Peter Kraft

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint Accounting for haplotype uncertainty in matched association studies: a comparison of simple and flexible techniques
    Peter Kraft
    Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
    Genet Epidemiol 28:261-72. 2005
  2. pmc A family-based test for correlation between gene expression and trait values
    Peter Kraft
    Department of Biostatistics, University of California at Los Angeles, Los Angeles, CA 90095 1772, USA
    Am J Hum Genet 72:1323-30. 2003
  3. ncbi request reprint Group 6: Pleiotropy and multivariate analysis
    Peter Kraft
    Department of Biostatistics, University of California at Los Angeles, 90095 1772, USA
    Genet Epidemiol 25:S50-6. 2003
  4. pmc Improved ancestry inference using weights from external reference panels
    Chia Yen Chen
    Department of Epidemiology, Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
    Bioinformatics 29:1399-406. 2013
  5. pmc A comprehensive analysis of common IGF1, IGFBP1 and IGFBP3 genetic variation with prospective IGF-I and IGFBP-3 blood levels and prostate cancer risk among Caucasians
    Fredrick R Schumacher
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
    Hum Mol Genet 19:3089-101. 2010
  6. 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
  7. pmc Artifact due to differential error when cases and controls are imputed from different platforms
    Jennifer A Sinnott
    Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
    Hum Genet 131:111-9. 2012
  8. ncbi request reprint CYP17 genetic variation and risk of breast and prostate cancer from the National Cancer Institute Breast and Prostate Cancer Cohort Consortium (BPC3)
    Veronica Wendy Setiawan
    Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033, USA
    Cancer Epidemiol Biomarkers Prev 16:2237-46. 2007
  9. ncbi request reprint The genetics of gene expression and gene mapping
    Peter Kraft
    Department of Biostatistics, UCLA School of Public Health, Box 951772 51 236C CHS, Los Angeles, CA 90095 1772, USA
    Trends Biotechnol 21:377-8. 2003
  10. pmc Analysis of case-control association studies with known risk variants
    Noah Zaitlen
    Department of Epidemiology, Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
    Bioinformatics 28:1729-37. 2012

Detail Information

Publications50

  1. ncbi request reprint Accounting for haplotype uncertainty in matched association studies: a comparison of simple and flexible techniques
    Peter Kraft
    Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
    Genet Epidemiol 28:261-72. 2005
    ..An application to progesterone-receptor haplotypes and endometrial cancer further illustrates that the performance of all these methods depends on how well the observed haplotypes "tag" the unobserved causal variant...
  2. pmc A family-based test for correlation between gene expression and trait values
    Peter Kraft
    Department of Biostatistics, University of California at Los Angeles, Los Angeles, CA 90095 1772, USA
    Am J Hum Genet 72:1323-30. 2003
    ....
  3. ncbi request reprint Group 6: Pleiotropy and multivariate analysis
    Peter Kraft
    Department of Biostatistics, University of California at Los Angeles, 90095 1772, USA
    Genet Epidemiol 25:S50-6. 2003
    ....
  4. pmc Improved ancestry inference using weights from external reference panels
    Chia Yen Chen
    Department of Epidemiology, Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
    Bioinformatics 29:1399-406. 2013
    ....
  5. pmc A comprehensive analysis of common IGF1, IGFBP1 and IGFBP3 genetic variation with prospective IGF-I and IGFBP-3 blood levels and prostate cancer risk among Caucasians
    Fredrick R Schumacher
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
    Hum Mol Genet 19:3089-101. 2010
    ....
  6. 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...
  7. pmc Artifact due to differential error when cases and controls are imputed from different platforms
    Jennifer A Sinnott
    Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
    Hum Genet 131:111-9. 2012
    ..Every SNP found with genome-wide significance should be validated on another platform to verify that its significance is not an artifact of study design...
  8. ncbi request reprint CYP17 genetic variation and risk of breast and prostate cancer from the National Cancer Institute Breast and Prostate Cancer Cohort Consortium (BPC3)
    Veronica Wendy Setiawan
    Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033, USA
    Cancer Epidemiol Biomarkers Prev 16:2237-46. 2007
    ..Our findings do not support the hypothesis that common germ line variation in CYP17 makes a substantial contribution to postmenopausal breast or prostate cancer susceptibility...
