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Integrative multi-omics analyses to identify the genetic and functional mechanisms underlying ovarian cancer risk regions

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收录情况: ◇ SCIE ◇ 自然指数

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机构: [1]Cedars Sinai Med Ctr, Cedars Sinai Genom Core, Los Angeles, CA 90048 USA [2]Cedars Sinai Med Ctr, Ctr Bioinformat & Funct Genom, Los Angeles, CA 90048 USA [3]Univ Cambridge, Dept Publ Hlth & Primary Care, Ctr Canc Genet Epidemiol, Cambridge, England [4]Univ Virginia, Dept Publ Hlth Sci, Charlottesville, VA USA [5]Univ Cambridge, Dept Oncol, Ctr Canc Genet Epidemiol, Cambridge, England [6]Cedars Sinai Med Ctr, Appl Gen Computat & Translat Core, Los Angeles, CA 90048 USA [7]Dana Farber Canc Inst, Dept Med Oncol, Boston, MA 02115 USA [8]Dana Farber Canc Inst, Ctr Funct Canc Epigenet, Boston, MA 02115 USA [9]Cedars Sinai Med Ctr, Samuel Oschin Comprehens Canc Inst, Womens Canc Program, Los Angeles, CA 90048 USA [10]Cedars Sinai Med Ctr, Dept Obstet & Gynecol, Div Gynecol Oncol, Los Angeles, CA 90048 USA [11]Radboud Univ Nijmegen, Radboud Inst Hlth Sci, Med Ctr, Nijmegen, Netherlands [12]Netherlands Comprehens Canc Org, Utrecht, Netherlands [13]Univ Calif Irvine, Genet Epidemiol Res Inst, Dept Med, Irvine, CA USA [14]N N Alexandrov Res Inst Oncol & Med Radiol, Minsk, BELARUS [15]Agii Anargiri Canc Hosp, Athens, Greece [16]Rutgers Canc Inst New Jersey, Canc Prevent & Control Program, New Brunswick, NJ USA [17]NCI, Dept Hlth & Human Serv, Div Canc Epidemiol & Genet, NIH, Bethesda, MD USA [18]Friedrich Alexander Univ Erlangen Nuremberg, Univ Hosp Erlangen, Dept Gynecol & Obstet, Comprehens Canc Ctr Erlangen EMN, Erlangen, Germany [19]Vanderbilt Univ, Div Epidemiol, Dept Med,Sch Med, Vanderbilt Epidemiol Ctr,Vanderbilt Ingram Canc C, Nashville, TN USA [20]Spanish Natl Canc Res Ctr CNIO, Human Genet Grp, Madrid, Spain [21]Inst Salud Carlos III, Ctr Biomed Network Res Rare Dis CIBERER, Madrid, Spain [22]Univ Hlth Network, Princess Margaret Hosp, Div Gynecol Oncol, Toronto, ON, Canada [23]Haukeland Hosp, Dept Obstet & Gynecol, Bergen, Norway [24]Univ Bergen, Dept Clin Sci, Ctr Canc Biomarkers CCBIO, Bergen, Norway [25]NCI, Div Canc Epidemiol & Genet, Bethesda, MD USA [26]Hannover Med Sch, Dept Radiat Oncol, Hannover, Germany [27]Hannover Med Sch, Gynaecol Res Unit, Hannover, Germany [28]Washington Univ, Div Biol & Biomed Sci, St Louis, MO USA [29]Univ Cambridge, Canc Res UK, Cambridge Inst, Cambridge, England [30]Maria Sklodowska Curie Natl Res Inst Oncol, Dept Pathol & Lab Diagnost, Warsaw, Poland [31]Univ Helsinki, Helsinki Univ Hosp, Dept Pathol, Helsinki, Finland [32]Peter MacCallum Canc Ctr, Div Res, Canc Genet Lab, Melbourne, Vic, Australia [33]Univ Melbourne, Sir Peter MacCallum Dept Oncol, Melbourne, Vic, Australia [34]Roswell Pk Comprehens Canc Ctr, Div Canc Prevent & Populat Sci, Canc Pathol & Prevent, Buffalo, NY USA [35]German Canc Res Ctr, Div Canc Epidemiol, Heidelberg, Germany [36]Univ Med Ctr Hamburg Eppendorf, Univ Canc Ctr Hamburg UCCH, Canc Epidemiol Grp, Hamburg, Germany [37]Tianjin Med Univ, Canc Inst & Hosp, Dept Epidemiol, Tianjin, Peoples R China [38]QIMR Berghofer Med Res Inst, Dept Genet & Computat Biol, Brisbane, Qld, Australia [39]Westmead Inst Med Res, Ctr Canc Res, Sydney, NSW, Australia [40]Westmead Hosp, Dept Gynaecol Oncol, Sydney, NSW, Australia [41]Univ Colorado, Sch Publ Hlth, Epidemiol, Aurora, CO USA [42]Univ Calgary, Community Hlth Sci, Calgary, AB, Canada [43]Univ Sydney, Canc Council NSW, Daffodil Ctr, Sydney, NSW, Australia [44]Univ Utah, Huntsman Canc Inst, Dept Populat Hlth Sci, Salt Lake City, UT USA [45]Dr Horst Schmidt Klin, Dept Gynecol & Gynecol Oncol, HSK, Wiesbaden, Wiesbaden, Germany [46]Evangel Kliniken Essen Mitte KEM, Dept Gynecol & Gynecol Oncol, Essen, Germany [47]Friedrich Schiller Univ, Dept Gynaecol, Jena Univ Hosp, Jena, Germany [48]Univ Southampton, Fac Med, Southampton, Hants, England [49]Imperial Coll London, Div Canc & Ovarian Canc Action Res Ctr, Dept Surg & Canc, London, England [50]Natl Ctr Sci Res Demokritos, Mol Diagnost Lab, INRASTES, Athens, Greece [51]UCL, Inst Clin Trials Methodol, MRC Clin Trials Unit, London, England [52]Canc Council Victoria, Canc Epidemiol Div, Melbourne, Vic, Australia [53]Univ Melbourne, Melbourne Sch Populat & Global Hlth, Ctr Epidemiol & Biostat, Melbourne, Vic, Australia [54]Monash Univ, Sch Clin Sci, Precis Med, Monash Hlth, Clayton, Vic, Australia [55]Cedars Sinai Med Ctr, Canc Prevent & Control Program, Cedars Sinai Canc, Los Angeles, CA USA [56]Pomeranian Med Univ, Dept Genet & Pathol, Int Hereditary Canc Ctr, Szczecin, Poland [57]Univ Southern Calif, Keck Sch Med, Dept Prevent Med, Los Angeles, CA USA [58]Karolinska Inst, Inst Environm Med, Stockholm, Sweden [59]Evangel Kliniken Essen Mitte, Ctr Pathol, Essen, Germany [60]Univ Texas MD Anderson Canc Ctr, Dept Epidemiol, Houston, TX USA [61]Univ Copenhagen, Herlev Hosp, Dept Pathol, Copenhagen, Denmark [62]Univ Copenhagen, Dept Gynaecol, Rigshosp, Copenhagen, Denmark [63]Roswell Pk Comprehens Canc Ctr, Ctr Immunotherapy, Buffalo, NY USA [64]Danish Canc Soc Res Ctr, Dept Virus Lifestyle & Genes, Copenhagen, Denmark [65]Inst Canc Res, Div Genet & Epidemiol, London, England [66]Seoul Natl Univ, Dept Prevent Med, Coll Med, Seoul, South Korea [67]Seoul Natl Univ, Canc Res Inst, Seoul, South Korea [68]Univ Calif Los Angeles, David Geffen Sch Med, Dept Obstet & Gynecol, Los Angeles, CA USA [69]Univ Calif Davis, Dept Pathol & Lab Med, Med Ctr, Sacramento, CA USA [70]Med Univ South Carolina, Hollings Canc Ctr, Charleston, SC USA [71]Univ Sydney, Sydney, NSW, Australia [72]Russian Acad Sci, Inst Biochem & Genet, Ufa Fed Res Ctr, Ufa, Russia [73]Bashkir State Univ, Dept Genet & Fundamental Med, Ufa, Russia [74]FMSS Univ Sherbrooke, Dept Immunol & Cell Biol, Sherbrooke, PQ, Canada [75]Katholieke Univ Leuven, Dept Human Genet, Lab Translat Genet, Leuven, Belgium [76]VIB, VIB Ctr Canc Biol, Leuven, Belgium [77]Mayo Clin, Div Clin Trials & Biostat, Dept Quantitat Hlth Sci, Rochester, MN USA [78]BC Canc, Canc Control Res, Vancouver, BC, Canada [79]Duke Univ Hosp, Dept Surg, Durham, NC USA [80]Aichi Canc Ctr Res Inst, Div Canc Epidemiol & Prevent, Nagoya, Aichi, Japan [81]Nagoya Univ, Grad Sch Med, Div Canc Epidemiol, Nagoya, Aichi, Japan [82]Samuel Lunenfeld Res Inst, Publ Hlth Ontario, Toronto, ON, Canada [83]Imperial Coll London, Dept Surg & Canc, Act Res Ctr, Div Canc & Ovarian Canc, London, England [84]Univ Glasgow, Inst Canc Sci, Glasgow, Lanark, Scotland [85]Brigham andWomens Hosp, Channing Div Network Med, Dept Med, Boston, MA USA [86]Harvard Med Sch, Boston, MA 02115 USA [87]Brigham & Womens Hosp, Obstetr & Gynecol Epidemiol Ctr, Boston, MA USA [88]Harvard T H Chan Sch Publ Hlth, Dept Epidemiol, Boston, MA USA [89]Magee Womens Res Inst, Womens Canc Res Ctr, Pittsburgh, PA USA [90]Hillman Canc Ctr, Pittsburgh, PA USA [91]Univ Pittsburgh, Sch Med, Dept Obstet Gynecol & Reprod Sci, Pittsburgh, PA USA [92]Roswell Pk Comprehens Canc Ctr, Dept Gynecol Oncol, Buffalo, NY USA [93]H Lee Moffitt Canc Ctr & Res Inst, Dept Canc Epidemiol, Tampa, FL USA [94]Roswell Pk Canc Inst, Dept Canc Prevent & Control, Buffalo, NY USA [95]Univ Toronto, Womens Coll Res Inst, Toronto, ON, Canada [96]Univ Melbourne, Dept Clin Pathol, Melbourne, Vic, Australia [97]Univ Chicago Med, Comprehens Canc Ctr, Chicago, IL USA [98]Univ Chicago, Dept Obstet & Gynecol, Chicago, IL USA [99]Lund Univ, Dept Clin Sci, Oncol, Lund, Sweden [100]Univ Utrecht, Julius Ctr Hlth Sci & Primary Care, UMC Utrecht, Utrecht, Netherlands [101]Seoul Natl Univ, Integrated Major Innovat Med Sci, Coll Med, Seoul, South Korea [102]Oregon Hlth & Sci Univ, Dept Obstet & Gynecol, Portland, OR USA [103]Oregon Hlth & Sci Univ, Knight Canc Inst, Portland, OR USA [104]Duke Univ Hosp, Dept Gynecol Oncol, Durham, NC USA [105]Yale Sch Publ Hlth, Chron Dis Epidemiol, New Haven, CT USA [106]Spanish Natl Canc Res Ctr CNIO, Hereditary Endocrine Canc Grp, Madrid, Spain [107]Fred Hutchinson Canc Res Ctr, Div Publ Hlth Sci, Program Epidemiol, Seattle, WA USA [108]Univ Washington, Dept Epidemiol, Seattle, WA USA [109]NIEHS, Epidemiol Branch, NIH, Res Triangle Pk, NC USA [110]Hebei Med Univ, Fourth Hosp, Dept Obstet & Gynaecol, Shijiazhuang, Hebei, Peoples R China [111]Univ Cambridge, Dept Publ Hlth & Primary Care, Cambridge, England [112]Univ Alberta, Div Gynecol Oncol, Dept Obstet & Gynecol, Edmonton, AB, Canada [113]Alberta Hlth Serv, Sect Gynecol Oncol Surg, North Zone, Edmonton, AB, Canada [114]Univ S Florida, Coll Med, Epidemiol Ctr, Tampa, FL USA [115]Inst Canc Res, Div Breast Canc Res, London, England [116]Canc Res Malaysia, Breast Canc Res Programme, Subang Jaya, Selangor, Malaysia [117]Univ Malaya, Dept Surg, Fac Med, Kuala Lumpur, Malaysia [118]Brigham & Womens Hosp, Dept Obstet & Gyneocl, Obstet & Gynecol Epidemiol Ctr, Boston, MA USA [119]Cedars Sinai Med Ctr, Samuel Oschin Comprehens Canc Inst, Canc Prevent & Genet Program, Los Angeles, CA USA [120]Univ Southern Maine, Muskie Sch Publ Serv, Portland, ME USA [121]Univ Oxford, Canc Epidemiol Unit, Oxford, England [122]Leuven Canc Inst, Div Gynecol Oncol, Dept Gynecol & Obstet, Leuven, Belgium [123]Vanderbilt Univ, Med Ctr, Dept Obstet & Gynecol, Dept Biomed Sci,Womens Hlth Res,Div Quantitat Sci, Nashville, TN USA [124]QIMR Berghofer Med Res Inst, Populat Hlth Dept, Brisbane, Qld, Australia [125]NIEHS, Biostat & Computat Biol Branch, NIH, Res Triangle Pk, NC USA [126]Univ Hawaii, Canc Epidemiol Program, Canc Ctr, Honolulu, HI USA [127]Fred Hutchinson Canc Res Ctr, Seattle, WA USA [128]Mayo Clin, Div Computat Biol, Dept Quantitat Hlth Sci, Rochester, MN USA [129]Uppsala Univ, Dept Surg Sci, Uppsala, Sweden [130]Univ Malaya, Med Ctr, Dept Obstet & Gynaecol, Kuala Lumpur, Malaysia [131]Univ Southern Calif, Keck Sch Med, Norris Comprehens Canc Ctr, Dept Prevent Med, Los Angeles, CA USA [132]Hebei Med Univ, Hosp 4, Dept Mol Biol, Shijiazhuang, Hebei, Peoples R China [133]Mayo Clin, Dept Quantitat Hlth Sci, Div Epidemiol, Rochester, MN USA [134]Univ British Columbia, Dept Obstet & Gynecol, Vancouver, BC, Canada [135]BC Canc Res Ctr, Dept Mol