Ancestry-matched Controls Research Articles

Characteristics of Rare Germline ATM Variants in Chronic Lymphocytic Leukemia (CLL)

Background The use of next-generation sequencing in the clinic has increasingly uncovered new variants of unknown significance (VUS), which are often ignored clinically. Ataxia telangiectasia mutated (ATM) is a tumor-suppressor gene that has a critical role in DNA double-strand break repair and has been implicated in the pathogenesis of CLL. In this study, we assessed rare germline ATM variants including VUS using a novel variant calling algorithm, evaluated their impact on the clinical characteristics of CLL and functionally assessed their effect on ATM kinase activity. Methods We evaluated the entire ATM coding region via germline whole exome sequencing from 885 CLL patients representing three different previously reported cohorts (327 DFCI; 276 German CLL Study Group, and 282 ICGC), along with a cohort of ancestry matched controls. We utilized DeepVariant (Poplin et al Nature Biotech 2018) to detect germline variants, followed by a standardized quality control workflow (AlDubayan et al JAMA 2020). All individuals harbored ATM germline variants. Variants were annotated using dbSNP, Clinvar and Varsome, and variants with GnomAD population allele frequency (AF) < 1% were defined as rare. For clinical characterization of CLL patients with rare germline ATM missense variants, we focused on the DFCI cohort. For functional analysis, we evaluated ATM kinase activity by ATM and KAP1 phosphorylation in response to 1 Gy gamma-irradiation using flow cytometry in primary CLL samples with/without rare germline ATM missense variants. We also generated CRISPR/Cas9 engineered cell lines to evaluate the function of ATM p.L2307F which was frequent in our CLL cohort and which we previously demonstrated as enriched in CLL, yet generally annotated as a VUS. Results We identified a total of 130 ATM germline variants among the CLL cases, including 87 missense, and 9 splice site alterations. 80 of 87 missense variants were rare and 59 were annotated as VUS. The top 5 most frequent rare germline missense variants with high odds ratio for association with CLL were ATM p.L2332P (AF cases vs controls, 0.328% vs 0.0188%, OR 17.46), p.L2307F (OR 16.88), p.F763L (OR 18.89), p.Y1442H (OR 35.39) and p.S99G (OR 16.28). In 63 DFCI patients with rare missense variants, the median age at diagnosis was 55 (31-82), 21.7% had a familial history of CLL and 29% had del(11q). Phosphorylation of ATM and KAP1 (pATM, pKAP1) in response to gamma-irradiation was reduced in 12 patients assessed (8 rare and 4 non-rare) with germline ATM variants (ATM variant alone group) compared to those without any somatic or germline ATM aberrancy (WT group) (P<0.01). Similar results were seen when the analysis was restricted to the 8 CLL patients with rare ATM variants. Phosphorylation levels were also significantly lower in 17 patients with rare germline ATM variants with concurrent del(11q) (del 11q + ATM variant group) compared to 13 of those with del(11q) alone (del 11q group) (P<0.01) (Figure 1). Altogether, these results suggest that germline ATM variants have a functional impact on DNA damage response in primary CLL cells. We previously identified the VUS variant ATM p.L2307F as particularly enriched among CLL patients (Tiao G et al., Leukemia. 2017). We therefore generated ATM L2307F knock-in NALM-6 cell lines via CRISPR/Cas9. We generated 7 cell lines including ATM wild type (+/+), ATM monoallelic mutated (+/L2307F), ATM monoallelic knocked out (+/-), ATM monoallelic mutated with knock out of the other allele (-/L2307F), and ATM biallelic knockout (-/-). The induction of both pATM and pKAP1 levels by gamma irradiation was reduced in proportion to ATM mutational status as shown in Figure 2. Conclusions We demonstrate that rare ATM germline variants are common in CLL and affect the DNA damage response in primary CLL cells when controlling for somatic 11q deletion. We further characterize the p.L2307F variant using CRISPR and demonstrate that this allele represents a functional hypomorph in cell-based assays. Further studies are needed to assess the impact of each individual rare germline variant on the function of ATM, CLL pathogenesis and the inherited risk of CLL. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Investigating the role of common and rare variants in multiplex multiple sclerosis families reveals an increased burden of common risk variation

Many multiple sclerosis (MS)-associated common risk variants as well as candidate low-frequency and rare variants have been identified; however, approximately half of MS heritability remains unexplained. We studied seven multiplex MS families, six of which with parental consanguinity, to identify genetic factors that increase MS risk. Candidate genomic regions were identified through linkage analysis and homozygosity mapping, and fully penetrant, rare, and low-frequency variants were detected by exome sequencing. Weighted sum score and polygenic risk score (PRS) analyses were conducted in MS families (24 affected, 17 unaffected), 23 sporadic MS cases, 63 individuals in 19 non-MS control families, and 1272 independent, ancestry-matched controls. We found that familial MS cases had a significantly higher common risk variation burden compared with population controls and control families. Sporadic MS cases tended to have a higher PRS compared with familial MS cases, suggesting the presence of a higher rare risk variation burden in the families. In line with this, score distributions among affected and unaffected family members within individual families showed that known susceptibility alleles can explain disease development in some high-risk multiplex families, while in others, additional genetic contributors increase MS risk.

