Using Prior Information from the Medical Literature in GWAS of Oral Cancer Identifies Novel Susceptibility Variant on Chromosome 4-the AdAPT Method

被引：14

作者：

Johansson, Mattias ^{[1
]}

Roberts, Angus ^{[2
]}

Chen, Dan ^{[1
]}

Li, Yaoyong ^{[3
]}

Delahaye-Sourdeix, Manon ^{[1
]}

Aswani, Niraj ^{[2
]}

Greenwood, Mark A. ^{[2
]}

Benhamou, Simone ^{[4
,5
]}

Lagiou, Pagona ^{[6
]}

Holcatova, Ivana ^{[7
]}

Richiardi, Lorenzo ^{[8
]}

Kjaerheim, Kristina ^{[9
]}

Agudo, Antonio ^{[10
]}

Castellsague, Xavier ^{[10
,11
]}

Macfarlane, Tatiana V. ^{[12
]}

Barzan, Luigi ^{[13
]}

Canova, Cristina ^{[14
,15
]}

Thakker, Nalin S. ^{[16
]}

Conway, David I. ^{[17
]}

Znaor, Ariana ^{[18
]}

Healy, Claire M. ^{[19
]}

Ahrens, Wolfgang ^{[20
,21
]}

Zaridze, David ^{[22
]}

Szeszenia-Dabrowska, Neonilia ^{[23
]}

Lissowska, Jolanta ^{[24
,25
]}

Fabianova, Eleonora ^{[26
]}

Mates, Ioan Nicolae ^{[27
]}

Bencko, Vladimir ^{[7
]}

Foretova, Lenka ^{[28
]}

Janout, Vladimir ^{[29
]}

Curado, Maria Paula ^{[30
,31
]}

Koifman, Sergio ^{[32
]}

Menezes, Ana ^{[33
]}

Wuensch-Filho, Victor ^{[34
]}

Eluf-Neto, Jose ^{[34
]}

Boffetta, Paolo ^{[30
,35
]}

Franceschi, Silvia ^{[1
]}

Herrero, Rolando ^{[36
]}

Fernandez Garrote, Leticia ^{[37
]}

Talamini, Renato ^{[38
]}

Boccia, Stefania ^{[39
,40
]}

Galan, Pilar ^{[41
,42
]}

Vatten, Lars ^{[43
]}

Thomson, Peter ^{[44
]}

Zelenika, Diana ^{[45
]}

Lathrop, Mark ^{[45
,46
]}

Byrnes, Graham ^{[1
]}

Cunningham, Hamish ^{[2
]}

Brennan, Paul ^{[1
]}

Wakefield, Jon ^{[47
,48
]}

机构：

[1] Int Agcy Res Canc IARC, Sect Infect, Lyon, France

[2] Univ Sheffield, Dept Comp Sci, GATE Team, Sheffield S10 2TN, S Yorkshire, England

[3] Univ Manchester, Paterson Inst Canc Res, Manchester, Lancs, England

[4] INSERM, U946, Paris, France

[5] Inst Gustave Roussy, CNRS, UMR8200, Villejuif, France

[6] Univ Athens, Sch Med, Dept Hyg Epidemiol & Med Stat, GR-11527 Athens, Greece

[7] Charles Univ Prague, Inst Hyg & Epidemiol, Fac Med 1, Prague, Czech Republic

[8] Univ Turin, Canc Epidemiol Unit, Turin, Italy

[9] Canc Registry Norway, Oslo, Norway

[10] IDIBELL, Inst Catala Oncol ICO, Lhospitalet De Llobregat, Catalonia, Spain

[11] CIBER Epidemiol & Salud Publ CIBERESP, Madrid, Spain

[12] Univ Aberdeen, Sch Med & Dent, Aberdeen, Scotland

[13] Gen Hosp Pordenone, Pordenone, Italy

[14] Univ Padua, Dept Mol Med, Padua, Italy

[15] Univ London Imperial Coll Sci Technol & Med, MRC HPA Ctr Environm & Hlth Resp Epidemiol & Publ, Natl Heart & Lung Inst, London, England

