Genomic DNA pooling for whole-genome association scans in complex disease: Empirical demonstration of efficacy in rheumatoid arthritis

Genes and Immunity

Volumn 8, Issue 1, 2007, Pages 57-68

  Steer, S ^a   Abkevich, V ^b   Gutin, A ^b   Cordell, H J ^c   Gendall, K L ^d   Merriman, M E ^d   Rodger, R A ^d   Rowley, K A ^d   Chapman, P ^e   Gow, P ^f   Harrison, A A ^g   Highton, J ^g   Jones, P B B ^h   O'Donnell, J ^e   Stamp, L ^e   Fitzgerald, L ^b   Iliev, D ^b   Kouzmine, A ^b   Tran, T ^b   Skolnick, M H ^b   Timms, K M ^b   Lanchbury, J S ^b   Merriman, T R ^d   more..

^a KING'S COLLEGE LONDON   (United Kingdom)

^b Myriad Genetic Laboratories   (United States)

^c NEWCASTLE UNIVERSITY   (United Kingdom)

^d UNIVERSITY OF OTAGO   (New Zealand)

^e CHRISTCHURCH HOSPITAL   (New Zealand)

^f MIDDLEMORE HOSPITAL   (New Zealand)

^g UNIVERSITY OF OTAGO   (New Zealand)

^h QE Hospital   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; HLA ANTIGEN; MEMBRANE ASSOCIATED GUANYLATE CYCLASE KINASE; MEMBRANE ASSOCIATED GUANYLATE CYCLASE KINASE 3; PROTEIN TYROSINE PHOSPHATASE; PROTEIN TYROSINE PHOSPHATASE 22; UNCLASSIFIED DRUG;

ADULT; ARTICLE; CASE CONTROL STUDY; COHORT ANALYSIS; CONTROLLED STUDY; DNA MICROARRAY; DNA PROBE; EMPIRICAL RESEARCH; FEASIBILITY STUDY; FEMALE; GENE FREQUENCY; GENE IDENTIFICATION; GENE LOCUS; GENETIC ASSOCIATION; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOTYPE; HUMAN; HUMAN CELL; MAJOR CLINICAL STUDY; MALE; NEW ZEALAND; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RHEUMATOID ARTHRITIS; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL SIGNIFICANCE; UNITED KINGDOM;

ARTHRITIS, RHEUMATOID; CASE-CONTROL STUDIES; COHORT STUDIES; DNA; FEMALE; GENETIC PREDISPOSITION TO DISEASE; GENOME, HUMAN; GENOMICS; HLA ANTIGENS; HUMANS; MALE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEIN-TYROSINE-PHOSPHATASE;

EID: 33846509234     PISSN: 14664879     EISSN: 14765470     Source Type: Journal    
DOI: 10.1038/sj.gene.6364359     Document Type: Article

References (48)

