutation burden of MP-D cSCCs was higher than W-D cSCCs. • More driver mutations were observed in MP-D cSCC than W-D cSCC groups. • CSMD3 , COL22A1 , FMN2 , and ASXL3 mutations are highly frequent than the results of previous reports in cSCC of Caucasians. [ABSTRACT FROM AUTHOR]

DNAJC7 has recently been identified as an amyotrophic lateral sclerosis (ALS) gene via large-scale exome analysis, and its involvement in ALS is still unclear in various populations. This study aimed to determine the frequencies and characteristics of the DNAJC7 variants in a Japanese ALS cohort. A total of 807 unrelated Japanese patients with sporadic ALS were screened via exome analysis. In total, we detected six rare missense variants and one splice-site variant of the DNAJC7 gene, which are not reported in the Japanese public database. Furthermore, the missense variants are located around the TPR domain, which is important for the function of DNAJC7. The total frequency of the DNAJC7 variants in Japanese ALS patients was estimated at 0.87%. Collectively, these results suggest that variants of DNAJC7 are rare cause of Japanese patients with sporadic ALS. [ABSTRACT FROM AUTHOR]

Super-refractory status epilepticus (SRSE) is associated with significant morbidity and mortality in children. We explored the clinical spectrum, specific characteristics, and outcome in SRSE patients admitted in a pediatric intensive care unit (PICU) and investigated how well current diagnostic or treatment modalities perform compared to Status Epilepticus (SE) and Refractory SE (RSE) patients. Retrospective analysis of PICU patients admitted with convulsive SE during 2009–2019. Eighty-six patients were classified as SE, RSE, and SRSE. New-onset RSE (NORSE) and febrile infection-related epilepsy syndrome (FIRES) were also identified. Functional outcome was evaluated by the modified Rankin scale. Patients with SRSE (n = 20) had longer weaning off anesthetics (p = 0.014), length of stay, mechanical ventilation duration, higher illness severity scores, and poorer outcome compared to SE (n = 13) or RSE (n = 53) patients (all p < 0.001). Diagnosis, mainly expressed by high prevalence of NORSE (n = 13) and FIRES (n = 9), was independently associated with SRSE (p = 0.024). Abnormal MRI findings (p = 0.005), and epilepsy-related pathogenic variants identified by whole-exome sequencing (WES) were mostly found in SRSE patients. Compared to intravenous immunoglobulins and steroid pulses, plasmapheresis and ketogenic diet, more often used in SRSE (p < 0.01), contributed better to seizure control. Only SRSE (AUROC > 0.80, 95% CI = 0.68–0.94, p < 0.001) and diagnosis (AUROC > 0.70, 95% CI = 0.55–0.83, p = 0.02) could predict a poor outcome. The majority of SRSE patients are characterized by considerable functional decline and morbidity. WES analysis may reveal epilepsy-related pathogenic variants while early aggressive immunotherapy and/or ketogenic diet might prove beneficial. Multicenter studies for prediction models of outcome are needed. • SRSE is associated with considerable functional decline and significant mortality. • NORSE and FIRES are independently associated with SRSE. • Whole exome sequencing has a role in revealing epilepsy-related pathogenic variants. • Plasmapheresis and/or ketogenic diet might be beneficial if promptly implemented. [ABSTRACT FROM AUTHOR]

• Rare genetic variant is an important factor contributing to differential GH responsiveness. • Mutant genes for short stature in GHD patients involved in GH secretion or growth plate development. • Diagnosis of growth hormone deficiency is based on clinical and genetic evaluation. • Genetic testing should be factored into accurate diagnosis and treatment decision making. Growth hormone is an effective therapy for growth hormone deficiency (GHD) but with a rather variable individual sensitivity. It is unclear whether rare genetic variants may contribute to the differential GH responsiveness. The present study aims to investigate the molecular etiology of GHD in Chinese children and adolescents and evaluate the impact of rare variants on therapeutic efficacies of GH. Twenty-one rare heterozygous variant were classified as promising uncertain significance (n = 14), pathogenic (n = 5) or likely pathogenic (n = 2) for 21 of the 93 GHD patients. After GHD patients harboring these rare variants were excluded, inter-individual variability in the response to GH therapy obviously reduced and the negative correlation between initiation age of treatment and height SDS change became stronger in the group without rare variants. Among rare variants, 7 (likely) pathogenic variants (7.5%, 7/93) involved a total of 6 genes not only associated with GH secretion (PROKR2 , LZTR1), but also growth plate chondrocyte signaling (ACAN , FBN1 , COL9A1) or genetic syndromes (PTPN11). Rare genetic variants are an important factor contributing to differential GH responsiveness and genetic testing should be factored into accurate diagnosis and treatment decision making in the future. Clinical Trial Registration Number: ChiCTR1900026510. [ABSTRACT FROM AUTHOR]

To clarify the diagnostic utility and the cost-effectiveness of whole-exome sequencing (WES) as a routine early-diagnostic tool in children with progressive neurological disorders. Patients with infantile-onset severe neurological diseases or childhood-onset progressive neurological disorders were prospectively recruited to this WES study, in the pediatric neurology clinic at Helsinki University Hospital during 2016–2018. A total of 48 patients underwent a singleton WES. A control group of 49 children underwent traditional diagnostic examinations and were retrospectively collected from the hospital records. Their use of health care services, related to the diagnostic process, was gathered. Incremental cost-effectiveness ratio (ICER) per additional diagnosis was calculated from the health care provider perspective. Bootstrapping methods were used to estimate the uncertainty of cost-effectiveness outcomes. WES provided a better diagnostic yield (38%) than diagnostic pathway that did not prioritize WES in early diagnosis (25%). WES outperformed other diagnostic paths especially when made early, within one year of first admission (44%). Cost-effectiveness in our results are conservative, affected by WES costs during 2016–18. WES is an efficient and cost-effective diagnostic tool that should be prioritized in early diagnostic path of children with progressive neurological disorders. The progressively decreasing price of the test improves cost-effectiveness further. [ABSTRACT FROM AUTHOR]

• Whole-exome sequencing (WES) was conducted to investigate the genetic mutations among NMD Jordanian patients. • Utilization of WES is helpful in facilitating rapid and accurate diagnosis of patients with NMDs. • WES helps in the identifying genetic risks among consanguineous couples. Neuromuscular disorders (NMDs) encompass a large group of genetic and acquired diseases affecting muscles, leading to progressive muscular weakness. These disorders are frequently inherited in an autosomal-recessive (AR) pattern with extreme heterogeneity and various clinical presentations. Consanguinity increases the likelihood of AR disorders, with high rates of cousin inbreeding in Jordan and other Arab countries. In Jordan, the implementation of genetic diagnosis is limited, with delayed or misdiagnosis of genetic disorders. Thus, the lack of genetic counselling and specialized treatment options is frequently encountered in the country. Whole-exome sequencing (WES) was conducted for eleven probands from ten Jordanian families who have been formerly diagnosed with limb-girdle dystrophy (LGMD) and Charcot-Marie-Tooth disease (CMT). The previous diagnoses were established principally on clinical examination in the absence of genetic testing. Additionally, Sanger sequencing and segregation analysis were used to validate the resulted pathogenic variants. Multiple variants were identified using WES: For DYSF gene, a missense variant (c. 4076 T > C, p.Leu1359Pro) in exon 38; a nonsense variant (c. 4321C > T, p.Gln1441Ter) in exon 39; a single‐nucleotide deletion (c. 5711delG, p.Gly1904AlafsTer101) in exon 51. Other variants included a missense variant (c. 122G > A, p.Arg41Gln) in exon 3 of MPV17 gene, a single‐nucleotide deletion (c. 859 delC, p.Lue287Ser fs14*) in exon 6 of SGCB gene, a missense variant (c. 311G > A, p.Gly104Asp) in exon 2 of SLC25A46 gene, a nonsense variant (c. 496C > T, p.Arg166Ter) in exon 5 of SGCG gene, and a nonsense variant (c.3202C > T, p.Gln1068Ter) in exon 13 of SH3TC2 gene. Utilization of WES is helpful to facilitate rapid and accurate NMDs diagnosis, complementing a thorough clinical evaluation. This approach can be invaluable to aid in the identification of genetic risks among consanguineous couples. Subsequently, well-informed genetic counselling and potential individualized treatment can be provided. [ABSTRACT FROM AUTHOR]

