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minimac2: faster genotype imputation

Christian Fuchsberger, Gonçalo R. Abecasis, David A. Hinds
2014 Bioinformatics  
Based on our computer simulations (Table 1) , we expect substantial gains in imputation accuracy (measured as the r 2 between imputed genotypes and the true simulated genotypes) and in association information  ...  locality 4.5Â 13.2Â Vectorization 3.8Â 12.3Â Adaptive precision 1.5Â 5.8Â Overall 18Â 55Â Table 1 . 1 Expected imputation accuracy Reference panel sample size Imputation accuracy (mean r  ... 
doi:10.1093/bioinformatics/btu704 pmid:25338720 pmcid:PMC4341061 fatcat:ee6ksulnu5bi7j76a6i25pqrmi

GAS Power Calculator: web-based power calculator for genetic association studies [article]

Jennifer Li Johnson, Goncalo R Abecasis
2017 bioRxiv   pre-print
Availability: The GAS Power Calculator can be accessed from the web interface at http://csg.sph.umich.edu/abecasis/gas_power_calculator/.  ...  We are also grateful to th Abecasis Lab and our users for their feedback and ideas to improve GAS Powe Calculator.  ... 
doi:10.1101/164343 fatcat:u46jx6vsc5asbku52qje2tzi3m

Using haplotype blocks to map human complex trait loci

Lon R. Cardon, Gonçalo R. Abecasis
2003 Trends in Genetics  
Corresponding author: Lon R. Cardon (lon.cardon@well.ox.ac.uk).  ... 
doi:10.1016/s0168-9525(03)00022-2 pmid:12615007 fatcat:oxwlr2q635e2tmyyhu5jrzeruy

Pedigree tests of transmission disequilibrium

Gonçalo R Abecasis, William OC Cookson, Lon R Cardon
2000 European Journal of Human Genetics  
Then the goodness of fit statistic R 2 -R 2 w =0 (1 -R 2 w =0 )/(K -3) FQTL = is distributed as F with one and K -3 degree of freedom in the absence of linkage disequilibrium.  ...  If a single offspring per family is considered, define R 2 w = 0 as the residual sum of squares when the model is fitted with w = 0 and R 2 as the residual sum of squares when the model is fitted with  ... 
doi:10.1038/sj.ejhg.5200494 pmid:10909856 fatcat:zsagln3objhz3abkcw3e37mjsi

Linkage Disequilibrium: Ancient History Drives the New Genetics

Gonçalo R. Abecasis, Debashis Ghosh, Thomas E. Nichols
2005 Human Heredity  
Specifi cally, knowledge of patterns of linkage disequilibrium in the genome means that carefully selected sets of SNPs [Johnson et al., 2001; Cardon and Abecasis, 2003; Carlson et al., 2004] can provide  ...  demonstration of natural selection, the use of linkage disequilibrium data that has generated the most interest is in the detection of association between common variants and common disease [Cardon and Abecasis  ... 
doi:10.1159/000085226 pmid:15838181 fatcat:kuixdirrhzb6higziwoooanuke

Variance Components Linkage Analysis with Repeated Measurements

Liming Liang, Wei-Min Chen, Pak C. Sham, Gonçalo R. Abecasis
2008 Human Heredity  
An R package is provided to determine optimal number of repeated measures for given measurement error and cost.  ...  Web Resource MERLIN and MERLIN-REGRESS: http://www.sph.umich. edu/csg/abecasis/Merlin/  ...  The R code to help determine the optimal number of repeated measures is available from our website. Precise trade-offs can be obtained by examining figure 2 and the R package.  ... 
doi:10.1159/000194977 pmid:19172083 pmcid:PMC2880721 fatcat:ilgea4xj55dkvluypuri6wbsvm

2014 Curt Stern Award: Adventures in Human Genetics1

Gonçalo R. Abecasis
2015 American Journal of Human Genetics  
doi:10.1016/j.ajhg.2015.02.006 pmid:25748353 pmcid:PMC4375429 fatcat:nzr27vbtxzcd3mwpworiubsx6e

Global Properties and Functional Complexity of Human Gene Regulatory Variation

Daniel J. Gaffney, Gonçalo R. Abecasis
2013 PLoS Genetics  
Identification and functional interpretation of gene regulatory variants is a major focus of modern genomics. The application of genetic mapping to molecular and cellular traits has enabled the detection of regulatory variation on genome-wide scales and revealed an enormous diversity of regulatory architecture in humans and other species. In this review I summarise the insights gained and questions raised by a decade of genetic mapping of gene expression variation. I discuss recent extensions
more » ... this approach using alternative molecular phenotypes that have revealed some of the biological mechanisms that drive gene expression variation between individuals. Finally, I highlight outstanding problems and future directions for development.
doi:10.1371/journal.pgen.1003501 pmid:23737752 pmcid:PMC3667745 fatcat:t7ajtdaszvbsnpg2o6prrybdq4

