Considerations for the processing and analysis of GoldenGate-based two-colour Illumina platforms

Statistical Methods in Medical Research

Volumn 18, Issue 5, 2009, Pages 437-452

  Lynch, Andy G ^a   Dunning, M J ^a   Iddawela, M ^a   Barbosa Morais, N L ^a   Ritchie, M E ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MESSENGER RNA;

ALLELE; ANALYTIC METHOD; CPG ISLAND; DNA METHYLATION; DNA MICROARRAY; DNA SEQUENCE; GENE ACTIVITY; GENE EXPRESSION; GENE PROBE; GENE TARGETING; GENETIC VARIABILITY; GENOTYPE; HUMAN; HYBRIDIZATION; MICROARRAY ANALYSIS; POLYMERASE CHAIN REACTION; PROMOTER REGION; REVIEW; RNA DEGRADATION; SINGLE NUCLEOTIDE POLYMORPHISM; VALIDATION PROCESS;

ALLELES; COLOR; DATA INTERPRETATION, STATISTICAL; DNA METHYLATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENOMICS; GENOTYPE; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 70349588328     PISSN: 09622802     EISSN: None     Source Type: Journal    
DOI: 10.1177/0962280208099451     Document Type: Review

References (44)

1. Quackenbush J. Computational analysis of microarray data. Nature Review Genetics 2001; 2:418-27.
2. Fan JB, Yeakley JM, Bibikova M., Chudin E., Wickham E., Chen J., Doucet D., Rigault P., Zhang B., Shen R., McBride C., Li HR, Fu XD, Oliphant A., Barker DL, Chee MS A versatile assay for high-throughput gene expression profiling on universal array matrices. Genome Research 2004; 14(5):878-85.
3. Gunderson KL, Kruglyak S., Graige MS, Garcia FB, Kermani G., Zhao C., Che D., Dickinson T., Wickham E., Bierle J., Doucet D., Milewski M., Yang R., Siegmund C., Haas J., Zhou L., Oliphant A., Fan JB, Barnard S., Chee MS Decoding randomly ordered DNA arrays. Genome Research 2004; 14(5):870-77.
4. Dunning MJ, Barbosa-Morais NL, Lynch AG, Tavaré S., Ritchie ME Statistical issues in the analysis of Illumina data. BMC Bioinformatics 2008; 9(85) pp.
5. Kerr MK, Churchill GA Statistical design and the analysis of gene expression microarray data. Genetic Research 2001; 77(2):123-28.
6. Dai M., Wang P., Boyd AD, Kostov G., Athey B., Jones EG, Bunney WE, Myers RM, Speed TP, Akil H., Watson SJ, Meng F. Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Research 2005; 33(20):e175.
7. Durbin BP, Hardin JS, Hawkins DM, Rocke DM A variance-stabilizing transformation for gene-expression microarray data. Bioinformatics 2002; 18(Suppl. 1):S105-S110.
8. Huber W., Heydebreck AV, Sultmann H., Poustka A., Vingron M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 2002; 18(Suppl. 1):S960-S104.
9. Lin SM, Du P., Huber W., Kibbe WA Model-based variance-stabilizing transformation for Illumina microarray data. Nucleic Acids Research 2008; 36(2): E11.
10. Suarez-Farinas M., Haider A., Wittkowski KM "Harshlighting" small blemishes on microarrays. BMC Bioinformatics 2005; 6(65).
11. Barnes M., Freudenberg J., Thompson S., Aronow B., Pavlidis P. Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms. Nucleic Acids Research 2005; 33(18): 5914-23.
12. Tseng G., Oh MK, Rohlin L., Liao J., Wong W. Issues in cDNA microarray analysis: Quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Research 2001; 29: 2549-57.
13. Smyth GK, Speed T. Normalization of cDNA microarray data. Methods 2003; 31(4): 265-73.
14. Irizarry RA, Ladd-Acosta C., Carvalho B., Wu amd H., Brandenburg SA, Jeddeloh JA, Wen B., Feinberg AP Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Research 2008; 18(5): 780-90.
