Genome-wide association of familial prostate cancer cases identifies evidence for a rare segregating haplotype at 8q24.21

The PRACTICAL consortium; International Consortium for Prostate Cancer Genetics

doi:10.1007/s00439-016-1690-6

Genome-wide association of familial prostate cancer cases identifies evidence for a rare segregating haplotype at 8q24.21

The PRACTICAL consortium, International Consortium for Prostate Cancer Genetics

Urology

Research output: Contribution to journal › Article › peer-review

38 Scopus citations

Abstract

Previous genome-wide association studies (GWAS) of prostate cancer risk focused on cases unselected for family history and have reported over 100 significant associations. The International Consortium for Prostate Cancer Genetics (ICPCG) has now performed a GWAS of 2511 (unrelated) familial prostate cancer cases and 1382 unaffected controls from 12 member sites. All samples were genotyped on the Illumina 5M+exome single nucleotide polymorphism (SNP) platform. The GWAS identified a significant evidence for association for SNPs in six regions previously associated with prostate cancer in population-based cohorts, including 3q26.2, 6q25.3, 8q24.21, 10q11.23, 11q13.3, and 17q12. Of note, SNP rs138042437 (p = 1.7e⁻⁸) at 8q24.21 achieved a large estimated effect size in this cohort (odds ratio = 13.3). 116 previously sampled affected relatives of 62 risk-allele carriers from the GWAS cohort were genotyped for this SNP, identifying 78 additional affected carriers in 62 pedigrees. A test for an excess number of affected carriers among relatives exhibited strong evidence for co-segregation of the variant with disease (p = 8.5e⁻¹¹). The majority (92 %) of risk-allele carriers at rs138042437 had a consistent estimated haplotype spanning approximately 100 kb of 8q24.21 that contained the minor alleles of three rare SNPs (dosage minor allele frequencies <1.7 %), rs183373024 (PRNCR1), previously associated SNP rs188140481, and rs138042437 (CASC19). Strong evidence for co-segregation of a SNP on the haplotype further characterizes the haplotype as a prostate cancer predisposition locus.

Original language	English (US)
Pages (from-to)	923-938
Number of pages	16
Journal	Human Genetics
Volume	135
Issue number	8
DOIs	https://doi.org/10.1007/s00439-016-1690-6
State	Published - Aug 1 2016

Funding

This research was supported by the National Cancer Institute Grant U01 CA 89600 (Support for the ICPCG), and a grant from the Center for Inherited Disease Research supported the genotyping aspect of the study (contract no. HHSN268201200008I; PI Cannon-Albright). The Geneva Coordinating Center at the University of Washington conducted quality control aspects of the study and submitted public facing data to the database of Genotypes and Phenotypes (dbGaP) at the National Center for Biotechnology Information. The authors acknowledge the Keith and Susan Warshaw Fund, the Maurice Warshaw Fund, the C. Scott Watkins Fund, and the Tennity Family Fund. The FHCRC portion of the study was supported by NIH grants R01 CA080122, R01 CA056678, and R01 CA092579, Fred Hutchinson Cancer Research Center and the Prostate Cancer Foundation. Funding for the iCOGS infrastructure (PRACTICAL data) came from the European Community’s Seventh Framework Programme under grant agreement no 223175 (HEALTH-F2-2009-223175) (COGS), Cancer Research UK (C1287/A10118, C1287/A 10710, C12292/A11174, C1281/A12014, C5047/A8384, C5047/A15007, C5047/A10692, C8197/A16565), the National Institutes of Health (CA128978) and Post-Cancer GWAS initiative (1U19 CA148537, 1U19 CA148065, and 1U19 CA148112—the GAME-ON initiative), the Department of Defence (W81XWH-10-1-0341), the Canadian Institutes of Health Research (CIHR) for the CIHR Team in Familial Risks of Breast Cancer, Komen Foundation for the Cure, the Breast Cancer Research Foundation, and the Ovarian Cancer Research Fund. The Biomedical Research Centre at the Institute of Cancer Research (UK) acknowledges the support of the National Institute of Health Research, the Royal Marsden NHS Foundation Trust, and Prostate Cancer UK. This research was supported by the National Cancer Institute Grant U01 CA 89600 (Support for the ICPCG), and a grant from the Center for Inherited Disease Research supported the genotyping aspect of the study (contract no. HHSN268201200008I; PI Cannon-Albright). The Geneva Coordinating Center at the University of Washington conducted quality control aspects of the study and submitted public facing data to the database of Genotypes and Phenotypes (dbGaP) at the National Center for Biotechnology Information. The authors acknowledge the Keith and Susan Warshaw Fund, the Maurice Warshaw Fund, the C. Scott Watkins Fund, and the Tennity Family Fund. The FHCRC portion of the study was supported by NIH grants R01 CA080122, R01 CA056678, and R01 CA092579, Fred Hutchinson Cancer Research Center and the Prostate Cancer Foundation. Funding for the iCOGS infrastructure (PRACTICAL data) came from the European Communityâs Seventh Framework Programme under grant agreement no 223175 (HEALTH-F2-2009-223175) (COGS), Cancer Research UK (C1287/A10118, C1287/A 10710, C12292/A11174, C1281/A12014, C5047/A8384, C5047/A15007, C5047/A10692, C8197/A16565), the National Institutes of Health (CA128978) and Post-Cancer GWAS initiative (1U19 CA148537, 1U19 CA148065, and 1U19 CA148112âthe GAME-ON initiative), the Department of Defence (W81XWH-10-1-0341), the Canadian Institutes of Health Research (CIHR) for the CIHR Team in Familial Risks of Breast Cancer, Komen Foundation for the Cure, the Breast Cancer Research Foundation, and the Ovarian Cancer Research Fund. The Biomedical Research Centre at the Institute of Cancer Research (UK) acknowledges the support of the National Institute of Health Research, the Royal Marsden NHS Foundation Trust, and Prostate Cancer UK.

