A multilevel model to address batch effects in copy number estimation using SNP arrays

Biostatistics

Volumn 12, Issue 1, 2011, Pages 33-50

  Scharpf, Robert B ^a   Ruczinski, Ingo ^b   Carvalho, Benilton ^b   Doan, Betty ^a   Chakravarti, Aravinda ^a   Irizarry, Rafael A ^b  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

Bioinformatics; DNA copy number variations; Hierarchical models; Single nucleotide polymorphism array

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; BIPOLAR DISORDER; DOWN SYNDROME; GENE DOSAGE; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENETICS; GENOTYPE; HUMAN; METHODOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL MODEL;

ALGORITHMS; BIPOLAR DISORDER; DOWN SYNDROME; GENE DOSAGE; GENETIC VARIATION; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; MODELS, GENETIC; MODELS, STATISTICAL; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 77956880496     PISSN: 14654644     EISSN: 14684357     Source Type: Journal    
DOI: 10.1093/biostatistics/kxq043     Document Type: Article

References (25)

1. AUTISM GENOME PROJECT CONSORTIUM. (2007). "Mapping autism risk loci using genetic linkage and chromosomal rearrangements." Nature Genetics 39, 319-328.
2. BEROUKHIM, R., GETZ, G., NGHIEMPHU, L., BARRETINA, J., HSUEH, T., LINHART, D., VIVANCO, I., LEE, J. C., HUANG, J. H., ALEXANDER, S. and others (2007). Assessing the signifcance of chromosomal aberrations in cancer: Methodology and application to glioma. Proceedings of the National Academy of Sciences of the United States of America 104, 20007-20012.
3. CAPPUZZO, F., MARCHETTI, A., SKOKAN, M., ROSSI, E., GAJAPATHY, S., FELICIONI, L., GRAMMASTRO, M. D., SCIARROTTA, M. G., BUTTITTA, F., INCARBONE, M., and others (2009). Increased MET gene copy number negatively affects survival of surgically resected non-small-cell lung cancer patients. Journal of Clinical Oncology 27, 1667-1674.
4. CARVALHO, B. S., LOUIS, T. A. AND IRIZARRY, R. A. (2010). "Quantifying uncertainty in genotype calls." Bioinformatics 26(2), 242-249.
5. CARVALHO, M. A., MARSILLAC, S. M., KARCHIN, R., MANOUKIAN, S., GRIST, S., SWABY, R. F., URMENYI, T. P., RONDINELLI, E., SILVA, R., GAYOL, L. and others (2007). Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis. Cancer Research 67, 1494-1501.
6. GOLDEN HELIX. (2009). Copy Number Variation Analysis with SVS 7. Golden Helix Manual for SNP and Variation Suite. http://www.goldenhelix.com/SNP Variation/tutorials/cnv/introduction.html
7. GU, W., ZHANG, F.AND LUPSKI, J. R. (2008). Mechanisms for human genomic rearrangements. Pathogenetics 1, 4.
8. HUANG, J., WEI, W., CHEN, J., ZHANG, J., LIU, G., DI, X., MEI, R., ISHIKAWA, S., ABURATANI, H., JONES, K. W. and others (2006). CARAT: a novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays. BMC Bioinformatics, 7, 83.
9. KIDD, J. M., COOPER, G. M., DONAHUE, W. F., HAYDEN, H. S., SAMPAS, N., GRAVES, T., HANSEN, N., TEAGUE, B., ALKAN, C., ANTONACCI, F. and others (2008). Mapping and sequencing of structural variation from eight human genomes. Nature 453, 56-64.
10. KORN, J. M., KURUVILLA, F. G., MCCARROLL, S. A., WYSOKER, A., NEMESH, J., CAWLEY, S., HUBBELL, E., VEITCH, J., COLLINS, P. J., DARVISHI, K. and others (2008). Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nature Genetics 40, 1253-1260.
