Software comparison for evaluating genomic copy number variation for Affymetrix 6.0 SNP array platform

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Eckel Passow, Jeanette E ^a   Atkinson, Elizabeth J ^a   Maharjan, Sooraj ^a   Kardia, Sharon L R ^b   de Andrade, Mariza ^a  

^a MAYO CLINIC   (United States)

^b UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIAS AND VARIANCE; COPY NUMBER DATUM; COPY NUMBER VARIATIONS; GENOME-WIDE ASSOCIATION STUDIES; MULTIPLE ALGORITHMS; PROVIDE GUIDANCES; SOFTWARE COMPARISONS; SOFTWARE DEVELOPER;

GENES; HIDDEN MARKOV MODELS; OPTIMIZATION; SOFTWARE PACKAGES; STATISTICAL TESTS;

QUALITY CONTROL;

ALGORITHM; ARTICLE; COMPUTER PROGRAM; COPY NUMBER VARIATION; DNA MICROARRAY; GENE DOSAGE; GENETIC ASSOCIATION; GENOME; GENOTYPE; HUMAN; HUMAN GENOME; METHODOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; DNA COPY NUMBER VARIATIONS; GENE DOSAGE; GENOME; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE;

EID: 79957638660     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-220     Document Type: Article

References (15)

1. Scharpf RB, Ruczinski I, Carvalho B, Doan B, Chakravarti A, Irizarry RA. A multilevel model to address batch effects in copy number estimation using SNP arrays. Biostatistics 2011, 12:33-50. 10.1093/biostatistics/kxq043, 20625178.
2. Baross A, Delaney AD, Li HI, Nayar T, Flibotte S, Qian H, Chan SY, Asano J, Ally A, Cao M, Birch P, Brown-John M, Fernandes N, Go A, Kennedy G, Langlois S, Eydoux P, Friedman JM, Marra MA. Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data. BMC Bioinformatics 2007, 8:368. 10.1186/1471-2105-8-368, 2148068, 17910767.
3. Winchester L, Yau C, Ragoussis J. Comparing CNV detection methods for SNP arrays. Briefings in Functional Genomics and Proteomics 2009, 8:353-366. 10.1093/bfgp/elp017, 19737800.
4. Wang K, Li M, Hadley D, Liu R, Glessner J, Grant S, Hakonarson H, Bucan M. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Research 2007, 17:1665-1674. 10.1101/gr.6861907, 2045149, 17921354.
5. Bengtsson H, Wirapati P, Speed T. GenomeWideSNP 5 & 6. Bioinformatics 2009, 25(17):2149-2156. 10.1093/bioinformatics/btn016, 18204055.
6. Bengtsson H, Simpson K, Bullard J, Hansen K. Aroma.affymetrix: A generic framework in R for analyzing small to very large Affymetrix data sets in bounded memory. Report 745, Department of Statistics, University of California, Berkeley, 2008
7. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Exploration, normalization and summaries of high density oligonucleotide array proble level data. Biostatistics 2003, 4:249-264. 10.1093/biostatistics/4.2.249, 12925520.
8. Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19:185-193. 10.1093/bioinformatics/19.2.185, 12538238.
9. Marioni JC, Thorne NP, Valsesia A, Fitzgerald T, Redon R, Fiegler H, Andrews TD, Stranger BE, Lynch AG, Dermitzakis ET, Carter NP, Tavaré S, Hurles ME. Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization. Genome Biology 2007, 8:R228. 10.1186/gb-2007-8-10-r228, 2246302, 17961237.
10. Diskin SJ, Li M, Hou C, Yang S, Glessner J, Hakonarson H, Bucan M, Maris JM, Wang K. Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms. Nucleic Acids Research 2008, 36:e126. 10.1093/nar/gkn556, 2577347, 18784189.
11. Altman DG, Bland JM. Measurement in medicine: the analysis of method comparison studies. The Statistician 1983, 32:307-317.
12. Scharpf RB, Parmigiani G, Pevsner J, Ruczinski I. Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays. The Annals of Applied Statistics 2008, 2:687-713. 10.1214/07-AOAS155, 2710854, 19609370.
13. The 1000 Genomes Project Consortium A map of human genome variation from population - scale sequencing. Nature 2010, 467:1061-1073. 10.1038/nature09534, 3042601, 20981092, The 1000 Genomes Project Consortium.
14. Oldridge DA, Banerjee S, Setlur SR, Sboner A, Demichelis F. Optimizing copy number variation analysis using genome-wide short sequence oligonucleotide arrays. Nucleic Acids Research 2010, 38:3275-86. 10.1093/nar/gkq073, 2879534, 20156996.
15. Lai WR, Johnson MD, Kucherlapati R, Park PJ. Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics 2005, 21:3763-70. 10.1093/bioinformatics/bti611, 2819184, 16081473.