  9. ncbi request reprint The genetics of gene expression and gene mapping
    Peter Kraft
    Department of Biostatistics, UCLA School of Public Health, Box 951772 51 236C CHS, Los Angeles, CA 90095 1772, USA
    Trends Biotechnol 21:377-8. 2003
    ....
  10. pmc Analysis of case-control association studies with known risk variants
    Noah Zaitlen
    Department of Epidemiology, Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
    Bioinformatics 28:1729-37. 2012
    ..Roughly, this method estimates model parameters for each known variant while accounting for the published disease prevalence from the epidemiological literature...
  11. pmc Multiple imputation methods for longitudinal blood pressure measurements from the Framingham Heart Study
    Terri Kang
    Department of Preventive Medicine, University of Southern California, Los Angeles, California, USA
    BMC Genet 4:S43. 2003
    ..This suggests that if missingness patterns are correlated within families, then imputation methods that do not allow this correlation can yield biased results...
  12. pmc Genomic screening in family-based association testing
    Amy Murphy
    Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
    BMC Genet 6:S115. 2005
    ..004) and ttth1-ttth4 (p = 0.004) phenotype(s). We find that both univariate- and multivariate-based screening techniques are powerful tools for detecting an association...
  13. pmc Genome-wide association study identifies new prostate cancer susceptibility loci
    Fredrick R Schumacher
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
    Hum Mol Genet 20:3867-75. 2011
    ..72 and P= 0.61, respectively). Further studies will be needed to assess whether these or other loci are differentially associated with PrCa subtypes...
  14. pmc Powerful SNP-set analysis for case-control genome-wide association studies
    Michael C Wu
    Department of Biostatistics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Am J Hum Genet 86:929-42. 2010
    ..When the correlation is low, both individual-SNP analysis and the SNP-set analysis tend to have low power. We apply SNP-set analysis to analyze the Cancer Genetic Markers of Susceptibility (CGEMS) breast cancer GWAS discovery-phase data...
  15. ncbi request reprint Quantifying bias due to allele misclassification in case-control studies of haplotypes
    Usha S Govindarajulu
    Department of Biostatistics, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
    Genet Epidemiol 30:590-601. 2006
    ..Here, we considered the impact of SNP allele misclassification on haplotype odds ratio estimates from case-control studies of unrelated individuals...
  16. pmc Phenotype harmonization and cross-study collaboration in GWAS consortia: the GENEVA experience
    Siiri N Bennett
    Collaborative Health Studies Coordinating Center, Department of Biostatistics, University of Washington, Seattle, Washington 98115, USA
    Genet Epidemiol 35:159-73. 2011
    ..GENEVA's harmonization efforts and policy of promoting data sharing and collaboration, not only within GENEVA but also with outside collaborations, can provide important guidance to ongoing and new consortia...
  17. ncbi request reprint RHD maternal-fetal genotype incompatibility and schizophrenia: extending the MFG test to include multiple siblings and birth order
    Peter Kraft
    Department of Epidemiology and Biostatistics, Harvard School of Public Health, University of California, Los Angeles, USA
    Eur J Hum Genet 12:192-8. 2004
    ..7, consistent with earlier estimates. Our extension of the MFG test has general application to family-based studies of maternal-genotype and MFG interaction effects...
  18. pmc High concentrations of long interspersed nuclear element sequence distinguish monoallelically expressed genes
    Elena Allen
    Department of Human Genetics, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 100:9940-5. 2003
    ..The sequence characteristics that distinguished the high-LINE-1 category were used to identify more than 1,000 additional genes from the human and mouse genomes as candidate genes for monoallelic expression...
  19. pmc Multivariate variance-components analysis of longitudinal blood pressure measurements from the Framingham Heart Study
    Peter Kraft
    Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
    BMC Genet 4:S55. 2003
    ..2 and 2.4, respectively). In this study, multivariate analysis provides no increase in power; this is likely due to the strong positive correlation in systolic blood pressure measured at different ages...