Optimal sequencing strategies for identifying disease-associated singletons

Sara Rashkin, Goo Jun, Sai Chen, Goncalo R. Abecasis, Guillaume Lettre
2017 PLoS Genetics  
These quantities can be defined as: PðsingletonjcaseÞ ¼ prf =L prf =L þ ð1 À p=LÞf ¼ pr=L pr=L þ ð1 À p=LÞ PðsingleonjcontrolÞ ¼ p=Lðrp=L þ 1 À p=L À rf Þ ð1 À f Þðrp=L þ 1 À p=LÞ where r is relative risk  ... 
doi:10.1371/journal.pgen.1006811 pmid:28640830 pmcid:PMC5501675 fatcat:7lbzzcsxufem3jfxd32rh4wpl4

Unified representation of genetic variants

Adrian Tan, Gonçalo R. Abecasis, Hyun Min Kang
2015 Computer applications in the biosciences : CABIOS  
A genetic variant can be represented in the Variant Call Format (VCF) in multiple different ways. Inconsistent representation of variants between variant callers and analyses will magnify discrepancies between them and complicate variant filtering and duplicate removal. We present a software tool vt normalize that normalizes representation of genetic variants in the VCF. We formally define variant normalization as the consistent representation of genetic variants in an unambiguous and concise
more » ... y and derive a simple general algorithm to enforce it. We demonstrate the inconsistent representation of variants across existing sequence analysis tools and show that our tool facilitates integration of diverse variant types and call sets. Availability and implementation: The source code is available for download at
doi:10.1093/bioinformatics/btv112 pmid:25701572 pmcid:PMC4481842 fatcat:rsoe7ewrgjc5dl2xtawpwjkdm4

Estimating the power of variance component linkage analysis in large pedigrees

Wei-Min Chen, Gonçalo R. Abecasis
2006 Genetic Epidemiology  
., 1999; Cardon and Abecasis, 2000] .  ...  Suppose the size of a sibship is s and the correlation between any two siblings is r. Let J denote a matrix consisting of 1's, and I denote an identity matrix.  ... 
doi:10.1002/gepi.20160 pmid:16685720 fatcat:r73fhh6x3bd6zc2dzxbkvqp2le

In silico method for inferring genotypes in pedigrees

Joshua T Burdick, Wei-Min Chen, Gonçalo R Abecasis, Vivian G Cheung
2006 Nature Genetics  
high-density genotype data for a subset of individuals in a pedigree to infer genotypes for the remaining relatives (see http://genomics.med.upenn. edu/genotypeinference and http:// www.sph.umich.edu/csg/abecasis  ...  Boehnke and R. Spielman for discussion and critical reading of the manuscript. This work was supported by grants from the US National Institutes of Health to G.R.A. and V.G.C.  ... 
doi:10.1038/ng1863 pmid:16921375 pmcid:PMC3005330 fatcat:zwid7tcbhjcades7vmp4cuqjii

Response to Graffelman: Tests of Hardy-Weinberg Equilibrium

David J. Cutler, Gonçalo R. Abecasis
2010 American Journal of Human Genetics  
doi:10.1016/j.ajhg.2010.03.012 pmcid:PMC2869040 fatcat:khwybzldabbq7bbdrdpnrskszi

Family-Based Association Tests for Genomewide Association Scans

Wei-Min Chen, Gonçalo R. Abecasis
2007 American Journal of Human Genetics  
Resources The URLs for data presented herein are as follows: Ghost, http://www.sph.umich.edu/csg/chen/ghost/ (for the Elston-Stewart-based implementation of our method) Merlin, http://www.sph.umich.edu/csg/abecasis  ...  et al. 30 to take advantage of recurring terms in likelihood calculations, and the methods of Abecasis and Wigginton 25 to model linkage disequilibrium within clusters of tightly linked markers.  ...  Thus, for any i and j, we haveĒ(g ) p E(g ) p 2 Pr (G p ij ij ij . is approxi- 2 S C O R E A/A) ϩ Pr (G p A/a) p 2p ϩ 2p(1 Ϫ p) p 2p Q E(y ) i i statistic should provide a useful and computationally ef-SCORE  ... 
doi:10.1086/521580 pmid:17924335 pmcid:PMC2265659 fatcat:52df3q2ctbcg5hqd6yatytljf4

Optimal designs for two-stage genome-wide association studies

Andrew D. Skol, Laura J. Scott, Gonçalo R. Abecasis, Michael Boehnke
2007 Genetic Epidemiology  
We have developed an interactive power calculator CaTS (www.sph.umich.edu/csg/abecasis/CaTS/) for two-stage GWA studies which implements these calculations and allows investigators to calculate power,  ...  If we define R E as the cost ratio estimated at design time and R A as the actual cost ratio when the study is carried out, then inefficiency due to misspecifying R (R E 6 ¼R A ) can be quantified as the  ...  Our tool is freely available at www.sph.umich.edu/csg/ abecasis/CaTS/. then the optimal two-stage design would use p samples 5 .565, p markers 5 .010, and cost 62.6% that of the one-stage study design.  ... 
doi:10.1002/gepi.20240 pmid:17549752 fatcat:t5t6ynvhgfdetmrghlgapqippu
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