Rare Functional Variants Research Articles

Large-scale whole-exome sequencing association studies identify rare functional variants influencing serum urate levels

Elevated serum urate levels can cause gout, an excruciating disease with suboptimal treatment. Previous GWAS identified common variants with modest effects on serum urate. Here we report large-scale whole-exome sequencing association studies of serum urate and kidney function among ≤19,517 European ancestry and African-American individuals. We identify aggregate associations of low-frequency damaging variants in the urate transporters SLC22A12 (URAT1; p = 1.3 × 10−56) and SLC2A9 (p = 4.5 × 10−7). Gout risk in rare SLC22A12 variant carriers is halved (OR = 0.5, p = 4.9 × 10−3). Selected rare variants in SLC22A12 are validated in transport studies, confirming three as loss-of-function (R325W, R405C, and T467M) and illustrating the therapeutic potential of the new URAT1-blocker lesinurad. In SLC2A9, mapping of rare variants of large effects onto the predicted protein structure reveals new residues that may affect urate binding. These findings provide new insights into the genetic architecture of serum urate, and highlight molecular targets in SLC22A12 and SLC2A9 for lowering serum urate and preventing gout.

Association of TYK2 rs34536443 polymorphism with Susceptibility to Systemic Lupus Erythematous in the Iranian Population

Systemic lupus erythematous (SLE) is a multifactorial autoimmune disorder which affects many organs and displays various symptoms. Genetic components contribute to the incidence and development of SLE. A rare functional variant within the tyrosine kinase 2 (TYK2) gene (rs34536443) is a common genetic candidate for several autoimmune diseases, including SLE. This case control study was performed to investigate the possible association of TYK2 single nucleotide polymorphism (SNP) with a predisposition for and clinical features of SLE in the Iranian population.Genotyping was conducted on 600 patients with SLE and 600 sex-, age- and ethnicity-matched control subjects from the Iranian population. Patient and control samples were genotyped for one SNP (rs34536443) by applying allelic discrimination real-time PCR.Statistical analysis of the allele distribution revealed no significant association (OR = 0.67, CI: 0.38-1.17, P value = 0.163) between the rs34536443 C allele and susceptibility to SLE. The CC genotype was not detected in either the patients or controls. Moreover, the CG genotypes showed no significant association with the risk of SLE (OR = 0.66, CI: 0.37-1.72, P value = 0.15).These findings suggest that TYK2 rs34536443 is not associated with SLE susceptibility in the Iranian population. Further investigation is required to examine the mechanisms by which polymorphisms in this gene lead to SLE development.

Genome-wide association study of lung function and clinical implication in heavy smokers

BackgroundThe aim of this study is to identify genetic loci associated with post-bronchodilator FEV1/FVC and FEV1, and develop a multi-gene predictive model for lung function in COPD.MethodsGenome-wide association study (GWAS) of post-bronchodilator FEV1/FVC and FEV1 was performed in 1645 non-Hispanic White European descent smokers.ResultsA functional rare variant in SERPINA1 (rs28929474: Glu342Lys) was significantly associated with post-bronchodilator FEV1/FVC (p = 1.2 × 10− 8) and FEV1 (p = 2.1 × 10− 9). In addition, this variant was associated with COPD (OR = 2.3; p = 7.8 × 10− 4) and severity (OR = 4.1; p = 0.0036). Heterozygous subjects (CT genotype) had significantly lower lung function and higher percentage of COPD and more severe COPD than subjects with the CC genotype. 8.6% of the variance of post-bronchodilator FEV1/FVC can be explained by SNPs in 10 genes with age, sex, and pack-years of cigarette smoking (P < 2.2 × 10− 16).ConclusionsThis study is the first to show genome-wide significant association of rs28929474 in SERPINA1 with lung function. Of clinical importance, heterozygotes of rs28929474 (4.7% of subjects) have significantly reduced pulmonary function, demonstrating a major impact in smokers. The multi-gene model is significantly associated with CT-based emphysema and clinical outcome measures of severity. Combining genetic information with demographic and environmental factors will further increase the predictive power for assessing reduced lung function and COPD severity.

