Combined Annotation Dependent Depletion Score Research Articles

Genetic Variant Score and Arrhythmogenic Right Ventricular Cardiomyopathy Phenotype in Plakophilin-2 Mutation Carriers

Introduction: Whether detailed genetic information contributes to risk stratification of patients with arrhythmogenic right ventricular cardiomyopathy (ARVC) remains uncertain. Pathogenic genetic variants in some genes seem to carry a higher risk for arrhythmia and earlier disease onset than others, but comparisons between variants in the same gene have not been done. Combined Annotation Dependent Depletion (CADD) score is a bioinformatics tool that measures the pathogenicity of each genetic variant. We hypothesized that a higher CADD score is associated with arrhythmic events and earlier age at ARVC manifestations in individuals carrying pathogenic or likely pathogenic genetic variants in plakophilin-2 (PKP2). Methods: CADD scores were calculated using the data from pooled Scandinavian and North American ARVC cohorts, and their association with cardiac events defined as ventricular tachycardia/ventricular fibrillation (VT/VF) or syncope and age at definite ARVC diagnosis were assessed. Results: In total, 33 unique genetic variants were reported in 179 patients (90 males, 71 probands, 96 with definite ARVC diagnosis at a median age of 35 years). Cardiac events were reported in 76 individuals (43%), of whom 53 had sustained VT/VF (35%). The CADD score was neither associated with age at cardiac events (HR 1.002, 95% CI: 0.953–1.054, p = 0.933) nor with age at definite ARVC diagnosis (HR 0.992, 95% CI: 0.947–1.039, p = 0.731). Conclusion: No correlation was found between CADD scores and clinical manifestations of ARVC, indicating that the score has no additional risk stratification value among carriers of pathogenic or likely pathogenic PKP2 genetic variants.

Human SMAD4 Genomic Variants Identified in Individuals with Heritable and Early-Onset Thoracic Aortic Disease.

Thoracic aortic aneurysms (TAAs) that progress to acute thoracic aortic dissections (TADs) are life threatening vascular events that have been associated with altered transforming growth factor (TGF) β signaling. In addition to TAA, multiple genetic vascular disorders, including hereditary hemorrhagic telangiectasia (HHT), involve altered TGFβ signaling and vascular malformations. Due to the importance of TGFβ, genomic variant databases have been curated for activin receptor-like kinase 1 (ALK1) and endoglin (ENG). This case report details seven variants in SMAD4 that are associated with either heritable or early onset aortic dissections and compares them to pathogenic exon variants in gnomAD v2.1.1. The TAA and TAD variants were identified through whole exome sequencing of 346 unrelated heritable thoracic aortic disease (HTAD) and 355 individuals of early onset (age ≤ 56 years old) of thoracic aortic dissection (ESTAD). An allele frequency filter of less than 0.05% was applied in the Genome Aggregation Database (gnomAD exome v2.1.1) with a combined annotation dependent depletion score (CADD) greater than 20. These seven variants also have a higher REVEL score (>0.2), indicating pathogenic potential. Further in vivo and in vitro analysis is needed to evaluate how these variants affect mRNA stability and SMAD4 protein activity in association with thoracic aortic disease.

Rare Hypomorphic Sucrase Isomaltase Variants in Relation to Irritable Bowel Syndrome Risk in UK Biobank

Rare Hypomorphic Sucrase Isomaltase Variants in Relation to Irritable Bowel Syndrome Risk in UK Biobank

Molecular Genetic Dissection of Inflammatory Linear Verrucous Epidermal Naevus Leads to Successful Targeted Therapy

Molecular Genetic Dissection of Inflammatory Linear Verrucous Epidermal Naevus Leads to Successful Targeted Therapy

The prognosis of epilepsy patients with CACNA1H missense variants: A longitudinal cohort study