Objective: To explore the genetic causes of Herlyn-Werner-Wunderlich syndrome (HWWS) using whole-exome sequencing.Design: Retrospective genetic study.Setting: Academic medical center.Patient(s): Twelve patients with HWWS.Intervention(s): Whole-exome sequencing was performed for each patient. Sanger sequencing was used to confirm the potential causative genetic variants. In silico analysis and American College of Medical Genetics and Genomics guidelines were used to classify the pathogenicity of each variant.Main Outcome Measure(s): Rare sequence variants associated with müllerian duct development and renal agenesis were identified and included in subsequent analyses.Result(s): A total of 11 variants were identified in 10 of 12 patients (83.3%) and were considered to constitute a molecular genetic diagnosis of HWWS. These 11 variants were related to 9 genes: CHD1L, TRIM32, TGFBR3, WNT4, RET, FRAS1, FAT1, FOXF1, and PCSK5. All variants were heterozygous and confirmed by Sanger sequencing. The changes included one frameshift variant, one splice-site variant, and eight missense variants. All of the identified variants were absent or rare in Genome Aggregation Database East Asian populations. One of the 11 variants (9.1%) was classified as a pathogenic variant according to the American College of Medical Genetics and Genomics guidelines, and 8 of the 11 variants (72.7%) were classified as variants of uncertain significance.Conclusion(s): To our knowledge, this is the first report of the genetic causes of HWWS. Renal agenesis-related genes, such as CHD1L, TRIM32, RET, and WNT4, may be associated with HWWS. Identification of these variants can not only help us understand the etiology of HWWS and the relationship between reproductive tract development and urinary system development, but additionally improve the level of genetic counseling for HWWS. [ABSTRACT FROM AUTHOR]

Aromatic L-amino acid decarboxylase (AADC) deficiency, caused by a pathogenic variant in the dopa decarboxylase (DDC) gene, is a rare neurometabolic disorder in which catecholamine and serotonin are not synthesized. From a large number of reports, it has been recognized that most affected patients show severe developmental delay in a bedridden state and are unable to speak. On the other hand, patients with a mild phenotype with AADC deficiency have been reported, but they number only a few cases. Therefore, the variation of phenotypes of the disease appears to be broad, and it may be challenging to diagnose an atypical phenotype as AADC deficiency. We report novel compound heterozygous variants in DDC (c.202G > A and c.254C > T) in two sisters, whose main complaint was mild developmental delay, by whole-exome sequencing (WES). Additionally, we describe their clinical features and provide an image that shows the variants located at different sites responsible for the catalysis of AADC in a three-dimensional structure. The patients were prescribed a Monoamine oxidase (MAO) inhibitor after diagnosis. Our cases indicate that a comprehensive genomic approach helps to diagnose AADC deficiency with atypical features, and underscore the significance of understanding the variations of this disorder for diagnosis and appropriate treatment. [ABSTRACT FROM AUTHOR]

Congenital diarrheal disorders (CDDs) are a rare group of enteropathies that typically present in the early few months of life and pose a diagnostic challenge. We aimed to analyze the clinical findings and outcome of infants with CDDs and share experience about genetic testing. Demographic, clinical and genetic findings, and outcome of the patients (n = 24) with CDDs were recorded from hospital files. The onset of diarrhea was within the neonatal period in 45.8% of the patients. The most frequent causes of CDDs were defects in digestion, absorption and transport of nutrients and electrolytes (DATN) (n = 11, 45.8%) and defects in intestinal immune-related homeostasis (IIH) (n = 6, 25%). Fat malabsorption (n = 6) was the leading cause of defects in DATN. Extraintestinal manifestations including neurological involvement (25%) and renal involvement (20.8%) were common among the patients. Genetic analyses were performed for 16 patients (targeted gene analysis in 9, congenital diarrhea panel in 3, immune deficiency panel in 1 and whole-exome sequencing in 3 patients). Genetic diagnosis was achieved in 14 of 16 patients (87.5%) with therapeutic consequences in 8 of 16 patients (50%). During the follow-up, 6 patients (25%) died. The percentage of undefined etiology decreased, and treatment of the patients improved with the increased number of genetic testing in patients with CDDs. [ABSTRACT FROM AUTHOR]