Whole-exome sequencing identifies rare genetic variations in German families with pulmonary sarcoidosis.

Genome-wide and candidate gene studies for pulmonary sarcoidosis have highlighted several candidate variants among different populations. However, the genetic basis of functional rare variants in sarcoidosis still needs to be explored. To identify functional rare variants in sarcoidosis, we sequenced exomes of 22 sarcoidosis cases from six families. Variants were prioritized using linkage and high-penetrance approaches, and filtered to identify novel and rare variants. Functional networking and pathway analysis of identified variants was performed using gene ontology based gene-phenotype, gene-gene, and protein-protein interactions. The linkage (n = 1007-7640) and high-penetrance (n = 11,432) prioritized variants were filtered to select variants with (a) reported allele frequency < 5% in databases (1.2-3.4%) or (b) novel (0.7-2.3%). Further selection based on functional properties and validation revealed a panel of 40 functional rare variants (33 from linkage region, 6 highly penetrant and 1 shared by both approaches). Functional network analysis implicated these gene variants in immune responses, such as regulation of pro-inflammatory cytokines including production of IFN-γ and anti-inflammatory cytokine IL-10, leukocyte proliferation, bacterial defence, and vesicle-mediated transport. The KEGG pathway analysis indicated inflammatory bowel disease as most relevant. This study highlights the subsets of functional rare gene variants involved in pulmonary sarcoidosis, such as, regulations of calcium ions, G-protein-coupled receptor, and immune system including retinoic acid binding. The implicated mechanisms in etiopathogenesis of familial sarcoidosis thus include Wnt signalling, inflammation mediated by chemokine and cytokine signalling and cadherin signalling pathways.

Common Variant of POC5 Is Associated With the Susceptibility of Adolescent Idiopathic Scoliosis.

A case-control study. To validate the relationship between POC5 and adolescent idiopathic scoliosis (AIS) in the Chinese patients and to further investigate the functional role of POC5. Three rare functional variants in the POC5 were recently reported to be strongly associated with the disease in a large family with multiple members affected with idiopathic scoliosis. To our knowledge, the association between the mutations of POC5 and AIS remains undetermined in the Chinese population. Single nucleotide variants c.1336G>A, c.1286C>T, and c.1363G>C of POC5 were genotyped in 2432 patients with AIS and 2292 healthy controls using multiple ligase detection reactions. Common variants covering POC5 gene were genotyped in 1446 patients and 2080 controls. The mRNA expression of POC5 was determined in the paraspinal muscles collected from 98 patients and 28 controls. The Student t test was used to compare mRNA expression level between the patients and the controls. In addition, the POC5 expression was compared among different genotypes of the remarkably associated single nucleotide polymorphism (SNP) with analysis of variance test. There was no case of mutation for the three reported variants of POC5. SNP rs6892146 was observed to have significantly different distribution of minor allele frequency in the two group (0.485 vs. 0.446, P = 0.004). The mRNA expression of POC5 was 1.5-fold higher in patients than in the controls (0.00012 ± 0.00009 vs. 0.00008 ± 0.00006, P = 0.02). Patients with genotype GG have a significantly increased expression of POC5 than those with CC (0.00014 ± 0.00007 vs. 0.00009 ± 0.00007, P = 0.03). Common variant rs6892146 of POC5 is associated with the development of AIS in the Chinese population. Targeted regional sequencing of POC5 may help identify novel mutations associated with AIS. 4.

Abstract 618: Identification of Novel Disease Genes for Metabolic Syndrome

Factors that underlie the association of diverse traits of the metabolic syndrome have remained largely unknown. The strong heritable nature of this condition provides an exceptional avenue for discovery of the disease mechanisms by using modern techniques of human molecular genetics. Strikingly, efforts by genome-wide association studies to identify common variants that show association with two or more traits have largely failed. Growing evidence indicates excess of rare genetic variants through recent exponential population growth, raising the possibility for their causal role in common diseases. With the advent of high throughput sequencing the power for identification of functional rare variants has dramatically increased. By biasing for extreme phenotypes and utilizing traditional method of segregation analysis we have discovered a number of disease genes for metabolic syndrome and coronary artery disease. A major benefit of this strategy is that true causal relationships has been established between rare variations in a gene, its cognate pathways and the disease of interest. These, in turn, have provided fundamental new insight into pathogenesis of poorly understood diseases such as plaque erosion, and logical starting points for identifying new targets and pathways for therapeutic intervention. By dissecting cognate pathways, we have identified novel targets, including Dyrk1B kinase, a novel incretin and components of Wnt signaling pathway to treat CAD, diabetes and hyperlipidemia and have implemented those succesfuly in animal models.

