GALC Deletions Increase the Risk of Primary Open-Angle Glaucoma: The Role of Mendelian Variants in Complex Disease

DNA copy number variants (CNVs) have been reported in many human diseases including autism and schizophrenia. Primary Open Angle Glaucoma (POAG) is a complex adult-onset disorder characterized by progressive optic neuropathy and vision loss. Previous studies have identified rare CNVs in POAG; however, their low frequencies prevented formal association testing. We present here the association between POAG risk and a heterozygous deletion in the galactosylceramidase gene (GALC). This CNV was initially identified in a dataset containing 71 Caucasian POAG cases and 478 ethnically matched controls obtained from dbGAP (study accession phs000126.v1.p1.) (p = 0.017, fisher's exact test). It was validated with array comparative genomic hybridization (arrayCGH) and realtime PCR, and replicated in an independent POAG dataset containing 959 cases and 1852 controls (p = 0.021, OR (odds ratio) = 3.5, 95% CI −1.1–12.0). Evidence for association was strengthened when the discovery and replication datasets were combined (p = 0.002; OR = 5.0, 95% CI 1.6–16.4). Several deletions with different endpoints were identified by array CGH of POAG patients. Homozygous deletions that eliminate GALC enzymatic activity cause Krabbe disease, a recessive Mendelian disorder of childhood displaying bilateral optic neuropathy and vision loss. Our findings suggest that heterozygous deletions that reduce GALC activity are a novel mechanism increasing risk of POAG. This is the first report of a statistically-significant association of a CNV with POAG risk, contributing to a growing body of evidence that CNVs play an important role in complex, inherited disorders. Our findings suggest an attractive biomarker and potential therapeutic target for patients with this form of POAG

A High-Density Genome-Wide Association Screen of Sporadic ALS in US Veterans

Following reports of an increased incidence of amyotrophic lateral sclerosis (ALS) in U.S. veterans, we have conducted a high-density genome-wide association study (GWAS) of ALS outcome and survival time in a sample of U.S. veterans. We tested ∼1.3 million single nucleotide polymorphisms (SNPs) for association with ALS outcome in 442 incident Caucasian veteran cases diagnosed with definite or probable ALS and 348 Caucasian veteran controls. To increase power, we also included genotypes from 5909 publicly-available non-veteran controls in the analysis. In the survival analysis, we tested for association between SNPs and post-diagnosis survival time in 639 Caucasian veteran cases with definite or probable ALS. After this discovery phase, we performed follow-up genotyping of 299 SNPs in an independent replication sample of Caucasian veterans and non-veterans (ALS outcome: 183 cases and 961 controls; survival: 118 cases). Although no SNPs reached genome-wide significance in the discovery phase for either phenotype, three SNPs were statistically significant in the replication analysis of ALS outcome: rs6080539 (177 kb from PCSK2), rs7000234 (4 kb from ZNF704), and rs3113494 (13 kb from LOC100506746). Two SNPs located in genes that were implicated by previous GWA studies of ALS were marginally significant in the pooled analysis of discovery and replication samples: rs17174381 in DPP6 (p = 4.4×10−4) and rs6985069 near ELP3 (p = 4.8×10−4). Our results underscore the difficulty of identifying and convincingly replicating genetic associations with a rare and genetically heterogeneous disorder such as ALS, and suggest that common SNPs are unlikely to account for a substantial proportion of patients affected by this devastating disorder