Oncol, Vancouver, BC, Canada [136]Univ Michigan, Sch Publ Hlth, Dept Epidemiol, Ann Arbor, MI USA [137]Univ NSWSydney, Sch Womens & Childrens Hlth, Fac Med & Hlth, Sydney, NSW, Australia [138]Univ NSW Sydney, Adult Canc Program, Lowy Canc Res Ctr, Sydney, NSW, Australia [139]TAS Consulting LLC, Portland, OR USA [140]Emory Univ, Rollins Sch Publ Hlth, Dept Epidemiol, Atlanta, GA USA [141]Cedars Sinai Med Ctr, Samuel Oschin Comprehens Canc Inst, Ctr Bioinformat & Funct Biol, Los Angeles, CA USA [142]Univ Bristol, MRC Integrat Epidemiol Unit, Bristol, Avon, England [143]Univ Bristol, Bristol Med Sch, Div Populat Hlth Sci, Sect Translat Epidemiol, Bristol, Avon, England
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摘要:
To identify credible causal risk variants (CCVs) associated with different histotypes of epithelial ovarian cancer (EOC), we performed genome-wide association analysis for 470,825 genotyped and 10,163,797 imputed SNPs in 25,981 EOC cases and 105,724 controls of European origin. We identified five histotype-specific EOC risk regions (p value <5 x 10(-8)) and confirmed previously reported associations for 27 risk regions. Conditional analyses identified an additional 11 signals independent of the primary signal at six risk regions (p value <10(-5)). Fine mapping identified 4,008 CCVs in these regions, of which 1,452 CCVs were located in ovarian cancer-related chromatin marks with significant enrichment in active enhancers, active promoters, and active regions for CCVs from each EOC histotype. Transcriptome-wide association and colocalization analyses across histotypes using tissue-specific and cross-tissue datasets identified 86 candidate susceptibility genes in known EOC risk regions and 32 genes in 23 additional genomic regions that may represent novel EOC risk loci (false discovery rate <0.05). Finally, by integrating genome-wide HiChIP interactome analysis with transcriptome-wide association study (TWAS), variant effect predictor, transcription factor ChIP-seq, and motifbreakR data, we identified candidate gene-CCV interactions at each locus. This included risk loci where TWAS identified one or more candidate susceptibility genes (e.g., HOXD-AS2, HOXD8, and HOXD3 at 2q31) and other loci where no candidate gene was identified (e.g., MYC and PVT1 at 8q24) by TWAS. In summary, this study describes a functional framework and provides a greater understanding of the biological significance of risk alleles and candidate gene targets at EOC susceptibility loci identified by a genome-wide association study.

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大类 | 1 区 生物学
小类 | 1 区 遗传学
最新[2025]版:
大类 | 1 区 生物学
小类 | 1 区 遗传学
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Q1 GENETICS & HEREDITY
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Q1 GENETICS & HEREDITY

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第一作者机构: [3]Univ Cambridge, Dept Publ Hlth & Primary Care, Ctr Canc Genet Epidemiol, Cambridge, England
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通讯机构: [1]Cedars Sinai Med Ctr, Cedars Sinai Genom Core, Los Angeles, CA 90048 USA [2]Cedars Sinai Med Ctr, Ctr Bioinformat & Funct Genom, Los Angeles, CA 90048 USA [3]Univ Cambridge, Dept Publ Hlth & Primary Care, Ctr Canc Genet Epidemiol, Cambridge, England [5]Univ Cambridge, Dept Oncol, Ctr Canc Genet Epidemiol, Cambridge, England
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