ASJC Scopus subject areas

Genetics
Genetics(clinical)

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1007/s00439-016-1690-6

Cite this

@article{cac763fc789b43e89f425609f3d76005,

title = "Genome-wide association of familial prostate cancer cases identifies evidence for a rare segregating haplotype at 8q24.21",

abstract = "Previous genome-wide association studies (GWAS) of prostate cancer risk focused on cases unselected for family history and have reported over 100 significant associations. The International Consortium for Prostate Cancer Genetics (ICPCG) has now performed a GWAS of 2511 (unrelated) familial prostate cancer cases and 1382 unaffected controls from 12 member sites. All samples were genotyped on the Illumina 5M+exome single nucleotide polymorphism (SNP) platform. The GWAS identified a significant evidence for association for SNPs in six regions previously associated with prostate cancer in population-based cohorts, including 3q26.2, 6q25.3, 8q24.21, 10q11.23, 11q13.3, and 17q12. Of note, SNP rs138042437 (p = 1.7e−8) at 8q24.21 achieved a large estimated effect size in this cohort (odds ratio = 13.3). 116 previously sampled affected relatives of 62 risk-allele carriers from the GWAS cohort were genotyped for this SNP, identifying 78 additional affected carriers in 62 pedigrees. A test for an excess number of affected carriers among relatives exhibited strong evidence for co-segregation of the variant with disease (p = 8.5e−11). The majority (92 %) of risk-allele carriers at rs138042437 had a consistent estimated haplotype spanning approximately 100 kb of 8q24.21 that contained the minor alleles of three rare SNPs (dosage minor allele frequencies <1.7 %), rs183373024 (PRNCR1), previously associated SNP rs188140481, and rs138042437 (CASC19). Strong evidence for co-segregation of a SNP on the haplotype further characterizes the haplotype as a prostate cancer predisposition locus.",

author = "{The PRACTICAL consortium} and {International Consortium for Prostate Cancer Genetics} and Teerlink, {Craig C.} and Daniel Leongamornlert and Tokhir Dadaev and Alun Thomas and James Farnham and Stephenson, {Robert A.} and Shaun Riska and McDonnell, {Shannon K.} and Schaid, {Daniel J.} and Catalona, {William J.} and Zheng, {S. Lilly} and Cooney, {Kathleen A.} and Ray, {Anna M.} and Zuhlke, {Kimberly A.} and Lange, {Ethan M.} and Giles, {Graham G.} and Southey, {Melissa C.} and Fitzgerald, {Liesel M.} and Antje Rinckleb and Manuel Luedeke and Christiane Maier and Stanford, {Janet L.} and Ostrander, {Elaine A.} and Kaikkonen, {Elina M.} and Csilla Sipeky and Teuvo Tammela and Johanna Schleutker and Wiley, {Kathleen E.} and Isaacs, {Sarah D.} and Walsh, {Patrick C.} and Isaacs, {William B.} and Jianfeng Xu and Geraldine Cancel-Tassin and Olivier Cussenot and Diptasri Mandal and Cecelia Laurie and Cathy Laurie and Thibodeau, {Stephen N.} and Eeles, {Rosalind A.} and Zsofia Kote-Jarai and Lisa Cannon-Albright",

note = "Publisher Copyright: {\textcopyright} 2016, Springer-Verlag Berlin Heidelberg.",

year = "2016",

month = aug,

day = "1",

doi = "10.1007/s00439-016-1690-6",

language = "English (US)",

volume = "135",

pages = "923--938",

journal = "Human Genetics",

issn = "0340-6717",

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number = "8",

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T1 - Genome-wide association of familial prostate cancer cases identifies evidence for a rare segregating haplotype at 8q24.21

AU - The PRACTICAL consortium

AU - International Consortium for Prostate Cancer Genetics

AU - Teerlink, Craig C.

