Genomes and Genes
Affiliation: Washington University School of Medicine
- Twins, tissue, and time: an assessment of SNPs and CNVsPaul Scheet
Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
Twin Res Hum Genet 15:737-45. 2012..These results suggest that DNA from buccal samples perform as well as DNA from blood samples on the current generation of micro-array technologies...
- Linkage disequilibrium-based quality control for large-scale genetic studiesPaul Scheet
Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America
PLoS Genet 4:e1000147. 2008..Our method is implemented in the software package fastPHASE, available from the Stephens Lab website (http://stephenslab.uchicago.edu/software.html)...
- A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phasePaul Scheet
Department of Statistics, University of Washington, Seattle, 98195 4322, USA
Am J Hum Genet 78:629-44. 2006..The methods described in this article are implemented in a software package, fastPHASE, which is available from the Stephens Lab Web site...
- Diversity of human copy number variation and multicopy genesPeter H Sudmant
Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
Science 330:641-6. 2010..Our approach makes ~1000 genes accessible to genetic studies of disease association...
- Automating sequence-based detection and genotyping of SNPs from diploid samplesMatthew Stephens
Department of Statistics, University of Washington, Seattle, Washington 98195, USA
Nat Genet 38:375-81. 2006..9% genotyping accuracy. This algorithm is implemented in a software package, PolyPhred version 5.0, which is freely available for academic use...
- Genotype, haplotype and copy-number variation in worldwide human populationsMattias Jakobsson
Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
Nature 451:998-1003. 2008..Our results produce new inferences about inter-population variation, support the utility of CNVs in human population-genetic research, and serve as a genomic resource for human-genetic studies in diverse worldwide populations...
- MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypesYun Li
Department of Genetics, Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, USA
Genet Epidemiol 34:816-34. 2010..Finally, we illustrate how association analyses of unobserved variants will benefit from ongoing advances such as larger HapMap reference panels and whole genome shotgun sequencing technologies...
- Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traitsElizabeth K Speliotes
Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, Michigan, United States of America
PLoS Genet 7:e1001324. 2011....
- Interactions of dietary whole-grain intake with fasting glucose- and insulin-related genetic loci in individuals of European descent: a meta-analysis of 14 cohort studiesJennifer A Nettleton
Division of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas Health Sciences Center, Houston, Houston, Texas, USA
Diabetes Care 33:2684-91. 2010..We tested the hypothesis that whole-grain food intake and genetic variation interact to influence concentrations of fasting glucose and insulin...
- A comparison of approaches to account for uncertainty in analysis of imputed genotypesJin Zheng
Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
Genet Epidemiol 35:102-10. 2011..However, for most realistic settings, we find that regressing the phenotype on the estimated allelic or genotypic dosage provides an attractive compromise between accuracy and computational tractability...
- Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputationMatthew Stephens
Department of Statistics, University of Washington, Seattle, WA 98195 4322, USA
Am J Hum Genet 76:449-62. 2005..Our method is implemented in the software package PHASE (v2.1.1), available from the Stephens Lab Web site...
- Genotype-imputation accuracy across worldwide human populationsLucy Huang
Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
Am J Hum Genet 84:235-50. 2009..Our results can serve as a guide for selecting appropriate reference panels for imputation-based GWA analysis in diverse populations...
- Haploscope: a tool for the graphical display of haplotype structure in populationsF Anthony San Lucas
Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
Genet Epidemiol 36:17-21. 2012..Haploscope, which has flexible options for annotation and inspection of haplotypes, is available for download at http://scheet.org/software...
- Nicotinic acetylcholine receptor region on chromosome 15q25 and lung cancer risk among African Americans: a case-control studyChristopher I Amos
Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
J Natl Cancer Inst 102:1199-205. 2010..Thus, among African American persons, multiple loci in the region of chromosome 15q25.1 appear to be strongly associated with lung cancer risk...
- New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes riskJosee Dupuis
Department of Biostatistics, Boston University School of Public Health, Massachusetts, USA
Nat Genet 42:105-16. 2010....
- Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant toolsF Anthony San Lucas
Department of Epidemiology, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
Bioinformatics 28:421-2. 2012..However, building flexible pipelines that support the tracking of variants alongside their samples, while enabling updated annotation and reanalyses, is not a simple task...
- Common variants near MC4R are associated with fat mass, weight and risk of obesityRuth J F Loos
MRC Epidemiology Unit, Addenbrooke s Hospital, Cambridge CB2 0QQ, UK
Nat Genet 40:768-75. 2008....