Exome Cohort Research Articles

Incidence of hypercholesterolemia actionable variants in a 10000+ exome cohort

Incidence of hypercholesterolemia actionable variants in a 10000+ exome cohort

Monogenic conditions and central nervous system anomalies: A prospective study, systematic review and meta-analysis.

Determine the incremental diagnostic yield of prenatal exome sequencing (pES) over chromosome microarray (CMA) or G-banding karyotype in fetuses with central nervous system (CNS) abnormalities. Data were collected via electronic searches from January 2010 to April 2022 in MEDLINE, Cochrane, Web of Science and EMBASE. The NHS England prenatal exome cohort was also included. Incremental yield was calculated as a pooled value using a random-effects model. Thirty studies were included (n=1583 cases). The incremental yield with pES for any CNS anomaly was 32% [95%CI 27%-36%; I2=72%]. Subgroup analysis revealed apparent incremental yields in; (a) isolated CNS anomalies; 27% [95%CI 19%-34%; I2=74%]; (b) single CNS anomaly; 16% [95% CI 10%-23%; I2=41%]; (c) more than one CNS anomaly; 31% [95% Cl 21%-40%; I2=56%]; and (d) the anatomical subtype with the most optimal yield was Type 1 malformation of cortical development, related to abnormal cell proliferation or apoptosis, incorporating microcephalies, megalencephalies and dysplasia; 40% (22%-57%; I2=68%). The commonest syndromes in isolated cases were Lissencephaly 3 and X-linked hydrocephalus. Prenatal exome sequencing provides a high incremental diagnostic yield in fetuses with CNS abnormalities with optimal yields in cases with multiple CNS anomalies, particularly those affecting the midline, posterior fossa and cortex.

Investigation of cancer predisposition in Fanconi anemia heterozygotes: A DiscovEHR cohort population study.

10589 Background: Fanconi anemia (FA) is a cancer predisposition syndrome caused by biallelic pathogenic variants in one of 22 genes involved in DNA intrastrand crosslink repair. 20 of these genes have an autosomal recessive inheritance pattern. Of the FA genes, 5 ( BRCA1, BRCA2, BRIP1, PALB2, RAD51C) are known cancer predisposition genes (CPG) when inherited in monoallelic autosomal dominant manner, though the heterozygous predisposition status of the remaining 15 remains unclear. Large population-level exome sequencing projects with linked health records such as the DiscovEHR cohort serve as promising tools to establish sufficient power to investigate all FA genes. Quantifying cancer risk is important for the counseling and surveillance of FA heterozygotes, especially with the ever-increasing use of genetic testing identifying these individuals. Methods: 170,503 individuals enrolled in the DiscovEHR Cohort were analyzed for pathogenic/likely pathogenic variants in 22 FA genes and identified 5834 subjects, the case group. ICD10 phenotype classifications for these subjects were curated to Phecodes and ICD-O-3 Site Recodes for two control arms of analysis. The first control arm included all DiscovEHR subjects excluding the case group and those with a variant of uncertain significance in the genes of interest with a deleterious in-silico score. The second control arm included individuals from the Surveillance, Epidemiology, and End Results (SEER) database. Phecode analysis yielded odds ratios adjusted for age, sex, race, smoking status, and BMI. SEER analysis yielded Standardized Incidence Ratio scores adjusted for age, sex, and birth cohort. When both arms of the analysis were completed Phecodes and SEER analyses were matched and positive signals for cancer risk were defined by statistically significant ratios in both. Results: The 5 known CPGs demonstrated multiple signals for cancer predisposition as expected (p < 0.0001). Results for FANCA (p = 0.4231) and FANCC (p = 0.8142) heterozygotes validated recent results from our group showing no increased risk of cancer in relatives of FA patients with these genotypes. Ten other FA genes also showed no increased risk of cancer. 3 genes suggested a possible increased risk of specific cancers in heterozygotes and are currently being evaluated in a second large population exome cohort to validate these findings. Conclusions: This is the largest study to date on the cancer predisposition risk in Fanconi anemia heterozygotes. We have confirmed the known risk in 5 well-described CPGs and the lack of risk amongst FANCA and FANCC heterozygotes, the most common in population. Further analysis via an additional large population cohort is underway to validate any possible novel cancer predispositions in 3 genes. For the remaining FA genes, this population analysis supports previous literature on known CPGs and the lack of cancer predisposition in most FA genes.

