Identification of susceptibility genes and genetic modifiers of human diseases

Progress in Biomedical Optics and Imaging - Proceedings of SPIE

Volumn 5699, Issue , 2005, Pages 491-502

  Abel, Kenneth ^a   Kammerer, Stefan ^a   Hoyal, Carolyn ^a   Reneland, Rikard ^a   Marnellos, George ^a   Nelson, Matthew R ^a   Braun, Andreas ^a  

^a SEQUENOM INC   (United States)

Author keywords

Disease susceptibility genes; DNA pooling; Genome wide association; Genotyping; MALDI TOF; Mass spectrometry; SNP

Indexed keywords

BIOMARKERS; CHEMICAL ANALYSIS; DISEASES; DNA; GENES; MASS SPECTROMETRY; PATIENT MONITORING; PROTEINS;

DISEASE SUSCEPTIBILITY GENES; DNA POOLING; GENOME-WIDE ASSOCIATION; GENOTYPING; MALDI-TOF; SNP;

GENETIC ENGINEERING;

EID: 21844439461     PISSN: 16057422     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1117/12.604620     Document Type: Conference Paper

References (48)

1. Botstein D and Risch N, "Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease." Nature Genet, 33 Suppl, 228-237, 2003.
2. Risch NJ, "Searching for genetic determinants in the new millennium." Nature, 405, 847-856, 2000.
3. Risch N and Merikangas K, "The future of genetic studies of complex human diseases." Science, 273, 1516-1517, 1996.
4. Collins FS, Guyer MS, and Charkravarti A, "Variations on a theme: cataloging human DNA sequence variation." Science, 278 1580-1581, 1997.
5. Goldstein DB, Ahmadi KR, Weale ME, and Wood NW, "Genome scans and candidate gene approaches in the study of common diseases and variable drug responses." Trends Genet, 19, 615-622, 2003.
6. Braun A, Little DP, and Koster H, "Detecting CFTR gene mutations by using primer oligo base extension and mass spectrometry." Clinical Chemistry, 43: 1151-1158, 1997.
7. Freking BA, Murphy SK, Wylie AA, Rhodes SJ, Keele JW, Leymaster KA, Jirtle RL, and Smith TP, "Identification of the single base change causing the callipyge muscle hypertrophy phenotype, the only known example of polar overdominance in mammals." Genome Res 12: 1496-1506, 2002.
8. Little DP, Braun A, Darnhofer-Demar B, and Koster H, "Identification of apolipoprotein E polymorphisms using temperature cycled primer oligo base extension and mass spectrometry." Eur J Clin Chem Clin Biochem 35: 545-548, 1997.
9. Sabeti PC, Reich DE, Higgins JM, Levine HZ, Richter DJ, Schaffner SF, Gabriel SB, Platko JV, Patterson NJ, McDonald GJ, Ackerman HC, Campbell SJ, Altshuler D, Cooper R, Kwiatkowski D, Ward R, and Lander ES, "Detecting recent positive selection in the human genome from haplotype structure." Nature 419: 832-837, 2002.
10. Sklar P, Gabriel SB, McInnis MG, Bennett P, Lim YM, Tsan G, Schaffner S, Kirov G, Jones I, Owen M, Craddock N, DePaulo JR, and Lander ES, "Family-based association study of 76 candidate genes in bipolar disorder. BDNF is a potential risk locus. Brain-derived neutrophic factor." Mol Psychiatry 7, 579-593, 2002.
11. Carlson CS, Eberle MA, Rieder MJ, Smith JD, Kruglyak L, and Nickerson DA, "Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans." Nature Genet, 33, 518-521, 2003.
12. Kruglyak L and Nickerson DA, "Variation is the spice of life." Nature Genet, 27, 234-236, 2001.
13. Reich DE, Gabriel SB, and Altshuler D, "Quality and completeness of SNP databases." Nature Genet, 33, 457-458, 2003.
14. Barcellos LF, Klitz W, Field LL, Tobias R, Bowcock AM, Wilson R, Nelson MP, Nagatomi J, and Thomson G, "Association mapping of disease loci, by use of a pooled DNA genomic screen." Am J Hum Genet 61, 734-747, 1997.
