Tag: gcta

NOTE: This collection was originally posted at SeqAnswers.com. Creating a copy here to preserve the information.Part I is available here: Yes .. BBMap can do that! – Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)Part II is available here: Yes .. BBMap can…

Szekanecz, Z. et al. Autoinflammation and autoimmunity across rheumatic and musculoskeletal diseases. Nat. Rev. Rheumatol. 17, 585–595 (2021). Article  CAS  PubMed  Google Scholar  Rosenblum, M. D., Remedios, K. A. & Abbas, A. K. Mechanisms of human autoimmunity. J. Clin. Invest. 125, 2228–2233 (2015). Article  PubMed  PubMed Central  Google Scholar  Wang,…

Dinkler L, Bryant-Waugh R. Assessment of avoidant restrictive food intake disorder, pica and rumination disorder: interview and questionnaire measures. Curr Opin Psychiatry. 2021;34(6):532–42. Article  Google Scholar  American Psychiatric Association. Diagnostic and Statistical Manual of Mental Disorders (5th ed.). Arlington, VA: American Psychiatric Publishing; 2013. Thomas JJ, Lawson EA, Micali N, Misra…

van Es MA, Hardiman O, Chio A, Al-Chalabi A, Pasterkamp RJ, Veldink JH, van den Berg LH. Amyotrophic Lateral Sclerosis. Lancet (London England). 2017;390:2084–98. Article  PubMed  Google Scholar  Liu MS, Cui LY, Fan DS. Age at onset of Amyotrophic Lateral Sclerosis in China. Acta Neurol Scand. 2014;129:163–7. Article  CAS  PubMed …

Summary Description: We are looking for a talented bioinformatician or computational biologist who specializes in utilizing polygenic scores and machine learning techniques to analyze genomic data, particularly for predicting complex disease and trait phenotypes. The ideal candidate will possess a solid understanding of genetics and genomics, along with expertise in…

MacDonald SW, Li SC, Bäckman L. Neural underpinnings of within-person variability in cognitive functioning. Psychol Aging. 2009;24:792–808. Article  PubMed  Google Scholar  Haynes BI, Bunce D, Kochan NA, Wen W, Brodaty H, Sachdev PS. Associations between reaction time measures and white matter hyperintensities in very old age. Neuropsychologia. 2017;96:249–55. Article  PubMed …

Significance testing of top vs. random SNPs 0 After performing GWAS, I calculated the percentage of phenotypic variance (SNP-based heritability) for top SNPs and random SNPs using GREML (GCTA). The variance of random SNPs was calculated for 3 different groups of randomly chosen SNPs and then averaged to get the…

Hekselman, I. & Yeger-Lotem, E. Mechanisms of tissue and cell-type specificity in heritable traits and diseases. Nat. Rev. Genet. 21, 137–150 (2020). Article  CAS  PubMed  Google Scholar  Ongen, H. et al. Estimating the causal tissues for complex traits and diseases. Nat. Genet. 49, 1676–1683 (2017). Article  CAS  PubMed  Google Scholar …

Doebley, J. F., Gaut, B. S. & Smith, B. D. The molecular genetics of crop domestication. Cell 127, 1309–1321 (2006). Article  CAS  PubMed  Google Scholar  Allaby, R. G., Fuller, D. Q. & Brown, T. A. The genetic expectations of a protracted model for the origins of domesticated crops. Proc. Natl…

Mitchell, K. S. et al. Binge eating disorder: a symptom-level investigation of genetic and environmental influences on liability. Psychol. Med. 40, 1899–1906 (2010). Article  CAS  PubMed  PubMed Central  Google Scholar  Reichborn-Kjennerud, T., Bulik, C. M., Tambs, K. & Harris, J. R. Genetic and environmental influences on binge eating in the…

99, 12451260 (2016). Genet. eCollection 2023. 36, 29362937 (2020). Genet. These assays include massively parallel regulatory assays134, which test synthetic regulatory sequences by screening variants in thousands of untranscribed or untranslated sequences for functional effects in a single experiment, and CRISPR techniques that allow for the introduction of mutations into…

Degenhardt L, Grebely J, Stone J, Hickman M, Vickerman P, Marshall BDL, et al. Global patterns of opioid use and dependence: harms to populations, interventions, and future action. Lancet. 2019;394:1560–79. Article  CAS  PubMed  PubMed Central  Google Scholar  Patten DK, Schultz BG, Berlau DJ. The Safety and Efficacy of Low-Dose Naltrexone…

Hi all, this is my first time posting on BioStars! I thought I’d easily find a bash one-liner to take care of this task but I’ve been searching with no luck. I have a fasta, samples.fasta, that looks like this: >sample01/contig002 ATCG >sample02/contig001 GCTA >sample11/contig003 CAGT I have a text…

Common variants associated with TAAD We designed a two-phased GWAS. The initial MVP discovery analysis was composed of 8,626 individuals (7,050 European, 1,266 African and 310 Hispanic ancestry participants) with TAAD and 453,043 disease-free individuals from the same ancestral groups (Supplementary Fig. 1); their baseline characteristics are presented in Supplementary…

Study design and participants The GCKD study is an ongoing prospective observational study that enrolled 5,217 adult persons with CKD between 2010 and 2012. Patients regularly seen by nephrologists with eGFR between 30 and 60 ml min−1 per 1.73 m2 or eGFR >60 ml min−1 per 1.73 m2 with UACR > 300 mg per g (or urinary protein/creatinine ratio > 500 mg…

