Tag: GRM

Scalable Integrative Analysis of Large Biobank-Scale Whole Genome Sequencing Studies With Functional Data

Whole Genome/Exome Sequencing (WGS/WES) data and Electronic Health Records (EHRs), such as large scale national and institutional biobanks, have emerged rapidly worldwide. In this talk, I will discuss the analytic tools and resources for scalable analysis of large scale biobank- and population-based Whole Genome Sequencing (WGS) association studies of common…

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Tandem NBPF 3mer HORs (Olduvai triplets) in Neanderthal and two novel HOR tandem arrays in human chromosome 1 T2T-CHM13 assembly

High-quality Neanderthal genome sequence Impressive progress by Pääbo et al. in high-quality sequencing of Neanderthal’s genome has opened new avenues in studying relation of modern humans and our closest extinct relatives Neanderthals, in quest of searching “what makes us human”1,2,3,4,5,6. The high-quality genomes Denisova 5 AltaiNea.hg197,8, Chagyrskaya 86, and Vindija…

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Nuclear genetic control of mtDNA copy number and heteroplasmy in humans

Overview of mtSwirl Here we develop mtSwirl, a scalable pipeline for mtCN and variant calling which makes calls relative to an internally generated per-sample consensus sequence before mapping all calls back to GRCh38. In addition to GRCh38 reference files and WGS data, the mtSwirl pipeline takes as input nuclear genome…

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Direct inference and control of genetic population structure from RNA sequencing data

In this study, we constructed the RGStraP pipeline to calculate RG-PCs from genetic variants called from RNAseq data. RGStraP relies on GATK for its variant calling suite, as well as PLINK and flashPCA to filter the SNPs and calculate genetic principal components from them, respectively (Methods). We make RGStraP available…

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Pathogens | Free Full-Text | Association of CYP2C19, CYP2D6 and CYP3A4 Genetic Variants on Primaquine Hemolysis in G6PD-Deficient Patients

3.2. Laboratory Characteristics A hematological analysis demonstrated values below normal for both groups but with no statistical difference for erythrocytes, hematocrit (Ht), hemoglobin (Hb) and thrombocytopenia (p > 0.05). In the G6PDd group, there was a higher frequency of anemia and jaundice with no significant statistical difference. Biochemical markers of…

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Infinite value present in GRM, between sample ‘XXXX’ and itself

when I try to run –pca command Iget the Error massge:” Infinite value present in GRM, between sample ‘XXXX’ and itself”what the problem can be?command:../scripts/plink2  –vcf filterxy.vcf.gz –pca allele-wts  –exclude pca-clean.prune.out –freq counts –remove pca-clean.king.cutoff.out.id –out pca-clean log: PLINK v2.00a5LM 64-bit Intel (16 May 2023)     www.cog-genomics.org/plink/2.0/(C) 2005-2023 Shaun Purcell,…

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Biobank-scale inference of ancestral recombination graphs enables genealogical analysis of complex traits

ARG-Needle and ASMC-clust algorithms We introduce two algorithms to construct the ARG of a set of samples, called ARG-Needle and ASMC-clust. Both approaches leverage output from the ASMC algorithm11, which takes as input a pair of genotyping array or sequencing samples and outputs a posterior distribution of the TMRCA across…

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Genetic correlates of vitamin D-binding protein and 25-hydroxyvitamin D in neonatal dried blood spots

Samples This study was based on the Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH) sample37, a population-based case-cohort design to study the genetic and environmental factors associated with severe mental disorders. The iPSYCH2012 sample is nested within the entire Danish population born between 1981 and 2005 (N = 1,472,762). In total,…

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Master mitotic kinases regulate viral genome delivery during papillomavirus cell entry

Marsh, M. & Helenius, A. Virus entry: open sesame. Cell 124, 729–740 (2006). Article  CAS  Google Scholar  Roe, T., Reynolds, T. C., Yu, G. & Brown, P. O. Integration of murine leukemia virus DNA depends on mitosis. EMBO J. 12, 2099–2108 (1993). Article  CAS  Google Scholar  Bieniasz, P. D., Weiss,…

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Genetic footprints of assortative mating in the Japanese population

Study cohort description We used data on a total of 172,270 individuals of Japanese and East Asian ancestry. Of these, data on 165,098 individuals were obtained from BBJ, which has enrolled ≥200,000 participants to date. BBJ is a multi-institutional hospital-based genome cohort that collected participants affected with at least one…

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Genetic and chemotherapeutic influences on germline hypermutation

DNM filtering in 100,000 Genomes Project We analysed DNMs called in 13,949 parent–offspring trios from 12,609 families from the rare disease programme of the 100,000 Genomes Project. The rare disease cohort includes individuals with a wide array of diseases, including neurodevelopmental disorders, cardiovascular disorders, renal and urinary tract disorders, ophthalmological…

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Calculation of the GRM in GCTA

Calculation of the GRM in GCTA 0 Hi experts, I am new to the field. I have some questions wrt the calculation of the GRM: by using the GCTA software: Let’s say I have a population of genome data for N= 4800000, and the original genotype SNPs, and also the…

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