  20. ncbi request reprint A conditional-on-exchangeable-parental-genotypes likelihood that remains unbiased at the causal locus under multiple-affected-sibling ascertainment
    Peter Kraft
    Genet Epidemiol 29:87-90. 2005
  21. ncbi request reprint Quantification of the power of Hardy-Weinberg equilibrium testing to detect genotyping error
    David G Cox
    Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
    Hum Hered 61:10-4. 2006
    ..While these methods are fairly reliable, they are also costly and time consuming...
  22. doi request reprint Multiple loci identified in a genome-wide association study of prostate cancer
    Gilles Thomas
    Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892, USA
    Nat Genet 40:310-5. 2008
    ..Our findings point to multiple loci with moderate effects associated with susceptibility to prostate cancer that, taken together, in the future may predict high risk in select individuals...
  23. pmc Sequence variants of elaC homolog 2 (Escherichia coli) (ELAC2) gene and susceptibility to prostate cancer in the Health Professionals Follow-Up Study
    Yen Ching Chen
    Department of Medicine, Channing Laboratory, Brigham and Women s Hospital, Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA
    Carcinogenesis 29:999-1004. 2008
    ..43, snp3: OR = 0.69, hap1: OR = 1.47, hap2: OR = 0.72, hap4: OR = 1.51; global P-value for all common haplotypes = 0.11). Common SNPs and haplotypes of ELAC2 were associated with risk of aggressive prostate cancer...
  24. pmc Genetic variation in the HSD17B1 gene and risk of prostate cancer
    Peter Kraft
    Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
    PLoS Genet 1:e68. 2005
    ..These results suggest that the germline variants in HSD17B1 characterized by these htSNPs do not substantially influence the risk of prostate cancer in U.S. and European whites...
  25. pmc Common variants near MC4R are associated with fat mass, weight and risk of obesity
    Ruth J F Loos
    MRC Epidemiology Unit, Addenbrooke s Hospital, Cambridge CB2 0QQ, UK
    Nat Genet 40:768-75. 2008
    ....
  26. pmc IGF-1, IGFBP-1, and IGFBP-3 polymorphisms predict circulating IGF levels but not breast cancer risk: findings from the Breast and Prostate Cancer Cohort Consortium (BPC3)
    Alpa V Patel
    Department of Epidemiology and Surveillance Research, American Cancer Society, Atlanta, Georgia, United States of America
    PLoS ONE 3:e2578. 2008
    ..In summary, the impact of genetic variation in IGF1 and IGFBP3 on circulating IGF levels does not appear to substantially influence breast cancer risk substantially among primarily Caucasian postmenopausal women...
  27. pmc The common obesity variant near MC4R gene is associated with higher intakes of total energy and dietary fat, weight change and diabetes risk in women
    Lu Qi
    Department of Nutrition, Harvard School of Public Health, Boston, MA02115, USA
    Hum Mol Genet 17:3502-8. 2008
    ..In addition, the SNP was related to greater long-term weight change and increased risk of diabetes in women...
  28. pmc Common variants of FUT2 are associated with plasma vitamin B12 levels
    Aditi Hazra
    Department of Epidemiology, Harvard School of Public Health, Program in Molecular and Genetic Epidemiology, Boston, Massachusetts 02115, USA
    Nat Genet 40:1160-2. 2008
    ..This allele is in strong linkage disequilibrium with the FUT2 nonsecretor variant encoding W143X, suggesting a plausible mechanism for altered B(12) absorption and plasma levels...
  29. ncbi request reprint Androgen receptor polymorphisms and endometrial cancer risk
    Monica McGrath
    Department of Epidemiology, Harvard School of Public Health, 181 Longwood Avenue, Boston, MA 02115, USA
    Int J Cancer 118:1261-8. 2006
    ..supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7136/suppmat/index.html)...