AU - Leongamornlert, Daniel

AU - Dadaev, Tokhir

AU - Thomas, Alun

AU - Farnham, James

AU - Stephenson, Robert A.

AU - Riska, Shaun

AU - McDonnell, Shannon K.

AU - Schaid, Daniel J.

AU - Catalona, William J.

AU - Zheng, S. Lilly

AU - Cooney, Kathleen A.

AU - Ray, Anna M.

AU - Zuhlke, Kimberly A.

AU - Lange, Ethan M.

AU - Giles, Graham G.

AU - Southey, Melissa C.

AU - Fitzgerald, Liesel M.

AU - Rinckleb, Antje

AU - Luedeke, Manuel

AU - Maier, Christiane

AU - Stanford, Janet L.

AU - Ostrander, Elaine A.

AU - Kaikkonen, Elina M.

AU - Sipeky, Csilla

AU - Tammela, Teuvo

AU - Schleutker, Johanna

AU - Wiley, Kathleen E.

AU - Isaacs, Sarah D.

AU - Walsh, Patrick C.

AU - Isaacs, William B.

AU - Xu, Jianfeng

AU - Cancel-Tassin, Geraldine

AU - Cussenot, Olivier

AU - Mandal, Diptasri

AU - Laurie, Cecelia

AU - Laurie, Cathy

AU - Thibodeau, Stephen N.

AU - Eeles, Rosalind A.

AU - Kote-Jarai, Zsofia

AU - Cannon-Albright, Lisa

PY - 2016/8/1

Y1 - 2016/8/1

N2 - Previous genome-wide association studies (GWAS) of prostate cancer risk focused on cases unselected for family history and have reported over 100 significant associations. The International Consortium for Prostate Cancer Genetics (ICPCG) has now performed a GWAS of 2511 (unrelated) familial prostate cancer cases and 1382 unaffected controls from 12 member sites. All samples were genotyped on the Illumina 5M+exome single nucleotide polymorphism (SNP) platform. The GWAS identified a significant evidence for association for SNPs in six regions previously associated with prostate cancer in population-based cohorts, including 3q26.2, 6q25.3, 8q24.21, 10q11.23, 11q13.3, and 17q12. Of note, SNP rs138042437 (p = 1.7e−8) at 8q24.21 achieved a large estimated effect size in this cohort (odds ratio = 13.3). 116 previously sampled affected relatives of 62 risk-allele carriers from the GWAS cohort were genotyped for this SNP, identifying 78 additional affected carriers in 62 pedigrees. A test for an excess number of affected carriers among relatives exhibited strong evidence for co-segregation of the variant with disease (p = 8.5e−11). The majority (92 %) of risk-allele carriers at rs138042437 had a consistent estimated haplotype spanning approximately 100 kb of 8q24.21 that contained the minor alleles of three rare SNPs (dosage minor allele frequencies <1.7 %), rs183373024 (PRNCR1), previously associated SNP rs188140481, and rs138042437 (CASC19). Strong evidence for co-segregation of a SNP on the haplotype further characterizes the haplotype as a prostate cancer predisposition locus.

AB - Previous genome-wide association studies (GWAS) of prostate cancer risk focused on cases unselected for family history and have reported over 100 significant associations. The International Consortium for Prostate Cancer Genetics (ICPCG) has now performed a GWAS of 2511 (unrelated) familial prostate cancer cases and 1382 unaffected controls from 12 member sites. All samples were genotyped on the Illumina 5M+exome single nucleotide polymorphism (SNP) platform. The GWAS identified a significant evidence for association for SNPs in six regions previously associated with prostate cancer in population-based cohorts, including 3q26.2, 6q25.3, 8q24.21, 10q11.23, 11q13.3, and 17q12. Of note, SNP rs138042437 (p = 1.7e−8) at 8q24.21 achieved a large estimated effect size in this cohort (odds ratio = 13.3). 116 previously sampled affected relatives of 62 risk-allele carriers from the GWAS cohort were genotyped for this SNP, identifying 78 additional affected carriers in 62 pedigrees. A test for an excess number of affected carriers among relatives exhibited strong evidence for co-segregation of the variant with disease (p = 8.5e−11). The majority (92 %) of risk-allele carriers at rs138042437 had a consistent estimated haplotype spanning approximately 100 kb of 8q24.21 that contained the minor alleles of three rare SNPs (dosage minor allele frequencies <1.7 %), rs183373024 (PRNCR1), previously associated SNP rs188140481, and rs138042437 (CASC19). Strong evidence for co-segregation of a SNP on the haplotype further characterizes the haplotype as a prostate cancer predisposition locus.

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DO - 10.1007/s00439-016-1690-6

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SN - 0340-6717

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JO - Human Genetics

JF - Human Genetics

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ER -

Genome-wide association of familial prostate cancer cases identifies evidence for a rare segregating haplotype at 8q24.21

Abstract

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ASJC Scopus subject areas

UN SDGs

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