Burton, G. J., Redman, C. W., Roberts, J. M. & Moffett, A. Pre-eclampsia: pathophysiology and clinical implications. BMJ 366, l2381 (2019). Article  PubMed  Google Scholar  Jiang, L. et al. A global view of hypertensive disorders and diabetes mellitus during pregnancy. Nat. Rev. Endocrinol. 18, 760–775 (2022). Article  PubMed  PubMed Central …

We analyzed data from a total of 2,733 participants from the GALA II16 and SAGE17 asthma case–control studies who self-identified as African American (AA; n = 757), Puerto Rican (PR; n = 893), Mexican American (MX; n = 784) or other Latino American (LA; n = 299) (Table 1 and Supplementary Table 1). The median age of the…

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…

GWAS-level and post-GWAS analyses GWAS of PD have nominated 90 independent risk signals in individuals of European ancestry, explaining ~16–36% of the heritable risk7, as well as two additional risk signals in Asian populations8. Typically, published GWAS are accompanied by various follow-up analyses, but performing these analyses is not always…

#119126 Bioinformatics Programmer II – Hybrid/Remote Extended Deadline: Tue 2/21/2023 This position will remain open until a successful candidate has been identified. UCSD Layoff from Career Appointment: Apply by 10/03/2022 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor. Special Selection Applicants: Apply by 10/13/2022….

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,…

This position will remain open until a successful candidate has been identified. UCSD Layoff from Career Appointment: Apply by 10/03/2022 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor. Special Selection Applicants: Apply by 10/13/2022. Eligible Special Selection clients should contact their Disability Counselor for…

Faraone, S. V. et al. Attention-deficit/hyperactivity disorder. Nat. Rev. Dis. Prim. 1, 15020 (2015). Article  Google Scholar  Franke, B. et al. The genetics of attention deficit/hyperactivity disorder in adults, a review. Mol. Psychiatry 17, 960–987 (2012). Article  CAS  Google Scholar  Dalsgaard, S., Leckman, J. F., Mortensen, P. B., Nielsen, H….

Tuttle KR, Bakris GL, Bilous RW, Chiang JL, de Boer IH, Goldstein-Fuchs J, et al. Diabetic kidney disease: a report from an ADA Consensus Conference. Diabetes Care. 2014;37(10):2864–83. Article  Google Scholar  Jha V, Garcia-Garcia G, Iseki K, Li Z, Naicker S, Plattner B, et al. Chronic kidney disease: global dimension…

Ellis, E. C. et al. Anthropogenic transformation of the biomes, 1700 to 2000. Glob. Ecol. Biogeogr. 19(5), 589–606 (2010). Google Scholar  Soleimani, T., Hermesch, S. & Gilbert, H. Economic and environmental assessments of combined genetics and nutrition optimization strategies to improve the efficiency of sustainable pork production. J. Anim. Sci….

Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421–427 (2014). PubMed Central  Article  CAS  Google Scholar  Visscher, P. M. et al. 10 years of GWAS discovery: biology, function, and translation. Am. J. Hum. Genet. 101, 5–22 (2017). CAS  PubMed  PubMed Central …

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…

Sampson, J. N. et al. Analysis of heritability and shared heritability based on genome-wide association studies for thirteen cancer types. J. Natl Cancer Inst. 107, djv279 (2015). PubMed  PubMed Central  Article  CAS  Google Scholar  Bosse, Y. & Amos, C. I. A decade of GWAS results in lung cancer. Cancer Epidemiol….

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…

Cooper, G. S., Bynum, M. L. K. & Somers, E. C. Recent insights in the epidemiology of autoimmune diseases: improved prevalence estimates and understanding of clustering of diseases. J. Autoimmun. 33, 197–207 (2009). PubMed  PubMed Central  Google Scholar  El-Gabalawy, H., Guenther, L. C. & Bernstein, C. N. Epidemiology of immune-mediated…

What software to use for GWAS with repeated longitudinal quantitative phenotype data? 0 I have quantitative data that has been collected at 4 different time points. Before treatment, 1 month after, 1 year after and 2 year after. I have generated Linear Mixed Models in R to obtain the residuals….

1. Wang, J. & Jia, H. Metagenome-wide association studies: fine-mining the microbiome. Nat. Rev. Microbiol. 14, 508–522 (2016). CAS  PubMed  Google Scholar  2. Moschen, A. R. et al. Lipocalin 2 protects from inflammation and tumorigenesis associated with gut microbiota alterations. Cell Host Microbe 19, 455–469 (2016). CAS  PubMed  Google Scholar …

Reference panel data to be used for GCTA-COJO 0 I performed a genome-wide meta-analysis based on summary statistics from the four cohorts to identify significant loci. Next, I would like to perform a conditional analysis using GCTA-COJO to search for SNPs independent of significant lead SNPs. I know that GCTA…

How long does it take to carry out the GWAS workflow? 0 Including these steps: 1) raw data format transformation for five companies 2) update positions for all SNPs to hg37 version 3) Quality control within companies 4) Pre-phasing (SHAPEIT2) and imputation (IMPUTE2) for all SNPs of each company 5)…

Understanding Conditional analysis 1 Hello, I’m new to data analysis and I’m having some trouble understanding the process and need help with a few questions. I am running a conditional analysis on chromosome 19 in relation to Alzheimer’s disease, I understand that conditional analysis tests whether SNPs have association independent…

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…