Genetic Predisposition to Coronary Artery Disease in Type 2 Diabetes Mellitus

This work was supported by the European Union Framework Programme 7 (FP7/2007-2013) for the Innovative Medicine Initiative (IMI) under grant agreement n° IMI/115006 (the SUMMIT [Surrogate Markers for Micro- and Macro-Vascular Hard End Points for Innovative Diabetes Tools] consortium); Aarno Koskelo Foundation; Academy of Finland (no. 263401; no. 2676882); American Heart Association (13SDG14330006); AstraZeneca; AtheroSysMed (Systems medicine of coronary heart disease and stroke); British Heart Foundation Centre of Research Excellence at Oxford; ERC269045-Gene Target T2D grant; Estonian Research Council (IUT20-60, PUT1660 and PUT1665P); Estonian Center of Genomics/Roadmap II (project No. 2014-2020.4.01.16-0125); European Union (no. 692145; no. 633589; no. 313010; LSHM-CT-2007-037273; no. 201668; 2014-2020.4.01.15-0012;QLG1-CT-2002-00896; EU/QLRT-2001-01254; QLG2-CT-2002-01254 HEALTH-F2-2013-601456); Finnish Foundation for Cardiovascular research; Gentransmed - Centre of Excellence for Genomics and Translational Medicine; German Ministry of Education and Research (no. 01ZX1313A-K); Helsinki University Central Hospital special government funds (TYH7215, TKK2012005, TYH2012209, TYH2014312); Juvenile Diabetes Research Foundation (JDRF, 2-SRA-2014-276-Q-R); National Institute of Diabetes and Digestive and Kidney diseases (NIDDK, 5R01DK106236; U01-DK066134; U01-DK105535; R01DK101478); National Heart, Lung and Blood Institute (NLHBI, R01HL103866); National Institute for Health Research (NIHR); Personalized diagnostics and treatment of high risk coronary artery disease patients (RiskyCAD; 305739); Sigrid Juselius Foundation; Finnish Academy (no. 269517); Finnish Foundation for Cardiovascular Research; Foundation for Strategic Research and Stockholm County Council (560283; 592229); Juho Vainio Foundation; Knut and Alice Wallenberg Foundation; Ministry for Higher Education; Strategic Cardiovascular and Diabetes Programmes of Karolinska Institutet and Stockholm County Council; Swedish Foundation for Strategic Research (SSF; ICA08-0047); Swedish Heart-Lung Foundation; Swedish Research Council (project 8691; 2015-02558; 2016-00598; M-2005-1112 and 2009-2298); Torsten and Ragnar Söderberg Foundation; W.W. Smith Charitable Trust (H1201); Wellcome Trust Institutional strategic support fund; Yrjö Jahnsson Foundation. Publisher Copyright: © 2020 Lippincott Williams and Wilkins. All rights reserved.Background: Coronary artery disease (CAD) is accelerated in subjects with type 2 diabetes mellitus (T2D). Methods: To test whether this reflects differential genetic influences on CAD risk in subjects with T2D, we performed a systematic assessment of genetic overlap between CAD and T2D in 66 643 subjects (27 708 with CAD and 24 259 with T2D). Variants showing apparent association with CAD in stratified analyses or evidence of interaction were evaluated in a further 117 787 subjects (16 694 with CAD and 11 537 with T2D). Results: None of the previously characterized CAD loci was found to have specific effects on CAD in T2D individuals, and a genome-wide interaction analysis found no new variants for CAD that could be considered T2D specific. When we considered the overall genetic correlations between CAD and its risk factors, we found no substantial differences in these relationships by T2D background. Conclusions: This study found no evidence that the genetic architecture of CAD differs in those with T2D compared with those without T2D.Peer reviewe

Metabolomic profiling identifies complex lipid species and amino acid analogues associated with response to weight loss interventions.

Obesity is an epidemic internationally. While weight loss interventions are efficacious, they are compounded by heterogeneity with regards to clinically relevant metabolic responses. Thus, we sought to identify metabolic biomarkers that are associated with beneficial metabolic changes to weight loss and which distinguish individuals with obesity who would most benefit from a given type of intervention. Liquid chromatography mass spectrometry-based profiling was used to measure 765 metabolites in baseline plasma from three different weight loss studies: WLM (behavioral intervention, N = 443), STRRIDE-PD (exercise intervention, N = 163), and CBD (surgical cohort, N = 125). The primary outcome was percent change in insulin resistance (as measured by the Homeostatic Model Assessment of Insulin Resistance [%ΔHOMA-IR]) over the intervention. Overall, 92 individual metabolites were associated with %ΔHOMA-IR after adjustment for multiple comparisons. Concordantly, the most significant metabolites were triacylglycerols (TAGs; p = 2.3e-5) and diacylglycerols (DAGs; p = 1.6e-4), with higher baseline TAG and DAG levels associated with a greater improvement in insulin resistance with weight loss. In tests of heterogeneity, 50 metabolites changed differently between weight loss interventions; we found amino acids, peptides, and their analogues to be most significant (4.7e-3) in this category. Our results highlight novel metabolic pathways associated with heterogeneity in response to weight loss interventions, and related biomarkers which could be used in future studies of personalized approaches to weight loss interventions

Whole blood sequencing reveals circulating microRNA associations with high-risk traits in non-ST-segment elevation acute coronary syndrome

10.1016/j.atherosclerosis.2017.03.041ATHEROSCLEROSIS26119-2

Associations of osteopontin and NT-proBNP with circulating miRNA levels in acute coronary syndrome

10.1152/physiolgenomics.00033.2019PHYSIOLOGICAL GENOMICS5110506-51