Shedding new light on genetic dark matter

Genome Medicine

Volumn 2, Issue 10, 2010, Pages

  Melhem, Nadine ^a   Devlin, Bernie ^a  

^a UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASSOCIATION; DISEASE ASSOCIATION; ENVIRONMENTAL FACTOR; GENE EXPRESSION; GENE INTERACTION; GENETIC RISK; GENETIC VARIABILITY; GENETICS; GENOME; HEREDITY; HERITABILITY; HUMAN; KNOWLEDGE; NOTE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 78751681096     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/gm200     Document Type: Note

References (21)

1. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A, Cho JH, Guttmacher AE, Kong A, Kruglyak L, Mardis E, Rotimi CN, Slatkin M, Valle D, Whittemore AS, Boehnke M, Clark AG, Eichler EE, Gibson G, Haines JL, Mackay TF, McCarroll SA, Visscher PM. Finding the missing heritability of complex diseases. Nature 2009, 461:747-753. 10.1038/nature08494, 2831613, 19812666.
2. McGovern DP, Gardet A, Törkvist L, Goyette P, Essers J, Taylor KD, Neale BM, Ong RT, Lagacé C, Li C, Green T, Stevens CR, Beauchamp C, Fleshner PR, Carlson M, D'Amato M, Halfvarson J, Hibberd ML, Lördal M, Padyukov L, Andriulli A, Colombo E, Latiano A, Palmieri O, Bernard EJ, Deslandres C, Hommes DW, de Jong DJ, Stokkers PC, Weersma RK, et al. Genome-wide association identifies multiple ulcerative colitis susceptibility loci. Nat Genet 2010, 42:332-337. 10.1038/ng.549, 20228799.
3. Imielinski M, Baldassano RN, Griffiths A, Russell RK, Annese V, Dubinsky M, Kugathasan S, Bradfield JP, Walters TD, Sleiman P, Kim CE, Muise A, Wang K, Glessner JT, Saeed S, Zhang H, Frackelton EC, Hou C, Flory JH, Otieno G, Chiavacci RM, Grundmeier R, Castro M, Latiano A, Dallapiccola B, Stempak J, Abrams DJ, Taylor K, McGovern D, et al. Western Regional Alliance for Pediatric IBD Common variants at five new loci associated with early-onset inflammatory bowel disease. Nat Genet 2009, 41:1335-1340. 10.1038/ng.489, 19915574, Western Regional Alliance for Pediatric IBD.
4. Risch N. Linkage strategies for genetically complex traits. I. Multilocus models. Am J Hum Genet 1990, 46:222-228. 1684987, 2301392.
5. Naukkarinen J, Surakka I, Pietiläinen KH, Rissanen A, Salomaa V, Ripatti S, Yki-Järvinen H, van Duijn CM, Wichmann HE, Kaprio J, Taskinen MR, Peltonen L. ENGAGE Consortium: Use of genome-wide expression data to mine the "Gray Zone" of GWA studies leads to novel candidate obesity genes. PLoS Genet 2010, 6:e1000976. 10.1371/journal.pgen.1000976, 2880558, 20532202.
6. Frayling TM, Timpson NJ, Weedon MN, Zeggini E, Freathy RM, Lindgren CM, Perry JR, Elliott KS, Lango H, Rayner NW, Shields B, Harries LW, Barrett JC, Ellard S, Groves CJ, Knight B, Patch AM, Ness AR, Ebrahim S, Lawlor DA, Ring SM, Ben-Shlomo Y, Jarvelin MR, Sovio U, Bennett AJ, Melzer D, Ferrucci L, Loos RJ, Barroso I, Wareham NJ, et al. A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity. Science 2007, 316:889-894. 10.1126/science.1141634, 2646098, 17434869.
7. Wells PS, Anderson JL, Scarvelis DK, Doucette SP, Gagnon F. Factor XIII Val34Leu variant is protective against venous thromboembolism: a HuGE review and meta-analysis. Am J Epidemiol 2006, 164:101-109. 10.1093/aje/kwj179, 16740590.
8. Nicolae DL, Gamazon E, Zhang W, Duan S, Dolan ME, Cox NJ. Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet 2010, 6:e1000888. 10.1371/journal.pgen.1000888, 2848547, 20369019.
9. Wang K, Li M, Bucan M. Pathway-based approaches for analysis of genomewide association studies. Am J Hum Genet 2007, 81:1278-1283.