ObjectiveCACNA1H is regarded as a gene conferring susceptibility to generalised epilepsy. However, the prognosis of epilepsy patients carrying the CACNA1H missense variants of uncertain significance (VUS) is unknown. A prospective cohort was generated to determine the deleterious effects of these variants and to check whether the presence of these variants affects the prognosis of epilepsy patients. MethodThis study was conducted at Xijing Hospital in Xian, China. All patients were followed up for at least 1 year. Previous reports were searched for previously reported variants. Ensembl database was searched for variants in the general population. Combined Annotation Dependent Depletion (CADD) was used to evaluate the deleterious effect of variants. Logistic regression and Cox regression were used for data analysis. ResultsThe study included 176 epilepsy patients with or without CACNA1H variants. In epilepsy patients with missense variants, we found 35 different variants, including 33 variants with uncertain significance and 2 likely benign variants. No significant difference was observed between the distribution of CADD scores of the variants from this cohort, of the general population, and of those found in previous reports. Among epilepsy patients with missense variants, the number of antiepileptic drugs (AEDs) administered to the patients, a first-degree family history of epilepsy, and possibly the presence of abnormalities in brain radiology findings were correlated with the poorer prognosis. Among the entire cohort, the type of epilepsy, number of AEDs administered, and presence of abnormalities in brain radiology findings were associated with the prognosis of these patients. The deleterious effect of CACNA1H missense variants or their presence was not related to the prognosis of epilepsy patients. ConclusionThe results of our study suggest that CACNA1H variants are related to multiple epilepsy syndromes. However, there is no strong evidence of the correlation between CACNA1H missense variants and a certain type of epilepsy. In our study cohort, both the deleterious effects and the presence of CACNA1H variants were found to be unrelated to the prognosis of patients with epilepsy. These findings suggest that CACNA1H missense variants that are classified as VUS might not influence the outcome of epilepsy.

Mutation burden in patients with small unrepaired atrial septal defects

BackgroundIn a recent nationwide cohort study, we have discovered that patients living with an atrial septal defect (ASD) have a shorter life expectancy, increased risk of atrial fibrillation, pneumonia, and psychiatric issues compared to the general population. The pathophysiological mechanisms are still unknown. The objective of this study is to investigate if this group of patients is burdened by mutations in genes associated with ASD. MethodsWe included 147 patients with an unrepaired ASD. We curated a list of ASD candidate genes, and patients were analyzed for genetic variants in these genes, using targeted next generation sequencing. We filtered for protein altering variants (PAVs) and protein truncating variants (PTVs) with minor allele frequency (MAF) < 0.01 and we predicted pathogenicity using the Combined Annotation Dependent Depletion (CADD) method. The number of rare and pathogenic variants in cases were compared with variants identified in 33,370 controls of European ancestry. ResultsWe identified 384 rare (MAF<0.01) PAVs, including 41 PTVs, in 59 genes. ASD patients were significantly enriched for very rare (MAF<0.0001) PAVs compared to controls (P = 0.0001). The frequency of PAVs with CADD score ≥30 was significantly higher in ASD patients, compared to controls (P = 0.0042). ConclusionsPatients with a small, unrepaired ASD were enriched for rare PAVs within 59 ASD candidate disease genes. Our results suggest that recurrence risk of congenital heart defects in offspring may be increased for this group of patients and warrants further investigations.

O21: GENOME-WIDE ASSOCIATION STUDY OF VARICOSE VEINS IN 810,625 INDIVIDUALS IDENTIFIES 45 GENETIC RISK LOCI

Abstract Introduction Varicose veins (VV) impact a third of the UK adult population; 10% of patients develop lipodermatosclerosis and ulceration. VV often requires surgical management, however, there is a high-risk of recurrence. VV is a complex disease, where genetic and non-genetic components contribute to overall phenotypic expression. The genetic architecture of VV is poorly understood; we aimed to uncover its genetic basis. Method We conducted hitherto the largest genome-wide association study of VV. In stage one, using UK Biobank, we compared 22,473 VV patients and 379,183 controls. In stage two, replication and meta-analysis were performed in an independent cohort of 113,041 VV cases and 295,928 controls from 23&amp;Me (California, USA). In-silico analysis was conducted in FUMA, MAGMA, and XGR. Result 109 genome-wide significant (P≤ 5×10-8) loci were identified in UK Biobank, 45 of which successfully replicated in the 23&amp;Me cohort. Twenty-seven loci have not been previously reported. FUMA positionally-mapped 128 genes at the replicated loci, with 84 having a combined annotation-dependent depletion score (CADD) &amp;gt;12.37, suggesting functional, deleterious variants. MAGMA analysis implicated pathways involved in cardiovascular system development (P=1.57×10-08) and tube morphogenesis (P=9.35×10-08). Furthermore, XGR revealed enriched pathways in downstream signalling in naive CD8+ T cells (P=0.0017), and encoding structural and core extracellular glycoproteins (both P=0.007). Conclusion We identified 45 variants conferring risk of VV, which provide insights into disease biology. Implicated genes are enriched in pathways involved in vascular development, immune cell activity and extracellular matrix function, and provide new targets for therapeutic development. Take-home message Unravelling the genetic architecture of varicose veins may facilitate our understanding of the disease and guide therapeutic approaches.