Abstract MP62: Role of Rare and Low-Frequency Variants in Gene-Alcohol Interactions on Plasma Lipid Levels

Introduction: Alcohol intake modifies plasma lipid levels and such effects may be modulated by genetic variants. We use emerging statistical methods that extend well-established common variant approaches to characterize the role of aggregated rare and low-frequency variants in gene by alcohol consumption interactions associated with fasting plasma lipid levels. Methods: Up to 247,870 exonic variants on the Illumina HumanExome BeadChip and fasting plasma triglycerides (TG), and high- and low-density lipoprotein cholesterol (HDL-c and LDL-c) were measured in 46,443 European Americans from 4 studies (the Atherosclerosis Risk in Communities (ARIC) study, the Framingham Heart Study, the Netherlands Epidemiology of Obesity Study and the Women’s Genome Health Study) of the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium. Using the gene-based rareGE method, we conducted exome-wide gene-environment (GxE) tests with genetic main effects estimated as fixed and random effects, and a joint analysis of genetic main and GxE interaction effects. Rare and low-frequency (minor allele frequency ≤ 5%) functional variants, (i.e. frameshift, nonsynonymous, stop/gain, stop/loss, and splicing) were aggregated by genes. Two dichotomous self-reported alcohol consumption variables, current drinker (at least 1 drink per week, yes/no) and regular drinker (at least 2 drinks per week, yes/no) were considered. A sample size weighted Z-test (weighted Stouffer’s method) was used to meta-analyze study-specific p -values. Exome-wide significance level was set at p &lt; 3.7*10 -6 (0.05/13368 genes), using a Bonferroni procedure to correct for multiple testing. Results: We identified 24 gene-lipid associations at 13 known lipid loci (within 500kb) harboring rare and low-frequency variants through the joint analysis. In ARIC, numerous genes ( PCSK9, LPL, LIPG, ANGPTL4, APOB, APOC3-A5 ) remained significant after conditioning on common index single nucleotide polymorphisms (SNPs), suggesting an independent role for rare variants at loci highlighted by previous genome-wide association studies. However, no significant gene-alcohol interactions were observed with rare and low-frequency variants on TG, HDL-c or LDL-c. Conclusion: This study applied new statistical approaches to investigate the role of rare and low-frequency variants in gene-alcohol consumption interactions on lipid levels. Results show promise for other larger scale studies analyzing rare variant GxE interactions.

ASSOCIATION OF RARE FUNCTIONAL VARIANTS IN TRIGLYCERIDE RELATED GENES WITH CIRCULATING TRIGLYCERIDE LEVELS

Hypertriglyceridemia increases the risk of coronary heart disease. We investigated the association between rare functional variants in candidate genes involved in triglyceride (TG) metabolism with circulating TG levels. We performed targeted sequencing in 2533 individuals recruited from Mayo Clinic

Whole-exome sequencing identifies common and rare variant metabolic QTLs in a Middle Eastern population

Metabolomics-genome-wide association studies (mGWAS) have uncovered many metabolic quantitative trait loci (mQTLs) influencing human metabolic individuality, though predominantly in European cohorts. By combining whole-exome sequencing with a high-resolution metabolomics profiling for a highly consanguineous Middle Eastern population, we discover 21 common variant and 12 functional rare variant mQTLs, of which 45% are novel altogether. We fine-map 10 common variant mQTLs to new metabolite ratio associations, and 11 common variant mQTLs to putative protein-altering variants. This is the first work to report common and rare variant mQTLs linked to diseases and/or pharmacological targets in a consanguineous Arab cohort, with wide implications for precision medicine in the Middle East.

