High-throughput association testing on DNA pools to identify genetic variants that confer susceptibility to acute myeloid leukemia

Cancer Epidemiology Biomarkers and Prevention

Volumn 13, Issue 5, 2004, Pages 795-800

  Rollinson, Sara ^a   Allan, James M ^a   Law, Graham R ^a   Roddam, Philippa L ^a   Smith, Martyn T ^b   Skibola, Christine ^b   Smith, Alexandra G ^a   Forrest, Matthew S ^b   Sibley, Kathryn ^a   Higuchi, Russell ^c   Germer, Soren ^c   Morgan, Gareth J ^a  

^a UNIVERSITY OF LEEDS   (United Kingdom)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c ROCHE MOLECULAR SYSTEMS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; ARGININE; DNA; GLUTAMINE; GUANINE; ISOLEUCINE; LEUCINE; LYSINE; PRIMER DNA; PROLINE; SERINE; TRYPTOPHAN; VALINE;

ACCURACY; ACUTE GRANULOCYTIC LEUKEMIA; ALLELE; ALLELE SPECIFIC POLYMERASE CHAIN REACTION; APOPTOSIS; ARTICLE; CANCER RISK; CANCER SUSCEPTIBILITY; CELL CYCLE; CYCLIN D1 GENE; DISEASE ASSOCIATION; DNA REPAIR; EVALUATION; FAS GENE; GENE FREQUENCY; GENETIC RISK; GENETIC SCREENING; GENETIC VARIABILITY; GENOTYPE; GSTP1 GENE; HMLH1 GENE; HUMAN; HUMAN TISSUE; LTALPHA GENE; ONCOGENE; P21 GENE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REGULATOR GENE; RISK ASSESSMENT; VALIDATION PROCESS; XRCC1 GENE;

BASE SEQUENCE; CASE-CONTROL STUDIES; CONFIDENCE INTERVALS; FEMALE; GENE FREQUENCY; GENOTYPE; HUMANS; LEUKEMIA, MYELOCYTIC, ACUTE; MALE; MOLECULAR SEQUENCE DATA; ODDS RATIO; REFERENCE VALUES; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS);

EID: 2942542639     PISSN: 10559965     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (37)