Pharmacogenetic Polygenic Risk Score for Bronchodilator Response in Children and Adolescents with Asthma: Proof-of-Concept.

Genome-wide association studies (GWAS) of response to asthma medications have primarily focused on Caucasian populations, with findings that may not be generalizable to minority populations. We derived a polygenic risk score (PRS) for response to albuterol as measured by bronchodilator response (BDR), and examined the PRS in a cohort of Hispanic school-aged children with asthma. We leveraged a published GWAS of BDR to identify relevant genetic variants, and ranked the top variants according to their Combined Annotation Dependent Depletion (CADD) scores. Variants with CADD scores greater than 10 were used to compute the PRS. Once we derived the PRS, we determined the association of the PRS with BDR in a cohort of Hispanic children with asthma (the Genetics of Asthma in Costa Rica Study (GACRS)) in adjusted linear regression models. Mean BDR in GACRS participants was5.6% with a standard deviation of 10.2%. We observed a 0.63% decrease in BDR in response to albuterol for a standard deviation increase in the PRS (p = 0.05). We also observed decreased odds of a BDR response at or above the 12% threshold for a one standard deviation increase in the PRS (OR = 0.80 (95% CI 0.67 to 0.95)). Our findings show that combining variants from a pharmacogenetic GWAS into a PRS may be useful for predicting medication response in asthma.

Rare, Protein-Altering Variants in AS3MT and Arsenic Metabolism Efficiency: A Multi-Population Association Study.

Background:Common genetic variation in the arsenic methyltransferase (AS3MT) gene region is known to be associated with arsenic metabolism efficiency (AME), measured as the percentage of dimethylarsinic acid (DMA%) in the urine. Rare, protein-altering variants in AS3MT could have even larger effects on AME, but their contribution to AME has not been investigated.Objectives:We estimated the impact of rare, protein-coding variation in AS3MT on AME using a multi-population approach to facilitate the discovery of population-specific and shared causal rare variants.Methods:We generated targeted DNA sequencing data for the coding regions of AS3MT for three arsenic-exposed cohorts with existing data on arsenic species measured in urine: Health Effects of Arsenic Longitudinal Study (HEALS, ), Strong Heart Study (SHS, ), and New Hampshire Skin Cancer Study (NHSCS, ). We assessed the collective effects of rare (allele frequency ), protein-altering AS3MT variants on DMA%, using multiple approaches, including a test of the association between rare allele carrier status (yes/no) and DMA% using linear regression (adjusted for common variants in 10q24.32 region, age, sex, and population structure).Results:We identified 23 carriers of rare-protein-altering AS3MT variant across all cohorts (13 in HEALS and 5 in both SHS and NHSCS), including 6 carriers of predicted loss-of-function variants. DMA% was 6–10% lower in carriers compared with noncarriers in HEALS [ (95% CI: , )], SHS [ (95% CI: , )], and NHSCS [ (95% CI: , )]. In meta-analyses across cohorts, DMA% was 8.7% lower in carriers [ (95% CI: , )].Discussion:Rare, protein-altering variants in AS3MT were associated with lower mean DMA%, an indicator of reduced AME. Although a small percentage of the population (0.5–0.7%) carry these variants, they are associated with a 6–10% decrease in DMA% that is consistent across multiple ancestral and environmental backgrounds. https://doi.org/10.1289/EHP8152

FUNCTIONAL IN SILICO ANALYSIS OF GENETIC VARIANTS FROM GENOME-WIDE ASSOCIATION STUDIES OF BLOOD PRESSURE AND HYPERTENSION