Association of ultra-rare coding variants with genetic generalized epilepsy: A case-control whole exome sequencing study.

We aimed to identify genes associated with genetic generalized epilepsy (GGE) by combining large cohorts enriched with individuals with a positive family history. Secondarily, we set out to compare the association of genes independently with familial and sporadic GGE. We performed a case-control whole exome sequencing study in unrelated individuals of European descent diagnosed with GGE (previously recruited and sequenced through multiple international collaborations) and ancestry-matched controls. The association of ultra-rare variants (URVs; in 18834 protein-coding genes) with epilepsy was examined in 1928 individuals with GGE (vs. 8578 controls), then separately in 945 individuals with familial GGE (vs. 8626 controls), and finally in 1005 individuals with sporadic GGE (vs. 8621 controls). We additionally examined the association of URVs with familial and sporadic GGE in two gene sets important for inhibitory signaling (19genes encoding γ-aminobutyric acid type A [GABAA ] receptors, 113genes representing the GABAergic pathway). GABRG2 was associated with GGE (p=1.8×10-5 ), approaching study-wide significance in familial GGE (p=3.0×10-6 ), whereas no gene approached a significant association with sporadic GGE. Deleterious URVs in the most intolerant subgenic regions in genes encoding GABAA receptors were associated with familial GGE (odds ratio [OR]=3.9, 95% confidence interval [CI]=1.9-7.8, false discovery rate [FDR]-adjusted p=.0024), whereas their association with sporadic GGE had marginally lower odds (OR=3.1, 95% CI=1.3-6.7, FDR-adjusted p=.022). URVs in GABAergic pathway genes were associated with familial GGE (OR=1.8, 95% CI=1.3-2.5, FDR-adjusted p=.0024) but not with sporadic GGE (OR=1.3, 95% CI=.9-1.9, FDR-adjusted p=.19). URVs in GABRG2 are likely an important risk factor for familial GGE. The association of gene sets of GABAergic signaling with familial GGE is more prominent than with sporadic GGE.

Abstract PR-16: Serum prostate-specific antigen levels and prostate cancer risk in a multiethnic population

Abstract Purpose: While prostate-specific antigen (PSA) is the most commonly used biomarker for prostate cancer (PCa) screening, multiple studies in the U.S. and Europe have shown that PSA levels in midlife, many years before a PCa diagnosis, are associated with increased risk of PCa later in life. However, limited information is available on the relationship between PSA levels measured years before diagnosis and risk of PCa in non-White populations. Methods: We examined whether a PSA level in older adult men measured up to 10+ years before a PCa diagnosis is associated with risk of overall PCa and aggressive PCa (Gleason score&amp;gt;7, non-localized disease, or death from PCa) in a nested case-control study of African American (AA), Latino (LA), Japanese (JP), Native Hawaiian (NH), and Non-Hispanic White (WH) men in the Multiethnic Cohort (MEC). Pre-diagnostic blood levels of total PSA were measured among 2,245 incident PCa cases and 2,203 age and ancestry matched controls. We also assessed the discriminative ability of PSA, years before diagnosis, relative to a polygenic risk score (PRS) for PCa. Results: The mean age at blood draw when PSA was measured for cases and controls was 68 (range: 47-86) and 69 (47-87), respectively. Among cases, the average duration between blood draw and a PCa diagnosis was 4.9 years (range: &amp;lt;1 year to 18 years). Compared to men with PSA below the median, men with PSA above the median had odds ratios (ORs) (95% CIs) for total PCa of 26.15 (16.73-40.87), 7.56 (5.60-10.22) and 3.67 (2.40-5.61), when measured &amp;lt;5, 5-10, and 10+ years before a PCa diagnosis, respectively. The magnitude of the associations were similar for aggressive disease. In men with PSA measured &amp;lt;5, 5-10 and 10+ years before a diagnosis, 95%, 89% and 75% of total PCa cases, respectively, were found to occur among men with a PSA level above the median, while 58%, 28% and 19% of cases, respectively, occurred among men with a PSA level in the top 10th percentile. By race/ethnicity group, the percentages of cases occurred among men with a PSA level above the median measured &amp;lt;5, 5-10 and 10+ years before a diagnosis were: 98%, 89%, 76% in AA; 93%, 90%, 80% in LA; 95%, 91%, 80% in JP; 96%, 95%, 69% in NH, and; 95%, 82%, 65% in WH, respectively. In analysis of the PRS, 25% of cases occurred among those in the top 10th percentile of the PRS distribution. At 10+ years, the independent effect of PSA on total PCa (OR per SD increase: 1.88, CI: 1.45-2.46) was comparable to the independent effect of the PRS (OR per SD increase: 2.12, CI: 1.55-2.93) in a model that mutually adjusted the effects of both PSA and PRS. Conclusions: Our findings in this study among older men suggest that PSA is informative as a marker of risk within 10 years of diagnosis, whereas the PRS can be used to define a man's risk earlier in life. Citation Format: Alisha Chou, Burcu F. Darst, Lynne R. Wilkens, Loïc Le Marchand, Hans G. Lilja, David V. Conti, Christopher A. Haiman. Serum prostate-specific antigen levels and prostate cancer risk in a multiethnic population [abstract]. In: Proceedings of the AACR Virtual Conference: 14th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2021 Oct 6-8. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr PR-16.