10. Roeder K, Wasserman L. Genome-wide significance levels and weighted hypothesis testing. Stat Sci 2009, 24:398-413. 10.1214/09-STS289, 2920568, 20711421.
11. Eichler EE, Flint J, Gibson G, Kong A, Leal SM, Moore JH, Nadeau JH. Missing heritability and strategies for finding the underlying causes of complex disease. Nat Rev Genet 2010, 11:446-450. 10.1038/nrg2809, 20479774.
12. Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras JB, Stephens M, Gilad Y, Pritchard JK. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 2010, 464:768-772. 10.1038/nature08872, 20220758.
13. Kong A, Steinthorsdottir V, Masson G, Thorleifsson G, Sulem P, Besenbacher S, Jonasdottir A, Sigurdsson A, Kristinsson KT, Jonasdottir A, Frigge ML, Gylfason A, Olason PI, Gudjonsson SA, Sverrisson S, Stacey SN, Sigurgeirsson B, Benediktsdottir KR, Sigurdsson H, Jonsson T, Benediktsson R, Olafsson JH, Johannsson OT, Hreidarsson AB, Sigurdsson G, Ferguson-Smith AC, Gudbjartsson DF, Thorsteinsdottir U, Stefansson K. DIAGRAM Consortium Parental origin of sequence variants associated with complex diseases. Nature 2009, 462:868-874. 10.1038/nature08625, 20016592, DIAGRAM Consortium.
14. Glessner JT, Wang K, Cai G, Korvatska O, Kim CE, Wood S, Zhang H, Estes A, Brune CW, Bradfield JP, Imielinski M, Frackelton EC, Reichert J, Crawford EL, Munson J, Sleiman PM, Chiavacci R, Annaiah K, Thomas K, Hou C, Glaberson W, Flory J, Otieno F, Garris M, Soorya L, Klei L, Piven J, Meyer KJ, Anagnostou E, Sakurai T, et al. Autism genome-wide copy number variation reveals ubiquitin and neuronal genes. Nature 2009, 459:569-573. 10.1038/nature07953, 2925224, 19404257.
15. Craddock N, Hurles ME, Cardin N, Pearson RD, Plagnol V, Robson S, Vukcevic D, Barnes C, Conrad DF, Giannoulatou E, Holmes C, Marchini JL, Stirrups K, Tobin MD, Wain LV, Yau C, Aerts J, Ahmad T, Andrews TD, Arbury H, Attwood A, Auton A, Ball SG, Balmforth AJ, Barrett JC, Barroso I, Barton A, Bennett AJ, Bhaskar S, et al. Wellcome Trust Case Control Consortium Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature 2010, 464:713-720. 10.1038/nature08979, 2892339, 20360734, Wellcome Trust Case Control Consortium.
16. Cohen JC, Kiss RS, Pertsemlidis A, Marcel YL, McPherson R, Hobbs HH. Multiple rare alleles contribute to low plasma levels of HDL cholesterol. Science 2004, 305:869-872. 10.1126/science.1099870, 15297675.
17. Yang J, Benyamin B, McEvoy BP, Gordon S, Henders AK, Nyholt DR, Madden PA, Heath AC, Martin NG, Montgomery GW, Goddard ME, Visscher PM. Common SNPs explain a large proportion of the heritability for human height. Nat Genet 2010, 42:565-569. 10.1038/ng.608, 20562875.
18. Purcell SM, Wray NR, Stone JL, Visscher PM, O'Donovan MC, Sullivan PF, Sklar P. International Schizophrenia Consortium Common polygenic variation contributes to risk of schizophrenia and bipolar disorder. Nature 2009, 460:748-752. International Schizophrenia Consortium.
19. Park JH, Wacholder S, Gail MH, Peters U, Jacobs KB, Chanock SJ, Chatterjee N. Estimation of effect size distribution from genome-wide association studies and implications for future discoveries. Nat Genet 2010, 42:570-575. 10.1038/ng.610, 20562874.
20. Nadeau JH. Transgenerational genetic effects on phenotypic variation and disease risk. Hum Mol Genet 2009, 18:R202-R210. 10.1093/hmg/ddp366, 2758712, 19808797.
21. Reed LK, Williams S, Springston M, Brown J, Freeman K, DesRoches CE, Sokolowski MB, Gibson G. Genotype-by-diet interactions drive metabolic phenotype variation in Drosophila melanogaster. Genetics 2010, 185:1009-1019. 10.1534/genetics.109.113571, 20385784.