Rare coding variants in CHRNB2 reduce the likelihood of smoking.

Human genetic studies of smoking behavior have been thus far largely limited to common variants. Studying rare coding variants has the potential to identify drug targets. We performed an exome-wide association study of smoking phenotypes in up to 749,459 individuals and discovered a protective association in CHRNB2, encoding the ß2 subunit of the α4ß2 nicotine acetylcholine receptor. Rare predicted loss-of-function and likely deleterious missense variants in CHRNB2 in aggregate were associated with a 35% decreased odds for smoking heavily (odds ratio (OR) = 0.65, confidence interval (CI) = 0.56-0.76, P = 1.9 × 10-8). An independent common variant association in the protective direction ( rs2072659 ; OR = 0.96; CI = 0.94-0.98; P = 5.3 × 10-6) was also evident, suggesting an allelic series. Our findings in humans align with decades-old experimental observations in mice that ß2 loss abolishes nicotine-mediated neuronal responses and attenuates nicotine self-administration. Our genetic discovery will inspire future drug designs targeting CHRNB2 in the brain for the treatment of nicotine addiction.

Common and rare variant associations with clonal haematopoiesis phenotypes.

Clonal haematopoiesis involves the expansion of certain blood cell lineages and has been associated with ageing and adverse health outcomes1-5. Here we use exome sequence data on 628,388 individuals to identify 40,208 carriers of clonal haematopoiesis of indeterminate potential (CHIP). Using genome-wide and exome-wide association analyses, we identify 24 loci (21 of which are novel) where germline genetic variation influences predisposition to CHIP, including missense variants in the lymphocytic antigen coding gene LY75, which are associated with reduced incidence of CHIP. We also identify novel rare variant associations with clonal haematopoiesis and telomere length. Analysis of 5,041 health traits from the UK Biobank (UKB) found relationships between CHIP and severe COVID-19 outcomes, cardiovascular disease, haematologic traits, malignancy, smoking, obesity, infection and all-cause mortality. Longitudinal and Mendelian randomization analyses revealed that CHIP is associated with solid cancers, including non-melanoma skin cancer and lung cancer, and that CHIP linked to DNMT3A is associated with the subsequent development of myeloid but not lymphoid leukaemias. Additionally, contrary to previous findings from the initial 50,000 UKB exomes6, our results in the full sample do not support a role for IL-6 inhibition in reducing the risk of cardiovascular disease among CHIP carriers. Our findings demonstrate that CHIP represents a complex set of heterogeneous phenotypes with shared and unique germline genetic causes and varied clinical implications.

Multiancestry exome sequencing reveals INHBE mutations associated with favorable fat distribution and protection from diabetes.

Body fat distribution is a major, heritable risk factor for cardiometabolic disease, independent of overall adiposity. Using exome-sequencing in 618,375 individuals (including 160,058 non-Europeans) from the UK, Sweden and Mexico, we identify 16 genes associated with fat distribution at exome-wide significance. We show 6-fold larger effect for fat-distribution associated rare coding variants compared with fine-mapped common alleles, enrichment for genes expressed in adipose tissue and causal genes for partial lipodystrophies, and evidence of sex-dimorphism. We describe an association with favorable fat distribution (p = 1.8 × 10-09), favorable metabolic profile and protection from type 2 diabetes (~28% lower odds; p = 0.004) for heterozygous protein-truncating mutations in INHBE, which encodes a circulating growth factor of the activin family, highly and specifically expressed in hepatocytes. Our results suggest that inhibin ßE is a liver-expressed negative regulator of adipose storage whose blockade may be beneficial in fat distribution-associated metabolic disease.

Germline Mutations in CIDEB and Protection against Liver Disease.

