SAQC: SNP Array Quality Control

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Yang, Hsin Chou ^a   Lin, Hsin Chi ^a   Kang, Meijyh ^b   Chen, Chun Houh ^a   Lin, Chien Wei ^a   Li, Ling Hui ^b   Wu, Jer Yuarn ^b   Chen, Yuan Tsong ^b   Pan, Wen Harn ^b  

^a INSTITUTE OF STATISTICAL SCIENCE   (Taiwan)

^b INSTITUTE OF BIOMEDICAL SCIENCES   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY AND PRECISION; CONFIDENCE INTERVAL METHOD; DETECTION METHODS; EMPIRICAL DISTRIBUTIONS; LOG-NORMAL DISTRIBUTION; SINGLE-NUCLEOTIDE POLYMORPHISMS; STATISTICAL PROPERTIES; USER-FRIENDLY TOOL;

DNA; GENES; POPULATION STATISTICS; QUALITY ASSURANCE; QUALITY CONTROL;

FISH;

DNA;

ARTICLE; DNA MICROARRAY; GENE FREQUENCY; HUMAN; HUMAN GENOME; METHODOLOGY; QUALITY CONTROL; SINGLE NUCLEOTIDE POLYMORPHISM; STANDARD;

DNA; GENE FREQUENCY; GENOME, HUMAN; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; QUALITY CONTROL;

EID: 79955110841     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-100     Document Type: Article

References (55)

