A pipeline for copy number variation detection based on principal component analysis

Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS

Volumn , Issue , 2011, Pages 6975-6978

  Chen, Jiayu ^a,b   Liu, Jingyu ^a,b   Boutte, David ^b   Calhoun, Vince D ^a,b  

^a University of New Mexico   (United States)

^b MIND RESEARCH NETWORK   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COPY NUMBER; DATA CORRECTIONS; DATA QUALITY; DATA SETS; FALSE POSITIVE RATES; HUMAN GENOMES; LOW SIGNAL-TO-NOISE RATIO; POTENTIAL EFFECTS; STRUCTURAL VARIATIONS; SUBSTANTIAL REDUCTION; TESTED DATA;

SIGNAL TO NOISE RATIO;

PRINCIPAL COMPONENT ANALYSIS;

DNA;

ADULT; ANALYSIS OF VARIANCE; ARTICLE; COMPUTER SIMULATION; COPY NUMBER VARIATION; FEMALE; GENETIC PREDISPOSITION; GENOTYPE; HUMAN; HUMAN GENOME; LABORATORY DIAGNOSIS; MALE; NORMAL DISTRIBUTION; PRINCIPAL COMPONENT ANALYSIS; REPRODUCIBILITY; SIGNAL PROCESSING; SINGLE NUCLEOTIDE POLYMORPHISM;

ADULT; ANALYSIS OF VARIANCE; COMPUTER SIMULATION; DNA; DNA COPY NUMBER VARIATIONS; FALSE POSITIVE REACTIONS; FEMALE; GENETIC PREDISPOSITION TO DISEASE; GENOME, HUMAN; GENOTYPE; HUMANS; MALE; NORMAL DISTRIBUTION; POLYMORPHISM, SINGLE NUCLEOTIDE; PRINCIPAL COMPONENT ANALYSIS; REPRODUCIBILITY OF RESULTS; SIGNAL PROCESSING, COMPUTER-ASSISTED;

EID: 84864615967     PISSN: 1557170X     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/IEMBS.2011.6091763     Document Type: Conference Paper

References (20)

1. J. S. Beckmann, et al., "Copy number variants and genetic traits: closer to the resolution of phenotypic to genotypic variability," Nat Rev Genet, Vol. 8, pp. 639-646, 2007.
2. A. Shlien, et al., "Excessive genomic DNA copy number variation in the Li-Fraumeni cancer predisposition syndrome," P Natl Acad Sci USA, Vol. 105, pp. 11264-11269, 2008.
3. E. Gonzalez, et al., "The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility," Science, Vol. 307, pp. 1434-1440, 2005.
4. J. Sebat, et al., "Strong association of de novo copy number mutations with autism," Science, Vol. 316, pp. 445-449, 2007.
5. L. A. Weiss, et al., "Association between microdeletion and microduplication at 16p11.2 and autism," New Engl J Med, Vol. 358, pp. 667-675, 2008.
6. T. Walsh, et al., "Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia," Science, Vol. 320, pp. 539-543, 2008.
7. J. L. Stone, et al., "Rare chromosomal deletions and duplications increase risk of schizophrenia," Nature, Vol. 455, pp. 237-241, 2008.
8. J. R. Pollack, et al., "Genome-wide analysis of DNA copy-number changes using cDNA microarrays," Nat Genet, Vol. 23, pp. 41-46, 1999.
9. R. Mei, et al., "Genome-wide detection of allelic imbalance using human SNPs and high-density DNA arrays," Genome Res, Vol. 10, pp. 1126-1137, 2000.
10. D. J. Schaid, et al., "Comparison of microsatellites versus singlenucleotide polymorphisms in a genome linkage screen for prostate cancer-susceptibility loci," Am J Hum Genet, Vol. 75, pp. 948-965, 2004.
11. N. P. Carter, "Methods and strategies for analyzing copy number variation using DNA microarrays," Nat Genet, Vol. 39, pp. S16-S21, 2007.
12. L. Bernardini, et al., "High-resolution SNP arrays in mental retardation diagnostics: how much do we gain?," Eur J Hum Genet, Vol. 18, pp. 178-185, 2010.
13. S. W. Scherer, et al., "Challenges and standards in integrating surveys of structural variation," Nat Genet, Vol. 39, pp. S7-S15, 2007.
14. K. Wang, et al., "PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data," Genome Res, Vol. 17, pp. 1665-1674, 2007.
15. S. J. Diskin, et al., "Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms," Nucleic Acids Res, Vol. 36, pp. e126, 2008.
16. A. B. Olshen, et al., "Circular binary segmentation for the analysis of array-based DNA copy number data," Biostatistics, Vol. 5, pp. 557- 572, 2004.
17. A. C. Need, et al., "A Genome-Wide Investigation of SNPs and CNVs in Schizophrenia," Plos Genet, Vol. 5, pp. e1000373, 2009.
18. M. Bucan, et al., "Genome-Wide Analyses of Exonic Copy Number Variants in a Family-Based Study Point to Novel Autism Susceptibility Genes," Plos Genet, Vol. 5, pp. e1000536, 2009.
19. Y. Nannya, et al., "A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays," Cancer Res, Vol. 65, pp. 6071-6079, 2005.
20. Illumina, "Interpreting Infinium Assay Data for Whole-Genome Structural Variation," Technical Note: DNA Analysis.