BACKGROUND: Exome sequencing in hundreds of thousands of persons may enable the identification of rare protein-coding genetic variants associated with protection from human diseases like liver cirrhosis, providing a strategy for the discovery of new therapeutic targets. METHODS: We performed a multistage exome sequencing and genetic association analysis to identify genes in which rare protein-coding variants were associated with liver phenotypes. We conducted in vitro experiments to further characterize associations. RESULTS: The multistage analysis involved 542,904 persons with available data on liver aminotransferase levels, 24,944 patients with various types of liver disease, and 490,636 controls without liver disease. We found that rare coding variants in APOB, ABCB4, SLC30A10, and TM6SF2 were associated with increased aminotransferase levels and an increased risk of liver disease. We also found that variants in CIDEB, which encodes a structural protein found in hepatic lipid droplets, had a protective effect. The burden of rare predicted loss-of-function variants plus missense variants in CIDEB (combined carrier frequency, 0.7%) was associated with decreased alanine aminotransferase levels (beta per allele, -1.24 U per liter; 95% confidence interval [CI], -1.66 to -0.83; P = 4.8×10-9) and with 33% lower odds of liver disease of any cause (odds ratio per allele, 0.67; 95% CI, 0.57 to 0.79; P = 9.9×10-7). Rare coding variants in CIDEB were associated with a decreased risk of liver disease across different underlying causes and different degrees of severity, including cirrhosis of any cause (odds ratio per allele, 0.50; 95% CI, 0.36 to 0.70). Among 3599 patients who had undergone bariatric surgery, rare coding variants in CIDEB were associated with a decreased nonalcoholic fatty liver disease activity score (beta per allele in score units, -0.98; 95% CI, -1.54 to -0.41 [scores range from 0 to 8, with higher scores indicating more severe disease]). In human hepatoma cell lines challenged with oleate, CIDEB small interfering RNA knockdown prevented the buildup of large lipid droplets. CONCLUSIONS: Rare germline mutations in CIDEB conferred substantial protection from liver disease. (Funded by Regeneron Pharmaceuticals.).

Exome sequencing and analysis of 454,787 UK Biobank participants.

A major goal in human genetics is to use natural variation to understand the phenotypic consequences of altering each protein-coding gene in the genome. Here we used exome sequencing1 to explore protein-altering variants and their consequences in 454,787 participants in the UK Biobank study2. We identified 12 million coding variants, including around 1 million loss-of-function and around 1.8 million deleterious missense variants. When these were tested for association with 3,994 health-related traits, we found 564 genes with trait associations at P ≤ 2.18 × 10-11. Rare variant associations were enriched in loci from genome-wide association studies (GWAS), but most (91%) were independent of common variant signals. We discovered several risk-increasing associations with traits related to liver disease, eye disease and cancer, among others, as well as risk-lowering associations for hypertension (SLC9A3R2), diabetes (MAP3K15, FAM234A) and asthma (SLC27A3). Six genes were associated with brain imaging phenotypes, including two involved in neural development (GBE1, PLD1). Of the signals available and powered for replication in an independent cohort, 81% were confirmed; furthermore, association signals were generally consistent across individuals of European, Asian and African ancestry. We illustrate the ability of exome sequencing to identify gene-trait associations, elucidate gene function and pinpoint effector genes that underlie GWAS signals at scale.

Exome sequencing and characterization of 49,960 individuals in the UK Biobank.

The UK Biobank is a prospective study of 502,543 individuals, combining extensive phenotypic and genotypic data with streamlined access for researchers around the world1. Here we describe the release of exome-sequence data for the first 49,960 study participants, revealing approximately 4 million coding variants (of which around 98.6% have a frequency of less than 1%). The data include 198,269 autosomal predicted loss-of-function (LOF) variants, a more than 14-fold increase compared to the imputed sequence. Nearly all genes (more than 97%) had at least one carrier with a LOF variant, and most genes (more than 69%) had at least ten carriers with a LOF variant. We illustrate the power of characterizing LOF variants in this population through association analyses across 1,730 phenotypes. In addition to replicating established associations, we found novel LOF variants with large effects on disease traits, including PIEZO1 on varicose veins, COL6A1 on corneal resistance, MEPE on bone density, and IQGAP2 and GMPR on blood cell traits. We further demonstrate the value of exome sequencing by surveying the prevalence of pathogenic variants of clinical importance, and show that 2% of this population has a medically actionable variant. Furthermore, we characterize the penetrance of cancer in carriers of pathogenic BRCA1 and BRCA2 variants. Exome sequences from the first 49,960 participants highlight the promise of genome sequencing in large population-based studies and are now accessible to the scientific community.