Objective: Hypertension is a complex disease with a strong genetic component. Genome wide association studies (GWAS) have identified hundreds of variants associated with hypertension and its defining traits [systolic blood pressure(SBP), diastolic blood pressure(DBP), pulse pressure(PP)]. Our goal was to catalogue all sentinel variants identified by GWAS of hypertension and investigate their functional effects on transcription/translation in silico. Design and method: We compiled a list of all common (minor allele frequency &gt;0.05) sentinel variants associated with SBP, DBP and PP in at least one GWAS at genome-wide level of statistical significance (P &lt; 5x10-8). In silico analyses were conducted to characterise putative biological consequences of these variants at mRNA/protein level. All sentinel variants (and their statistical proxies) were characterised using Ensembl variant effect predictor (VEP) GRCh37 release 90 to identify effects on coding and non-coding exons. Data from the University of California Santa Cruz (UCSC) CpG islands was used to map variants to regulatory regions of open chromatin. Combined Annotation Dependent Depletion (CADD) scores quantified the overall genetic deleteriousness of variants. Results: A total of 892 variants were significantly associated with at least one BP-defining trait in GWAS. The effects of each allele copy of these variants on blood pressure ranged from 0.15–1.58mmHg (for SBP) and 0.09–0.81mmHg (for DBP). A total of 599 (67%) variants received at least one functional annotation. Only 92 (10.3%) variants led to missense changes in encoded proteins. A significant number of variants directly mapped to regulatory regions of active chromatin such as active enhancers and transcription start sites [258 (28.9%) and 225 (25.2%), respectively]. Only three variants [rs16859180 in the gene Serine/Threonine Kinase 36(STK36), rs328 in lipoprotein lipase(LPL) and rs11556924 in zinc finger C3HC-type protein 1(ZC3HC1)] had CADD scores &gt;30 (placing them in the top 0.1% of most deleterious variants in the human genome). Conclusions: The majority of BP GWAS variants do not alter the amino-acid content of encoded proteins. A significant proportion are located within regions of regulatory importance to transcription, suggesting that many BP GWAS variants operate through quantitative effect on expression of key genes in specific cells and tissues.

A Survey of Compound Heterozygous Variants in Pediatric Cancers and Structural Birth Defects.

Compound heterozygous (CH) variants occur when two recessive alleles are inherited and the variants are located at different loci within the same gene in a given individual. CH variants are important contributors to many different types of recessively inherited diseases. However, many studies overlook CH variants because identification of this type of variant requires knowing the parent of origin for each nucleotide. Using computational methods, haplotypes can be inferred using a process called “phasing,” which estimates the chromosomal origin of most nucleotides. In this paper, we used germline, phased, whole-genome sequencing (WGS) data to identify CH variants across seven pediatric diseases (adolescent idiopathic scoliosis: n = 16, congenital heart defects: n = 709, disorders of sex development: n = 79, ewing sarcoma: n = 287, neuroblastoma: n = 259, orofacial cleft: n = 107, and syndromic cranial dysinnervation: n = 172), available as parent-child trios in the Gabriella Miller Kids First Data Resource Center. Relatively little is understood about the genetic underpinnings of these diseases. We classified CH variants as “potentially damaging” based on minor allele frequencies (MAF), Combined Annotation Dependent Depletion scores, variant impact on transcription or translation, and gene-level frequencies in the disease group compared to a healthy population. For comparison, we also identified homozygous alternate (HA) variants, which affect both gene copies at a single locus; HA variants represent an alternative mechanism of recessive disease development and do not require phasing. Across all diseases, 2.6% of the samples had a potentially damaging CH variant and 16.2% had a potentially damaging HA variant. Of these samples with potentially damaging variants, the average number of genes per sample was 1 with a CH variant and 1.25 with a HA variant. Across all samples, 5.1 genes per disease had a CH variant, while 35.6 genes per disease had a HA variant; on average, only 4.3% of these variants affected common genes. Therefore, when seeking to identify potentially damaging variants of a putatively recessive disease, CH variants should be considered as potential contributors to disease development. If CH variants are excluded from analysis, important candidate genes may be overlooked.