15. Bolstad BM, Irizarry RA, Astrand M., Speed TP A comparison of normalization methods for high density oligonucleotide array data based on bias and variance. Bioinformatics 2003; 19(2): 185-93.
16. Workman C., Jensen LJ, Jarmer H., Berka R., Gautier L., Nielsen HB, Saxild HH, Nielsen C., Brunak S., Knudsen S. A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biology 2002; 3(9).
17. Sachidanandam R., Weissman D., Schmidt S., Kakol J., Stein L., Marth G., Sherry S., Mullikin J., Mortimore B., Willey D., Hunt S., Cole C., Coggill P., Rice C., Ning Z., Rogers J., Bentley D., Kwok P., Mardis E., Yeh R., Schultz B., Cook L., Davenport R., Dante M., Fulton L., Hillier L., Waterston R., McPherson J., Gilman B., Schaffner S., Van Etten W., Reich D., Higgins J., Daly M., Blumenstiel B., Baldwin J., Stange-Thomann N., Zody M., Linton L., Lander E., Altshuler D. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 2001; 409: 928-33.
18. 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: 661-78.
19. International HapMap Consortium I. The International HapMap Project. Nature 2003; 426(6968): 789-96.
20. Fan JB, Oliphant A., Shen R., Kermani BG, Garcia F., Gunderson KL, Hansen M., Steemers F., Butler SL, Deloukas P., Galver L., Hunt S., McBride C., Bibikova M., Rubano T., Chen J., Wickham E., Doucet D., Chang W., Campbell D., Zhang B., Kruglyak S., Bentley D., Haas J., Rigault P., Zhou L., Stuelpnagel J., Chee MS Highly Parallel SNP Genotyping. Cold Spring Harbor Symposia on Quantitative Biology 2003; 68: 69-78.
21. Murray SS, Oliphant A., Shen R., McBride C., Steeke RJ, Shannon SG, Rubano T., Kermani BG, Fan JB, Chee MS, Hansen, MS A highly informative SNP linkage panel for human genetic studies. Nature Methods 2004; 1: 113-17.
22. Fan JB, Gunderson KL, Bibikova M., Yeakley JM, Chen J., Wickham Garcia E., Lebruska LL, Laurent M., Shen R., Barker D. Illumina universal bead arrays. Methods in Enzymology 2006; 410: 57-73.
23. Teo YY, Inouye M., Small KS, Gwilliam R., Deloukas P., Kwiatkowski DP, Clark TG A genotype calling algorithm for the Illumina BeadArray platform. Bioinformatics 2007; 23(20): 2741-46.
24. Colella S., Yau C., Taylor JM, Mirza G., Butler H., Clouston P., Bassett AS, Seller A., Holmes CC, Ragoussis J. QuantiSNP: An objective bayes hidden-markov model to detect and accurately map copy number variation using SNP genotyping data. Nucleic Acids Research 2007; 35(5): 2013-25.
25. Oosting J., Lips EH, Von Eijk R., Eilers PHC, Szuhai K., Wijmenga C., Morreau H., Von Wezel T. High Resolution copy number analysis of paraffin-embedded archival tissue using SNP BeadArrays. Genome Research 2007; 17(3): 368-76.
26. Bibikova M., Talantov D., Chudin E., Yeakley JM, Chen J., Doucet D., Wickham E., Atkins D., Barker D., Chee M., Wang Y., Fantitle JB Quantitative gene expression profiling in formalin-fixed, paraffin-embedded tissues using universal bead arrays. American Journals of Pathology 2004; 165(5): 1799-807.
27. Zhang C., Li HR, Fan JB, Wang-Rodriguez J., Downs T., Fu XD, Zhang MQ Profiling alternatively spliced mRNA isoforms for prostate cancer classification. BMC Bioinformatics 2006; 7(202).
28. Haller A., Kanakapalli D., Walter R., Alhasan S., Eliason J., Everson R. Transcriptional profiling of degraded RNA in cryopreserved and fixed tissue samples obtained at autopsy. BMC Clinical Pathology 2006; 6(9).