Herpes Simplex Virus Hepatitis in an Immunocompetent Host Resembling Hepatic Pyogenic Abscesses.

Herpes simplex virus (HSV) hepatitis represents a rare complication of HSV infection, which can progress to acute liver failure and, in some cases, death. We describe an immunocompetent 67-year-old male who presented with one week of fever and abdominal pain. Computed tomography (CT) scan and magnetic resonance imaging (MRI) of the abdomen showed multiple bilobar hepatic lesions, some with rim enhancement, compatible with liver abscesses. Subsequent liver biopsy, however, revealed hepatocellular necrosis, HSV-type intranuclear inclusions, and immunostaining positive for herpes virus type 2 (HSV-2). Though initially treated with broad-spectrum antibiotics, following histologic diagnosis of HSV hepatitis, the patient was transitioned to intravenous acyclovir for four weeks and he achieved full clinical recovery. Given its high mortality and nonspecific presentation, one should consider HSV hepatitis in all patients with acute hepatitis with multifocal hepatic lesions of unknown etiology. Of special note, this is only the second reported case of HSV liver lesions mimicking pyogenic abscesses on CT and MRI.

Determining the natural history of pancreatic cystic neoplasms: a Manitoban cohort study.

BACKGROUND: Most pancreatic cystic neoplasms (PCN) are thought to harbor a low malignant potential. This historical cohort study attempts to describe the natural history of these lesions in a provincial cohort, to assess the safety of non-surgical management. Pathological diagnosis of malignancy was the primary outcome measure of interest. METHODS: All adult patients (age 18+) with PCN seen between 2000 and 2012 by the two main institutions in Manitoba were included in this study. PCN were graded as high and low risk, which dictated initial treatment plan (surgery or observation). Predictors of initial surgical treatment, delayed surgery in the observation group and the clinical/radiological predictors of malignancy were determined. RESULTS: 497 patients were included in this study. 43 (8.7%) high-risk lesions underwent initial surgery, with 13 (30.2%) cases of malignancy discovered. 450 (90.5%) low-risk cysts were observed for a median of 17.3 months (range: 0.00-142.3). 29 (6.4%) cases of delayed surgery occurred, with malignancy discovered in five (17.2%). CONCLUSIONS: This study supports current selection criteria for management of PCNs. Due to the low incidence of malignancy in low-risk PCN, it appears that long-term observation is safe and should be the treatment modality of choice in the absence of high-risk features.

Yield of tissue sampling for subepithelial lesions evaluated by EUS: a comparison between forceps biopsies and endoscopic submucosal resection.

BACKGROUND: In most circumstances, subepithelial tumors lack distinct endoscopic and ultrasonographic features. Consequently, definitive diagnosis usually requires tissue acquisition and pathologic confirmation. Establishing a tissue diagnosis is difficult because the yield of forceps biopsies is low. However, prospective data evaluating tissue sampling techniques for subepithelial lesions are currently lacking. OBJECTIVE: Our purpose was to prospectively determine the diagnostic yield of endoscopic submucosal-mucosal resection (ESMR) compared with forceps biopsy for lesions limited to the submucosa (third endosonographic layer) of the GI tract. DESIGN: A prospective head-to-head comparison was performed. SETTING: The study was performed in a tertiary care hospital. PATIENTS: Study patients were 23 adults with subepithelial lesions limited to the submucosa. INTERVENTION: All submucosal lesions underwent forceps biopsy followed by endoscopic submucosal resection. Biopsy specimens were obtained with large-capacity "jumbo" forceps. A total of 4 double passes (8 biopsy specimens) were collected from each lesion with use of the bite-on-bite technique. Endoscopic resection was then performed with an electrosurgical snare or cap-fitted endoscopic mucosal resection device. MAIN OUTCOME MEASUREMENT: The main outcome measurement was the diagnostic yield of biopsy forceps compared with endoscopic submucosal resection. RESULTS: Twenty-three patients with lesions limited to the submucosa were identified by endoscopic ultrasonography. All lesions underwent forceps biopsy followed by ESMR. The diagnostic yield of the jumbo forceps biopsy was 4 of 23 (17%), whereas the diagnostic yield of ESMR was 20 of 23 (87%) (P = .0001, McNemar test). CONCLUSION: In the evaluation of subepithelial lesions limited to the submucosa, ESMR has a significantly higher diagnostic yield than jumbo forceps biopsy with use of the bite-on-bite technique.