Linkage of Alzheimer disease families with Puerto Rican ancestry identifies a chromosome 9 locus

The genetic admixture of Caribbean Hispanics provides an opportunity to discover novel genetic factors in Alzheimer disease (AD). We sought to identify genetic variants for AD through a family-based design using the Puerto Rican (PR) Alzheimer Disease Initiative (PRADI). Whole-genome sequencing (WGS) and parametric linkage analysis were performed for 100 individuals from 23 multiplex PRADI families. Variants were prioritized by minor allele frequency (<0.01), functional potential [combined annotation dependent depletion score (CADD) >10], and co-segregation with AD. Variants were further ranked using an independent PR case-control WGS dataset (PR10/66). A genome-wide significant linkage peak was found in 9p21 with a heterogeneity logarithm of the odds score (HLOD) >5.1, which overlaps with an AD linkage region from two published independent studies. The region harbors C9orf72, but no expanded repeats were observed in the families. Seven variants prioritized by the PRADI families also displayed evidence for association in the PR10/66 (p < 0.05), including a missense variant in UNC13B. Our study demonstrated the importance of family-based design and WGS in genetic study of AD.

Exome Sequencing of 21 Bardet-Biedl Syndrome (BBS) Genes to Identify Obesity Variants in 6,851 American Indians.

ObjectiveIn an ongoing effort to identify the genetic variation that contributes to obesity in American Indians, known Bardet–Biedl syndrome (BBS) genes were analyzed for an effect on BMI and leptin signaling.MethodsPotentially deleterious variants (Combined Annotation Dependent Depletion score > 20) in BBS genes were identified in whole‐exome sequence data from 6,851 American Indians informative for BMI. Common variants (detected in ≥ 10 individuals) were analyzed for association with BMI; rare variants (detected in < 10 individuals) were analyzed for mean BMI of carriers. Functional assessment of variants’ effect on signal transducer and activator of transcription 3 (STAT3) activity was performed in vitro.ResultsOne common variant, rs59252892 (Thr549Ile) in BBS9, was associated with BMI (P = 0.0008, β = 25% increase per risk allele). Among rare variants for which carriers had severe obesity (mean BMI > 40 kg/m2), four were in BBS9. In vitro analysis of BBS9 found the Ile allele at Thr549Ile had a 20% increase in STAT3 activity compared with the Thr allele (P = 0.01). Western blot analysis showed the Ile allele had a 15% increase in STAT3 phosphorylation (P = 0.006). Comparable functional results were observed with Ser545Gly and Val209Leu but not Leu665Phe and Lys810Glu.ConclusionsPotentially functional variants in BBS genes in American Indians are reported. However, functional evidence supporting a causal role for BBS9 in obesity is inconclusive.

Human myelomeningocele risk and ultra-rare deleterious variants in genes associated with cilium, WNT-signaling, ECM, cytoskeleton and cell migration

Myelomeningocele (MMC) affects one in 1000 newborns annually worldwide and each surviving child faces tremendous lifetime medical and caregiving burdens. Both genetic and environmental factors contribute to disease risk but the mechanism is unclear. This study examined 506 MMC subjects for ultra-rare deleterious variants (URDVs, absent in gnomAD v2.1.1 controls that have Combined Annotation Dependent Depletion score ≥ 20) in candidate genes either known to cause abnormal neural tube closure in animals or previously associated with human MMC in the current study cohort. Approximately 70% of the study subjects carried one to nine URDVs among 302 candidate genes. Half of the study subjects carried heterozygous URDVs in multiple genes involved in the structure and/or function of cilium, cytoskeleton, extracellular matrix, WNT signaling, and/or cell migration. Another 20% of the study subjects carried heterozygous URDVs in candidate genes associated with gene transcription regulation, folate metabolism, or glucose metabolism. Presence of URDVs in the candidate genes involving these biological function groups may elevate the risk of developing myelomeningocele in the study cohort.

Von Willebrand factor antigen levels are associated with burden of rare nonsynonymous variants in the VWF gene

Approximately 35% of patients with type 1 von Willebrand disease (VWD) do not have a known pathogenic variant in the von Willebrand factor (VWF) gene. We aimed to understand the impact of VWF coding variants on VWD risk and VWF antigen (VWF:Ag) levels, studying 527 patients with low VWF and VWD and 210 healthy controls. VWF sequencing was performed and VWF:Ag levels assayed. A combined annotation-dependent depletion (CADD) score >20 was used as a predicted pathogenicity measure. The number of rare nonsynonymous VWF variants significantly predicted VWF:Ag levels (P = 1.62 × 10−21). There was an association between average number of rare nonsynonymous VWF variants with VWD type 1 (P = 2.4 × 10−13) and low VWF (P = 1.6 × 10−27) compared with healthy subjects: type 1 subjects possessed on average >2 times as many rare variants as those with low VWF and 8 times as many as healthy subjects. The number of rare nonsynonymous variants significantly predicts VWF:Ag levels even after controlling for presence of a variant with a CADD score >20 or a known pathogenic variant in VWF (P = 2.7 × 10−14). The number of rare nonsynonymous variants in VWF as well as the presence of a variant with CADD >20 are both significantly associated with VWF levels. The association with rare nonsynonymous variants holds even when controlling for known pathogenic variants, suggesting that additional variants, in VWF or elsewhere, are associated with VWF:Ag levels. Patients with higher VWF:Ag levels with fewer rare nonsynonymous VWF gene variants could benefit from next-generation sequencing to find the cause of their bleeding.