15. Carmi R, Rokhlina T, Kwitek-Black AE, Elbedour K, Nishimura D, Stone EM, and Sheffield VC, "Use of a DNA pooling strategy to identify a human obesity syndrome locus on chromosome 15." Hum Mol Genet, 4, 9-13, 1995.
16. Risch N and Teng J, "The relative power of family-based and case-control designs for linkage disequilibrium studies of complex human diseases. I. DNA pooling." Genome Res, 8, 1273-1288, 1998.
17. Shaw SH, Carrasquillo MM, Kashuk C, Puffenberger EG, and Chakravarti A, 1998 "Allele frequency distributions in pooled DNA samples: applications to mapping complex disease genes." Genome Res, 8, 111-123, 1998.
18. Barratt BJ, Payne F, Rance HE, Nutland S, Todd JA, and Clayton DG, "Identification of the sources of error in allele frequency estimations from pooled DNA indicates an optimal experimental design." Ann Hum Genet, 66, 393-405, 2002.
19. Herbon N, Werner M, Braig C, Gohlke H, Dutsch G, Illig T, Altmuller J, Hampe J, Lantermann A, Schreiber S, Bonifacio E, Ziegler A, Schwab A, Wildenauer D, van den Boom D, Braun A, Knapp M, Reitmeir P, and Wjst M, "High-resolution SNP scan of chromosome 6p21 in pooled samples from patients with complex diseases." Genomics, 81, 510-518, 2003.
20. Le Hellard S, Ballereau SJ, Visscher PM, Torrance HS, Pinson J, Morris SW, Thomson ML, Semple CA, Muir WJ, Blackwood DH, Porteous DJ, and Evans KL, "SNP genotyping on pooled DNAs: comparison of genotyping technologies and a semi automated method for data storage and analysis." Nucleic Acids Res, 30, e74, 2002.
21. Mohlke KL, Erdos MR, Scott LJ, Fingerlin TE, Jackson AU, Silander K, Hollstein P, Boehnke M, and Collins FS, "High-throughput screening for evidence of association by using mass spectrometry genotyping on DNA pools." Proc Natl Acad Sci USA, 99, 16928-16933, 2002.
22. Visscher PM and Hellard SL, "Simple method to analyze SNP-based association studies using DNA pools." Genet Epidemiol, 24, 291-296, 2003.
23. Werner M, Sych M, Herbon N, Illig T, Konig IR, and Wjst M, "Large-scale determination of SNP allele frequencies in DNA pools using MALDI-TOF mass spectrometry." Hum Mutat, 20, 57-64, 2002.
24. Bansal A, van den Boom D, Kammerer S, Honisch C, Adam G, Cantor CR, Kleyn P, and Braun A, "Association testing by DNA pooling: an effective initial screen." Proc Natl Acad Sci USA, 99, 16871-16874, 2002.
25. Freeman DJ, Packard CJ, Shepherd J, Gaffney D, "Polymorphisms in the gene coding for cholesteryl ester transfer protein are related to plasma high-density lipoprotein cholesterol and transfer protein activity." Clin Sci (Lond), 79, 575-581, 1990.
26. Corbex M, Poirier O, Fumeron F, Betoulle D, Evans A, Ruidavets JB, Arveiler D, Luc G, Tiret L, Cambien F, "Extensive association analysis between the CETP gene and coronary heart disease phenotypes reveals several putative functional polymorphisms and gene-environment interaction." Genet Epidemiol, 19, 64-80, 2000.
27. Dachet C, Poirier O, Cambien F, Chapman J, Rouis M, "New functional promoter polymorphism, CETP/-629, in cholesteryl ester transfer protein (CETP) gene related to CETP mass and high density lipoprotein cholesterol levels: role of Sp1/Sp3 in transcriptional regulation." Arterioscler Thromb Vase Biol, 20, 507-515, 2000.
28. Schork NJ, Nath SK, Fallin D, and Chakravarti A, "Linkage disequilibrium analysis of biallelic DNA markers, human quantitative trait loci, and threshold-defined case and control subjects." Am J Hum Genet, 67, 1208-1218, 2000.
29. The International HapMap Consortium, "The International HapMap Project." Nature 426, 789-796, 2003.