A practical approach to curate clonal hematopoiesis of indeterminate potential in human genetic data sets

AbstractClonal hematopoiesis of indeterminate potential (CHIP) is a common form of age-related somatic mosaicism that is associated with significant morbidity and mortality. CHIP mutations can be identified in peripheral blood samples that are sequenced using approaches that cover the whole genome, the whole exome, or targeted genetic regions; however, differentiating true CHIP mutations from sequencing artifacts and germ line variants is a considerable bioinformatic challenge. We present a stepwise method that combines filtering based on sequencing metrics, variant annotation, and population-based associations to increase the accuracy of CHIP calls. We apply this approach to ascertain CHIP in ∼550 000 individuals in the UK Biobank complete whole exome cohort and the All of Us Research Program initial whole genome release cohort. CHIP ascertainment on this scale unmasks recurrent artifactual variants and highlights the importance of specialized filtering approaches for several genes, including TET2 and ASXL1. We show how small changes in filtering parameters can considerably increase CHIP misclassification and reduce the effect size of epidemiological associations. Our high-fidelity call set refines previous population-based associations of CHIP with incident outcomes. For example, the annualized incidence of myeloid malignancy in individuals with small CHIP clones is 0.03% per year, which increases to 0.5% per year among individuals with very large CHIP clones. We also find a significantly lower prevalence of CHIP in individuals of self-reported Latino or Hispanic ethnicity in All of Us, highlighting the importance of including diverse populations. The standardization of CHIP calling will increase the fidelity of CHIP epidemiological work and is required for clinical CHIP diagnostic assays.

De novo variants in H3-3A and H3-3B are associated with neurodevelopmental delay, dysmorphic features, and structural brain abnormalities

The histone H3 variant H3.3, encoded by two genes H3-3A and H3-3B, can replace canonical isoforms H3.1 and H3.2. H3.3 is important in chromatin compaction, early embryonic development, and lineage commitment. The role of H3.3 in somatic cancers has been studied extensively, but its association with a congenital disorder has emerged just recently. Here we report eleven de novo missense variants and one de novo stop-loss variant in H3-3A (n = 6) and H3-3B (n = 6) from Baylor Genetics exome cohort (n = 11) and Matchmaker Exchange (n = 1), of which detailed phenotyping was conducted for 10 individuals (H3-3A = 4 and H3-3B = 6) that showed major phenotypes including global developmental delay, short stature, failure to thrive, dysmorphic facial features, structural brain abnormalities, hypotonia, and visual impairment. Three variant constructs (p.R129H, p.M121I, and p.I52N) showed significant decrease in protein expression, while one variant (p.R41C) accumulated at greater levels than wild-type control. One H3.3 variant construct (p.R129H) was found to have stronger interaction with the chaperone death domain-associated protein 6.

Contribution of uniparental disomy in a clinical trio exome cohort of 2675 patients.

BackgroundUniparental disomy (UPD) is the inheritance of two homologous chromosomes from the same parent. UPD may result in clinical phenotypes when occurring on chromosomes with specific imprinting pattern, when leading to homozygosity of a deleterious recessive allele inherited from one carrier parent, or when associated with a mosaic aneuploidy. Due to the importance of UPD in genetic disease etiology, UPD analysis has started to be implemented in the context of exome sequencing (ES) or genome sequencing.MethodsWe developed an in‐house algorithm TRIPS (Trio Parentage/UPD Studies) to identify UPD events in trio ES cases. This method identifies regions with uniparental inheritance by utilizing the trio genotyping data obtained from the concurrent SNP array to delineate the parental origin of the SNPs in the proband.ResultsWe identified 16 UPD events from 2675 ES trios. Among those, four events led to imprinting disorders, seven unmasked a pathogenic/likely pathogenic variant in a recessive disease gene, and two were consistent with a mosaic genome wide paternal UPD pattern. Twelve of these UPD events directly contributed to the molecular diagnosis of the patients.ConclusionOur study demonstrated the contribution of UPD to the molecular diagnosis in one clinical ES cohort, thus UPD analysis should be incorporated into routine clinical ES interpretation.