1. MacGregor AJ, Snieder H, Rigby AS, Koskenvuo M, Kaprio J, Aho K, Silman AJ. Characterising the quantitative genetic contribution to rheumatoid arthritis using data from twins. Arthritis Rheum 2000; 43: 30-37.
2. Gregersen PK, Silver J, Winchester RJ. The shared epitope hypothesis. An approach to understanding the molecular genetics of susceptibility to rheumatoid arthritis. Arthritis Rheum 1987; 30: 1205-1213.
3. Gregersen PK, Lee HS, Batliwalla F, Begovich AB. PTPN22: Setting thresholds for autoimmunity. Semin Immunol 2006; 18: 214-223.
4. Iwamoto T, Ikari K, Nakamura T, Kuwahara M, Toyama Y, Tomatsu T et al. Association between PADI4 and rheumatoid arthritis: A meta-analysis. Rheumatology 2006; 45: 804-807.
5. Plenge RM, Padyukov L, Remmers EF, Purcell S, Lee AT, Karlson EW et al. Replication of putative candidate-gene associations with rheumatoid arthritis in >4000 samples from North America and Sweden: Association of susceptibility with PTPN22, CTLA4, and PAD14. Am J Hum Genet 2005; 77: 1044-1060.
6. Matsuzaki H, Dong S, Loi H, Di X, Liu G, Hubbell E et al. Genotyping over 100 000 SNPs on a pair of oligonucleotide arrays. Nat Methods 2004; 1: 109-111.
7. Gunderson KL, Steemers FJ, Lee G, Mendoza LG, Chee MS. A genome-wide scalable SNP genotyping assay using microarray technology. Nat Genet 2005; 37: 549-554.
8. Gunderson KL, Kuhn KM, Steemers FJ, Ng P, Murray SS, Shen R. Whole-genome genotyping of haplotype tag single nucleotide polymorphisms. Pharmacogenomics 2006; 7: 641-648.
9. Klein RJ, Zeiss C, Chew EY, Tsai JY, Sackler RS, Haynes C et al. Complement factor H polymorphism in age-related macular degeneration. Science 2005; 308: 385-389.
10. Herbert A, Gerry NP, McQueen MB, Heid IM, Pfeufer A, Illig T et al. A common genetic variant is associated with adult and childhood obesity. Science 2006; 312: 279-283.
11. Smyth DJ, Cooper JD, Bailey R, Field S, Burren O, Smink LJ et al. A genome-wide association study of nonsynonymous SNPs identifies a type 1 diabetes locus in the interferon-induced helicase (IFIH1) region. Nat Genet 2006; 38: 617-619.
12. Zuo Y, Zuo G, Zhao H. Two-stage designs in case-control association analysis. Genetics 2006; 173: 1747-1760.
13. Skol AD, Scott LJ, Abecasis GR, Boehnke M. Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies. Nat Genet 2006; 38: 209-213.
14. Fisher PJ, Turic D, Williams NM, McGuffin P, Asherson P, Ball D et al. DNA pooling identifies QTLs on chromosome 4 for general cognitive ability in children. Hum Mol Genet 1999; 8: 915-922.
15. Bansal A, van den Boom D, Kammerer S, Honisch C, Adam G, Cantor CR et al. Association testing by DNA pooling: An effective initial screen. Proc Natl Acad Sci USA 2002; 99: 16871-16874.
16. Begovich AB, Carlton VE, Honigberg LA, Schrodi SJ, Chokkalingam AP, Alexander HC et al. A missense single-nucleotide polymorphism in a gene encoding a protein tyrosine phosphatase (PTPN22) is associated with rheumatoid arthritis. Am J Hum Genet 2004; 75: 330-337.
17. Spector TD, Reneland RH, Mah S, Valdes AM, Hart DJ, Kammerer S et al. Association between a variation in LRCH1 and knee osteoarthritis. Arthritis Rheum 2006; 54: 524-532.
18. Spinola M, Meyer P, Kammerer S, Falvella FS, Boettger ME, Hoyal CR et al. Association of the PDCD5 locus with lung cancer risk and prognosis in smokers. J Clin Oncol 2006; 24: 1672-1678.
19. Meaburn E, Butcher LM, Schalkwyk LC, Plomin R. Genotyping pooled DNA using 100K SNP microarrays: A step towards genomewide association scans. Nucl Acids Res 2006; 34: E27.
20. Downes K, Barratt BJ, Akan P, Bumpstead SJ, Taylor SD, Clayton DG, Deloukas P. SNP allele frequency estimation in DNA pools and variance components analysis. Biotechniques 2004; 5: 840-845.
21. Carlton VE, Hu X, Chokkalingam AP, Schrodi SJ, Brandon R, Alexander HC et al. PTPN22 genetic variation: Evidence for multiple variants associated with rheumatoid arthritis. Am J Hum Genet 2005; 77: 567-581.
22. Altshuler D, Hirschhorn JN, Klannemark M, Lindgren CM, Vohl MC, Nemesh J et al. The common PPARgamma Pro12Ala polymorphism is associated with decreased risk of type 2 diabetes. Nat Genet 2000; 26: 76-80.
23. Barrett JC, Cardon LR. Evaluating coverage of genome-wide association studies. Nat Genet 2006; 38: 659-662.
24. Moskvina V, Norton N, Williams N, Holmans P, Owen M, O'Donovan M. Streamlined analysis of pooled genotype data in SNP-based association studies. Genet Epidemiol 2005; 28: 273-282.