Polygenic burden could explain high rates of affective disorders in a community with restricted founder population

This study investigates if genetic factors could contribute to the high rate of mood disorders reported in a U.S. community known to have a restricted early founder population (confirmed here through runs of homozygosity analysis). Polygenic scores (PGSs) for eight common diseases, disorders, or traits, including psychiatric disorders, were calculated in 274 participants (125 mood disorder cases) who each reported three or four grandparents born in the community. Ancestry-matched controls were selected from the UK Biobank (UKB; three sets of N= 1,822 each). The mean PGSs were significantly higher in the community for major depression PRS (p= 2.1× 10-19 , 0.56 SD units), bipolar disorder (p= 2.5× 10-15 , 0.56 SD units), and schizophrenia (p= 3.8× 10-21 , 0.64 SD units). The PGSs were not significantly different between the community participants and UKB controls for the traits of body mass index, Type 2 diabetes, coronary artery disease, and chronotype. The mean PGSs for height were significantly lower in the community sample compared to controls (-0.21 SD units, p= 1.2× 10-5 ). The results are consistent with enrichment of polygenic risk factors for psychiatric disorders in this community.

Genomic Autopsy of Sudden Deaths in Young Individuals

Postmortem genetic testing of young individuals with sudden death has previously identified pathogenic gene variants. However, prior studies primarily considered highly penetrant monogenic variants, often without detailed decedent and family clinical information. To assess genotype and phenotype risk in a diverse cohort of young decedents with sudden death and their families. Pathological and whole-genome sequence analysis was conducted in a cohort referred from a national network of medical examiners. Cases were accrued prospectively from May 2015 to March 2019 across 24 US states. Analysis began September 2016 and ended November 2020. Evaluation of autopsy and clinical data integrated with whole-genome sequence data and family member evaluation. A total of 103 decedents (mean [SD] age at death, 23.7 [11.9] years; age range, 1-44 years), their surviving family members, and 140 sex- and genetic ancestry-matched controls were analyzed. Among 103 decedents, autopsy and clinical data review categorized 36 decedents with postmortem diagnoses, 23 decedents with findings of uncertain significance, and 44 with sudden unexplained death. Pathogenic/likely pathogenic (P/LP) genetic variants in arrhythmia or cardiomyopathy genes were identified in 13 decedents (12.6%). A multivariable analysis including decedent phenotype, ancestry, and sex demonstrated that younger decedents had a higher burden of P/LP variants and select variants of uncertain significance (effect size, -1.64; P = .001). These select, curated variants of uncertain significance in cardiac genes were more common in decedents than controls (83 of 103 decedents [86%] vs 100 of 140 controls [71%]; P = .005), and decedents harbored more rare cardiac variants than controls (2.3 variants per individual vs 1.8 in controls; P = .006). Genetic testing of 31 parent-decedent trios and 14 parent-decedent dyads revealed 8 transmitted P/LP variants and 1 de novo P/LP variant. Incomplete penetrance was present in 6 of 8 parents who transmitted a P/LP variant. Whole-genome sequencing effectively identified P/LP variants in cases of sudden death in young individuals, implicating both arrhythmia and cardiomyopathy genes. Genomic analyses and familial phenotype association suggest potentially additive, oligogenic risk mechanisms for sudden death in this cohort.

Burden of Cardiomyopathic Genetic Variation in Lethal Pediatric Myocarditis.