The role of cytokine gene polymorphisms in determining disease susceptibility and phenotype in inflammatory bowel disease.

BACKGROUND AND AIMS: Emerging data indicate that alterations in cytokine synthesis may play a role in inflammatory bowel disease (IBD) pathogenesis. The differential production of cytokines has been linked to single nucleotide polymorphisms in gene promoter regions, signal sequences, and gene introns. The aim of this study was to assess the relationship between polymorphisms involving five cytokine genes (TNF-alpha, TGF-beta, IL-10, IL-6, and IFN-gamma), and IBD susceptibility and disease phenotype. METHODS: Cytokine genotyping was performed utilizing polymerase chain reaction. The specific gene polymorphisms that were probed for included: -1082(G/A), -819(T/C), and -592(A/C) in the IL-10 promoter, -308(G/A) in the TNF-alpha promoter, codon 10 (T/C), and codon 25 (G/C) of the TGF-beta signal sequence, +874(T/A) of intron 1 of IFN-gamma, and -174(C/G) in the IL-6 promoter. RESULTS: A total of 193 IBD patients (138 Crohn's disease (CD) and 55 ulcerative colitis (UC)) and 92 controls were evaluated. No association between IBD, UC, or CD susceptibility and the cytokine gene polymorphisms were found. Patients with ileocolonic CD were more likely to possess the IL-6 -174 GG genotype compared to those with nonileocolonic disease (p= 0.006). Patients with ileal CD were more likely to possess the IL-6 -174 GC genotype compared to those with nonileal disease (p= 0.0004). An increased number of CD patients with isolated colonic disease possessed the IL-6 -174 CC genotype compared to those with nonisolated colonic disease (p= 0.032). CONCLUSION: The cytokine gene polymorphisms studied here do not appear to influence IBD susceptibility. There does, however, appear to be an influence on disease phenotype, particularly on CD site.

Mining OMIM for insight into complex diseases.

Understanding clinical phenotypes through their corresponding genotypes is one of the principal goals of genetic research. Though achieving this goal is relatively simple with single gene syndromes, more complex diseases often consist of varied clinical phenotypes that may be the result of interactions among multiple genetic loci. Microarray technology has brought the phenotype -genotype relationship to the molecular level, using differently behaving cancers, for example, as the basis for comparing patterns of gene expression. With this feasibility study, we attempted to use similar methods of analysis at the clinical level, in order to evaluate our hypothesis that the clustering of clinical phenotypes would provide information that would be useful in elucidating their underlying genotypes. Because of its breadth of content and detailed descriptions, we used OMIM as our source material for phenotypic and genetic information. After processing the source material, we then performed self-organizing map and hierarchical clustering analysis on representative diseases by phenotypic category. Through pre-determined queries over this analysis, we made two findings of potential clinical significance, one concerning diabetes and another concerning progressive neurologic diseases. Our methods provide a formal approach to analyzing phenotypes among diverse diseases, and may help indicate fruitful areas for further research into their underlying genetic causes.

A knowledge framework for computational molecular-disease relationships in cancer.

Biomedical knowledge is growing at an exponential rate, with new discoveries being published across a range of information sources. A coded, fully-computable, and integrated approach to this information could increase the efficiency of its use, through improved retrieval as well as the eventual ability to apply decision support tools to the knowledge base. Though multiple knowledge bases (KBs) and databases (DBs) concerning gene-disease relationships exist, few present the information in a coded, easily computable form. Focusing on molecular-disease relationships in cancer (gene-disease and protein-disease), we evaluated articles in major biomedical journals, in order to develop both the framework for a knowledge model as well as evaluation criteria. We then used these criteria to evaluate major KBs, DBs, and terminologies. We discovered that although both the high-level as well as the specific molecular-disease relationships present in our test set were mapped in many of the databases, they generally were not applied together in a coded form. We propose a rationale behind a model mediated schema for the integration of these resources.