P164 USING EXOME SEQUENCING TO EXPAND THE GENETIC ARCHITECTURE OF INFLAMMATORY BOWEL DISEASE

IBD studies over the past decade have confirmed association to 250 gene loci. A handful of associations have led to specific validated functional variants highlighting intracellular response to microbes and regulation of adaptive immunity in IBD pathogenesis. For the vast majority, however, the specific implicated gene and causal functional variants remain unknown. In partnership with IBD researchers around the world, we launched an exome sequencing initiative to define the full allelic spectrum of protein-altering variation in genes associated to CD and/or UC, assess their role in clinical course and response to therapy, and to determine whether truncating variants confer risk or protection in each IBD gene in order to highlight opportune therapeutic targets. We have already completed exomes of 13,000 IBD cases providing a high-resolution view of coding variation at each GWAS hit and demonstrated a convincing excess of rare exome signal collectively. The cases are drawn from individual substudies that focus on isolated populations (Ashkenazi, Finnish, French-Canadian), admixed populations and clinical extremes, each providing unique opportunities for discovery. Early findings include novel protective truncating variants, the complete allelic series (including unique founder population alleles), non-additive inheritance models at known genes such as NOD2, overlooked low-frequency coding variants that explain GWAS hits (PRDM1, NRIP1). The integration of low frequency and rare functional variants with GWAS is moving us much closer towards completion of the genetic architecture of IBD. Early analyses of the data have revealed novel non-coding associations in known IBD genes as well as coding variants that implicate genes at loci in which the ‘causative’ gene was unknown. Furthermore, initial results have suggested variation in enrichment of different processes across different ethnicities.

Population-Specific Associations of Deleterious Rare Variants in Coding Region of P2RY1-P2RY12 Purinergic Receptor Genes in Large-Vessel Ischemic Stroke Patients.

The contribution of low-frequency and damaging genetic variants associated with platelet function to ischemic stroke (IS) susceptibility remains unknown. We employed a deep re-sequencing approach in Polish patients in order to investigate the contribution of rare variants (minor allele frequency, MAF < 1%) to the IS genetic susceptibility in this population. The genes selected for re-sequencing consisted of 26 genes coding for proteins associated with the surface membrane of platelets. Targeted pooled re-sequencing (Illumina HiSeq 2500) was performed on genomic DNA of 500 cases (patients with history of clinically proven diagnosis of large-vessel IS) and 500 controls. After quality control and prioritization based on allele frequency and damaging probability, follow-up individual genotyping of deleterious rare variants was performed in patients from the original cohort. Gene-based analyses identified an association between IS and 6 rare functional and damaging variants in the purinergic genes (P2RY1 and P2RY12 locus). The predicted properties of the most damaging rare variants in P2RY1 and P2RY12 were confirmed by using mouse fibroblast cell cultures transfected with plasmid constructs containing cDNA of mutated variants (FLIPR on FlexStation3). This study identified a putative role for rare variants in P2RY1 and P2RY12 genes involved in platelet reactivity on large-vessel IS susceptibility in a Polish population.

Analysis of population-specific pharmacogenomic variants using next-generation sequencing data

Functional rare variants in drug-related genes are believed to be highly differentiated between ethnic- or racial populations. However, knowledge of population differentiation (PD) of rare single-nucleotide variants (SNVs), remains widely lacking, with the highest fixation indices, (Fst values), from both rare and common variants annotated to specific genes, having only been marginally used to understand PD at the gene level. In this study, we suggest a new, gene-based PD method, PD of Rare and Common variants (PDRC), for analyzing rare variants, as inspired by Generalized Cochran-Mantel-Haenszel (GCMH) statistics, to identify highly population-differentiated drug response-related genes (“pharmacogenes”). Through simulation studies, we reveal that PDRC adequately summarizes rare and common variants, due to PD, over a specific gene. We also applied the proposed method to a real whole-exome sequencing dataset, consisting of 10,000 datasets, from the Type 2 Diabetes Genetic Exploration by Next-generation sequencing in multi-Ethnic Samples (T2D-GENES) initiative, and 3,000 datasets from the Genetics of Type 2 diabetes (Go-T2D) repository. Among the 48 genes annotated with Very Important Pharmacogenetic summaries (VIPgenes), in the PharmGKB database, our PD method successfully identified candidate genes with high PD, including ACE, CYP2B6, DPYD, F5, MTHFR, and SCN5A.

