Thomas J Hoffmann

Summary

Affiliation: University of California
Country: USA

Publications

  1. doi request reprint Strategies for Imputing and Analyzing Rare Variants in Association Studies
    Thomas J Hoffmann
    Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94143 USA Electronic address
    Trends Genet 31:556-63. 2015
  2. pmc Genome-wide association and admixture analysis of glaucoma in the Women's Health Initiative
    Thomas J Hoffmann
    Department of Epidemiology and Biostatistics and Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
    Hum Mol Genet 23:6634-43. 2014
  3. pmc Design and coverage of high throughput genotyping arrays optimized for individuals of East Asian, African American, and Latino race/ethnicity using imputation and a novel hybrid SNP selection algorithm
    Thomas J Hoffmann
    Institute for Human Genetics, University of California, San Francisco, CA 94143 0794, USA
    Genomics 98:422-30. 2011
  4. doi request reprint Genotyping Informatics and Quality Control for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort
    Mark N Kvale
    Institute for Human Genetics, University of California, San Francisco, California 94143
    Genetics 200:1051-60. 2015
  5. doi request reprint Automated Assay of Telomere Length Measurement and Informatics for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort
    Kyle Lapham
    Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158 2517
    Genetics 200:1061-72. 2015
  6. pmc Next generation genome-wide association tool: design and coverage of a high-throughput European-optimized SNP array
    Thomas J Hoffmann
    Institute for Human Genetics, University of California, San Francisco 94143 0794, CA, USA
    Genomics 98:79-89. 2011
  7. doi request reprint Characterizing Race/Ethnicity and Genetic Ancestry for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort
    Yambazi Banda
    Institute for Human Genetics, University of California, San Francisco, California 94143 0794
    Genetics 200:1285-95. 2015
  8. doi request reprint A large multiethnic genome-wide association study of prostate cancer identifies novel risk variants and substantial ethnic differences
    Thomas J Hoffmann
    Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California Institute for Human Genetics, University of California, San Francisco, San Francisco, California
    Cancer Discov 5:878-91. 2015
  9. doi request reprint Detecting gene-environment interactions in human birth defects: Study designs and statistical methods
    Caroline G Tai
    Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
    Birth Defects Res A Clin Mol Teratol 103:692-702. 2015
  10. pmc The impact of improved microarray coverage and larger sample sizes on future genome-wide association studies
    Karla J Lindquist
    Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94158 9001, USA
    Genet Epidemiol 37:383-92. 2013

