Gary K Chen

Summary

Affiliation: University of Southern California
Country: USA

Publications

  1. pmc Mendel-GPU: haplotyping and genotype imputation on graphics processing units
    Gary K Chen
    Department of Preventive Medicine, USC, Los Angeles, CA 90089, USA
    Bioinformatics 28:2979-80. 2012
  2. pmc Enhancing the discovery of rare disease variants through hierarchical modeling
    Gary K Chen
    Division of Biostatistics, Department of Preventive Medicine, University of Southern California, 2001 North Soto Street, SSB 202Q, MC 9234, Los Angeles, CA 90089 9234, USA
    BMC Proc 5:S16. 2011
  3. pmc A scalable and portable framework for massively parallel variable selection in genetic association studies
    Gary K Chen
    Division of Biostatistics, Department of Preventive Medicine, Los Angeles, CA 90089, USA
    Bioinformatics 28:719-20. 2012
  4. doi request reprint Using biological knowledge to discover higher order interactions in genetic association studies
    Gary K Chen
    Division of Biostatics, Department of Preventive Medicine, University of Southern California, Los Angeles, California 90089 9601, USA
    Genet Epidemiol 34:863-78. 2010
  5. pmc Characterizing genetic risk at known prostate cancer susceptibility loci in African Americans
    Christopher A Haiman
    Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
    PLoS Genet 7:e1001387. 2011
  6. pmc A genome-wide association study of breast cancer in women of African ancestry
    Fang Chen
    Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
    Hum Genet 132:39-48. 2013
  7. pmc A genome-wide scan for breast cancer risk haplotypes among African American women
    Chi Song
    Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
    PLoS ONE 8:e57298. 2013
  8. pmc The potential for enhancing the power of genetic association studies in African Americans through the reuse of existing genotype data
    Gary K Chen
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California, United States of America
    PLoS Genet 6:e1001096. 2010
  9. pmc A common variant at the TERT-CLPTM1L locus is associated with estrogen receptor-negative breast cancer
    Christopher A Haiman
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, USA
    Nat Genet 43:1210-4. 2011
  10. pmc Precise inference of copy number alterations in tumor samples from SNP arrays
    Gary K Chen
    Department of Preventive Medicine, Zilkha Neurogenetic Institute and Department of Psychiatry, University of Southern California, Los Angeles, CA 90089, USA
    Bioinformatics 29:2964-70. 2013

Detail Information

Publications17

  1. pmc Mendel-GPU: haplotyping and genotype imputation on graphics processing units
    Gary K Chen
    Department of Preventive Medicine, USC, Los Angeles, CA 90089, USA
    Bioinformatics 28:2979-80. 2012
    ..However, the computational demands are so high that they prohibit researchers with limited computational resources from haplotyping large-scale sequence data...
  2. pmc Enhancing the discovery of rare disease variants through hierarchical modeling
    Gary K Chen
    Division of Biostatistics, Department of Preventive Medicine, University of Southern California, 2001 North Soto Street, SSB 202Q, MC 9234, Los Angeles, CA 90089 9234, USA
    BMC Proc 5:S16. 2011
    ....
  3. pmc A scalable and portable framework for massively parallel variable selection in genetic association studies
    Gary K Chen
    Division of Biostatistics, Department of Preventive Medicine, Los Angeles, CA 90089, USA
    Bioinformatics 28:719-20. 2012
    ..Open source code and documentation can be found at a Google Code repository under the URL http://bioinformatics.oxfordjournals.org/content/early/2012/01/10/bioinformatics.bts015.abstract...
  4. doi request reprint Using biological knowledge to discover higher order interactions in genetic association studies
    Gary K Chen
    Division of Biostatics, Department of Preventive Medicine, University of Southern California, Los Angeles, California 90089 9601, USA
    Genet Epidemiol 34:863-78. 2010
    ..We also apply the method to data from a GWAS for breast cancer, revealing a set of interactions enriched for the Gene Ontology terms growth, metabolic process, and biological regulation...
  5. pmc Characterizing genetic risk at known prostate cancer susceptibility loci in African Americans
    Christopher A Haiman
    Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
    PLoS Genet 7:e1001387. 2011
    ..Our findings with variants at 8q24 also reinforce the importance of this region as a major risk locus for prostate cancer in men of African ancestry...
  6. pmc A genome-wide association study of breast cancer in women of African ancestry
    Fang Chen
    Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
    Hum Genet 132:39-48. 2013
    ..Identification of novel risk variants for breast cancer in women of African ancestry will demand testing of a substantially larger set of markers from stage 1 in a larger replication sample...
  7. pmc A genome-wide scan for breast cancer risk haplotypes among African American women
    Chi Song
    Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
    PLoS ONE 8:e57298. 2013
    ....
  8. pmc The potential for enhancing the power of genetic association studies in African Americans through the reuse of existing genotype data
    Gary K Chen
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California, United States of America
    PLoS Genet 6:e1001096. 2010
    ....
  9. pmc A common variant at the TERT-CLPTM1L locus is associated with estrogen receptor-negative breast cancer
    Christopher A Haiman
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, USA
    Nat Genet 43:1210-4. 2011
    ..25, P = 1.1 × 10(-9)), particularly in younger women (<50 years of age) (OR = 1.48, P = 1.9 × 10(-9)). Our results identify a genetic locus associated with estrogen receptor negative breast cancer subtypes in multiple populations...
  10. pmc Precise inference of copy number alterations in tumor samples from SNP arrays
    Gary K Chen
    Department of Preventive Medicine, Zilkha Neurogenetic Institute and Department of Psychiatry, University of Southern California, Los Angeles, CA 90089, USA
    Bioinformatics 29:2964-70. 2013
    ....
  11. pmc Genotype imputation via matrix completion
    Eric C Chi
    Department of Human Genetics, University of California, Los Angeles, CA 90095, USA
    Genome Res 23:509-18. 2013
    ..Implementation in a lower-level language such as Fortran or C is apt to further improve computational efficiency...
  12. pmc Fast and flexible simulation of DNA sequence data
    Gary K Chen
    Department of Preventive Medicine, University of Southern California, Los Angeles, California 90033, USA
    Genome Res 19:136-42. 2009
    ..Practical usage of MaCS is demonstrated through a comparison of measures of linkage disequilibrium between generated program output and real genotype data from populations considered to be structured...
  13. pmc Accommodating chromosome inversions in linkage analysis
    Gary K Chen
    Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095 7088, USA
    Am J Hum Genet 79:238-51. 2006
    ..Our expanded cytogenetic analysis of these families further identifies inversion carriers and increases the evidence of linkage...
  14. pmc Fine-mapping of breast cancer susceptibility loci characterizes genetic risk in African Americans
    Fang Chen
    Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
    Hum Mol Genet 20:4491-503. 2011
    ..04, P = 6.1 × 10(-5)]. In this detailed analysis of the known breast cancer risk loci, we have validated and improved upon markers of risk that better characterize their association with breast cancer in women of African ancestry...
  15. pmc Association testing in a linked region using large pedigrees
    Rita M Cantor
    Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095 7088, USA
    Am J Hum Genet 76:538-42. 2005
    ..For the test results to be valid, good estimates of haplotype frequencies must be used in the analysis...
  16. pmc Genome-wide association study of prostate cancer in men of African ancestry identifies a susceptibility locus at 17q21
    Christopher A Haiman
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, California, USA
    Nat Genet 43:570-3. 2011
    ..Further studies are needed to investigate the biological contribution of this allele to prostate cancer risk. These findings emphasize the importance of conducting genome-wide association studies in diverse populations...