116
R. E. Graff et al.
Goring HH, Terwilliger JD, Blangero J (2001) Large upward bias in estimation of locus-specific
effects from genomewide scans. Am J Hum Genet 69:1357–1369
Gorlov IP, Gorlova OY, Sunyaev SR, Spitz MR, Amos CI (2008) Shifting paradigm of association
studies: value of rare single-nucleotide polymorphisms. Am J Hum Genet 82:100–112
Gray R, Wheatley K (1991) How to avoid bias when comparing bone marrow transplantation with
chemotherapy. Bone Marrow Transplant 7(Suppl 3):9–12
Greenwood CM, Rangrej J, Sun L (2007) Optimal selection of markers for validation or replication
from genome-wide association studies. Genet Epidemiol 31:396–407
Guey LT, Kravic J, Melander O et al (2011) Power in the phenotypic extremes: a simulation study
of power in discovery and replication of rare variants. Genet Epidemiol 35:236–246
Gusev A, Ko A, Shi H et al (2016) Integrative approaches for large-scale transcriptome-wide
association studies. Nat Genet 48:245–252
Hahn LW, Ritchie MD, Moore JH (2003) Multifactor dimensionality reduction software for
detecting gene-gene and gene-environment interactions. Bioinformatics 19:376–382
Han B, Eskin E (2011) Random-effects model aimed at discovering associations in meta-analysis
of genome-wide association studies. Am J Hum Genet 88:586–598
Haycock PC, Burgess S, Wade KH, Bowden J, Relton C, Davey SG (2016) Best (but oft-forgotten)
practices: the design, analysis, and interpretation of Mendelian randomization studies. Am J
Clin Nutr 103:965–978
Hindorff LA, Sethupathy P, Junkins HA et al (2009) Potential etiologic and functional implications
of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA
106:9362–9367
Hirschhorn JN, Altshuler D (2002) Once and again-issues surrounding replication in genetic
association studies. J Clin Endocrinol Metab 87:4438–4441
Hirschhorn JN, Lohmueller K, Byrne E, Hirschhorn K (2002) A comprehensive review of genetic
association studies. Genet Med 4:45–61
Ho LA, Lange EM (2010) Using public control genotype data to increase power and decrease cost
of case–control genetic association studies. Hum Genet 128:597–608
Hodges E, Xuan Z, Balija V et al (2007) Genome-wide in situ exon capture for selective
resequencing. Nat Genet 39:1522–1527
Hoffmann TJ, Kvale MN, Hesselson SE et al (2011a) Next generation genome-wide association
tool: design and coverage of a high-throughput European-optimized SNP array. Genomics
98:79–89
Hoffmann TJ, Zhan Y, Kvale MN et al (2011b) 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. Genomics 98:422–430
Hoffmann TJ, Van Den Eeden SK, Sakoda LC et al (2015) A large multiethnic genomewide association study of prostate cancer identifies novel risk variants and substantial ethnic
differences. Cancer Discov 5:878–891
Hoffmann TJ, Passarelli MN, Graff RE et al (2017) Genome-wide association study of prostatespecific antigen levels identifies novel loci independent of prostate cancer. Nat Commun
8:14248
Hong MG, Pawitan Y, Magnusson PK, Prince JA (2009) Strategies and issues in the detection of
pathway enrichment in genome-wide association studies. Hum Genet 126:289–301
Hong J, Lunetta KL, Cupples LA, Dupuis J, Liu CT (2016) Evaluation of a two-stage approach in
trans-ethnic meta-analysis in genome-wide association studies. Genet Epidemiol 40:284–292
Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR (2012) Fast and accurate genotype
imputation in genome-wide association studies through pre-phasing. Nat Genet 44:955–959
Huang BE, Lin DY (2007) Efficient association mapping of quantitative trait loci with selective
genotyping. Am J Hum Genet 80:567–576
Huang L, Li Y, Singleton AB et al (2009) Genotype-imputation accuracy across worldwide human
populations. Am J Hum Genet 84:235–250
Huang QQ, Ritchie SC, Brozynska M, Inouye M (2018) Power, false discovery rate and Winner’s