1. Cardon LR, Bell JI. Association study designs for complex diseases. Nature Reviews Genetics 2001, 2(2):91-99. 10.1038/35052543, 11253062.
2. Collins A, Lonjou C, Morton NE. Genetic epidemiology of single-nucleotide polymorphisms. Proceedings of the National Academy of Sciences of the United States of America 1999, 96(26):15173-15177. 10.1073/pnas.96.26.15173, 24792, 10611357.
3. Kruglyak L. Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nature Genetics 1999, 22(2):139-144. 10.1038/9642, 10369254.
4. The Wellcome Trust Case Control Consortium Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 2007, 447(7145):661-678. 10.1038/nature05911, 2719288, 17554300, The Wellcome Trust Case Control Consortium.
5. Yang H-C, Liang Y-J, Wu Y-L, Chung C-M, Chiang K-M, Ho H-Y, Ting C-T, Lin T-H, Sheu S-H, Tsai W-C, et al. Genome-wide association study of young-onset hypertension in the Han Chinese population of Taiwan. PLoS ONE 2009, 4(5):e5459. 10.1371/journal.pone.0005459, 2674219, 19421330.
6. Wang WYS, Barratt BJ, Clayton DG, Todd JA. Genome-wide association studies: Theoretical and practical concerns. Nature Reviews Genetics 2005, 6(2):109-118. 10.1038/nrg1522, 15716907.
7. Monzon FA, Hagenkord JM, Lyons-Weiler MA, Balani JP, Parwani AV, Sciulli CM, Li J, Chandran UR, Bastacky SI, Dhir R. Whole genome SNP arrays as a potential diagnostic tool for the detection of characteristic chromosomal aberrations in renal epithelial tumors. Modern Pathology 2008, 21(5):599-608. 10.1038/modpathol.2008.20, 18246049.
8. Pomares E, Riera M, Permanyer J, Mendez P, Castro-Navarro J, Andres-Gutierrez A, Marfany G, Gonzalez-Duarte R. Comprehensive SNP-chip for retinitis pigmentosa-Leber congenital amaurosis diagnosis: new mutations and detection of mutational founder effects. European Journal of Human Genetics 2010, 18(1):118-124. 10.1038/ejhg.2009.114, 2987167, 19584904.
9. Pomares E, Marfany G, Brion MJ, Carracedo A, Gonzalez-Duarte R. Novel high-throughput SNP genotyping cosegregation analysis for genetic diagnosis of autosomal recessive retinitis pigmentosa and Leber congenital amaurosis. Human Mutation 2007, 28(5):511-516. 10.1002/humu.20479, 17279538.
10. Pomeroy R, Duncan G, Sunar-Reeder B, Ortenberg E, Ketchum M, Wasiluk H, Reeder D. A low-cost, high-throughput, automated single nucleotide polymorphism assay for forensic human DNA applications. Analytical Biochemistry 2009, 395(1):61-67. 10.1016/j.ab.2009.07.041, 19646946.
11. Lessig R, Zoledziewska M, Fahr K, Edelmann J, Kostrzewa M, Dobosz T, Kleemann WJ. Y-SNP-genotyping - a new approach in forensic analysis. Forensic Science International 2005, 154(2-3):128-136. 10.1016/j.forsciint.2004.09.129, 16182959.
12. Zhao G, Yang Q, Huang D, Yu C, Yang R, Chen H, Mei K. Study on the application of parent-of-origin specific DNA methylation markers to forensic genetics. Forensic Science International 2005, 154(2-3):122-127. 10.1016/j.forsciint.2004.09.123, 16182958.
13. The International HapMap Consortium The International HapMap Project. Nature 2003, 426(6968):789-796. 10.1038/nature02168, 14685227, The International HapMap Consortium.
14. The International HapMap Consortium Integrating ethics and science in the international HapMap project. Nature Reviews Genetics 2004, 5(6):467-475. 10.1038/nrg1351, 2271136, 15153999, The International HapMap Consortium.
15. The International HapMap Consortium A haplotype map of the human genome. Nature 2005, 437(7063):1299-1320. 10.1038/nature04226, 1880871, 16255080, The International HapMap Consortium.
16. The International HapMap Consortium A second generation human haplotype map of over 3.1 million SNPs. Nature 2007, 449(7164):851-861. 10.1038/nature06258, 2689609, 17943122, The International HapMap Consortium.
17. Reich DE, Cargill M, Bolk S, Ireland J, Sabeti PC, Richter DJ, Lavery T, Kouyoumjian R, Farhadian SF, Ward R, et al. Linkage disequilibrium in the human genome. Nature 2001, 411(6834):199-204. 10.1038/35075590, 11346797.
18. Arnheim N, Calabrese P, Nordborg M. Hot and cold spots of recombination in the human genome: The reason we should find them and how this can be achieved. American Journal of Human Genetics 2003, 73(1):5-16. 10.1086/376419, 1180590, 12772086.