Acute myocarditis (AM) is a well-known cause of sudden death and heart failure, often caused by prevalent viruses. We previously showed that some pediatric AM correlates with putatively damaging variants in genes related to cardiomyocyte structure and function. We sought to evaluate whether deleterious cardiomyopathic variants were enriched among fatal pediatric AM cases in New York City compared with ancestry-matched controls. Twenty-four children (aged 3 weeks to 20 years) with death due to AM were identified through autopsy records; histologies were reviewed to confirm that all cases met Dallas criteria for AM and targeted panel sequencing of 57 cardiomyopathic genes was performed. Controls without cardiovascular disease were identified from a pediatric database and matched by genetic ancestry to cases using principal components from exome sequencing. Rates of putative deleterious variations (DV) were compared between cases and controls. Where available, AM tissues underwent viral analysis by polymerase chain reaction. DV were identified in 4 of 24 AM cases (16.7%), compared with 2 of 96 age and ancestry-matched controls (2.1%, P=0.014). Viral causes were proven for 6 of 8 AM cases (75%), including the one DV+ case where tissue was available for testing. DV+ cases were more likely to be female, have no evidence of chronic inflammation, and associate with sudden cardiac death than DV- cases. Deleterious variants in genes related to cardiomyocyte integrity are more common in children with fatal AM than controls, likely conferring susceptibility. Additionally, genetically mediated AM may progress more rapidly and be more severe.

Myopathic Cardiac Genotypes Increase Risk for Myocarditis

Background: Acute myocarditis (AM) is an important cause of heart failure and cardiomyopathy in adults and children, but risk factors are poorly understood. Mutations in genes related to cardiomyopathies have been implicated in children, suggesting overlap with other genetic myocardial disorders. Objectives: This study aimed to assess the prevalence of mutations in cardiac genes, including those associated with cardiomyopathies and neuromuscular disorders, among predominantly adult patients with AM. Methods: Genomic DNAs were obtained or extracted from blood from AM subjects from three separate cohorts (N=117; AM1=26, AM2=72, AM3=19), and next generation sequencing performed. Sex- and ancestry-matched controls without AM or cardiac disease and with available exome sequencing data from the BioMe biobank were included (N=468). Rates of deleterious variants (DV) in 93 cardiac genes were compared for cases and controls. Associations between DV status and histologic, viral and clinical outcomes were analyzed as secondary endpoints. Results: Based on a pooled burden meta-analysis (random effects), cardiac DV were statistically enriched in cases (AM1 19.2%, AM2 11.1%, AM3 31.6%) vs. respectively matched controls (5.6%, 7.6%, 7.9%) (P=0.013). Thirteen genes were implicated; of these, three (DYSF, DSP and TTN) were the source of DV for > 1 AM subject. No statistical differences were found between DV+ vs. DV- subjects for histologic AM classification, viral status or clinical outcome. Conclusions: Putatively damaging variants in genes related to cardiomyocyte structural integrity, classically associated with cardiomyopathy or neuromuscular disorders affecting the heart, are associated with increased risk for AM. Understanding viral-host genetic interactions may improve mechanistic insights in AM and clinical genetic testing may identify at-risk individuals.

Synaptic processes and immune-related pathways implicated in Tourette syndrome

Tourette syndrome (TS) is a neuropsychiatric disorder of complex genetic architecture involving multiple interacting genes. Here, we sought to elucidate the pathways that underlie the neurobiology of the disorder through genome-wide analysis. We analyzed genome-wide genotypic data of 3581 individuals with TS and 7682 ancestry-matched controls and investigated associations of TS with sets of genes that are expressed in particular cell types and operate in specific neuronal and glial functions. We employed a self-contained, set-based association method (SBA) as well as a competitive gene set method (MAGMA) using individual-level genotype data to perform a comprehensive investigation of the biological background of TS. Our SBA analysis identified three significant gene sets after Bonferroni correction, implicating ligand-gated ion channel signaling, lymphocytic, and cell adhesion and transsynaptic signaling processes. MAGMA analysis further supported the involvement of the cell adhesion and trans-synaptic signaling gene set. The lymphocytic gene set was driven by variants in FLT3, raising an intriguing hypothesis for the involvement of a neuroinflammatory element in TS pathogenesis. The indications of involvement of ligand-gated ion channel signaling reinforce the role of GABA in TS, while the association of cell adhesion and trans-synaptic signaling gene set provides additional support for the role of adhesion molecules in neuropsychiatric disorders. This study reinforces previous findings but also provides new insights into the neurobiology of TS.

Germline variants in HEY2 functional domains lead to congenital heart defects and thoracic aortic aneurysms

PurposeIn this study we aimed to establish the genetic cause of a myriad of cardiovascular defects prevalent in individuals from a genetically isolated population, who were found to share a common ancestor in 1728. MethodsTrio genome sequencing was carried out in an index patient with critical congenital heart disease (CHD); family members had either exome or Sanger sequencing. To confirm enrichment, we performed a gene-based association test and meta-analysis in two independent validation cohorts: one with 2685 CHD cases versus 4370 . These controls were also ancestry-matched (same as FTAA controls), and the other with 326 cases with familial thoracic aortic aneurysms (FTAA) and dissections versus 570 ancestry-matched controls. Functional consequences of identified variants were evaluated using expression studies. ResultsWe identified a loss-of-function variant in the Notch target transcription factor-encoding gene HEY2. The homozygous state (n = 3) causes life-threatening congenital heart defects, while 80% of heterozygous carriers (n = 20) had cardiovascular defects, mainly CHD and FTAA of the ascending aorta. We confirm enrichment of rare risk variants in HEY2 functional domains after meta-analysis (MetaSKAT p = 0.018). Furthermore, we show that several identified variants lead to dysregulation of repression by HEY2. ConclusionA homozygous germline loss-of-function variant in HEY2 leads to critical CHD. The majority of heterozygotes show a myriad of cardiovascular defects.