Genomic Landscape of Primary Cutaneous Diffuse Large B Cell Lymphoma, Leg Type

Primary cutaneous diffuse large B-cell lymphoma, leg type (DLBCL-LT) is an aggressive subtype of cutaneous B cell lymphoma (CBCL) with a poor prognosis. It is most often diagnosed on the legs of the elderly, frequently relapses, and has a tendency towards extracutaneous dissemination. Current treatment strategies are ineffective and revolve around surgical excision, multiagent chemotherapy (e.g. R-CHOP) and radiation therapy, with estimated 5-year survival rates of ~50%. Identifying genetic mutations and altered pathways specific for DLBCL-LT is crucial for the diagnosis and development of effective targeted therapies for this condition.We performed whole exome capture and massively parallel sequencing on 13 tumor samples of DLBCL-LT (4 matched and 9 unmatched) and 5 samples of cutaneous diffuse large B cell lymphoma, not otherwise specified (DLBCL-NOS) (1 matched and 4 unmatched). This is the largest whole exome cohort of cutaneous DLBCL to date. We applied algorithms routinely used by our lab to identify putative cancer promoting mutations and to compare the genetic landscape with DLBCL, both nodal and extranodal.Broadly, the landscape of mutations in DLBCL-LT is similar to that of activated B-cell like (ABC) DLBCL and most analogous to primary central nervous system lymphoma (PCNSL), a type of extranodal ABC DLBCL. Similar to PCNSL, we found frequent disease-defining oncogenic gene mutations in MYD88 (85%), CD79B (38%), and TBL1XR1 (38%), and loss of function mutations in tumor suppressor genes KMT2D (15%), CDKN1B (15%), and CD58 (8%). We observed frequent mutations in PIM1 (54%), OSBPL10 (31%), BTG2 (31%), and IGLL5 (15%), which are either known or proposed targets of activation-induced cytidine deaminase (AID) and aberrant somatic hypermutation (aSHM) also seen in PCNSL. Importantly and similarly to PCNSL, we found alterations at the PDL-1 and PDL-2 locus, but instead of copy number gains, we discovered frequent PD-L1 and PD-L2 translocations (40%) that may translate into overexpression of PD-L1 .This spectrum of mutations differed significantly compared to our DLBCL-NOS cohort, which did not have the above oncogenic mutations and lacked any PD-L1 or PD-L2 chromosomal alterations. Finally, we report novel oncogenic mutations in DLBCL-LT including MYD88 p.S243N, CD79B p.L199P, CCND3 p.T283P and p.P284S, BRAF p.V600E, and CARD11 p.R113Q and novel loss of function mutations in KMT2D, CDKN1B, CD58, MSH2, PIK3R1, MSH2, and BMF .Collectively, we identified recurrent mutations in multiple key cancer-related biological pathways, including epigenetic modulators (TBL1XR1, HIST1H1E, and KMT2D), NF-κB signaling pathway (MYD88, CD79B, and CARD11), MAPK signaling pathway (BRAF), PI3K signaling pathway (PIK3R1), JAK/STAT signaling pathway (PIM1), cell cycle regulators (CCND3, CDKN1B and BTG2), and immune escape (CD58). All of the DLBCL-LT samples in our cohort contained one or more gene mutations that can be targeted by agents that are currently FDA-approved or under clinical trials, such as BRAF inhibitors, JAK/STAT inhibitors, PIM inhibitors, PI3K inhibitors, NF-kB inhibitors, MYD88 inhibitors, and PD-1/PDL-1 inhibitors.Altogether, our data identified targetable putative driver gene mutations in DLBCL-LT. These mutational signatures bear broad similarities to PCNSL. Because of the relative rarity of this disease, we hope these efforts will allow for its inclusion, when relevant, in trials involving genotypically similar DLBCL. DisclosuresNo relevant conflicts of interest to declare.