[16] Univ Manchester, Sch Dent, Manchester, Lancs, England

[17] Univ Glasgow, Sch Dent, Glasgow, Lanark, Scotland

[18] Croatian Natl Inst Publ Hlth, Croatian Natl Canc Registry, Zagreb, Croatia

[19] Trinity Coll Dublin, Sch Dent Sci, Dublin, Ireland

[20] Inst Epidemiol & Prevent Res BIPS, Bremen, Germany

[21] Univ Bremen, Inst Stat, D-28359 Bremen, Germany

[22] Russian Acad Med Sci, Canc Res Ctr, Inst Carcinogenesis, Moscow, Russia

[23] Inst Occupat Med, Dept Epidemiol, Lodz, Poland

[24] M Sklodowska Curie Mem Canc Ctr, Dept Canc Epidemiol & Prevent, Warsaw, Poland

[25] Inst Oncol, Warsaw, Poland

[26] Reg Author Publ Hlth, Banska Bystrica, Slovakia

[27] Univ Med & Pharm Carol Davila, Bucharest, Romania

[28] Masaryk Mem Canc Inst, Dept Canc Epidemiol & Genet, Brno, Czech Republic

[29] Palacky Univ, CR-77147 Olomouc, Czech Republic

[30] Int Prevent Res Inst IPRI, Ecully, France

[31] Hosp Araujo Jorge ACCG, Goiania, Go, Brazil

[32] Fiocruz MS, Natl Sch Publ Hlth, BR-21045900 Rio De Janeiro, Brazil

[33] Univ Fed Pelotas, Pelotas, Brazil

[34] Univ Sao Paulo, Sao Paulo, Brazil

[35] Mt Sinai Sch Med, Tisch Canc Inst, New York, NY USA

[36] Inst Invest Epidemiol, San Jose, Costa Rica

[37] Inst Oncol & Radiobiol, Havana, Cuba

[38] IRCSS, Natl Canc Inst, Aviano, Italy

[39] Univ Cattolica Sacro Cuore, Inst Hyg, Rome, Italy

[40] IRCCS San Raffaele Pisana, Rome, Italy

[41] Univ Paris 13, INSERM, U557, UMR Inserm,INRA,CNAM, Paris, France

[42] CRNH IdF, Bobigny, France

[43] Norwegian Univ Sci & Technol, N-7034 Trondheim, Norway

[44] Newcastle Univ, Sch Dent, Newcastle Upon Tyne NE1 7RU, Tyne & Wear, England

[45] Commissariat Energie Atom, Ctr Natl Genotypage, Inst Genom, Evry, France

[46] Fondat Jean Dausset CEPH, Paris, France

[47] Univ Washington, Dept Biostat, Seattle, WA 98195 USA

[48] Univ Washington, Dept Stat, Seattle, WA 98195 USA

来源：

PLOS ONE | 2012年 / 7卷 / 05期

关键词：

GENOME-WIDE ASSOCIATION; LUNG-CANCER; POOLED ANALYSIS; 15Q25; LOCUS; DISEASES; EUROPE; GENES; RISK;

D O I：

10.1371/journal.pone.0036888

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Background: Genome-wide association studies (GWAS) require large sample sizes to obtain adequate statistical power, but it may be possible to increase the power by incorporating complementary data. In this study we investigated the feasibility of automatically retrieving information from the medical literature and leveraging this information in GWAS. Methods: We developed a method that searches through PubMed abstracts for pre-assigned keywords and key concepts, and uses this information to assign prior probabilities of association for each single nucleotide polymorphism (SNP) with the phenotype of interest - the Adjusting Association Priors with Text (AdAPT) method. Association results from a GWAS can subsequently be ranked in the context of these priors using the Bayes False Discovery Probability (BFDP) framework. We initially tested AdAPT by comparing rankings of known susceptibility alleles in a previous lung cancer GWAS, and subsequently applied it in a two-phase GWAS of oral cancer. Results: Known lung cancer susceptibility SNPs were consistently ranked higher by AdAPT BFDPs than by p-values. In the oral cancer GWAS, we sought to replicate the top five SNPs as ranked by AdAPT BFDPs, of which rs991316, located in the ADH gene region of 4q23, displayed a statistically significant association with oral cancer risk in the replication phase (per-rare-allele log additive p-value [p(trend)] = 2.5 x 10(-3)). The combined OR for having one additional rare allele was 0.83 (95% CI: 0.76-0.90), and this association was independent of previously identified susceptibility SNPs that are associated with overall UADT cancer in this gene region. We also investigated if rs991316 was associated with other cancers of the upper aerodigestive tract (UADT), but no additional association signal was found. Conclusion: This study highlights the potential utility of systematically incorporating prior knowledge from the medical literature in genome-wide analyses using the AdAPT methodology. AdAPT is available online (url: http://services.gate.ac.uk/lld/gwas/service/config).

引用

页数：10

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