19. Sharp AJ, Locke DP, McGrath SD, Cheng Z, Bailey JA, Vallente RU, Pertz LM, Clark RA, Schwartz S, Segraves R, et al. Segmental duplications and copy-number variation in the human genome. American Journal of Human Genetics 2005, 77(1):78-88. 10.1086/431652, 1226196, 15918152.
20. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Maner S, Massa H, Walker M, Chi MY, et al. Large-scale copy number polymorphism in the human genome. Science 2004, 305(5683):525-528. 10.1126/science.1098918, 15273396.
21. Conrad DF, Andrews TD, Carter NP, Hurles ME, Pritchard JK. A high-resolution survey of deletion polymorphism in the human genome. Nature Genetics 2006, 38(1):75-81. 10.1038/ng1697, 16327808.
22. Feuk L, Carson AR, Scherer SW. Structural variation in the human genome. Nature Reviews Genetics 2006, 7(2):85-97. 10.1038/nrg1767, 16418744.
23. The 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(7289):713-720. 10.1038/nature08979, 2892339, 20360734, The Wellcome Trust Case Control Consortium.
24. Stark M, Hayward N. Genome-wide loss of heterozygosity and copy number analysis in melanoma using high-density single-nucleotide polymorphism arrays. Cancer Research 2007, 67(6):2632-2642. 10.1158/0008-5472.CAN-06-4152, 17363583.
25. Abdulla MA, Ahmed I, Assawamakin A, Bhak J, Brahmachari SK, Calacal GC, Chaurasia A, Chen CH, Chen J, Chen YT, et al. Mapping human genetic diversity in Asia. Science 2009, 326(5959):1541-1545. 10.1126/science.1177074, 20007900.
26. Campbell MC, Tishkoff SA. African genetic diversity: Implications for human demographic history, modern human origins, and complex disease mapping. Annual Review of Genomics and Human Genetics 2008, 9:403-433. 10.1146/annurev.genom.9.081307.164258, 2953791, 18593304.
27. Goldstein DB, Cavalleri GL. Genomics - Understanding human diversity. Nature 2005, 437(7063):1241-1242. 10.1038/4371241a, 16251937.
28. Matsuzaki H, Dong SL, Loi H, Di XJ, Liu GY, Hubbell E, Law J, Berntsen T, Chadha M, Hui H, et al. Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays. Nature Methods 2004, 1(2):109-111. 10.1038/nmeth718, 15782172.
29. Kennedy GC, Matsuzaki H, Dong SL, Liu WM, Huang J, Liu GY, Xu X, Cao MQ, Chen WW, Zhang J, et al. Large-scale genotyping of complex DNA. Nature Biotechnology 2003, 21(10):1233-1237. 10.1038/nbt869, 12960966.
30. Steemers FJ, Chang WH, Lee G, Barker DL, Shen R, Gunderson KL. Whole-genome genotyping with the single-base extension assay. Nature Methods 2006, 3(1):31-33. 10.1038/nmeth842, 16369550.
31. Steemers FJ, Gunderson KL. Whole genome genotyping technologies on the BeadArray™ platform. Biotechnology journal 2007, 2(1):41-49. 10.1002/biot.200600213, 17225249.
32. Gunderson KL, Steemers FJ, Lee G, Mendoza LG, Chee MS. A genome-wide scalable SNP genotyping assay using microarray technology. Nature Genetics 2005, 37(5):549-554. 10.1038/ng1547, 15838508.
33. Hirschhorn JN, Daly MJ. Genome-wide association studies for common diseases and complex traits. Nature Reviews Genetics 2005, 6(2):95-108. 10.1038/nrg1521, 15716906.
34. Wong KK, Tsang YTM, Shen J, Cheng RS, Chang YM, Man TK, Lau CC. Allelic imbalance analysis by high-density single-nucleotide polymorphic allele (SNP) array with whole genome amplified DNA. Nucleic Acids Research 2004, 32(9):e69. 10.1093/nar/gnh072, 419627, 15148342.
35. Staaf J, Lindgren D, Vallon-Christersson J, Isaksson A, Goransson H, Juliusson G, Rosenquist R, Hoglund M, Borg A, Ringner M. Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays. Genome Biology 2008, 9(9). 10.1186/gb-2008-9-9-r136, 2592714, 18796136.
36. Puputti M, Sihto H, Isola J, Butzow R, Joensuu H, Nupponen NN. Allelic imbalance of HER2 variant in sporadic breast and ovarian cancer. Cancer Genetics and Cytogenetics 2006, 167(1):32-38. 10.1016/j.cancergencyto.2004.09.023, 16682283.
37. Ishikawa S, Komura D, Tsuji S, Nishimura K, Yamamoto S, Panda B, Huang J, Fukayama M, Jones KW, Aburatani H. Allelic dosage analysis with genotyping microarrays. Biochemical and Biophysical Research Communications 2005, 333(4):1309-1314. 10.1016/j.bbrc.2005.06.040, 15982637.
38. Primdahl H, Wikman FP, von der Maase H, Zhou XG, Wolf H, Orntoft TF. Allelic imbalances in human bladder cancer: Genome-wide detection with high-density single-nucleotide polymorphism arrays. Journal of the National Cancer Institute 2002, 94(3):216-223.