Coding and noncoding drivers of mantle cell lymphoma identified through exome and genome sequencing

AbstractMantle cell lymphoma (MCL) is an uncommon B-cell non-Hodgkin lymphoma (NHL) that is incurable with standard therapies. The genetic drivers of this cancer have not been firmly established, and the features that contribute to differences in clinical course remain limited. To extend our understanding of the biological pathways involved in this malignancy, we performed a large-scale genomic analysis of MCL using data from 51 exomes and 34 genomes alongside previously published exome cohorts. To confirm our findings, we resequenced the genes identified in the exome cohort in 191 MCL tumors, each having clinical follow-up data. We confirmed the prognostic association of TP53 and NOTCH1 mutations. Our sequencing revealed novel recurrent noncoding mutations surrounding a single exon of the HNRNPH1gene. In RNA-seq data from 103 of these cases, MCL tumors with these mutations had a distinct imbalance of HNRNPH1 isoforms. This altered splicing of HNRNPH1 was associated with inferior outcomes in MCL and showed a significant increase in protein expression by immunohistochemistry. We describe a functional role for these recurrent noncoding mutations in disrupting an autoregulatory feedback mechanism, thereby deregulating HNRNPH1 protein expression. Taken together, these data strongly imply a role for aberrant regulation of messenger RNA processing in MCL pathobiology.

SUN-LB107 Functional Characterisation of Human Heterozygous Non-Synonymous MC3R Variants

Background: Melanocortin 3 receptor (MC3R) is a member of the melanocortin family of G-protein coupled receptors predominantly expressed in hypothalamic tissue. Rodent models have implicated MC3R in the pathogenesis of obesity, however in humans the relationship between obesity phenotypes and impaired MC3R function is less well established than that observed for loss of function mutations in the homologous MC4R. Aim: Recently three heterozygous MC3R variants identified from candidate gene sequencing of an obese human cohort were reported to be pathogenic. We sought to functionally characterise the these MC3R non-synonymous variants (p.Q11X, p.I50T and p.A149V) in vitro and examine their associations to body mass index in an unselected population-based cohort. Methodology: Functional characterisation of each variant was undertaken in HEK293 cells transiently overexpressing either wild-type MC3R or the respective MC3R mutant where cAMP-dependant luciferase activity in response to alpha-melanocyte stimulating hormone (α-MSH) was measured. Body mass index (BMI) was compared between heterozygous carriers of the MC3R variants of interest and control participants (matched for age and sex and ethnicity) identified within the UK Biobank whole exome sequencing dataset. Results: Impairment of the canonical MC3R cAMP signalling response to α-MSH was observed for both p.Q11X and p.A149V MC3R variants when compared to wild-type MC3R receptor function in vitro. In contrast the cAMP signalling response of MC3R p.I50T to α-MSH was non-inferior to wild-type. Thirty-nine (male=18) heterozygous carriers of MC3R p.I50T were identified in the UK Biobank whole exome cohort. There was no statistical difference in median (IQR) BMI for female carriers 27.1(7.8) kg/m2 vs. matched female control participants 26.2(5.5) kg/m2 or male carriers 27.7(5.4) kg/m2 vs. matched male control participants 27.4(4.9) kg/m2. A single participant heterozygous for the MC3R p.Q11X variant (BMI= 28.3 kg/m2) and two participants heterozygous for MC3R p.A149V (BMI= 24.7 and 25.1 kg/m2 respectively) variant were identified in the UK Biobank whole exome cohort. BMI did not significantly differ from the match control population median for either of these variants. Conclusion: In vitro assessment and phenotype correlates suggest that MC3R p.I50T is not an obesity causing mutation. Despite evidence of impaired receptor function in vitro, MC3R p.Q11X and p.A149V did not associate with obesity in this unselected population and further study are required to elucidate their pathogenicity in humans.

A diagnostic ceiling for exome sequencing in cerebellar ataxia and related neurological disorders.

