Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs
Tóm tắt
Từ khóa
Tài liệu tham khảo
Rabbee, N. & Speed, T.P. A genotype calling algorithm for affymetrix SNP arrays. Bioinformatics 22, 7–12 (2006).
Nicolae, D.L., Wu, X., Miyake, K. & Cox, N.J. GEL: a novel genotype calling algorithm using empirical likelihood. Bioinformatics 22, 1942–1947 (2006).
McCarroll, S.A. et al. Common deletion polymorphisms in the human genome. Nat. Genet. 38, 86–92 (2006).
Conrad, D.F., Andrews, T.D., Carter, N.P., Hurles, M.E. & Pritchard, J.K. A high-resolution survey of deletion polymorphism in the human genome. Nat. Genet. 38, 75–81 (2006).
McCarroll, S.A. & Altshuler, D.M. Copy-number variation and association studies of human disease. Nat. Genet. 39 (Suppl.), S37–S42 (2007).
McCarroll, S.A. et al. Integrated detection and population-genetic analysis of SNPs and copy-number variation. Nat. Genet. advance online publication, 10.1038/ng.238 (7 September 2008).
Komura, D. et al. Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays. Genome Res. 16, 1575–1584 (2006).
Fiegler, H. et al. Accurate and reliable high-throughput detection of copy number variation in the human genome. Genome Res. 16, 1566–1574 (2006).
Olshen, A.B., Venkatraman, E.S., Lucito, R. & Wigler, M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5, 557–572 (2004).
Wang, K. et al. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res. 17, 1665–1674 (2007).
Bengtsson, H., Irizarry, R., Carvalho, B. & Speed, T.P. Estimation and assessment of raw copy numbers at the single locus level. Bioinformatics 24, 759–767 (2008); published online 19 January 2008.
The International HapMap Consortium. A haplotype map of the human genome. Nature 437, 1299–1320 (2005).
Macconaill, L.E., Aldred, M.A., Lu, X. & Laframboise, T. Toward accurate high-throughput SNP genotyping in the presence of inherited copy number variation. BMC Genomics 8, 211 (2007).
Dempster, A.P., Laird, N.M. & Rubin, D.B. Maximum likelihood from incomplete data via the EM algorithm. J. Roy. Statist. Soc. B 39, 1–38 (1977).
Viterbi, A.J. Error bounds for convolutional codes and an asymptotically optimum decoding algorithm. IEEE Trans Info Theory IT-13, 260–269 (1967).
Sebat, J. et al. Strong association of de novo copy number mutations with autism. Science 316, 445–449 (2007).
Laframboise, T., Harrington, D. & Weir, B.A. PLASQ: a generalized linear model-based procedure to determine allelic dosage in cancer cells from SNP array data. Biostatistics 8, 323–336 (2007).
Kidd, J.M. et al. Mapping and sequencing of structural variation from eight human genomes. Nature 453, 56–64 (2008).
Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007).
Clayton, D.G. et al. Population structure, differential bias and genomic control in a large-scale, case-control association study. Nat. Genet. 37, 1243–1246 (2005).
Weiss, L.A. et al. Association between microdeletion and microduplication at 16p11.2 and autism. N. Engl. J. Med. 358, 667–675 (2008); published online 9 January 2008.