30. Dausset J, Cann H, Cohen D, Lathrop M, Lalouel JM, and White R, "Centre d'etude du polymorphisme humain (CEPH): collaborative genetic mapping of the human genome." Genomics, 6, 575-7, 1990.
31. Buetow KH, Edmonson M, MacDonald R, Clifford R, Yip P, Kelley J, Little DP, Strausberg R, Koester H, Cantor CR, and Braun A, "High-throughput development and characterization of agenomewide collection of gene-based single nucleotide polymorphism markers by chip-based matrixassistedlaser desorption/ionization time-of-flight mass spectrometry." Proc Natl Acad Sci USA, 98, 581-4, 2001.
32. Nelson MR, Marnellos, G, Kammerer S, Hoyal CR, Shi MM, Cantor CR, and Braun A, "Large-scale validation of single nucleotide polymorphisms in gene regions." Genome Res, 14, 1664-8, 2004.
33. Barrett JC, Fry B, Maller J, Daly MJ, "Haploview: analysis and visualization of LD and haplotype maps." Bioinformatics, [Epub ahead of print, PubMed ID: 15297300], 2004.
34. International Human Genome Sequencing Consortium, "Finishing the euchromatic sequence of the human genome." Nature 431, 931-45, 2004.
35. Ripley BD, Pattern Recognition and Neural Networks, Cambridge University Press, Cambridge, 1996.
36. Hirschhorn JN, Lohmueller K, Byrne E, and Hirschhorn K, "A comprehensive review of genetic association studies." Genet Med, 4, 45-61, 2002.
37. Ioannidis JP, Ntzani EE, Trikalinos TA, and Contopoulos-Ioannidis DG, "Replication validity of genetic association studies." Nat Genet, 29, 306-309, 2001.
38. Lohmueller KE, Pearce CL, Pike M, Lander ES, and Hirschhorn JN, "Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease." NatureGenet, 33, 177-182, 2003.
39. Andrew T, Hart DJ, Snieder H, de Lange M, Spector TD, and MacGregor AJ, "Are twins and singletons comparable? A study of disease-related and lifestyle characteristics in adult women." Twin Res, 4, 464-477, 2001.
40. Jurinke C, Oeth P, and van den Boom D, "MALDI-TOF mass spectrometry: a versatile tool for high-performance DNA analysis." Mol Biotechnol 26, 147-164, 2004.
41. Sham P, Bader JS, Craig I, O'Donovan M, and Owen M, "DNA Pooling: a tool for large-scale association studies." Nat Rev Genet, 3, 862-871, 2002.
42. DerSimonian R and Laird N, "Meta-analysis in clinical trials." Control Clin Trials, 7, 177-188, 1986.
43. von Eckardstein A, Nofer JR, and Assmann G, "High density lipoproteins and arteriosclerosis: role of cholesterol efflux and reverse cholesterol transport." Arterioscler Thromb Vase Biol, 21, 13-27, 2001.
44. Knoblauch H, Bauerfeind A, Krahenbuhl C, Daury A, Rohde K, Bejanin S, Essioux L, Schuster H, Luft FC, and Reich JG, "Common haplotypes in five genes influence genetic variance of LDL and HDL cholesterol in the general population." Hum Mol Genet, 11, 1477-1485, 2002.
45. Kammerer S, Roth RB, Reneland R, Marnellos G, Hoyal CR, Markward NJ, Ebner F, Kiechle M, Schwarz-Boeger U, Griffiths LR, Ulbrich C, Chrobok K, Forster G, Praetorius GM, Meyer P, Rehbock J, Cantor CR, Nelson MR, and Braun A, "Large-scale association study identifies ICAM gene region as breast and prostate cancer susceptibility locus." Cancer Res, 64, 8906-8910, 2004.
46. Lopez-Otin C and Diamandis EP, "Breast and prostate cancer: an analysis of common epidemiological, genetic, and biochemical features." Endocr Rev, 19, 365-396, 1998.
47. Davies H, Bignell GR, Cox C et al., "Mutations of the BRAF gene in human cancer." Nature, 417, 949-954, 2002.
48. Pollock PM and Meltzer PS, "Lucky draw in the gene raffle." Nature, 417, 906-907, 2002.