ALZHEIMER'S DISEASE SEQUENCING PROJECT: CASE-CONTROL ANALYSES

Responding to a 2012 Presidential Initiative to fight Alzheimer's disease (AD), the National Institute on Aging (NIA) and National Human Genome Research Institute (NHGRI) jointly developed a project to analyze the genomes of well-characterized individuals with or without AD. This effort, the Alzheimer's Disease Sequencing Project (ADSP) has the overarching goals of identifying new (1) genes involved in AD, (2) genomic variation contributing to AD risk or protection, and (3) potential avenues for therapies and AD prevention. This presentation highlights findings from the ADSP Discovery Phase Case-Control Study, which analyzed whole exome sequence (WES) variation from unrelated participants of the Alzheimer's Disease Genetics Consortium (ADGC) and Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium. We selected European-ancestry cases and dementia-free controls based on age, sex, APOE genotype, and pathology, along with additional unrelated cases from AD families and Caribbean Hispanic controls to enrich the risk profile and diversity of the study. We analyzed individual common variants (minor allele count > 10) using logistic regression and aggregated rare (minor allele frequency < 5%) functional variants into genes using SKAT-O with filters based on predicted functional impact or loss-of-function. All models included adjustment for sequencing center and population structure. Sensitivity analyses adjusted for age, sex, and APOE genotype. Analyses were performed separately by ancestry and were combined using seqMeta/R. Statistical significance was established using a Bonferroni correction. After QC, the analysis included 5,740 cases and 5,096 controls (218 cases and 177 controls were Hispanic) and approximately 1.5 million SNVs and 50,000 indels. Significant associations from single variant and gene-based tests included common and rare variants in several known AD risk genes (TREM2, MS4A6A, ABCA7, PILRA), as well as potentially novel findings in GAS2L2, OPRL1, ZNF655, NSF and a long non-coding RNA. Several of these findings show preliminary evidence of replication in ongoing efforts among independent WES and imputed datasets. WES association analyses of ADSP case-control data replicated several known AD genes and identified novel associations; efforts to replicate these findings and characterize the biological mechanisms of the identified genes in AD are currently underway.

INCREASED BURDEN OF RARE LOSS-OF-FUNCTION VARIANTS IN ALZHEIMER’S DISEASE PATIENTS COMPARED TO CENTENARIANS

Late onset Alzheimer's disease (AD) has high estimated heritability, but the effects of common genetic variants could explain only 24% to 33% of total phenotypic variance for AD. In the present study we investigated the burden of rare loss-of-function variants in a whole genome sequencing study of 45 AD subjects and 53 cognitively healthy centenarians, all of Ashkenazi Jewish ancestry (AJ). We restricted our analysis to coding rare variants observed at most once in the 1000 Genomes database and having a minor allele frequency below 2% in our AJ sample. We compared the burden of predicted protein altering variants between cases and controls as normalized by the level of rare synonymous variants. We observed an increased burden among AD subjects for predicted loss-of-function variants (LoFs) defined as stop-gain, frame shift, initiation codon (INIT), and splice site mutations (n=930, OR=1.3, P=1.5xE-5). Among LoFs, the strongest burden was observed for INIT (OR=2.16, P=0.0097) and premature stop variants predicted to cause nonsense mediated decay in the majority of transcripts (NMD) (OR=1.98, P=0.02). Notably, this increased burden of NMD, INIT and splice variants was more pronounced in innate immune genes (Gene Ontology ID: 0045087) (OR=4.55, P=0.0043). Further comparison to additional whole exomes of age-matched AJ samples indicates that the difference in LoF burden originated both from the AD and centenarian sample. To exploration how non-coding variants differ between AD and centenarians, we obtained Combined Annotation Dependent Depletion CADD scores as a measure of deleteriousness for rare non-coding variants. In non-coding regions, the enrichment of potentially functional rare variants with the highest CADD scores (Phred>=40) compared to those with the lowest (Phred <=0.2) in AD patients and centenarians was not significant, but in the same direction (OR=1.3, P=0.21) as the LoFs in AD. In summary, we observed an overall increased burden of rare Loss-of-function variants in AD subjects as compared to centenarians, and this enrichment is more pronounced for innate immune genes. Replication of the coding region enrichment in a larger sample and investigation of non-coding functional variants are on ongoing.