Genetic ataxias are associated with mutations in hundreds of genes with high phenotypic overlap complicating the clinical diagnosis. Whole-exome sequencing (WES) has increased the overall diagnostic rate considerably. However, the upper limit of this method remains ill-defined, hindering efforts to address the remaining diagnostic gap. To further assess the role of rare coding variation in ataxic disorders, we reanalyzed our previously published exome cohort of 76 predominantly adult and sporadic-onset patients, expanded the total number of cases to 260, and introduced analyses for copy number variation and repeat expansion in a representative subset. For new cases (n = 184), our resulting clinically relevant detection rate remained stable at 47% with 24% classified as pathogenic. Reanalysis of the previously sequenced 76 patients modestly improved the pathogenic rate by 7%. For the combined cohort (n = 260), the total observed clinical detection rate was 52% with 25% classified as pathogenic. Published studies of similar neurological phenotypes report comparable rates. This consistency across multiple cohorts suggests that, despite continued technical and analytical advancements, an approximately 50% diagnostic rate marks a relative ceiling for current WES-based methods and a more comprehensive genome-wide assessment is needed to identify the missing causative genetic etiologies for cerebellar ataxia and related neurodegenerative diseases.

Peripheral myelin protein 2 \u2013 a novel cluster of mutations causing Charcot-Marie-Tooth neuropathy

BackgroundCharcot-Marie-Tooth (CMT) disease is the most common inherited neuromuscular disorder characterized by wide clinical, genetic and pathomechanistic heterogeneity. Recently, the gene encoding peripheral myelin protein 2 (PMP2) was identified as a novel cause for CMT neuropathy with three mutations that structurally cluster together (p.Ile43Asn, p.Thr51Pro, p.Ile52Thr) reported in five families.ResultsUsing whole exome sequencing and cohort screening we identified two novel missense substitutions in PMP2 in Bulgarian (p.Met114Thr, c.341C > T) and German (p.Val115Ala, c.344 T > C) families. The mutations affect adjacent and highly conserved amino acid residues outside of the known mutation-rich region in the protein. Crystal structure analysis positions the affected residues within a cluster of highly conserved fatty acid coordinating residues implying their functional significance. The clinical, electrophysiological and imaging features in both families were consistent with a childhood onset polyneuropathy with variable patterns of demyelination, slow to very slow progression, and most severe involvement of the peroneal muscles.ConclusionsWe expand the genetic and phenotypic spectrum of PMP2-related peripheral neuropathy. Our findings reveal a second mutational cluster in the protein.

Blacklisting variants common in private cohorts but not in public databases optimizes human exome analysis

Computational analyses of human patient exomes aim to filter out as many nonpathogenic genetic variants (NPVs) as possible, without removing the true disease-causing mutations. This involves comparing the patient's exome with public databases to remove reported variants inconsistent with disease prevalence, mode of inheritance, or clinical penetrance. However, variants frequent in a given exome cohort, but absent or rare in public databases, have also been reported and treated as NPVs, without rigorous exploration. We report the generation of a blacklist of variants frequent within an in-house cohort of 3,104 exomes. This blacklist did not remove known pathogenic mutations from the exomes of 129 patients and decreased the number of NPVs remaining in the 3,104 individual exomes by a median of 62%. We validated this approach by testing three other independent cohorts of 400, 902, and 3,869 exomes. The blacklist generated from any given cohort removed a substantial proportion of NPVs (11-65%). We analyzed the blacklisted variants computationally and experimentally. Most of the blacklisted variants corresponded to false signals generated by incomplete reference genome assembly, location in low-complexity regions, bioinformatic misprocessing, or limitations inherent to cohort-specific private alleles (e.g., due to sequencing kits, and genetic ancestries). Finally, we provide our precalculated blacklists, together with ReFiNE, a program for generating customized blacklists from any medium-sized or large in-house cohort of exome (or other next-generation sequencing) data via a user-friendly public web server. This work demonstrates the power of extracting variant blacklists from private databases as a specific in-house but broadly applicable tool for optimizing exome analysis.

EIF2AK3 variants in Dutch patients with Alzheimer's disease.