1. Mohrenweiser HW, Xi T, Vazquez-Matias J, Jones IM. Identification of 127 amino acid substitution variants in screening 37 DNA repair genes in humans. Cancer Epidemiol Biomark Prev 2002;11:1054-64.
2. Ronen A, Glickman BW. Human DNA repair genes. Environ Mol Mutagen 2001;37:241-83.
3. Germer S, Holland MJ, Higuchi R. High-throughput SNP allele-frequency determination in pooled DNA samples by kinetic PCR. Genome Res 2000;10:258-66.
4. Russell NH. Biology of acute leukemia. Lancet 1997;349:118-22.
5. Rollinson S, Roddam P, Kane E, Roman E, Cartwright R, Jack GJ. Polymorphic variation within the glutathione S-transferase genes and risk of adult acute leukemia. Carcinogenesis 2000;21:43-7.
6. Roddam PL, Rollinson S, Kane E, et al. Poor metabolizers at the cytochrome P450 2D6 and 2C19 loci are at increased risk of developing adult acute leukemia. Pharmacogenetics 2000;10:605-15.
7. Smith MT, Wang Y, Kane E, et al. Low NAD(P)H:quinone oxidoreductase 1 activity is associated with increased risk of acute leukemia in adults. Blood 2001;97:1422-6.
8. Allan JM, Wild CP, Rollinson S, et al. Polymorphism in glutathione S-transferase P1 is associated with susceptibility to chemotherapy-induced leukemia. Proc Natl Acad Sci USA 2001;98:11592-7.
9. Berwick M, Vineis P. Markers of DNA repair and susceptibility to cancer in humans: an epidemiologic review. J Natl Cancer Inst 2000;92:874-97.
10. Carreau M, Gan OI, Liu L, et al. Bone marrow failure in the Fanconi anemia group C mouse model after DNA damage. Blood 1998;91:2737-44.
11. Wu L, Davies SL, Levitt NC, Hickson ID. Potential role for the BLM helicase in recombinational repair via a conserved interaction with RAD51. J Biol Chem 2001;276:19375-81.
12. Canman CE, Lim DS. The role of ATM in DNA damage responses and cancer. Oncogene 1998;17:3301-8.
13. Rosenberg PS, Greene MH, Alter BP. Cancer incidence in persons with Fanconi anemia. Blood 2003;101:822-6.
14. Boultwood J. Ataxia telangiectasia gene mutations in leukemia and lymphoma. J Clin Pathol 2001;54:512-6.
15. van Brabant AJ, Stan R, Ellis NA. DNA helicases, genomic instability, and human genetic disease. Annu Rev Genomics Hum Genet 2000;1:409-59.
16. Kane EV, Roman E, Cartwright R, Parker J, Morgan G. Tobacco and the risk of acute leukemia in adults. Br J Cancer 1999;81:1228-33.
17. Welfare M, Monesola AA, Bassendine MF, Daly AK. Polymorphisms in GSTP1, GSTM1, and GSTT1 and susceptibility to colorectal cancer. Cancer Epidemiol Biomark Prev 1999;8:289-92.
18. Warzocha K, Ribeiro P, Bienvenu J, et al. Genetic polymorphisms in the tumor necrosis factor locus influence non-Hodgkin's lymphoma outcome. Blood 1998;91:3574-81.
19. Betticher DC, Thatcher N, Altermatt HJ, Hoban P, Ryder WD, Heighway J. Alternate splicing produces a novel cyclin D1 transcript. Oncogene 1995;11:1005-11.
20. Dunning AM, Healey CS, Pharoah PD, Teare MD, Ponder BA, Easton DF. A systematic review of genetic polymorphisms and breast cancer risk. Cancer Epidemiol Biomark Prev 1999;8:843-54.
21. Duell EJ, Wiencke JK, Cheng TJ, et al. Polymorphisms in the DNA repair genes XRCC1 and ERCC2 and biomarkers of DNA damage in human blood mononuclear cells. Carcinogenesis 2000;21:965-71.
22. Huang QR, Manolios N. Investigation of the -1377 polymorphism on the Apo-1/Fas promoter in systemic lupus erythematosus patients using allele-specific amplification. Pathology 2000;32:126-30.
23. Ito E, Yanagisawa Y, Iwahashi Y, et al. A core promoter and a frequent single-nucleotide polymorphism of the mismatch repair gene hMLH1. Biochem Biophys Res Commun 1999;256:488-94.
24. Tannergard P, Lipford JR, Kolodner R, Frodin JE, Nordenskjold M, Lindblom A. Mutation screening in the hMLH1 gene in Swedish hereditary nonpolyposis colon cancer families. Cancer Res 1995;55:6092-6.
25. Konishi R, Sakatani S, Kiyokane K, Suzuki K. Polymorphisms of p21 cyclin-dependent kinase inhibitor and malignant skin tumors. J Dermatol Sci 2000;24:177-83.
26. Shen MR, Jones IM, Mohrenweiser H. Nonconservative amino acid substitution variants exist at frequency in DNA repair genes in healthy humans. Cancer Res 1998;58:604-8.
27. Schlesselman JJ. Case-control studies: design, conduct, analysis. University press: Oxford, 1982.
28. Sjalander A, Birgander R, Rannug A, Alexandrie AK, Tornling G, Beckman G. Association between the p21 codon 31 A1 (arg) allele and lung cancer. Hum Hered 1996;46:221-5.
29. Inbar E, Yakir B, Darvasi A. An efficient haplotyping method with DNA pools. Nucleic Acids Res 2002;30:E76.
30. Lunn RM, Langlois RG, Hsieh LL, Thompson CL, Bell DA. XRCC1 polymorphisms: effects on aflatoxin B1-DNA adducts and glycophorin A variant frequency. Cancer Res 1999;59:2557-61.
31. Law GR, Rollinson S, Feltbower R, Allan JM, Roman E, Morgan GJ. Application of DNA pooling to large studies of disease. Stat Med. Submitted for publication, 2003.
32. Sibley K, Rollinson S, Allan JM, et al. Functional FAS promoter polymorphisms are associated with increased risk of acute myeloid leukemia. Cancer Res 2003;63:4327-30.
33. Yang Y, Zhang J, Hoh J, et al. Efficiency of single-nucleotide polymorphism haplotype estimation from pooled DNA. Proc Natl Acad Sci USA 2003;100:7225-30.
34. Wang S, Kidd KK, Zhao H. On the use of DNA pooling to estimate haplotype frequencies. Genet Epidemiol 2003;24:74-82.
35. Weinberg CR, Umbach DM. Using pooled exposure assessment to improve efficiency in case-control studies. Biometrics 1999;55:718-26.
36. Zhou G, Kamahori M, Okano K, Chuan G, Harada K, Kambara H. Quantitative detection of single nucleotide polymorphisms for a pooled sample by a bioluminometric assay coupled with modified primer extension reactions (BAMPER). Nucleic Acids Res 2001;29:E93.
37. Giordano M, Mellai M, Hoogendoorn B, Momigliano-Richiardi P. Determination of SNP allele frequencies in pooled DNAs by primer extension genotyping and denaturing high-performance liquid chromatography. J Biochem Biophys Methods 2001;47:101-10.