Ancestry-specific profiles of genetic determinants of severe hypertriglyceridemia

Susceptibility to severe hypertriglyceridemia (HTG), defined as plasma triglyceride (TG) levels ≥10mmol/L (880mg/dL), is conferred by both heterozygous rare variants in five genes involved in TG metabolism and numerous common single-nucleotide polymorphisms (SNPs) associated with TG levels. To date, these genetic susceptibility factors have been comprehensively assessed primarily in severe HTG patients of European ancestry. Here, we expand our analysis to HTG patients of East Asian and Hispanic ancestry. The genomic DNA of 336, 63 and 199 severe HTG patients of European, East Asian and Hispanic ancestry, respectively, was evaluated using a targeted next-generation sequencing panel to screen for: 1) rare variants in LPL, APOA5, APOC2, GPIHBP1 and LMF1; 2) common, small-to-moderate effect SNPs, quantified using a polygenic score; and 3) common, large-effect polymorphisms, APOA5 p.G185C and p.S19W. While the proportion of individuals with high polygenic scores was similar, frequency of rare variant carriers varied across ancestries. Compared with ancestry-matched controls, Hispanic patients were the most likely to have a rare variant (OR=5.02; 95% CI 3.07-8.21; p<0.001), while European patients were the least likely (OR=2.56; 95% CI 1.58-4.13; p<0.001). The APOA5 p.G185C polymorphism, exclusive to East Asians, was significantly enriched in patients compared with controls (OR=10.1; 95% CI 5.6-18.3; p<0.001), showing the highest enrichment among the measured genetic factors. While TG-associated rare variants and common SNPs are both found in statistical excess in severe HTG patients of different ancestral backgrounds, the overall genetic profiles of each ancestry group were distinct.

Abstract 13286: Finding the Missing Heritability of Serum Lipids: Leveraging the Relatedness in a Large-scale Biobank

Introduction: High prevalence of dyslipidemia in the United States results in elevated risk of cardiovascular disease. Although the high heritability of serum lipids has motivated many genome-wide association studies (GWAS), much of the heritability is still unexplained. Genomic regions shared with identity by descent (IBD) are inherited from the same common ancestor without recombination, and can be observed in both close and distant relatives. IBD segments provide an opportunity to discover genes that harbor low frequency, large effect variants that are undetectable in GWAS due to low power at rare and heterogeneous alleles. Methods: The Vanderbilt biobank (BioVU) comprises over 280,000 DNA samples from participants with linked electronic medical record (EMR). In this study, we extracted 18,337 European dyslipidemia cases, who have either diagnosed dyslipidemia or record of taking lipid-lowering drugs in linked EMR, and 18,337 sex, age, and ancestry-matched controls. The pairwise IBD shared segments were identified by GERMLINE using genotype data. To assess enrichment of IBD, we compared local shared IBD rates in case-case pairs and case-control pairs. Results: The greatest enrichment of IBD sharing was found on chromosome 5 (chr5: 169-171 MB, p-value=3.3х10 -5 ), and another three suggested regions were from chromosome 10, 18 and 22 (chr10: 86-87 MB, p-value=5.5х10 -4 , chr18: 10-11 MB, p-value=5.3х10 -4 , and chr22: 49.3-49.7 MB, p-value=2.1х10 -4 ). To further explore the molecular function, we used PrediXcan to impute the genetically regulated expression of the genes which locate within 1 MB of identified regions. A total of 31 unique genes in these regions exhibit significantly different predicted expression between risk IBD segment carriers and non-carriers, and are also significantly correlated with at least one serum lipids level. For instance, a novel long non-coding RNA, LINC01310, from chr22 associated with total glyceride (p-value=5.3х10 - 3 ) and expressed a lower level in risk people carrying the risk-associated IBD segment (p-value=1.2х10 - 6 ). Conclusions: Our results identity four genomic segments enriched in dyslipidemia cases, and, using GReX, we demonstrate the potential function of novel genes on the regulation of serum lipids.