Population Prevalence of Deleterious SGCE Variants.

Background:Myoclonus-Dystonia (M-D) is a pleiotropic neuropsychiatric disorder of variable penetrance. Pathogenic variants in SGCE, a maternally imprinted gene, are the most frequent known genetic cause of M-D. The population prevalence of SGCE-linked M-D is unknown, the pathogenicity of SGCE variants identified in patients with M-D may be indeterminant, and SGCE variants predicted to be deleterious by in silico analysis may appear in patients undergoing whole-exome or whole-genome sequencing for seemingly unrelated disorders. The Genome Aggregation Database (gnomAD) v2 provides variant data on 125,748 exomes and 15,708 genomes from unrelated individuals sequenced as part of various disease-specific and population genetic studies.Methods:SGCE variants included in the gnomAD v2 dataset were analyzed with Combined Annotation Dependent Depletion (CADD), and database for nonsynonymous single nucleotide polymorphisms’ functional predictions (dbNSFP). We determined the frequency of annotated SGCE variants, ranked by scores of deleteriousness, within the gnomAD v2 dataset. Deleteriousness scores were compared to a subset of published disease associated SGCE pathogenic variants.Results:Within gnomAD v2, there were 56, 408, and 1250 alleles harboring SGCE variants with CADD scores greater than 30, 25, and 20, respectively. We estimate that approximately 1/348 individuals in the United States population harbors an SGCE variant with a CADD score ≥ 25.Discussion:SGCE M-D may be underdiagnosed due to pleiotropy, mild phenotypes, variable penetrance, and impaired access to genetic testing. Due to the high population prevalence of deleterious SGCE variants, caution should be used when asserting pathogenicity without co-segregation analyses and expert neurological examination of phenotypes within pedigrees.HighlightsIn silico analyses of a large population database of genetic variants revealed that over 0.2% of individuals in the United States harbor a highly deleterious SGCE variant. This finding suggests that M-D and minor phenotypic variants such as mild isolated myoclonus may be underdiagnosed.

Rare coding variants in MYH6 are associated with atrial fibrillation: results from 45,596 exomes representing the general population

Abstract Background Atrial Fibrillation (AF) is the most common cardiac arrhythmia, and it is associated with serious complications; including an increased risk of stroke, heart failure, and death. It affects around 5% of the population above 65 years of age, and it is estimated that 2% of healthcare expenses are related to AF. The causes of AF are complex, and includes structural heart disease, hypertension, diabetes and genetic risk factors. To date 166 unique genetic loci have been identified to be associated with AF. While AF has traditionally been regarded as an electrical disease, structural genes, including the sarcomere gene, titin (TTN), has been associated with the disease. Recently, a large genome wide association study associated common variants in the gene MYH6 with AF. The gene encodes the protein alpha myosin heavy chain, and has previously been associated with sick-sinus syndrome and structural heart disease. Purpose We hypothesized that genetic variants in the sarcomere gene MYH6 were more prevalent in AF patients than non-AF patients supporting that this gene is important for the development of AF. Methods We analysed publicly available data from the UK Biobank, combining exome-sequencing data and health-related information on 45,596 participants. Using next-generation sequencing, we then examined the genetic variation in MYH6 in a cohort of 383 Danish, early-onset AF patients. The patients had onset of AF before age 40, had normal echocardiogram, and no other cardiovascular disease at onset of AF. Genetic variants were filtered by minor allele frequency (MAF) in the Genome Aggregation Database (GnomAD), and only rare variants with MAF&amp;lt;1% were included. We then predicted the potential deleteriousness of the variants using combined annotation dependent depletion (CADD) score. Results We found rare coding variants in MYH6 to be significantly associated with AF in exome-sequencing data on 45,596 participants from the UK Biobank (p=0.038). In our cohort of 383 Danish, early-onset AF patients with no other cardiovascular disease, we identified 12 rare, missense variants in MYH6. Of these variants, three were novel, and 11 had CADD scores &amp;gt;20, suggesting them to be in the top 1% of likely deleterious variants. Conclusion We identified rare genetic variants in MYH6 to be significantly associated with AF in a large population-based cohort. We also identified 12 rare coding variants in a highly selected cohort of early-onset AF patients. Most of these variants were predicted to be deleterious. Our results indicate that rare variants in MYH6 may increase susceptibility to AF, thus elaborating on the understanding of the pathophysiological mechanisms of AF, and the role of structural genes in the development of AF. Funding Acknowledgement Type of funding source: Foundation. Main funding source(s): Novo Nordisk Foundation Pre-Graduate Scholarships

