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RVTESTS: an efficient and comprehensive tool for rare variant association analysis using sequence data: Table 1

Xiaowei Zhan, Youna Hu, Bingshan Li, Goncalo R. Abecasis, Dajiang J. Liu
2016 Bioinformatics  
To answer this challenge, we developed RVTESTS, which implements a broad set of rare variant association statistics and supports the analysis of autosomal and X-linked variants for both unrelated and related  ...  RVTESTS also provides useful companion features for annotating sequence variants, integrating bioinformatics databases, performing data quality control and sample selection.  ...  Conclusion In summary, RVTESTS is an efficient and comprehensive tool for sequence-based association analyses.  ... 
doi:10.1093/bioinformatics/btw079 pmid:27153000 pmcid:PMC4848408 fatcat:siliq2a2vjbnpcbk7it75ys7wy

Deviation from baseline mutation burden provides powerful and robust rare-variants association test for complex diseases [article]

Lin Jiang, Hui Jiang, Sheng Dai, Ying Chen, Youqiang Song, Clara Sze-Man Tang, Binbin Wang, Maria-Mercedes Garcia-Barcelo, Paul Tam, Stacey S. Cherny, Pak Chung Sham, Miaoxin Li
2020 bioRxiv   pre-print
The proposed approach provides a powerful and robust method to identify rare risk variants for complex diseases.  ...  Here we propose a novel and powerful rare variants association test based on the deviation of the observed mutational burden in a genomic region from a baseline mutation burden predicted by weighted recursive  ...  For the gene-based association test by the three alternative methods [CMC 8 , KBAC 23 , and SKAT 10 ], KGGSeq produced all input of these tools and automatically launched RVTESTS for the analysis in  ... 
doi:10.1101/2020.07.04.186619 fatcat:5gmvkuxmmnckvb5gvdz4fnc5eu

RIC3 variants are not associated with Parkinson's Disease in large European, Latin American, or East Asian cohorts [article]

Kajsa Brolin, Sara Bandres Ciga, Hampton Leonard, Mary B Makarious, Cornelis Blauwendraat, Ignacio Mata, Jia Nee Foo, Lasse Pihlstrom, Maria Swanberg, Ziv Gan-Or, Manuela MX Tan, International Parkinson's Disease Genomics Consortium (IPDGC)
2021 medRxiv   pre-print
We further investigate the role of RIC3 variants in PD in European cohorts using individual-level genotyping data from 14,671 PD patients and 17,667 controls, as well as whole-genome sequencing data from  ...  Rare variants in RIC3 have been suggested to be associated with PD in the Indian population. However, replication studies yielded inconsistent results.  ...  In both datasets, we also assessed the 92 burden of rare variants in RIC3, using RVTESTS version 2.1.0 (Zhan et al., 2016) with standard 93 settings.  ... 
doi:10.1101/2021.06.22.21259012 fatcat:dei6is6b4zd3tj5bn5i4l2t5pq

Robust and rapid algorithms facilitate large-scale whole genome sequencing downstream analysis in an integrative framework

Miaoxin Li, Jiang Li, Mulin Jun Li, Zhicheng Pan, Jacob Shujui Hsu, Dajiang J. Liu, Xiaowei Zhan, Junwen Wang, Youqiang Song, Pak Chung Sham
2017 Nucleic Acids Research  
In the tests with whole genome sequencing data from 1000 Genomes Project, KG-GSeq annotated several thousand more reliable nonsynonymous variants than other widely used tools (e.g.  ...  Whole genome sequencing (WGS) is a promising strategy to unravel variants or genes responsible for human diseases and traits.  ...  ACKNOWLEDGEMENTS The authors acknowledge a number of institutes and projects for their free data sets used in this study: 1000 Genomes Project, Online Mendelian Inheritance in Man, dbNSFP, etc.  ... 
doi:10.1093/nar/gkx019 pmid:28115622 pmcid:PMC5435951 fatcat:7aohk5mghnabbep6cvvim73owa

Another Round of "Clue" to Uncover the Mystery of Complex Traits

Shefali Verma, Marylyn Ritchie
2018 Genes  
an alternative approach, investigating these clues comprehensively to help in elucidating the genetic architecture of complex traits.  ...  Testing of associations in model organisms has helped us in many ways, but the gap between validation of all possible genetic associations and the limited number that have been achieved lies in the potential  ...  Acknowledgments: We would like to thank current and previous members of Ritchie Lab, Sarah Pendergrass,  ... 
doi:10.3390/genes9020061 pmid:29370075 pmcid:PMC5852557 fatcat:ppy4ivjbgzewnj55k5yftceesi