Genome-wide association study identifies 18 new susceptibility variants loci associated with Brugada Syndrome

Abstract The Brugada Syndrome (BrS) is characterized by ST-segment elevation in the right precordial leads and is associated with an increased risk of sudden cardiac death. The disorder was initially described as a monogenic primary cardiac electrical disease. However, mutations in SCN5A, encoding the cardiac sodium channel (NaV1.5), which is the major gene associated with the disorder are found in only around 20% of cases and are associated with low penetrance. Furthermore many cases did not display familial aggregation. Based on a previous GWAS conducted on 312 BrS patients and the discovery of the unexpected strong effect of 3 common variants, we proposed that the BrS may comprise a more complex inheritance model. We conducted a genome-wide association study on 2820 individuals with BrS and 10001 ancestry-matched controls to uncover additional genetic loci that modulate susceptibility to BrS, to characterize further the BrS genetic architecture and to uncover new molecular mechanisms. We identified 21 susceptibility variants that passed the genome-wide statistical significance threshold (P&amp;lt;5.10–8), of which 18 were novel. Eight were located at the SCN5A-SCN10A locus, illustrating the central role of NaV1.5 in the disease. Interestingly, 9 occur in the vicinity of genes known to play a crucial role in cardiac development (HEY2, TBX20, GATA4, ZFPM2, WT1, TBX5, IRX3, IRX5) and / or control cardiac ion channel expression. Of note, 2 others signals occurred in the vicinity of microtubule / cytoskeleton associated proteins (MAPRE2 and MYO18B). Through studies in zebrafish and in human iPSC-derived cardiomyocytes, we demonstrate a role of MAPRE2 on NaV1.5 function. We identified 18 new susceptibility variants associated with BrS and uncovered a new pathophysiological molecular mechanism underlying BrS susceptibility. We provided further support for a complex genetic architecture underlying susceptibility for the disorder. Funding Acknowledgement Type of funding source: Public Institution(s). Main funding source(s): H2020 - Marie Sklodowska Curie IF grant, Rising star grant from the Pays de la Loire regional council

Epilepsy subtype-specific copy number burden observed in a genome-wide study of 17 458 subjects.

Cytogenic testing is routinely applied in most neurological centres for severe paediatric epilepsies. However, which characteristics of copy number variants (CNVs) confer most epilepsy risk and which epilepsy subtypes carry the most CNV burden, have not been explored on a genome-wide scale. Here, we present the largest CNV investigation in epilepsy to date with 10 712 European epilepsy cases and 6746 ancestry-matched controls. Patients with genetic generalized epilepsy, lesional focal epilepsy, non-acquired focal epilepsy, and developmental and epileptic encephalopathy were included. All samples were processed with the same technology and analysis pipeline. All investigated epilepsy types, including lesional focal epilepsy patients, showed an increase in CNV burden in at least one tested category compared to controls. However, we observed striking differences in CNV burden across epilepsy types and investigated CNV categories. Genetic generalized epilepsy patients have the highest CNV burden in all categories tested, followed by developmental and epileptic encephalopathy patients. Both epilepsy types also show association for deletions covering genes intolerant for truncating variants. Genome-wide CNV breakpoint association showed not only significant loci for genetic generalized and developmental and epileptic encephalopathy patients but also for lesional focal epilepsy patients. With a 34-fold risk for developing genetic generalized epilepsy, we show for the first time that the established epilepsy-associated 15q13.3 deletion represents the strongest risk CNV for genetic generalized epilepsy across the whole genome. Using the human interactome, we examined the largest connected component of the genes overlapped by CNVs in the four epilepsy types. We observed that genetic generalized epilepsy and non-acquired focal epilepsy formed disease modules. In summary, we show that in all common epilepsy types, 1.5-3% of patients carry epilepsy-associated CNVs. The characteristics of risk CNVs vary tremendously across and within epilepsy types. Thus, we advocate genome-wide genomic testing to identify all disease-associated types of CNVs.

Mitochondrial DNA Haplogroups and Susceptibility to Neuroblastoma.

Neuroblastoma is a childhood malignancy that arises from the developing sympathetic nervous system. Although mitochondrial dysfunctions have been implicated in the pathophysiology of neuroblastoma, the role of mitochondrial DNA (mtDNA) has not been extensively investigated. A total of 2404 Caucasian children diagnosed with neuroblastoma and 9310 ancestry-matched controls were recruited at the Children's Hospital of Philadelphia. The mtDNA haplogroups were identified from SNP array data of two independent cohorts. We conducted a case-control study to explore potential associations of mtDNA haplogroups with the susceptibility of neuroblastoma. The genetic effect of neuroblastoma was measured by odds ratios (ORs) of mitochondrial haplogroups. All tests were two-sided. Haplogroup K was statistically significantly associated with reduced risk of neuroblastoma in the discovery cohort consisting of 1474 cases and 5699 controls (OR = 0.72, 95% confidence interval [CI] = 0.57 to 0.90; P = 4.8 × 10-3). The association was replicated in an independent cohort (OR = 0.69, 95% CI = 0.53 to 0.92; P = .01) of 930 cases and 3611 controls. Pooled analysis was performed bycombining the two data sets. The association remained highly statistically significant after correction for multiple testing (OR = 0.71, 95% CI = 0.59 to 0.84, P = 1.96 × 10-4, Pcorrected = .002). Further analysis focusing on neuroblastoma subtypes indicated haplogroup K was more associated with high-risk neuroblastoma (OR = 0.57, 95% CI = 0.43 to 0.76; P = 1.46 × 10-4) than low-risk and intermediate-risk neuroblastoma. Haplogroup K is an independent genetic factor associated with reduced risk of developing neuroblastoma in European descents. These findings provide new insights into the genetic basis of neuroblastoma, implicating mitochondrial DNA encoded proteins in the etiology of neuroblastoma.