Molecular landscape of CAPN3 mutations in limb-girdle muscular dystrophy type R1: from a Chinese multicentre analysis to a worldwide perspective

BackgroundLimb-girdle muscular dystrophy type R1 (LGMDR1) can be caused by recessive CAPN3 mutations accounting for the majority of LGMD. To date, no systemic evaluation has been performed to analyse the...

Screening non-MAPT genes of the Chr17q21 H1 haplotype in Parkinson's disease

IntroductionThe microtubule-associated protein tau (MAPT) gene is considered a strong genetic risk factor for Parkinson's disease (PD) in Caucasians. MAPT is located within an inversion region of high linkage disequilibrium designated as H1 and H2 haplotype, and contains eight other genes which have been implicated in neurodegeneration. The aim of the current study was to identify common coding variants in strong linkage disequilibrium (LD) within the associated loci on chr17q21 harboring MAPT. MethodsSanger sequencing of coding exons in 90 Caucasian late-onset PD (LOPD) patients was performed. Specific gene sequencing for LRRC37A, LRRC37A2, ARL17A and ARL17B was not possible given the high homology, presence of pseudogenes and copy number variants that are in the region, and therefore four genes (NSF, KANSL1, SPPL2C, and CRHR1) were included in the analysis. Coding variants from these four genes that did not perfectly tag (r2 = 1) the MAPT H1/H2 haplotype were genotyped in an independent replication series of Caucasian PD cases (N = 851) and controls (N = 730). ResultsIn the 90 LOPD cases we identified 30 coding variants. Eleven non-synonymous variants tagged the MAPT H1/H2 haplotype, including two SPPL2C variants (rs12185233 and rs12373123) that had high pathogenic combined annotation dependent depletion (CADD) scores of >20. In the replication series, the non-synonymous KANSL1 rs17585974 variant was in very strong LD with MAPT H1/H2 and had a high CADD score of 24.7. ConclusionWe have identified several non-synonymous variants across neighboring genes of MAPT that may warrant further genetic and functional investigation within the biological etiology of PD.

TRPV6 variants confer susceptibility to chronic pancreatitis in the Chinese population.

Chronic pancreatitis (CP) is a progressive fibroinflammatory syndrome of the pancreatic tissue caused by genetic and environmental factors. Previously reported susceptibility genes in CP explain less than half of the apparent heritability. To uncover novel pathogenic mechanisms, we initially performed low-coverage whole-genome sequencing on 464 Chinese CP patients and 504 controls. The transient receptor potential cation channel, Subfamily V, Member 6 (TRPV6) gene was found to be significantly associated with CP after a burden test of aggregated rare nonsynonymous variants with a combined annotation dependent depletion score > 20 (p = .020). In the replication stage, we analyzed the entire coding sequence and exon/intron boundaries of the TPRV6 gene by Sanger sequencing in another 205 patients with CP and 105 controls. Integration of the findings from the two stages resulted in the identification of 25 TRPV6 variants: 1 rare nonsense variant, 20 rare missense variants, and 4 common missense variants. Loss-of-function variants, as determined by intracellular Ca2+ concentration in transfected HEK293T cells, were significantly overrepresented in patients as compared to controls (9/669 [1.35%] vs. 1/609 [0.16%]; odds ratio = 8.29; p = .022). This study provides evidence suggesting that TRPV6 is a novel susceptibility gene for CP.