  30. pmc Evaluation of markers for CpG island methylator phenotype (CIMP) in colorectal cancer by a large population-based sample
    Shuji Ogino
    Department of Pathology, Brigham and Women s Hospital, Harvard Medical School, Boston, MA 02115, USA
    J Mol Diagn 9:305-14. 2007
    ..In conclusion, a panel of markers including at least RUNX3, CACNA1G, IGF2, and MLH1 can serve as a sensitive and specific marker panel for CIMP-high...
  31. pmc Integrating epidemiology and genetic association: the challenge of gene-environment interaction
    Peter Kraft
    Departments of Epidemiology and Biostatistics, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
    Philos Trans R Soc Lond B Biol Sci 360:1609-16. 2005
    ..Such collaborations also ensure a common approach to measuring variation at a genetic locus, avoiding a problem that has led to difficulties when comparing results from genetic association studies...
  32. pmc Haplotype analysis of common variants in the BRCA1 gene and risk of sporadic breast cancer
    David G Cox
    Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
    Breast Cancer Res 7:R171-5. 2005
    ..Truncation mutations in the BRCA1 gene cause a substantial increase in risk of breast cancer. However, these mutations are rare in the general population and account for little of the overall incidence of sporadic breast cancer...
  33. ncbi request reprint Case-sibling gene-association studies for diseases with variable age at onset
    Peter Kraft
    Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
    Stat Med 23:3697-712. 2004
    ....
  34. ncbi request reprint Issues in association mapping with high-density SNP data and diverse family structures
    Heike Bickeböller
    Department of Genetic Epidemiology, Medical School, Georg August University Gottingen, Humboldtallee 32, D 37073 Gottingen, Germany
    Genet Epidemiol 31:S22-33. 2007
    ..Aside from these successes, the group 3 contributions highlight some interesting areas for future research...
  35. ncbi request reprint Model selection and Bayesian methods in statistical genetics: summary of group 11 contributions to Genetic Analysis Workshop 15
    Michael D Swartz
    Department of Epidemiology, University of Texas M D Anderson Cancer Center, Houston, TX, USA
    Genet Epidemiol 31:S96-102. 2007
    ..These group contributions exhibit the value of framing genetic problems in terms of model selection, and highlight the impact of variable selection for gene mapping...
  36. ncbi request reprint Inhibitor kappaB-alpha haplotype GTC is associated with susceptibility to acute respiratory distress syndrome in Caucasians
    Rihong Zhai
    Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA
    Crit Care Med 35:893-8. 2007
    ..Inhibitor kappaB-alpha (NFKBIA) inhibits NF-kappaB and controls its activities. The objective was to determine whether polymorphisms in NFKBIA gene would be associated with ARDS development...
  37. ncbi request reprint Exploiting gene-environment interaction to detect genetic associations
    Peter Kraft
    Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
    Hum Hered 63:111-9. 2007
    ..This makes the joint test an attractive tool for large-scale association scans where the true gene-environment interaction model is unknown...
  38. ncbi request reprint alpha-Linolenic acid, Delta6-desaturase gene polymorphism, and the risk of nonfatal myocardial infarction
    Ana Baylin
    Department of Community Health, Brown University, Providence, RI, USA
    Am J Clin Nutr 85:554-60. 2007
    ..Delta(6)-Desaturase (FADS2) is the rate-limiting step in the polyunsaturated fatty acid (PUFA) biosynthetic pathway...
  39. ncbi request reprint Genome-wide association study of prostate cancer identifies a second risk locus at 8q24
    Meredith Yeager
    SAIC Frederick, National Cancer Institute NCI Frederick Cancer Research and Development Center, Frederick, Maryland 21702, USA
    Nat Genet 39:645-9. 2007
    ..We estimate that the population attributable risk of the new locus, marked by rs6983267, is higher than the locus marked by rs1447295 (21% versus 9%)...
  40. ncbi request reprint A common 8q24 variant in prostate and breast cancer from a large nested case-control study
    Fredrick R Schumacher
    Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
    Cancer Res 67:2951-6. 2007
    ..590). Although the gene responsible has yet to be identified, the validation of this marker in this large sample of prostate cancer cases leaves little room for the possibility of a false-positive result...