Exome sequencing in amyotrophic lateral sclerosis implicates a novel gene, DNAJC7, encoding a heat-shock protein.

To discover novel genes underlying amyotrophic lateral sclerosis (ALS), we aggregated exomes from 3,864 cases and 7,839 ancestry-matched controls. We observed a significant excess of rare protein-truncating variants among ALS cases, and these variants were concentrated in constrained genes. Through gene level analyses, we replicated known ALS genes including SOD1, NEK1 and FUS. We also observed multiple distinct protein-truncating variants in a highly constrained gene, DNAJC7. The signal in DNAJC7 exceeded genome-wide significance, and immunoblotting assays showed depletion of DNAJC7 protein in fibroblasts in a patient with ALS carrying the p.Arg156Ter variant. DNAJC7 encodes a member of the heat-shock protein family, HSP40, which, along with HSP70 proteins, facilitates protein homeostasis, including folding of newly synthesized polypeptides and clearance of degraded proteins. When these processes are not regulated, misfolding and accumulation of aberrant proteins can occur and lead to protein aggregation, which is a pathological hallmark of neurodegeneration. Our results highlight DNAJC7 as a novel gene for ALS.

Contributions of Rare Gene Variants to Familial and Sporadic FSGS.

Over the past two decades, the importance of genetic factors in the development of FSGS has become increasingly clear. However, despite many known monogenic causes of FSGS, single gene defects explain only 30% of cases. To investigate mutations underlying FSGS, we sequenced 662 whole exomes from individuals with sporadic or familial FSGS. After quality control, we analyzed the exome data from 363 unrelated family units with sporadic or familial FSGS and compared this to data from 363 ancestry-matched controls. We used rare variant burden tests to evaluate known disease-associated genes and potential new genes. We validated several FSGS-associated genes that show a marked enrichment of deleterious rare variants among the cases. However, for some genes previously reported as FSGS related, we identified rare variants at similar or higher frequencies in controls. After excluding such genes, 122 of 363 cases (33.6%) had rare variants in known disease-associated genes, but 30 of 363 controls (8.3%) also harbored rare variants that would be classified as "causal" if detected in cases; applying American College of Medical Genetics filtering guidelines (to reduce the rate of false-positive claims that a variant is disease related) yielded rates of 24.2% in cases and 5.5% in controls. Highly ranked new genes include SCAF1, SETD2, and LY9. Network analysis showed that top-ranked new genes were located closer than a random set of genes to known FSGS genes. Although our analysis validated many known FSGS-causing genes, we detected a nontrivial number of purported "disease-causing" variants in controls, implying that filtering is inadequate to allow clinical diagnosis and decision making. Genetic diagnosis in patients with FSGS is complicated by the nontrivial rate of variants in known FSGS genes among people without kidney disease.

Emerging Concepts in Precision Medicine and Cardiovascular Diseases in Racial and Ethnic Minority Populations.

Cardiovascular diseases remain the leading cause of mortality and a major contributor to preventable deaths worldwide. The dominant modifiable risk factors and the social and environmental determinants that increase cardiovascular risk are known, and collectively, are as important in racial and ethnic minority populations as they are in majority populations. Their prevention and treatment remain the foundation for cardiovascular health promotion and disease prevention. Genetic and epigenetic factors are increasingly recognized as important contributors to cardiovascular risk and provide an opportunity for advancing precision cardiovascular medicine. In this review, we explore emerging concepts at the interface of precision medicine and cardiovascular disease in racial and ethnic minority populations. Important among these are the lack of racial and ethnic diversity in genomics studies and biorepositories; the resulting misclassification of benign variants as pathogenic in minorities; and the importance of ensuring ancestry-matched controls in variant interpretation. We address the relevance of epigenetics, pharmacogenomics, genetic testing and counseling, and their social and cultural implications. We also examine the potential impact of precision medicine on racial and ethnic disparities. The National Institutes of Health's All of Us Research Program and the National Heart, Lung, and Blood Institute's Trans-Omics for Precision Medicine Initiative are presented as examples of research programs at the forefront of precision medicine and diversity to explore research implications in minorities. We conclude with an overview of implementation research challenges in precision medicine and the ethical implications in minority populations. Successful implementation of precision medicine in cardiovascular disease in minority populations will benefit from strategies that directly address diversity and inclusion in genomics research and go beyond race and ethnicity to explore ancestry-matched controls, as well as geographic, cultural, social, and environmental determinants of health.

