Preprocessing and quality control strategies for Illumina DASL assay-based brain gene expression studies with semi-degraded samples

Frontiers in Genetics

Volumn 3, Issue FEB, 2012, Pages

  Chow, Maggie L ^a   Winn, Mary E ^b,c   Li, Hai Ri ^d   April, Craig ^e   Wynshaw Boris, Anthony ^f   Fan, Jian Bing ^e   Fu, Xiang Dong ^d   Courchesne, Eric ^a   Schork, Nicholas J ^c  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e ILLUMINA INC   (United States)

^f UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Data preprocessing; Gene expression; Microarray; Quality control

Indexed keywords

EID: 84873056124     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2012.00011     Document Type: Article

References (23)

1. Abramovitz, M., Ordanic-Kodani, M., Wang, Y., Li, Z., Catzavelos, C, Bouzyk, M., Sledge, G. W. Jr., Moreno, C. S., and Leyland-Jones, B. (2008). Optimization optimization of RNA extraction from FFPE tissues for expression profiling in the DASL assay. BioTechniques AA, A17-A23.
2. April, C, Klotzle, B., Royce, T., Wickham-Garcia, E., Boyaniwsky, T., Izzo, J., Cox, D., Jones, W., Rubio, R., Holton, K., Matulonis, U., Quacken-bush,J.,andFan,J.B. (2009).Whole-genome gene expression profiling of formalin-fixed, paraffin-embedded tissue samples. PLoS ONE 4, e8162. doi:10.1371/journal.pone.0008162
3. Bloss, C. S., and Courchesne, E. (2007). MRI neuroanatomy in young girls with autism: a preliminary study. J. Am. Acad. Child Adolesc. Psychiatry 46,515-23.
4. Chen, C, Grennan, K., Badner, J., Zhang, D., Gershon, E., Jin, L., and Liu, C. (2011). Removing batch effects in analysis of expression microarray data: an evaluation of six batch adjustment methods. PLoS ONE 6, el7238. doi:10.1371/journal.pone.0017238
5. Du, P., Kibbe, W A., and Lin, S. M. (2007). nuID: a universal naming scheme of oligonucleotides for Illumina, affymetrix, and other microarrays. Biol Direct 2, 16.
6. Du, P., Kibbe, W A., and Lin, S. M. (2008). Lumi: a pipeline for processing Illumina microarray. Bioinformatics 24,1547-1548.
7. Fan, J.-B., Yeakley, J. M., Bibikova, M., Chudin, E., Wickham, E., Chen, J., Doucet, D., Rigault, P., Zhang, B., Shen, R., McBride, C, Li, H. R., Fu, X. D., Oliphant, A., Barker, D. L, and Chee, M. S. (2004). A versatile assay for high-throughput gene expression profiling on universal array matrices. Genome Res. 14, 878-885.
8. Gentleman, R. C, Carey, V. J., Bates, D. M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., Hornik, K., Hothorn, T., Huber, W., Iacus, S., Irizarry, R., Leisch, E, Li, C, Maechler, M., Rossini, A. J., Sawitzki, G., Smith, C, Smyth, G., Tierney, L., Yang, J. Y, and Zhang, J. (2004). Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80.
9. Giles, P. J. (2003). Normality of oligonucleotide microarray data and implications for parametric statistical analyses. Bioinformatics 19, 2254-2262.
10. Gold, D. L., Wang, J., and Coombes, K. R. (2005). Inter-gene correlation on oligonucleotide arrays: how much does normalization matter? Am. J. Pharmacogenomics 5, 271-279.
11. Horvath, S., Janka, Z., and Mimics, K. (2010). Analyzing Schizophrenia by DNA Microarrays. Biol. Psychiatry 69, 157-162.
12. Johnson, W E., Li, C, and Rabinovic, A. (2007). Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8,118-127.