39. Yang HC, Lin HC, Huang MC, Li LH, Pan WH, Wu JY, Chen YT. A new analysis tool for individual-level allele frequency for genomic studies. BMC Genomics 2010, 11(1):415. 10.1186/1471-2164-11-415, 2996943, 20602748.
40. Ogiwara H, Kohno T, Nakanishi H, Nagayama K, Sato M, Yokota J. Unbalanced translocation, a major chromosome alteration causing loss of heterozygosity in human lung cancer. Oncogene 2008, 27(35):4788-4797. 10.1038/onc.2008.113, 18408757.
41. Zhou XF, Mok SC, Chen Z, Li Y, Wong DTW. Concurrent analysis of loss of heterozygosity (LOH) and copy number abnormality (CNA) for oral premalignancy progression using the Affymetrix 10K SNP mapping array. Human Genetics 2004, 115(4):327-330. 10.1007/s00439-004-1163-1, 15290239.
42. Gunduz E, Gunduz M, Ali MA, Beder L, Tamamura R, Katase N, Tominaga S, Yamanaka N, Shimizu K, Nagatsuka H. Loss of heterozygosity at the 9p21-24 region and identification of BRM as a candidate tumor suppressor gene in head and neck squamous cell carcinoma. Cancer Investigation 2009, 27(6):661-668. 10.1080/07357900802563010, 19488910.
43. Huggins R, Li LH, Lin YC, Yu AL, Yang HC. Nonparametric estimation of LOH using Affymetrix SNP genotyping arrays for unpaired samples. Journal of Human Genetics 2008, 53(11-12):983-990. 10.1007/s10038-008-0340-9, 18989737.
44. Kurashina K, Yamashita Y, Ueno T, Koinuma K, Ohashi J, Horie H, Miyakura Y, Hamada T, Haruta H, Hatanaka H, et al. Chromosome copy number analysis in screening for prognosis-related genomic regions in colorectal carcinoma. Cancer Science 2008, 99(9):1835-1840. 10.1111/j.1349-7006.2008.00881.x, 18564138.
45. Blauw HM, Veldink JH, van Es MA, van Vught PW, Saris CG, van der Zwaag B, Franke L, Burbach JPH, Wokke JH, Ophoff RA, et al. Copy-number variation in sporadic amyotrophic lateral scleroses: A genome-wide screen. Lancet Neurology 2008, 7(4):319-326. 10.1016/S1474-4422(08)70048-6, 18313986.
46. Huang J, Wei W, Zhang J, Liu G, Bignell GR, Stratton MR, Futreal PA, Wooster R, Jones KW, Shapero MH. Whole genome DNA copy number changes identified by high density oligonucleotide arrays. Human Genomics 2004, 1(4):287-299.
47. Di XJ, Matsuzaki H, Webster TA, Hubbell E, Liu GY, Dong SL, Bartell D, Huang J, Chiles R, Yang G, et al. Dynamic model based algorithms for screening and genotyping over 100K SNPs on oligonucleotide microarrays. Bioinformatics 2005, 21(9):1958-1963. 10.1093/bioinformatics/bti275, 15657097.
48. Rabbee N, Speed TP. A genotype calling algorithm for affymetrix SNP arrays. Bioinformatics 2006, 22(1):7-12. 10.1093/bioinformatics/bti741, 16267090.
49. Hua JP, Craig DW, Brun M, Webster J, Zismann V, Tembe W, Joshipura K, Huentelman MJ, Dougherty ER, Stephan DA. SNiPer-HD: Improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays. Bioinformatics 2007, 23(1):57-63. 10.1093/bioinformatics/btl536, 17062589.
50. Korn JM, Kuruvilla FG, McCarroll SA, Wysoker A, Nemesh J, Cawley S, Hubbell E, Veitch J, Collins PJ, Darvishi K, et al. Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nature Genetics 2008, 40(10):1253-1260. 10.1038/ng.237, 2756534, 18776909.
51. Laurie CC, Doheny KF, Mirel DB, Pugh EW, Bierut LJ, Bhangale T, Boehm F, Caporaso NE, Cornelis MC, Edenberg HJ, et al. Quality control and quality assurance in genotypic data for genome-wide association studies. Genet Epidemiol 2010, 34(6):591-602. 10.1002/gepi.20516, 20718045.
52. Pan WH, Fann CSJ, Wu JY, Hung YT, Ho MS, Tai TH, Chen YJ, Liao CJ, Yang ML, Cheng ATA, et al. Han Chinese cell and genome bank in Taiwan: Purpose, design and ethical considerations. Human Heredity 2006, 61(1):27-30. 10.1159/000091834, 16534213.
53. Affymetrix Inc BRLMM: An improved genotype calling method for the GeneChip human mapping 500K array set. 2006, Affymetrix Inc.
54. Yang HC, Liang YJ, Huang MC, Li LH, Lin CH, Wu JY, Chen YT, Fann CSJ. A genome-wide study of preferential amplification/hybridization in microarray-based pooled DNA experiments. Nucleic Acids Research 2006, 34(15):e106. 10.1093/nar/gkl446, 1616968, 16931491.
55. Massey FJ. The Kolmogorov-Smirnov test for goodness of fit. Journal of the American Statistical Association 1951, 46(253):68-78.