Collaborators

Detail Information

Publications17

  1. doi request reprint Strategies for Imputing and Analyzing Rare Variants in Association Studies
    Thomas J Hoffmann
    Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94143 USA Electronic address
    Trends Genet 31:556-63. 2015
    ....
  2. pmc Genome-wide association and admixture analysis of glaucoma in the Women's Health Initiative
    Thomas J Hoffmann
    Department of Epidemiology and Biostatistics and Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
    Hum Mol Genet 23:6634-43. 2014
    ..These results suggest the possibility of a distinct genetic architecture underlying glaucoma in individuals of African ancestry. ..
  3. pmc Design and coverage of high throughput genotyping arrays optimized for individuals of East Asian, African American, and Latino race/ethnicity using imputation and a novel hybrid SNP selection algorithm
    Thomas J Hoffmann
    Institute for Human Genetics, University of California, San Francisco, CA 94143 0794, USA
    Genomics 98:422-30. 2011
    ..The arrays provide excellent genome-wide coverage and are valuable additions for large-scale GWA studies...
  4. doi request reprint Genotyping Informatics and Quality Control for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort
    Mark N Kvale
    Institute for Human Genetics, University of California, San Francisco, California 94143
    Genetics 200:1051-60. 2015
    ....
  5. doi request reprint Automated Assay of Telomere Length Measurement and Informatics for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort
    Kyle Lapham
    Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158 2517
    Genetics 200:1061-72. 2015
    ..The GERA cohort represents the largest currently available such resource, linked to comprehensive electronic health and genotype data for analysis. ..
  6. pmc Next generation genome-wide association tool: design and coverage of a high-throughput European-optimized SNP array
    Thomas J Hoffmann
    Institute for Human Genetics, University of California, San Francisco 94143 0794, CA, USA
    Genomics 98:79-89. 2011
    ..At steady state, we have produced 462 million genotypes per week for each Axiom system. The new array provides a valuable addition to the repertoire of tools for large scale genome-wide association studies...
  7. doi request reprint Characterizing Race/Ethnicity and Genetic Ancestry for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort
    Yambazi Banda
    Institute for Human Genetics, University of California, San Francisco, California 94143 0794
    Genetics 200:1285-95. 2015
    ....
  8. doi request reprint A large multiethnic genome-wide association study of prostate cancer identifies novel risk variants and substantial ethnic differences
    Thomas J Hoffmann
    Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California Institute for Human Genetics, University of California, San Francisco, San Francisco, California
    Cancer Discov 5:878-91. 2015
    ..6% of disease heritability. The entire GWAS array explained approximately 33.4% of heritability, with a 4.3-fold enrichment within DNaseI hypersensitivity sites (P = 0.004)...
  9. doi request reprint Detecting gene-environment interactions in human birth defects: Study designs and statistical methods
    Caroline G Tai
    Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
    Birth Defects Res A Clin Mol Teratol 103:692-702. 2015
    ..Depending on the research objective, several analytic options exist to estimate G×E effects that use varying combinations of individuals drawn from available triads...
  10. pmc The impact of improved microarray coverage and larger sample sizes on future genome-wide association studies
    Karla J Lindquist
    Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94158 9001, USA
    Genet Epidemiol 37:383-92. 2013
    ..Furthermore, increasing sample size has a much larger impact than increasing coverage on the potential of future GWAS to detect additional SNP-disease associations and heritability...
  11. pmc Polygenic modeling of genome-wide association studies: an application to prostate and breast cancer
    John S Witte
    Institute for Human Genetics, Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
    OMICS 15:393-8. 2011
    ..This supports the further development and application of polygenic models to genomic data...
  12. pmc Imputation of the rare HOXB13 G84E mutation and cancer risk in a large population-based cohort
    Thomas J Hoffmann
    Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
    PLoS Genet 11:e1004930. 2015
    ..8x10-4) and more so in cases diagnosed with multiple cancer types, both those including and not including prostate cancer, strongly suggesting pleiotropic effects. [corrected]...
  13. doi request reprint Replication and heritability of prostate cancer risk variants: impact of population-specific factors
    Victor Virlogeux
    Department of Epidemiology and Biostatistics, University of California, San Francisco, California Department of Biology, Ecole Normale Superieure de Lyon, Lyon, France
    Cancer Epidemiol Biomarkers Prev 24:938-43. 2015
    ..To date, genome-wide association studies have identified 104 SNPs independently associated with prostate cancer in men of European ancestry...
  14. pmc Parallel biocomputing
    Kenneth S Kompass
    Department of Epidemiology and Biostatistics and Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
    Source Code Biol Med 6:4. 2011
    ..abstract:..
  15. pmc Use of principal components to aggregate rare variants in case-control and family-based association studies in the presence of multiple covariates
    Rémi Kazma
    Department of Epidemiology and Biostatistics and Institute for Human Genetics, University of California San Francisco, 1450 Third Street, Box 3110, San Francisco, CA 94148 3110, USA
    BMC Proc 5:S29. 2011
    ..The two methods provide a fast way to analyze simultaneously rare and common variants at the gene level while adjusting for covariates. However, further evaluation of the statistical efficiency of this approach is warranted...
  16. pmc Comprehensive approach to analyzing rare genetic variants
    Thomas J Hoffmann
    Department of Epidemiology and Biostatistics and Institute of Human Genetics, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 5:e13584. 2010
    ..This agnostic approach allows one to efficiently analyze the association between rare variants and disease while avoiding assumptions required by other approaches for grouping such variants...
  17. doi request reprint Evidence of reproductive stoppage in families with autism spectrum disorder: a large, population-based cohort study
    Thomas J Hoffmann
    Institute for Human Genetics, University of California, San Francisco2Department of Epidemiology and Biostatistics, University of California, San Francisco
    JAMA Psychiatry 71:943-51. 2014
    ..Few studies have examined the curtailment of reproduction (ie, stoppage) after the diagnosis of a child with autism spectrum disorder (ASD)...