  41. pmc A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer
    David J Hunter
    Channing Laboratory, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Genet 39:870-4. 2007
    ..Our summary results from the GWAS are available online in a form that should speed the identification of additional risk loci...
  42. ncbi request reprint Haplotype analysis of the HSD17B1 gene and risk of breast cancer: a comprehensive approach to multicenter analyses of prospective cohort studies
    Heather Spencer Feigelson
    Department of Epidemiology and Surveillance Research, American Cancer Society, National Home Office, Atlanta, Georgia 30329, USA
    Cancer Res 66:2468-75. 2006
    ..Although the probability that these ER-negative findings are false-positive results is high, these findings were consistent across each cohort examined and warrant further study...
  43. ncbi request reprint Drinking from the fire hose--statistical issues in genomewide association studies
    David J Hunter
    Harvard School of Public Health, Boston, USA
    N Engl J Med 357:436-9. 2007
  44. pmc Re: the use of inferred haplotypes in downstream analysis
    Peter Kraft
    Am J Hum Genet 81:863-5; author reply 865-6. 2007
  45. ncbi request reprint Ala12 variant of the peroxisome proliferator-activated receptor-gamma gene (PPARG) is associated with higher polyunsaturated fat in adipose tissue and attenuates the protective effect of polyunsaturated fat intake on the risk of myocardial infarction
    Edward A Ruiz-Narváez
    Department of Nutrition, Harvard School of Public Health, Boston, MA 02115, USA
    Am J Clin Nutr 86:1238-42. 2007
    ..The Ala12 allele of the peroxisome proliferator-activated receptor-gamma gene (PPARG) decreases the lipolysis of triacylglycerols in adipose tissue, which results in the accumulation of fatty acids in adipocytes...
  46. ncbi request reprint Sequence variants of estrogen receptor beta and risk of prostate cancer in the National Cancer Institute Breast and Prostate Cancer Cohort Consortium
    Yen Ching Chen
    Channing Laboratory, 181 Longwood Avenue, Boston, MA 02115, USA
    Cancer Epidemiol Biomarkers Prev 16:1973-81. 2007
    ..Estrogen receptor beta (ESR2) may play a role in modulating prostate carcinogenesis through the regulation of genes related to cell proliferation and apoptosis...
  47. ncbi request reprint Association between Toll-like receptor gene cluster (TLR6, TLR1, and TLR10) and prostate cancer
    Yen Ching Chen
    Channing Laboratory, Department of Medicine, Brigham and Women s Hospital, Harvard Medical School, Boston, 181 Longwood Avenue, Boston, MA 02115, USA
    Cancer Epidemiol Biomarkers Prev 16:1982-9. 2007
    ..We assessed if genetic polymorphisms of this gene cluster were associated with the risk of prostate cancer in a U.S. population...
  48. pmc Haplotypes of the estrogen receptor beta gene and breast cancer risk
    David G Cox
    Program in Molecular and Genetic Epidemiology, Epidemiology Department, Harvard School of Public Health, Boston, MA, USA
    Int J Cancer 122:387-92. 2008
    ..These data suggest that inherited variants in ESR2 (while possibly conferring a small increased risk of breast cancer) are not associated with appreciable (OR > 1.2) changes in breast cancer risk among Caucasian women...
  49. ncbi request reprint Sequence variants of Toll-like receptor 4 and susceptibility to prostate cancer
    Yen Ching Chen
    Channing Laboratory, Department of Medicine, Brigham and Women s Hospital, Harvard Medical School, Boston, MA, USA
    Cancer Res 65:11771-8. 2005
    ..02). Two common haplotypes were statistically significantly associated with altered risk of prostate cancer. Inherited polymorphisms of the innate immune gene TLR4 are associated with risk of prostate cancer...
  50. pmc Heterogeneity of breast cancer associations with five susceptibility loci by clinical and pathological characteristics
    Montserrat Garcia-Closas
    Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Marylan, United States of America
    PLoS Genet 4:e1000054. 2008
    ..Understanding the etiologic heterogeneity of breast cancer may ultimately result in improvements in prevention, early detection, and treatment...