Genomics of 1 million parent lifespans implicates novel pathways and common diseases and distinguishes survival chances

We use a genome-wide association of 1 million parental lifespans of genotyped subjects and data on mortality risk factors to validate previously unreplicated findings near CDKN2B-AS1, ATXN2/BRAP, FURIN/FES, ZW10, PSORS1C3, and 13q21.31, and identify and replicate novel findings near ABO, ZC3HC1, and IGF2R. We also validate previous findings near 5q33.3/EBF1 and FOXO3, whilst finding contradictory evidence at other loci. Gene set and cell-specific analyses show that expression in foetal brain cells and adult dorsolateral prefrontal cortex is enriched for lifespan variation, as are gene pathways involving lipid proteins and homeostasis, vesicle-mediated transport, and synaptic function. Individual genetic variants that increase dementia, cardiovascular disease, and lung cancer - but not other cancers - explain the most variance. Resulting polygenic scores show a mean lifespan difference of around five years of life across the deciles

GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19

Critical illness in COVID-19 is an extreme and clinically homogeneous disease phenotype that we have previously shown to be highly efficient for discovery of genetic associations. Despite the advanced stage of illness at presentation, we have shown that host genetics in patients who are critically ill with COVID-19 can identify immunomodulatory therapies with strong beneficial effects in this group. Here we analyse 24,202 cases of COVID-19 with critical illness comprising a combination of microarray genotype and whole-genome sequencing data from cases of critical illness in the international GenOMICC (11,440 cases) study, combined with other studies recruiting hospitalized patients with a strong focus on severe and critical disease: ISARIC4C (676 cases) and the SCOURGE consortium (5,934 cases). To put these results in the context of existing work, we conduct a meta-analysis of the new GenOMICC genome-wide association study (GWAS) results with previously published data. We find 49 genome-wide significant associations, of which 16 have not been reported previously. To investigate the therapeutic implications of these findings, we infer the structural consequences of protein-coding variants, and combine our GWAS results with gene expression data using a monocyte transcriptome-wide association study (TWAS) model, as well as gene and protein expression using Mendelian randomization. We identify potentially druggable targets in multiple systems, including inflammatory signalling (JAK1), monocyte–macrophage activation and endothelial permeability (PDE4A), immunometabolism (SLC2A5 and AK5), and host factors required for viral entry and replication (TMPRSS2 and RAB2A)

Similar prevalence of expanded CGG repeat lengths in the fragile X mental retardation I gene among infertile women and among women with proven fertility : a prospective study

Purpose:We sought to determine the usefulness of fragile X mental retardation 1 (FMR1) carrier testing among young infertile women with or without signs of ovarian insufficiency as compared with fertile women.Methods:Three cohorts of women were recruited to determine the cytosine-guanine-guanine (CGG) repeats trinucleotide repeat length in the 5'-untranslated region of the FMR1 gene in lymphocyte DNA. A total of 199 fertile women, who were reported to have conceived within 3 months, were recruited together with 372 infertile women with ongoing menstrual cycles and 48 infertile women with primary ovarian insufficiency. The various ranges of FMR1 CGG repeat lengths among infertile women were compared with those of fertile controls. In infertile women with ongoing menstrual cycles, the serum concentrations of follicle-stimulating hormone, anti-Muellerian hormone, and inhibin B were measured during the early follicular phase.Results:None of the three categories of FMR1 CGG repeat length expansions (premutation, intermediate range, and high normal range) were more prevalent among infertile women than among fertile women. The CGG repeat length was not correlated with any of the ovarian reserve parameters.Conclusion:In comparison with a generalized preconception screening strategy, infertility as a criterion, even together with reduced ovarian reserve, is not suitable for identifying a higher proportion of women with expanded FMR1 CGG repeat length.Genet Med advance online publication 10 October 2013Genetics in Medicine (2013); doi:10.1038/gim.2013.146

Genetic mechanisms of critical illness in COVID-19

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079,&nbsp;P&nbsp;=&nbsp;1.65&nbsp;&times;&nbsp;10&minus;8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1,&nbsp;OAS2&nbsp;and&nbsp;OAS3); on chromosome 19p13.2 (rs74956615,&nbsp;P&nbsp;=&nbsp;2.3&nbsp;&times;&nbsp;10&minus;8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069,&nbsp;P&nbsp;=&nbsp;3.98&nbsp;&times; 10&minus;12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757,&nbsp;P&nbsp;=&nbsp;4.99&nbsp;&times;&nbsp;10&minus;8) in the interferon receptor gene&nbsp;IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of&nbsp;IFNAR2, or high expression of&nbsp;TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte&ndash;macrophage chemotactic receptor&nbsp;CCR2&nbsp;is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice.</p