Rare Variant Analysis of Human and Rodent Obesity Genes in Individuals with Severe Childhood Obesity

Obesity is a genetically heterogeneous disorder. Using targeted and whole-exome sequencing, we studied 32 human and 87 rodent obesity genes in 2,548 severely obese children and 1,117 controls. We identified 52 variants contributing to obesity in 2% of cases including multiple novel variants in GNAS, which were sometimes found with accelerated growth rather than short stature as described previously. Nominally significant associations were found for rare functional variants in BBS1, BBS9, GNAS, MKKS, CLOCK and ANGPTL6. The p.S284X variant in ANGPTL6 drives the association signal (rs201622589, MAF~0.1%, odds ratio = 10.13, p-value = 0.042) and results in complete loss of secretion in cells. Further analysis including additional case-control studies and population controls (N = 260,642) did not support association of this variant with obesity (odds ratio = 2.34, p-value = 2.59 × 10−3), highlighting the challenges of testing rare variant associations and the need for very large sample sizes. Further validation in cohorts with severe obesity and engineering the variants in model organisms will be needed to explore whether human variants in ANGPTL6 and other genes that lead to obesity when deleted in mice, do contribute to obesity. Such studies may yield druggable targets for weight loss therapies.

Enrichment of low-frequency functional variants revealed by whole-genome sequencing of multiple isolated European populations

The genetic features of isolated populations can boost power in complex-trait association studies, and an in-depth understanding of how their genetic variation has been shaped by their demographic history can help leverage these advantageous characteristics. Here, we perform a comprehensive investigation using 3,059 newly generated low-depth whole-genome sequences from eight European isolates and two matched general populations, together with published data from the 1000 Genomes Project and UK10K. Sequencing data give deeper and richer insights into population demography and genetic characteristics than genotype-chip data, distinguishing related populations more effectively and allowing their functional variants to be studied more fully. We demonstrate relaxation of purifying selection in the isolates, leading to enrichment of rare and low-frequency functional variants, using novel statistics, DVxy and SVxy. We also develop an isolation-index (Isx) that predicts the overall level of such key genetic characteristics and can thus help guide population choice in future complex-trait association studies.

Region-based association tests for sequencing data on survival traits.

Family-based designs enriched with affected subjects and disease associated variants can increase statistical power for identifying functional rare variants. However, few rare variant analysis approaches are available for time-to-event traits in family designs and none of them applicable to the X chromosome. We developed novel pedigree-based burden and kernel association tests for time-to-event outcomes with right censoring for pedigree data, referred to FamRATS (family-based rare variant association tests for survival traits). Cox proportional hazard models were employed to relate a time-to-event trait with rare variants with flexibility to encompass all ranges and collapsing of multiple variants. In addition, the robustness of violating proportional hazard assumptions was investigated for the proposed and four current existing tests, including the conventional population-based Cox proportional model and the burden, kernel, and sum of squares statistic (SSQ) tests for family data. The proposed tests can be applied to large-scale whole-genome sequencing data. They are appropriate for the practical use under a wide range of misspecified Cox models, as well as for population-based, pedigree-based, or hybrid designs. In our extensive simulation study and data example, we showed that the proposed kernel test is the most powerful and robust choice among the proposed burden test and the existing four rare variant survival association tests. When applied to the Diabetes Heart Study, the proposed tests found exome variants of the JAK1 gene on chromosome 1 showed the most significant association with age at onset of type 2 diabetes from the exome-wide analysis.

Evaluation of IFITM3 rs12252 Association With Severe Pediatric Influenza Infection.