curse in eQTL studies. Nucleic Acids Res 46:e133
R. E. Graff et al.
Goring HH, Terwilliger JD, Blangero J (2001) Large upward bias in estimation of locus-specific
effects from genomewide scans. Am J Hum Genet 69:1357–1369
Gorlov IP, Gorlova OY, Sunyaev SR, Spitz MR, Amos CI (2008) Shifting paradigm of association
studies: value of rare single-nucleotide polymorphisms. Am J Hum Genet 82:100–112
Gray R, Wheatley K (1991) How to avoid bias when comparing bone marrow transplantation with
chemotherapy. Bone Marrow Transplant 7(Suppl 3):9–12
Greenwood CM, Rangrej J, Sun L (2007) Optimal selection of markers for validation or replication
from genome-wide association studies. Genet Epidemiol 31:396–407
Guey LT, Kravic J, Melander O et al (2011) Power in the phenotypic extremes: a simulation study
of power in discovery and replication of rare variants. Genet Epidemiol 35:236–246
Gusev A, Ko A, Shi H et al (2016) Integrative approaches for large-scale transcriptome-wide
association studies. Nat Genet 48:245–252
Hahn LW, Ritchie MD, Moore JH (2003) Multifactor dimensionality reduction software for
detecting gene-gene and gene-environment interactions. Bioinformatics 19:376–382
Han B, Eskin E (2011) Random-effects model aimed at discovering associations in meta-analysis
of genome-wide association studies. Am J Hum Genet 88:586–598
Haycock PC, Burgess S, Wade KH, Bowden J, Relton C, Davey SG (2016) Best (but oft-forgotten)
practices: the design, analysis, and interpretation of Mendelian randomization studies. Am J
Clin Nutr 103:965–978
Hindorff LA, Sethupathy P, Junkins HA et al (2009) Potential etiologic and functional implications
of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA
106:9362–9367
Hirschhorn JN, Altshuler D (2002) Once and again-issues surrounding replication in genetic
association studies. J Clin Endocrinol Metab 87:4438–4441
Hirschhorn JN, Lohmueller K, Byrne E, Hirschhorn K (2002) A comprehensive review of genetic
association studies. Genet Med 4:45–61
Ho LA, Lange EM (2010) Using public control genotype data to increase power and decrease cost
of case–control genetic association studies. Hum Genet 128:597–608
Hodges E, Xuan Z, Balija V et al (2007) Genome-wide in situ exon capture for selective
resequencing. Nat Genet 39:1522–1527
Hoffmann TJ, Kvale MN, Hesselson SE et al (2011a) Next generation genome-wide association
tool: design and coverage of a high-throughput European-optimized SNP array. Genomics
98:79–89
Hoffmann TJ, Zhan Y, Kvale MN et al (2011b) 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. Genomics 98:422–430
Hoffmann TJ, Van Den Eeden SK, Sakoda LC et al (2015) A large multiethnic genomewide association study of prostate cancer identifies novel risk variants and substantial ethnic
differences. Cancer Discov 5:878–891
Hoffmann TJ, Passarelli MN, Graff RE et al (2017) Genome-wide association study of prostatespecific antigen levels identifies novel loci independent of prostate cancer. Nat Commun
8:14248
Hong MG, Pawitan Y, Magnusson PK, Prince JA (2009) Strategies and issues in the detection of
pathway enrichment in genome-wide association studies. Hum Genet 126:289–301
Hong J, Lunetta KL, Cupples LA, Dupuis J, Liu CT (2016) Evaluation of a two-stage approach in
trans-ethnic meta-analysis in genome-wide association studies. Genet Epidemiol 40:284–292
Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR (2012) Fast and accurate genotype
imputation in genome-wide association studies through pre-phasing. Nat Genet 44:955–959
Huang BE, Lin DY (2007) Efficient association mapping of quantitative trait loci with selective
genotyping. Am J Hum Genet 80:567–576
Huang L, Li Y, Singleton AB et al (2009) Genotype-imputation accuracy across worldwide human
populations. Am J Hum Genet 84:235–250
Huang QQ, Ritchie SC, Brozynska M, Inouye M (2018) Power, false discovery rate and Winner’s
curse in eQTL studies. Nucleic Acids Res 46:e133