ALG12-CDG is a rare autosomal recessive type I congenital disorder of glycosylation (CDG) due to pathogenic variants in ALG12 which encodes the dolichyl-P-mannose:Man-7-GlcNAc-2-PP-dolichyl-alpha-6-mannosyltransferase. Thirteen patients from unrelated 11 families have been reported, most of them result in broad multisystem manifestations with clinical variability. It is important to validate abnormal glycosylation to establish causal relationship. Here, we report two siblings with novel compound heterozygous variants in ALG12 : c.443T>C, p.(Leu148Pro) and c.412_413insCGT, p.(Gln137_Phe138insSer). Both patients showed global developmental delay, microcephaly, hypotonia, failure to thrive, facial dysmorphism, skeletal malformations and coagulation abnormalities, which are common in ALG12-CDG. In addition, one of our patients showed left hydronephrosis, which is a novel clinical feature in ALG12-CDG. Brain MRI showed hypoplasia of cerebrum, brain stem and cerebellar vermis in both patients. N -glycosylation defects of trypsin digested transferrin peptides were revealed by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), and electrospray ionization MS verified the lack of N -glycans in transferrin. The present study can add hydronephrosis to phenotypic spectrum of ALG12-CDG. Since the symptoms of ALG12-CDG are quite diverse, the combination of whole-exome sequencing and transferrin glycopeptide analysis with MS, can help diagnosis of ALG12-CDG. [ABSTRACT FROM AUTHOR]

Congenital hereditary endothelial dystrophy (CHED) is a rare genetic disease of the corneal endothelium with a very early onset of bilateral corneal edema due to degeneration and dysfunction of the corneal endothelium. Currently SLC4A11 is the only established causative gene for CHED, but not all these reported CHED patients could be explained by SLC4A11 deficiency, indicating that the genetic predisposition of CHED still requires further exploration. Trio-based whole-exome sequencing was performed on a CHED patient and his unaffected parents. The GATK2 and an in-house bioinformatics pipeline were applied for variant analyses, following the 2015 American College of Medical Genetics and Genomics (ACMG) guidelines. Potential pathogenic variants were further validated by Sanger sequencing. The expression profiles of FAM149A in cell line, murine tissues or human corneal endothelia were determined by RT-qPCR. Small interfering RNA was used to knock down the expression of FAM149A in vitro. Cell viability was detected by a CCK-8 assay. ROS and 8-OHdG were examined by fluorometric analysis. The nuclear translocation of NRF2 was determined by western blotting. We identified a homozygous mutation (NM_015398.3: c.991A > G; p.R331G) in the FAM149A gene that related to the phenotype of CHED. FAM149A was found to be highly expressed in corneal endothelium, and up-regulated upon oxidative stress. Further functional investigations demonstrated that deficiency in FAM149A impaired Nrf2-antioxidant signaling, rendering cells more vulnerable to oxidative stress. Consistently, the expression of FAM149A was significantly reduced in patients with corneal endothelium dysfunction. This study demonstrated, for the first time, FAM149A as a plausible causative gene for CHED etiology, offering new insight for future investigation targeting CHED. [Display omitted] • FAM149A might be a plausible causative gene for congenital hereditary endothelial dystrophy (CHED) etiology. •FAM149A was found to be highly expressed in corneal endothelium, and up-regulated upon oxidative stress. • Deficiency in FAM149A impaired Nrf2-antioxidant signaling, rendering cells more vulnerable to oxidative stress. [ABSTRACT FROM AUTHOR]