Interferon-induced transmembrane protein 3 (IFITM3) restricts endocytic fusion of influenza virus. IFITM3 rs12252_C, a putative alternate splice site, has been associated with influenza severity in adults. IFITM3 has not been evaluated in pediatric influenza. The Pediatric Influenza (PICFLU) study enrolled children with suspected influenza infection across 38 pediatric intensive care units during November 2008 to April 2016. IFITM3 was sequenced in patients and parents were genotyped for specific variants for family-based association testing. rs12252 was genotyped in 54 African-American pediatric outpatients with influenza (FLU09), included in the population-based comparisons with 1000 genomes. Splice site analysis of rs12252_C was performed using PICFLU and FLU09 patient RNA. In PICFLU, 358 children had influenza infection. We identified 22 rs12252_C homozygotes in 185 white non-Hispanic children. rs12252_C was not associated with influenza infection in population or family-based analyses. We did not identify the Δ21 IFITM3 isoform in RNAseq data. The rs12252 genotype was not associated with IFITM3 expression levels, nor with critical illness severity. No novel rare IFITM3 functional variants were identified. rs12252 was not associated with susceptibility to influenza-related critical illness in children or with critical illness severity. Our data also do not support it being a splice site.

Inborn errors of metabolism associated with psychosis: literature review and case-control study using exome data from 5090 adult individuals.

A literature review was conducted, using the computerized "Online Mendelian Inheritance in Man" (OMIM) and PubMed, to identify inborn errors of metabolism (IEM) in which psychosis may be a predominant feature or the initial presenting symptom. Different combinations of the following keywords were searched using OMIM: "psychosis", "schizophrenia", or "hallucinations" and "metabolic", "inborn error of metabolism", "inborn errors of metabolism", "biochemical genetics", or "metabolic genetics". The OMIM search generated 126 OMIM entries, 40 of which were well known IEM. After removing IEM lacking evidence in PubMed for an association with psychosis, 29 OMIM entries were identified. Several of these IEM are treatable. They involve different small organelles (lysosomes, peroxisomes, mitochondria), iron or copper accumulation, as well as defects in other met-abolic pathways (e.g., defects leading to hyperammonemia or homocystinemia). A clinical checklist summarizing the key features of these conditions and a guide to clinical approach are provided. The genes corresponding to each of these con-ditions were identified. Whole exome data from 2545 adult cases with schizophrenia and 2545 unrelated controls, accessed via the Database of Genotypes and Phenotypes (dbGaP), were analyzed for rare functional variants in these genes. The odds ratio of having a rare functional variant in cases versus controls was calculated for each gene. Eight genes are significantly associated with schizophrenia (p < 0.05, OR >1) using an unselected group of adult patients with schizophrenia. Increased awareness of clinical clues for these IEM will optimize referrals and timely metabolic interventions.

Gene-based segregation method for identifying rare variants in family-based sequencing studies.

Whole-exome sequencing using family data has identified rare coding variants in Mendelian diseases or complex diseases with Mendelian subtypes, using filters based on variant novelty, functionality, and segregation with the phenotype within families. However, formal statistical approaches are limited. We propose a gene-based segregation test (GESE) that quantifies the uncertainty of the filtering approach. It is constructed using the probability of segregation events under the null hypothesis of Mendelian transmission. This test takes into account different degrees of relatedness in families, the number of functional rare variants in the gene, and their minor allele frequencies in the corresponding population. In addition, a weighted version of this test allows incorporating additional subject phenotypes to improve statistical power. We show via simulations that the GESE and weighted GESE tests maintain appropriate type I error rate, and have greater power than several commonly used region-based methods. We apply our method to whole-exome sequencing data from 49 extended pedigrees with severe, early-onset chronic obstructive pulmonary disease (COPD) in the Boston Early-Onset COPD study (BEOCOPD) and identify several promising candidate genes. Our proposed methods show great potential for identifying rare coding variants of large effect and high penetrance for family-based sequencing data. The proposed tests are implemented in an R package that is available on CRAN (https://cran.r-project.org/web/packages/GESE/).