Next-generation sequencing has contributed to our understanding of the genetics of Alzheimer's disease (AD) and has explained a substantial part of the missing heritability of familial AD. We sequenced 19 exomes from 8 Dutch families with a high AD burden and identified EIF2AK3, encoding for protein kinase RNA-like endoplasmic reticulum kinase (PERK), as a candidate gene. Gene-based burden analysis in a Dutch AD exome cohort containing 547 cases and 1070 controls showed a significant association of EIF2AK3 with AD (OR 1.84 [95% CI 1.07-3.17], p-value 0.03), mainly driven by the variant p.R240H. Genotyping of this variant in an additional cohort from the Rotterdam Study showed a trend toward association with AD (p-value 0.1). Immunohistochemical staining with pPERK and peIF2α of 3 EIF2AK3 AD carriers showed an increase in hippocampal neuronal cells expressing these proteins compared with nondemented controls, but no difference was observed in AD noncarriers. This study suggests that rare variants in EIF2AK3 may be associated with disease risk in AD.

Abstract 1304: Whole-exome analysis of 1,135 melanomas reveals new significantly mutated cancer genes and copy number alterations

Abstract Introduction: Identifying driver mutations and significantly mutated genes (SMGs) is critical to characterize therapeutic targets and understand biological subtypes. Past studies in melanoma have identified ~20 SMGs and 4 genomic subtypes (BRAF, NRAS, and NF1, and triple wildtype). Critically, these studies have been powered to detect SMGs only at a frequency of >~10%. However, clinically targetable drivers can occur at much lower frequencies (e.g. ALK-rearrangmenet in lung cancer). Thus, we hypothesized that a uniform meta-analysis of all publicly available melanoma whole exome sequences would provide power to identify clinically SMGs not previously associated with melanoma. Methods: We assembled and uniformly analyzed a cohort of 1,135 tumor and matched germline primary and metastatic non-uveal melanoma whole exomes. All samples were realigned to hg19 using the Picard best practice realignment pipeline. These samples passed several QC metrics that included coverage (DepthOfCoverage, 50X tumor and 20X normal), cross sample contamination (ContEst, < 5%), tumor purity (FACETS, > 20%), and tumor-in-normal (deTiN, < 30%). Mutational significance analysis was performed using MutSigCV2 followed by filtering via biological priors using OncoKB. CNA profiles were generated using GATK4 best practices pipeline. Results: We identified 77 SMGs (MutSig q < 0.1) that were implicated in either melanoma or other cancer types according to OncoKB's curated list of 1,018 cancer genes, some of which that have not been considered SMGs or previously reported in melanoma. Novel genes were involved in immune response [B2M (1.7%) and PTPRC (12.1%)], DNA damage checkpoints [MDC1 (7.5%)], negative regulation of the MAPK pathway [CBL (4.6%)], MYC suppression [MGA (9.4%)], and the PI3K/AKT pathway [PIK3CA (3.4%) and PIK3CB (3.5%)]. Within the “triple-wt” subset of melanomas (n=212), we identified additional SMGs including IDH1, SF3B1, CTNNB1, and MAPK2K1 present in 3-5% of tumors, suggesting additional potential therapeutic targets. Copy number profiles of the cohort were consistent with previous findings. By increasing the resolution from cytobands to 1Mb regions, we identified a 1Mb region in chromosome 3 (chr3:138Mb-139Mb) that was enriched in amplifications (29.2%). Genes in this region include MRAS, PI3KCB, FOXL2, and FAIM. Conclusion: Through assembly and uniform analysis of the largest melanoma whole exome cohort to date, we identified significantly mutated known cancer genes not previously associated with the disease, and identified additional drivers within an incompletely characterized subtype of melanoma. This also enabled us to find genome regions enriched in copy number alterations. Taken together, our findings may inform the additional classification of melanoma and identification of novel drivers to shed light on biological subtypes and identify potential therapeutic targets. Citation Format: Jake R. Conway, David Liu, Stephanie Wankowicz, Amaro Taylor-Weiner, Felix Dietlein, Eliezer Van Allen. Whole-exome analysis of 1,135 melanomas reveals new significantly mutated cancer genes and copy number alterations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1304.