25. Meaburn E, Butcher LM, Liu L, Fernandes C, Hansen V, Al-Chalabi A et al. Genotyping DNA pools on microarrays: Tackling the QTL problem of large samples and large numbers of SNPs. BMC Genomics 2005; 6: 52-59.
26. Kirov G, Nikolov I, Georgieva L, Moskvina V, Owen MJ, O'Donovan MC. Pooled DNA genotyping on Affymetrix SNP genotyping arrays. BMC Genomics 2006; 7: 27.
27. Wright GJ, Leslie JD, Ariza-McNaughton L, Lewis J. Delta proteins and MAGI proteins: An interaction of Notch ligands with intracellular scaffolding molecules and its significance for zebrafish development. Development 2004; 131: 5659-5669.
28. Ando K, Kanazawa S, Tetsuka T, Ohta S, Jiang X, Tada T et al. Induction of Notch signaling by tumor necrosis factor in rheumatoid synovial fibroblasts. Oncogene 2003; 22: 7796-7803.
29. Arking DE, Pfeufer A, Post W, Kao WHL, Newton-Cheh C, Ikeda M et al. A common genetic variant in the NOS1 regulator NOS1AP modulates cardiac repolarization. Nat Genet 2006; 644: 644-651.
30. Tamiya G, Shinya M, Imanishi T, Ikuta T, Makino S, Okamoto K et al. Whole genome association study of rheumatoid arthritis using 27 039 microsatellites. Hum Mol Genet 2005; 14: 2305-2321.
31. Newton J, Brown MA, Milicic A, Ackerman H, Darke C, Wilson JN et al. The effect of HLA-DR on susceptibility to rheumatoid arthritis is influenced by the associated lymphotoxin alpha-tumor necrosis factor haplotype. Arthritis Rheum 2003; 48: 90-96.
32. Newton JL, Harney SM, Timms AE, Sims AM, Rockett K, Darke C et al. Dissection of class III major histocompatibility complex haplotypes associated with rheumatoid arthritis. Arthritis Rheum 2004; 50: 2122-2129.
33. Jawaheer D, Li W, Graham RR, Chen W, Damle A, Xiao X et al. Dissecting the genetic complexity of the association between human leukocyte antigens and rheumatoid arthritis. Am J Hum Genet 2002; 71: 585-594.
34. Singal DP, Li J, Lei K. Genetics of rheumatoid arthritis (RA): Two separate regions in the major histocompatibility complex contribute to susceptibility to RA. Immunol Lett 1999; 69: 301-306.
35. Zanelli E, Jones G, Pascual M, Eerligh P, van der Slik AR, Zwinderman AH et al. The telomeric part of the HLA region predisposes to rheumatoid arthritis independently of the class II loci. Hum Immunol 2001; 62: 75-84.
36. Dyer PA, Thomson W, Sanders PA, Grennan DM. Are major histocompatibility system class III products independent markers for susceptibility to rheumatoid arthritis? Dis Markers 1986; 4: 151-155.
37. Fielder AH, Ollier W, Lord DK, Burley MW, Silman A, Awad J et al. HLA class III haplotypes in multicase rheumatoid arthritis families. Hum Immunol 1989; 25: 75-85.
38. Okamoto K, Makino S, Yoshikawa Y, Takaki A, Nagatsuka Y, Ota M et al. Identification of I kappa BL as the second major histocompatibility complex-linked susceptibility locus for rheumatoid arthritis. Am J Hum Genet 2003; 72: 303-312.
39. Brintnell W, Zeggini E, Barton A, Thomson W, Eyre S, Hinks A et al. Evidence for a novel rheumatoid arthritis susceptibility locus on chromosome 6p. Arthritis Rheum 2004; 50: 3823-3830.
40. Roeder K, Bacanu SA, Wasserman L, Devlin B. Using linkage genome scans to improve power of association in genome scans. Am J Hum Genet 2006; 78: 243-252.
41. Ehm MG, Nelson MR, Spurr NK. Guidelines for conducting and reporting whole genome/large-scale association studies. Hum Mol Genet 2005; 14: 2485-2488.
42. Arnett FC, Edworthy SM, Bloch DA, McShane DJ, Fries JF, Cooper NS et al. The American Rheumatism Association 1987 revised criteria for the classification of rheumatoid arthritis. Arthritis Rheum 1988; 31: 315-324.
43. Liu WM, Di X, Yang G, Matsuzaki H, Huang J, Mei R et al. Algorithms for large-scale genotyping microarrays. Bioinformatics 2003; 19: 2397-2403.
44. Clayton DG, Walker NM, Smyth DJ, Pask R, Cooper JD, Maier LM et al. Population structure, differential bias and genomic control in a large-scale, case-control association study. Nat Genet 2005; 37: 1243-1246.
45. Simkins HM, Merriman ME, Highton J, Chapman PT, O'Donnell JL, Jones PB et al. Association of the PTPN22 locus with rheumatoid arthritis in a New Zealand Caucasian cohort. Arthritis Rheum 2005; 52: 2222-2225.
46. Conrad DF, Andrews TD, Carter NP, Hurles ME, Pritchard JK. A high-resolution survey of deletion polymorphism in the human genome. Nat Genet 2006; 38: 75-81.
47. Shi YY, He L. SHEsis, a powerful software platform for analyses of linkage disequilibrium, haplotype construction, and genetic association at polymorphic loci. Cell Res 2005; 15: 97-98.
48. Dudbridge F. Pedigree disequilibrium tests for multilocus haplotypes. Genet Epidemiol 2003; 25: 115-121.