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...
- 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...
- 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...
- Rapid and powerful detection of subtle allelic imbalance from exome sequencing data with hapLOHseqF Anthony San Lucas
Department of Translational Molecular Pathology The Graduate School of Biomedical Sciences, The University of Texas Health Science Center at Houston, Houston, TX, USA
Bioinformatics 32:3015-7. 2016..We developed hapLOHseq for the detection of subtle allelic imbalance events from next-generation sequencing data...
- Role of CDKN2C Copy Number in Sporadic Medullary Thyroid CarcinomaElizabeth G Grubbs
1 Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
Thyroid 26:1553-1562. 2016..The objective of this study was to evaluate the association between tumor RET mutation status, CDKN2C loss, and aggressiveness of MTC in a cohort of patients with sporadic disease...
- 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...
- 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...
- 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...
- Haplotype-based profiling of subtle allelic imbalance with SNP arraysSelina Vattathil
Human and Molecular Genetics Program, The University of Texas Graduate School of Biomedical Sciences, Houston, Texas 77030, USA
Genome Res 23:152-8. 2013..We anticipate our approach will offer a new paradigm for genomic profiling of heterogeneous samples...
- Genome-wide analysis of BMI in adolescents and young adults reveals additional insight into the effects of genetic loci over the life courseMariaelisa Graff
Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27517, USA
Hum Mol Genet 22:3597-607. 2013..05). These results suggest that genetic loci for BMI can vary in their effects across the life course, underlying the importance of evaluating BMI at different ages...
- 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....
- Extensive Hidden Genomic Mosaicism Revealed in Normal TissueSelina Vattathil
Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX 77030, USA Electronic address
Am J Hum Genet 98:571-8. 2016..Finally, our results, in which we demonstrate a nearly 3-fold higher rate of clonal mosaicism, suggest that SNP-based population surveys of mosaic structural mutations should be conducted with haplotypes for optimal discovery...
- Preliminary whole-exome sequencing reveals mutations that imply common tumorigenicity pathways in multiple endocrine neoplasia type 1 patientsMinerva Angelica Romero Arenas
Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
Surgery 156:1351-7; discussion 1357-8. 2014..No sequencing has evaluated multiple endocrine neoplasia type 1 (MEN1)-related HPT. We sought to perform whole-exome sequencing in HPT patients to identify somatic mutations and associated biological pathways and tumorigenic networks...
- Cancer in silico drug discovery: a systems biology tool for identifying candidate drugs to target specific molecular tumor subtypesF Anthony San Lucas
The Graduate School of Biomedical Sciences, The University of Texas Health Science Center at Houston, Houston, Texas Department of Epidemiology, The University of Texas M D Anderson Cancer Center, Houston, Texas
Mol Cancer Ther 13:3230-40. 2014..CiDD identified EGFR and proteasome inhibitors, while proposing five cell lines for in vitro testing. CiDD facilitates phenotype-driven, systematic drug discovery based on clinical and molecular data from TCGA...
- Identification of allelic imbalance with a statistical model for subtle genomic mosaicismRui Xia
Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America Division of Biostatistics, The University of Texas School of Public Health, Houston, Texas, United States of America
PLoS Comput Biol 10:e1003765. 2014....
- Clonal evolution in breast cancer revealed by single nucleus genome sequencingYong Wang
The University of Texas MD Anderson Cancer Center, Department of Genetics, Houston, Texas 77030, USA
Nature 512:155-60. 2014..3×), whereas the ER(+) tumour cells did not. These findings have important implications for the diagnosis, therapeutic treatment and evolution of chemoresistance in breast cancer. ..
- 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....