13. Lein, E. S., Hawrylycz, M. J., Ao, N., Ayres, M., Bensinger, A., Bernard, A., Boe, A. E, Boguski, M. S., Brockway, K. S., Byrnes, E. J., Chen, L., Chen, L., Chen, T. M., Chin, M. C, Chong, J., Crook, B. E., Czaplinska, A., Dang, C. N., Datta, S., Dee, N. R., Desaki, A. L., Desta, T., Diep, E., Dolbeare, T. A., Donelan, M. J., Dong, H. W., Dougherty, J. G., Duncan, B. J., Ebbert, A. J., Eichele, G., Estin, L. K., Faber, C, Facer, B. A., Fields, R., Fischer, S. R., Fliss, T. P., Frensley, C, Gates, S. N., Glattfelder, K. J., Halverson, K. R., Hart, M. R., Hohmann, J. G., Howell, M. P., Jeung, D. P., Johnson, R. A., Karr, P. T., Kawal, R., Kidney, J. M., Knapik, R. H., Kuan, C. L., Lake, J. H., Laramee, A. R., Larsen, K. D., Lau, C, Lemon, T. A., Liang, A. J., Liu, Y, Luong, L. T., Michaels, J., Morgan, J. J., Morgan, R. J., Mortrud, M. T., Mosqueda, N. E, Ng, L. L., Ng, R., Orta, G. J., Overly, C. C, Pak, T. H., Parry, S. E., Pathak, S. D., Pearson, O. C, Puchalski, R. B., Riley, Z. L., Rockett, H. R., Rowland, S. A., Royall, J. J., Ruiz, M. J., Sarno, N. R., Schaffnit, K., Shapo-valova, N. V., Sivisay, T., Slaughter-beck, C. R., Smith, S. C, Smith, K. A., Smith, B. I., Sodt, A. J., Stewart, N. N., Stumpf, K. R., Sunkin, S. M., Sutram, M., Tarn, A., Teemer, C. D., Thaller, C, Thompson, C. L., Varnam, L. R., Visel, A., Whitlock, R. M., Wohnoutka, P. E., Wolkey, C. K., Wong, V. Y, Wood, M., Yaylaoglu, M. B., Young, R. C, Youngstrom, B. L., Yuan, X. E, Zhang, B., Zwingman, T. A., and Jones, A. R. (2007). Genome-wide atlas of gene expression in the adult mouse brain. Nature 445, 168-176.
14. Lim, W K., Wang, K., Lefebvre, C, and Califano, A. (2007). Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks. Bioinformatics 23, i282-i288.
15. Lin, S. M., Du, P., Huber, W., and Kibbe, WA. (2008). Model-based variance-stabilizing transformation for Illumina microarray data. Nucleic Acids Res. 36, ell
16. Lord, C, Risi, S., Lambrecht, L., Cook, E. H. Jr., Leventhal, B. L., DiLavore, P. C,Pickles,A.,andRutter.M. (2000). The autism diagnostic observation schedule-generic: a standard measure of social and communication deficits associated with the spectrum of autism. J. Autism Dev. Disord. 30, 205-223.
17. Lord, C, Rutter, M., and Couteur, A. (1994). Autism diagnostic interview-revised: a revised version of a diagnostic interview for caregivers of individuals with possible pervasive developmental disorders. J. Autism Dev. Disord. 24, 659-685.
18. Mimics, K., and Pevsner, J. (2004). Progress in the use of microarray technology to study the neurobiology of disease. Nat. Neurosd. 7, 434-439.
19. Oldham, M. C, Konopka, G., Iwamoto, K., Langfelder, P., Kato, T., Horvath, S., and Geschwind, D. H. (2008). Functional organization of the transcriptome in human brain. Nat. Neurosd. 11, 1271-1282.
20. Rehen, S. K., Yung, Y C, McCreight, M. P., Kaushal, D., Yang, A. H., Almeida, B. S. V., Kingsbury, M. A., Cabral, K. M. S., McConnell, M. J., Anliker, B., Fontanoz, M., and Chun, J. (2005). Constitutional aneuploidy in the normal human brain. Neurosd. 25, 2176-2180.
21. Schmid, R., Baum, P., Ittrich, C, Fundel-Clemens, K., Huber, W, Brors, B., Eils, R., Weith, A., Mennerich, D., and Quast, K. (2010). Comparison of normalization methods for Illumina BeadChip HumanHT-12 v3. BMC Genomics 11, 349. doi:10.1186/1471-2164-11-349
22. Tuchman, R., and Rapin, I. (2002). Epilepsy in autism. Lancet Neurol. 1, 352-358.
23. Zapala, M. A., and Schork, N. J. (2006). Multivariate regression analysis of distance matrices for testing associations between gene expression patterns and related variables. Proc. Natl. Acad. Sci. U.S.A. 103, 19430-19435.