De Novo Missense Variants in TRAF7 Cause Developmental Delay, Congenital Anomalies, and Dysmorphic Features

TRAF7 is a multi-functional protein involved in diverse signaling pathways and cellular processes. The phenotypic consequence of germline TRAF7 variants remains unclear. Here we report missense variants in TRAF7 in seven unrelated individuals referred for clinical exome sequencing. The seven individuals share substantial phenotypic overlap, with developmental delay, congenital heart defects, limb and digital anomalies, and dysmorphic features emerging as key unifying features. The identified variants are de novo in six individuals and comprise four distinct missense changes, including a c.1964G>A (p.Arg655Gln) variant that is recurrent in four individuals. These variants affect evolutionarily conserved amino acids and are located in key functional domains. Gene-specific mutation rate analysis showed that the occurrence of the de novo variants in TRAF7 (p = 2.6× 10-3) and the recurrent de novo c.1964G>A (p.Arg655Gln) variant (p = 1.9× 10-8) in our exome cohort was unlikely to have occurred by chance. Invitro analyses of the observed TRAF7 mutations showed reduced ERK1/2 phosphorylation. Our findings suggest that missense mutations in TRAF7 are associated with a multisystem disorder and provide evidence of a role for TRAF7 in human development.

Disclosure of cardiac variants of uncertain significance results in an exome cohort.

This study examined the impact of disclosing subclassifications of genetic variants of uncertain significance (VUS) on behavioral intentions. We studied return of VUS results to 79 individuals with a cardiomyopathy-associated VUS, subclassified into VUS-high or VUS-low. Primary outcomes were perceived risk (absolute and comparative), perceived severity, perceived value of information, self-efficacy, decision regret, and behavioral intentions to share results and change behaviors. There was no significant difference between the 2 subclasses in overall behavioral intentions (t = 0.023, P = .982) and each of the individual items on the behavioral intentions scale; absolute (t = -1.138, P = .259) or comparative (t = -0.463, P = .645) risk perceptions; perceived value of information (t = 0.582, P = .563) and self-efficacy (t = -0.733, P = .466). Decision regret was significantly different (t = 2.148, P = .035), with VUS-low (mean = 17.24, SD = 16.08) reporting greater regret. Combining the subclasses, perceived value of information was the strongest predictor of behavioral intentions (β = 0.524, P < .001). Participants generally understood the meaning of a genetic VUS result classification and reported satisfaction with result disclosure. No differences in behavioral intentions were found, but differences in decision regret suggest participants distinguish subclasses of VUS results. The perceived value of VUS may motivate recipients to pursue health-related behaviors.

Mutation screening of SCN2A in schizophrenia and identification of a novel loss-of-function mutation.

There is a growing body of evidence suggesting a shared genetic susceptibility between many neuropsychiatric disorders, including schizophrenia, autism, intellectual disability (ID) and epilepsy. The sodium channel, voltage-gated type II α subunit gene SCN2A has been shown to exhibit loss-of-function (LoF) mutations in individuals with seizure disorders, ID, autism and schizophrenia. The role of LoF mutations in schizophrenia is still uncertain with only one such mutation identified to date. To seek additional evidence for a role for LoF mutations at SCN2A in schizophrenia we performed mutation screening of the entire coding sequence in 980 schizophrenia cases. Given an absence of LoF mutations in a public exome cohort (ESP6500, N=6503), we did not additionally sequence controls. We identified a novel, nonsense (i.e. stop codon) mutation in one case (E169X) that is absent in 4300 European-American and 2203 African-American individuals from the NHLBI Exome Sequencing Project. This is the second LoF allele identified in a schizophrenia case to date. We also show a novel, missense variant, V1282F, that occurs in two cases and is absent in the control dataset. We argue that very rare, LoF mutations at SCN2A act in a moderately penetrant manner to increase the risk of developing several neuropsychiatric disorders including seizure disorders, ID, autism and schizophrenia.