The impact of rare and low-frequency genetic variants in common disease

Lorenzo Bomba, Klaudia Walter, Nicole Soranzo
2017 Genome Biology  
Advances in sequencing technology enable focused explorations on the contribution of low-frequency and rare variants to human traits.  ...  Here we review experimental approaches and current knowledge on the contribution of these genetic variants in complex disease and discuss challenges and opportunities for personalised medicine.  ...  Acknowledgements Lorenzo Bomba acknowledges Open Targets for funding. We acknowledge Jennifer Asimit for critical review of the manuscript.  ... 
doi:10.1186/s13059-017-1212-4 pmid:28449691 pmcid:PMC5408830 fatcat:jda6cwf3erazrewazw2xqit72e

VikNGS: A C++ Variant Integration Kit for Next Generation Sequencing association analysis [article]

Zeynep Baskurt, Scott Mastromatteo, Jiafen Gong, Richard F. Wintle, Stephen W. Scherer, Lisa J. Strug
2018 bioRxiv   pre-print
for vRVS, as well as conventional rare and common variant genotype-based association analysis approaches.  ...  To enable consortium research, the aggregation of several data sets for genetic association analysis of quantitative and binary traits with covariate adjustment is required, and we developed the Variant  ...  Acknowledgements Funding This work has been supported by Genome Canada (12404 to LJS and SWS) and the Natural Sciences and Engineering Council of Canada (2015-03742 to LJS).  ... 
doi:10.1101/504381 fatcat:ppuhbqlofnherohbjjpnntxx2a

Truncating variant burden in high-functioning autism and pleiotropic effects of LRP1 across psychiatric phenotypes

Bàrbara Torrico, Alex D. Shaw, Roberto Mosca, Norma Vivó-Luque, Amaia Hervás, Noèlia Fernàndez-Castillo, Patrick Aloy, Mònica Bayés, Janice M. Fullerton, Bru Cormand, Claudio Toma
2019 Journal of Psychiatry & Neuroscience  
We aim to investigate whether the load of inherited truncating mutations contributes similarly to high-functioning autism, and to characterize genes that harbour de novo variants in high-functioning autism  ...  Previous research has implicated de novo and inherited truncating mutations in autism-spectrum disorder.  ...  We performed analysis of rare variants in LRP1 using the sequencing data of schizophrenia, ASD and control cohorts (Appendix 1, Supplement).  ... 
doi:10.1503/jpn.180184 pmid:31094488 pmcid:PMC6710089 fatcat:y4dhashcjjhwrcsl7cdgs2gwwq

Non-Coding Genetic Analysis Implicates Interleukin 18 Receptor Accessory Protein 3′UTR in Amyotrophic Lateral Sclerosis [article]

Chen Eitan, Elad Barkan, Tsviya Olender, Kristel R. van Eijk, Matthieu Moisse, Sali M. K. Farhan, Aviad Siany, Shu-Ting Hung, Nancy Yacovzada, Johnathan Cooper-Knock, Kevin P. Kenna, Rick A. A. van der Spek (+22 others)
2021 bioRxiv   pre-print
Here, we developed analytical tools to identify rare variants in pre-miRNAs, miRNA recognition elements in 3′UTRs, and miRNA-target networks.  ...  UTR variants significantly enriched in non-ALS genomes, replicate in an independent cohort and associate with a five-fold reduced risk of developing ALS.  ...  RVTESTS: an efficient and comprehensive 606 tool for rare variant association analysis using sequence data. Bioinformatics 32, 1423-1426 (2016). 607 65. Raczy, C., et al.  ... 
doi:10.1101/2021.06.03.446863 fatcat:avbgt4xovzfrja42ggx3vshcym

A versatile toolkit for molecular QTL mapping and meta-analysis at scale [article]

Corbin Quick, Li Guan, Zilin Li, Xihao Li, Rounak Dey, Yaowu Liu, Laura Scott, Xihong Lin
2020 bioRxiv   pre-print
We developed APEX (All-in-one Package for Efficient Xqtl analysis), an efficient toolkit for xQTL mapping and meta-analysis that provides (a) highly optimized linear mixed models to account for relatedness  ...  Larger xQTL sample sizes are critical to help identify causal variants, improve predictive models, and increase power to detect rare associations.  ...  Liu, RVTESTS: an efficient and comprehensive tool for rare 526 variant association analysis using sequence data. Bioinformatics 32, 1423-1426 (2016). 527 39. X.  ... 
doi:10.1101/2020.12.18.423490 fatcat:47hocs23bncshdl546amkn7ndy

Identification of novel rare sequence variation underlying heritable pulmonary arterial hypertension [article]