11. LAFRAMBOISE, T., HARRINGTON, D. AND WEIR, B. A. (2007). PLASQ: a generalized linear model-based procedure to determine allelic dosage in cancer cells from SNP array data. Biostatistics 8, 323-336.
12. LÖ NNSTEDT, I. AND SPEED, T. (2001). Replicated microarray data. Statistica Sinica 12, 31.
13. LUPSKI, J. R. (2009). Genomic disorders ten years on. Genome Medicine 1, 42.
14. MA, O., CAI, W.-W., ZENDER, L., DAYARAM, T., SHEN, J., HERRON, A. J., LOWE, S. W., MAN, T.-K., LAU, C. C. AND DONEHOWER, L. A. (2009). MMP13, Birc2 (cIAP1), and Birc3 (cIAP2), amplifed on chromosome 9, collaborate with p53 defciency in mouse osteosarcoma progression. Cancer Research 69, 2559-2567.
15. MARSHALL, C. R., NOOR, A., VINCENT, J. B., LIONEL, A. C., FEUK, L., SKAUG, J., SHAGO, M., MOESSNER, R., PINTO, D., REN, Y. AND OTHERS (2008). Structural variation of chromosomes in autism spectrum disorder. American Journal of Human Genetics 82, 477-488.
16. MCCARROLL, S. A., KURUVILLA, F. G., KORN, J. M., CAWLEY, S., NEMESH, J., WYSOKER, A., SHAPERO, M. H., DE BAKKER, P. I. W., MALLER, J. B., KIRBY, A. and others (2008). Integrated detection and population-genetic analysis of SNPs and copy number variation. Nature Genetics 40, 1166-1174.
17. MCKINNEY, C., MERRIMAN, M. E., CHAPMAN, P. T., GOW, P. J., HARRISON, A. A., HIGHTON, J., JONES, P. B. B., MCLEAN, L., O'DONNELL, J. L., POKORNY, V. and others (2008). Evidence for an infuence of chemokine ligand 3-like 1 (CCL3L1) gene copy number on susceptibility to rheumatoid arthritis. Annals of the Rheumatic Diseases 67, 409-413.
18. NEED, A. C., GE, D., WEALE, M. E., MAIA, J., FENG, S., HEINZEN, E. L., SHIANNA, K. V., YOON, W., KASPERAVICITE, D., GENNARELLI, M. and others (2009). A genome-wide investigation of SNPs and CNVs in schizophrenia. PLoS Genetics 5, e1000373.
19. REDON, R., ISHIKAWA, S., FITCH, K. R., FEUK, L., PERRY, G. H., ANDREWS, T. D., FIEGLER, H., SHAPERO, M. H., CARSON, A. R., CHEN, W. and others (2006). Global variation in copy number in the human genome. Nature 444, 444-454. (Pubitemid 44809057)
20. SCHARPF, R. B., PARMIGIANI, G., PEVSNER, J., AND RUCZINSKI, I. (2008) Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays. Annals of Applied Statistics 2, 687-713.
21. SUTRALA, S. R., GOOSSENS, D., WILLIAMS, N. M., HEYRMAN, L., ADOLFSSON, R., NORTON, N., BUCKLAND, P. R., AND DEL-FAVERO, J. (2007). Gene copy number variation in schizophrenia. Schizophrenia Research 96, 93-99.
22. WANG, W., CARVALHO, B., MILLER, N., PEVSNER, J., CHAKRAVARTI, A., AND IRIZARRY, R. A. (2008). Estimating genome-wide copy number using allele specifc mixture models. Journal of Computational Biology 15, 857-866.
23. WOO, H. G., PARK, E. S., LEE, J.-S., LEE, Y.-H., ISHIKAWA, T., KIM, Y. J. AND THORGEIRSSON, S. S. (2009). Identifcation of potential driver genes in human liver carcinoma by genomewide screening. Cancer Research 69, 4059-4066.
24. WU, Z. AND IRIZARRY, R. A. (2007). A statistical framework for the analysis of microarray probe-level data. Annals of Applied Statistics, 1, 333-357.
25. ZHANG, D., CHENG, L., QIAN, Y., ALLIEY-RODRIGUEZ, N., KELSOE, J. R., GREENWOOD, T., NIEVERGELT, C., BARRETT, T. B., MCKINNEY, R., SCHORK, N., and others (2008). Singleton deletions throughout the genome increase risk of bipolar disorder. Molecular Psychiatry 14, 376-380.