Abstract 11800: Whole Exome Sequencing in a Large Pedigree With DCM Identifies a Novel Mutation in RBM20

Background and hypothesis: Familial dilated cardiomyopathy (DCM) is genetically heterogeneous and is associated with mutations in at least 30 different genes. None of these genes have an expected diagnostic yield of more than 10% complicating genetic diagnosis. Whole exome sequencing (WES) is a powerful alternative for the identification of the causal gene, however variant interpretation remains challenging. We performed WES in a large family with autosomal dominant DCM complicated by end stage heart failure and ventricular arrhythmias. The index of this family was evaluated previously by means of targeted gene panel analysis including 28 genes, but no causal mutation was found. Methods and results: WES was applied on 2 affected cousins. First, shared heterozygous variants (single nucleotide variants, small insertions and deletions) located inside the exon or at the exon/intron boundary were selected. Synonymous variants were excluded, except if they were located at the exon/intron boundaries. Variants with a minor allele frequency of &gt;0.1% in publically available exome databases (1000 Genomes and ESP) were excluded. Furthermore, variants that were present in an in-house exome cohort performed for other disease entities were also excluded since these probably represent local SNV’s. The remaining 19 variants were evaluated using a comprehensive scoring system that includes different in-silico analysis tools, orthologous and paralogous conservation and population frequencies. Subsequently Sanger sequencing was performed for 10 variants that were classified as likely pathogenic (N=1) or variants of unknown significance (N=9) according to the scoring system in order to confirm the presence of the variant and to evaluate co-segregation. Only one variant in exon 9 of the RBM20 gene (c.2714T&gt;A, p.Met950Lys, NM_001334363) showed full co-segregation in the 7 affected family members resulting in a maximum 2-point LOD score of 2.1 and suggesting this as the pathogenic mutation responsible for the phenotype. Recently mutations in RBM20 have been linked to dilated cardiomyopathy caused by defective splicing of the giant sarcomeric protein titin. Conclusions: We report the identification of a novel mutation in RBM20 by WES in a large pedigree with DCM.

Gender Disparity and Mutation Burden in Metastatic Melanoma.

Gender differences in melanoma incidence and outcome have been consistently observed but remain biologically unexplained. We hypothesized that tumors are genetically distinct between men and women and analyzed the mutation spectra in 266 metastatic melanomas (102 women and 164 men) from The Cancer Genome Atlas (TCGA). We found a statistically significantly greater burden of missense mutations among men (male median 298 vs female median = 211.5; male-to-female ratio [M:F] = 1.85, 95% confidence interval [CI] = 1.44 to 2.39). We validated these initial findings using available data from a separate melanoma exome cohort (n = 95) and found a similar increase in missense mutations among men (male median 393 vs female median 259; M:F = 1.59, 95% CI = 1.12 to 2.27). In addition, we found improved survival with increasing log-transformed missense mutation count (univariate hazard ratio = 0.82, 95% CI = 0.69 to 0.98) for TCGA samples. Our analyses demonstrate for the first time a gender difference in mutation burden in cutaneous melanoma.

Individualized Iterative Phenotyping for Genome-wide Analysis of Loss-of-Function Mutations

Next-generation sequencing provides the opportunity to practice predictive medicine based on identified variants. Putative loss-of-function (pLOF) variants are common in genomes and understanding their contribution to disease is critical for predictive medicine. To this end, we characterized the consequences of pLOF variants in an exome cohort by iterative phenotyping. Exome data were generated on 951 participants from the ClinSeq cohort and filtered for pLOF variants in genes likely to cause a phenotype in heterozygotes. 103 of 951 exomes had such a pLOF variant and 79 participants were evaluated. Of those 79, 34 had findings or family histories that could be attributed to the variant (28 variants in 18 genes), 2 had indeterminate findings (2 variants in 2 genes), and 43 had no findings or a negative family history for the trait (34 variants in 28 genes). The presence of a phenotype was correlated with two mutation attributes: prior report of pathogenicity for the variant (p = 0.0001) and prior report of other mutations in the same exon (p = 0.0001). We conclude that 1/30 unselected individuals harbor a pLOF mutation associated with a phenotype either in themselves or their family. This is more common than has been assumed and has implications for the setting of prior probabilities of affection status for predictive medicine.