Stefan Gräf, Matthias Haimel, Marta Bleda, Charaka Hadinnapola, Laura Southgate, Wei Li, Joshua Hodgson, Bin Liu, Richard M. Salmon, Mark Southwood, Rajiv D. Machado, Jennifer M. Martin (+53 others)
2017 bioRxiv   pre-print
Case-control analyses revealed significant overrepresentation of rare variants in novel genes, namely ATP13A3, AQP1 and SOX17, and provided independent validation of a critical role for GDF2 in PAH.  ...  Since the missing heritability likely involves genetic variation confined to small numbers of cases, we performed whole genome sequencing in 1038 PAH index cases and 6385 PAH-negative control subjects.  ...  Acknowledgements We gratefully acknowledge the participation of patients recruited to the UK National Institute of Health Research BioResource -Rare Diseases (NIHR BR-RD) Study.  ... 
doi:10.1101/185272 fatcat:wqjpzywc7ne6jjgoe2mphlifga

Association Study of Over 200,000 Subjects Detects Novel Rare Variants, Functional Elements, and Polygenic Architecture of Prostate Cancer Susceptibility [article]

Nima C Emami, Taylor B Cavazos, Sara R Rashkin, Clinton L Cario, Rebecca E Graff, Caroline G Tai, Joel A Mefford, Linda Kachuri, Eunice Wan, Simon Wong, David S Aaronson, Joseph Presti (+14 others)
2020 bioRxiv   pre-print
Six novel loci were genome-wide significant in our meta-analysis, including two rare variants (minor allele frequency < 0.01, at 3p21.31 and 8p12).  ...  To identify rare variants associated with PrCa susceptibility, and better characterize the mechanisms and cumulative disease risk associated with common risk variants, we analyzed large population-based  ...  RVTESTS: an efficient and comprehensive tool for rare variant association analysis using sequence data. Bioinformatics. 2016;32:1423-6. [ 20 ] 20 Lee S, Teslovich TM, Boehnke M, Lin X.  ... 
doi:10.1101/2020.02.12.929463 fatcat:eqqhysm2i5girikbkuysjxynqm

Whole-exome sequencing in 16,511 individuals reveals a role of the HTRA1 protease and its substrate EGFL8 in brain white matter hyperintensities [article]

Rainer Malik, Nathalie Beaufort, Simon Frerich, Benno Gesierich, Marios K Georgakis, Kristiina Rannikmae, Amy C Ferguson, Christof Haffner, Matthew Traylor, Michael Ehrmann, Cathie LM Sudlow, Martin Dichgans
2021 medRxiv   pre-print
We conducted a comprehensive analysis of WMH burden in the UK Biobank using publicly available whole-exome sequencing data (N=16,511) and found a splice-site variant in GBE1, encoding 1,4-alpha-glucan  ...  White matter hyperintensities (WMH) are among the most common radiological abnormalities in the ageing population and an established risk factor for stroke and dementia.  ...  , whole-exome sequencing (WES) data.  ... 
doi:10.1101/2021.03.26.21253954 fatcat:sqf6fddnrzgzpnpha6ayo7ftgm

A genome-wide association study implicates multiple mechanisms influencing raised urinary albumin-creatinine ratio

2019 Human Molecular Genetics  
After excluding variants at the CUBN locus, known to alter ACR via effects on renal absorption, an ACR genetic risk score was associated with a higher risk of hypertension, and less strongly, type 2 diabetes  ...  For some rare genotype combinations at the CUBN locus, most individuals had ACR levels above the microalbuminuria clinical threshold.  ...  Genet., 48, 1279-1283. 25 Zhan, X., Hu, Y., Li, B., Abecasis, G.R. and Liu, D.J. (2016) RVTESTS: an efficient and comprehensive tool for rare variant association analysis using sequence data.  ... 
doi:10.1093/hmg/ddz243 pmid:31630189 pmcid:PMC7246045 fatcat:c4tzc7skgndojm3njklhkfhqxu

Recessive genetic effects on type 2 diabetes-related metabolites in a consanguineous population [article]

Ayşe Demirkan, Jun Liu, Najaf Amin, Jan B van Klinken, Ko Willems van Dijk, Cornelia M. van Duijn
2019 bioRxiv   pre-print
By performing association according to the recessive genetic model within these selected regions, we identified and replicated two intronic variants: rs6759814 located in KCNH7 associated with valine and  ...  Additionally, we identified a rare intronic SNV in TBR1 for which the homozygous individuals were enriched for obesity.  ...  Liu, 2016 RVTESTS: an efficient and comprehensive tool for rare 373 variant association analysis using sequence data.  ... 
doi:10.1101/619262 fatcat:cip2jq7mmfgdxde24dq5vhr73i
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