29. Ravo M., Mutarelli M., Ferraro L., Grober OMV, Paris O., Tarallo R., Vigilante A., Cimino D., de Bortoli M., Nola E., Cicatiello L., Weisztitle A. Quantitative expression profiling of highly degraded RNA from formalin-fixed, paraffin-embedded breast tumor biopsies by oligonucleotide microarrays. Laboratory Investigation 2008; 88: 430-40.
30. Abramovitz M., Ordanic-Kodani M., Wang Y., Li Z., Catzavelos C., Bouzyk M., Sledge GW, Moreno CS, Leyland-Jones B. Optimization of RNA extraction from FFPE tissues for expression profiling in the DASL assay. Biotechniques 2008; 44: 417-23.
31. Knight JC Allele-specific gene expression uncovered. Trends Genetics 2004; 20(3): 113-16.
32. Lo HS, Wang Z., Hu Y., Yang HH, Gere S., Buetow KH, Lee MP Allelic variation in gene expression is common in the human genome. Genome Research 2003; 13(8): 1855-62.
33. Pant PV, Tao H., Beilharz EJ, Ballinger DG, Cox DR, Frazer KA Analysis of allelic differential expression in human white blood cells. Genome Research 2006; 16(3): 331-39.
34. Tan AC, Fan JB, Karikari C., Bibikova M., Garcia EW, Zhou L., Barker D., Serre D., Feldmann G., Hruban RH, Klein AP, Goggins M., Couch FJ, Hudson TJ, Winslow RL, Maitra A., Chakravarti A. Allele-specific expression in the germline of patients with familial pancreatic cancer: An unbiased approach to cancer gene discovery. Cancer Biology Therapy 2008; 7(1): 135-44.
35. Serre D., Gurd S., Ges B., Sladek R., Sinnett D. Differential allelic expression in the human genome: A robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression. PLoS Genet 2008; 4(2): E1000006.
36. Bird A. DNA methylation patterns and epigenetic memory. Genes and Development 2002; 16(1): 6-21.
37. Laird PW The power and the promise of DNA methylation markers. Natural Reviews Cancer 2003; 3(4): 253-66.
38. Jones PA, Baylin SB The epigenomics of cancer. Cell 2007; 128(4): 683-92.
39. Bibikova M., Lin Z., Zhou L., Chudin E., Garcia EW, Wu B., Doucet D., Thomas NJ, Wang Y., Vollmer E., Goldmann T., Seifart C., Jiang W., Barker DL, Chee MS, Floros J., Fan JB High-throughput DNA methylation profiling using universal bead arrays. Genome Research 2006; 16(3): 383-93.
40. Bibikova M., Chudin E., Wu B., Zhou L., Garcia EW, Liu Y., Shin S., Plaia TW, Auerbach JM, Arking DE, Gonzalez R., Crook J., Davidson B., Schulz TC, Robins A., Khanna A., Sartipy P., Hyllner J., Vanguri P., Savant-Bhonsale S., Smith AK, Chakravarti A., Maitra A., Rao M., Barker DL, Loring JF, Fan FB Human embryonic stem cells have a unique epigenetic signature. Genome Research 2006; 16(9): 1075-83.
41. Bjornsson HT, Brown LJ, Fallin MD, Rongione MA, Bibikova M., Wickham E., Fan JB, Feinberg AP Epigenetic specificity of loss of imprinting of the IGF2 gene in Wilms tumors. Journal of the National Cancer Institute 2007; 99(16): 1270-73.
42. Ladd-Acosta C., Pevsner J., Sabunciyan S., Yolken RH, Webster MJ, Dinkins T., Callinan PA, Fan JB, Potash JB, Feinberg AP DNA methylation signatures within the human brain. American Journal of Human Genetics 2007; 81(6): 1304-14.
43. Dunning MJ, Ritchie ME, Barbosa-Morais NL, Tavaré S., Lynch AG Spike-in validation of an Illumina-specific variance stabilizing transformation. BMC Research Notes 2008 ; 1 (18).
44. Yang YH, Dudoit S., Luu P., Lin DM, Peng V., Ngai J., Speed TP Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Research 2002; 30(4): E15.