PS1133 GENOMIC ARRAYS IDENTIFY HIGH-RISK CHRONIC LYMPHOCYTIC LEUKEMIA WITH GENOMIC COMPLEXITY: A MULTI-CENTER STUDY

Background: Chronic lymphocytic leukemia (CLL) is among the most heritable cancers, with 60% of disease risk genetically determined. However, most of the genetic heritability of CLL remains unexplained. Previously, we identified ATM as the first CLL risk gene. Aims: Here we leverage a deep-learning-based germline variant calling algorithm to explore germline mutational enrichment in DNA repair and cell cycle genes in CLL. Methods: A two-stage case-control analysis was conducted using gene-based mutational enrichment analysis of 50 established cancer predisposition DNA repair and cell cycle genes. In the discovery phase, a total of 285 Spanish patients and 5,608 ancestry-matched controls were evaluated. In the validation stage, an independent cohort of 514 European patients and 27,173 ancestry-matched controls were analyzed. An FDR correction was applied to both datasets and genes with a q-value <0.2 in both cohorts were considered significant. Results: Our joint analysis of 799 CLL patients from 2 genetically distinct cohorts and 32,781 ancestry-matched cancer-free controls identified ATM and CHEK2 as significantly enriched in both CLL datasets. First, our analysis recaptured the previously reported finding of ATM variant enrichment in CLL patients. Carriers of pathogenic ATM mutations in our cohorts (n = 9 patients, discovery: 1.05%, validation: 1.17%) were 2.8–3.7 times more likely to develop CLL compared to cancer-free individuals (discovery: OR = 2.8, 95%CI = 0.7–9.0, q-value = 0.181; validation: OR = 3.7, 95%CI = 1.6–8.3, q-value = 0.0454). In addition, our analysis identified 21 CLL patients carrying pathogenic CHEK2 alterations (discovery: 1.40%, validation: 3.31%), making CLL patients 4.4–8.0 times more likely to carry such alterations compared to controls (discovery: OR = 8.0, 95%CI = 2.3–27.0, q-value = 0.026; validation: OR = 4.4, 95%CI = 2.5–7.3, q-value <0.001). Summary/Conclusion: Our analysis of genetically distinct CLL cohorts, using a high-sensitivity variant calling algorithm, supports CHEK2 as a potentially novel CLL predisposition gene that may explain a portion of the missing monogenic heritability of CLL. In addition, this study highlights the DNA repair and cell cycle regulation pathways as potential drivers of CLL susceptibility.

Inherited DNA repair and cell cycle gene defects in chronic lymphocytic leukemia.

1508 Background: Chronic lymphocytic leukemia (CLL) is among the most heritable cancers, with 60% of disease risk genetically determined. However, most of the genetic heritability of CLL remains unexplained. Previously, we identified ATM as the first CLL risk gene. Here, we leverage a deep-learning-based germline variant calling algorithm to explore germline mutational enrichment in DNA repair and cell cycle genes in CLL. Methods: A two-stage case-control analysis was conducted using gene-based mutational enrichment analysis of 50 established cancer predisposition DNA repair and cell cycle genes. In the discovery phase, a total of 285 Spanish patients and 5,608 ancestry-matched controls were evaluated. In the validation stage, an independent cohort of 514 European patients and 27,173 ancestry-matched controls were analyzed. An FDR correction was applied to both datasets and genes with a q-value &lt; 0.2 in both cohorts were considered significant. Results: Our joint analysis of 799 CLL patients from 2 genetically distinct cohorts and 32,781 ancestry-matched cancer-free controls identified ATM and CHEK2 as significantly enriched in both CLL datasets. First, our analysis recaptured the previously reported finding of ATM variant enrichment in CLL patients. Carriers of pathogenic ATM mutations in our cohorts (n = 9 patients, discovery: 1.05%, validation: 1.17%) were 2.8–3.7 times more likely to develop CLL compared to cancer-free individuals (discovery: OR = 2.8, 95%CI = 0.7–9.0, q-value = 0.181; validation: OR = 3.7, 95%CI = 1.6–8.3, q-value = 0.0454). In addition, our analysis identified 21 CLL patients carrying pathogenic CHEK2 alterations (discovery: 1.40%, validation: 3.31%), making CLL patients 4.4-8.0 times more likely to carry such alterations compared to controls (discovery: OR = 8.0, 95%CI = 2.3–27.0, q-value = 0.026; validation: OR = 4.4, 95%CI = 2.5–7.3, q-value &lt; 0.001). Conclusions: Our analysis of genetically distinct CLL cohorts, using a high-sensitivity variant calling algorithm, supports CHEK2 as a potentially novel CLL predisposition gene that may explain a portion of the missing monogenic heritability of CLL. In addition, this study highlights the DNA repair and cell cycle regulation pathways as potential drivers of CLL susceptibility.