参考文献:第9章 变异检测
Dohm, J. C., et al. 2008. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res. 36(16): e105. [PubMed]
Lee, D., et al. 2015. Fast and accurate mapping of Complete Genomics reads. Methods. 79-80: 3-10. [PubMed]
Li, H., et al. 2008. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18(11): 1851-1858. [PubMed]
McCarroll, S. A., et al. 2008. Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet. 40(10): 1166-1174. [PubMed]
McKenna, A., et al. 2010. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20(9): 1297-1303. [PubMed]
Rozowsky, J., et al. 2009. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol. 27(1): 66-75. [PubMed]
Zhang, F., et al. 2009. Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet. 10: 451-481. [PubMed]
Altshuler, D. M., et al. 2010. Integrating common and rare genetic variation in diverse human populations. Nature. 467(7311): 52-58. [PubMed]
Bailey, J. A., et al. 2002. Recent segmental duplications in the human genome. Science. 297(5583): 1003-1007. [PubMed]
Barreiro, L. B., et al. 2008. Natural selection has driven population differentiation in modern humans. Nat Genet. 40(3): 340-345. [PubMed]
Bentley, D. R., et al. 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 456(7218): 53-59. [PubMed]
Berger, J., et al. 2001. Genetic mapping with SNP markers in Drosophila. Nat Genet. 29(4): 475-481. [PubMed]
Cardoso-Moreira, M. M. and M. Long. 2010. Mutational bias shaping fly copy number variation: implications for genome evolution. Trends Genet. 26(6): 243-247. [PubMed]
Carreto, L., et al. 2008. Comparative genomics of wild type yeast strains unveils important genome diversity. BMC Genomics. 9: 524. [PubMed]
Carter, N. P. 2007. Methods and strategies for analyzing copy number variation using DNA microarrays. Nat Genet. 39(7 Suppl): S16-21. [PubMed]
Cartwright, R. A. 2009. Problems and solutions for estimating indel rates and length distributions. Mol Biol Evol. 26(2): 473-480. [PubMed]
Chen, K., et al. 2009. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods. 6(9): 677-681. [PubMed]
Chew, M. 2000. Cracking the code: how will the Human Genome Project affect life as we know it? Med J Aust. 173(11-12): 590. [PubMed]
Chiang, D. Y., et al. 2009. High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods. 6(1): 99-103. [PubMed]
Collins, F. S., et al. 1987. Construction of a general human chromosome jumping library, with application to cystic fibrosis. Science. 235(4792): 1046-1049. [PubMed]
Conrad, D. F., et al. 2006. A high-resolution survey of deletion polymorphism in the human genome. Nat Genet. 38(1): 75-81. [PubMed]
Cooper, G. M., et al. 2008. Systematic assessment of copy number variant detection via genome-wide SNP genotyping. Nat Genet. 40(10): 1199-1203. [PubMed]
Daly, M. J., et al. 2001. High-resolution haplotype structure in the human genome. Nat Genet. 29(2): 229-232. [PubMed]
Dumas, L., et al. 2007. Gene copy number variation spanning 60 million years of human and primate evolution. Genome Res. 17(9): 1266-1277. [PubMed]
Graubert, T. A., et al. 2007. A high-resolution map of segmental DNA copy number variation in the mouse genome. PLoS Genet. 3(1): e3. [PubMed]
Hastings, P. J., et al. 2009. Mechanisms of change in gene copy number. Nat Rev Genet. 10(8): 551-564. [PubMed]
Hormozdiari, F., et al. 2011. Sensitive and fast mapping of di-base encoded reads. Bioinformatics. 27(14): 1915-1921. [PubMed]
Hyten, D. L., et al. 2010. High-throughput SNP discovery and assay development in common bean. BMC Genomics. 11: 475. [PubMed]
Iafrate, A. J., et al. 2004. Detection of large-scale variation in the human genome. Nat Genet. 36(9): 949-951. [PubMed]
Judson, R., et al. 2002. How many SNPs does a genome-wide haplotype map require? Pharmacogenomics. 3(3): 379-391. [PubMed]
Kidd, J. M., et al. 2008. Mapping and sequencing of structural variation from eight human genomes. Nature. 453(7191): 56-64. [PubMed]
Kim, T. M., et al. 2010. rSW-seq: algorithm for detection of copy number alterations in deep sequencing data. BMC Bioinformatics. 11: 432. [PubMed]
Klein, R. J., et al. 2005. Complement factor H polymorphism in age-related macular degeneration. Science. 308(5720): 385-389. [PubMed]
Koboldt, D. C., et al. 2009. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics. 25(17): 2283-2285. [PubMed]
Kondrashov, A. S. and I. B. Rogozin. 2004. Context of deletions and insertions in human coding sequences. Hum Mutat. 23(2): 177-185. [PubMed]
Korbel, J. O., et al. 2007. Paired-end mapping reveals extensive structural variation in the human genome. Science. 318(5849): 420-426. [PubMed]
Krawitz, P., et al. 2010. Microindel detection in short-read sequence data. Bioinformatics. 26(6): 722-729. [PubMed]
Lee, A. S., et al. 2008. Analysis of copy number variation in the rhesus macaque genome identifies candidate loci for evolutionary and human disease studies. Hum Mol Genet. 17(8): 1127-1136. [PubMed]
Li, H., et al. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 25(16): 2078-2079. [PubMed]
Li, R., et al. 2009. SNP detection for massively parallel whole-genome resequencing. Genome Res. 19(6): 1124-1132. [PubMed]
Lunter, G. 2007. Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes. Bioinformatics. 23(13): i289-296. [PubMed]
Lupski, J. R. 2007. An evolution revolution provides further revelation. Bioessays. 29(12): 1182-1184. [PubMed]
Malats, N. and F. Calafell. 2003. Basic glossary on genetic epidemiology. J Epidemiol Community Health. 57(7): 480-482. [PubMed]
McCarroll, S. A., et al. 2006. Common deletion polymorphisms in the human genome. Nat Genet. 38(1): 86-92. [PubMed]
Nachman, M. W. 2001. Single nucleotide polymorphisms and recombination rate in humans. Trends Genet. 17(9): 481-485. [PubMed]
Ng, S. B., et al. 2010. Exome sequencing identifies the cause of a mendelian disorder. Nat Genet. 42(1): 30-35. [PubMed]
Nguyen, D. Q., et al. 2008. Reduced purifying selection prevails over positive selection in human copy number variant evolution. Genome Res. 18(11): 1711-1723. [PubMed]
Ogurtsov, A. Y., et al. 2004. Indel-based evolutionary distance and mouse-human divergence. Genome Res. 14(8): 1610-1616. [PubMed]
Ossowski, S., et al. 2008. Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res. 18(12): 2024-2033. [PubMed]
Patil, N., et al. 2001. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science. 294(5547): 1719-1723. [PubMed]
Perry, G. H., et al. 2006. Hotspots for copy number variation in chimpanzees and humans. Proc Natl Acad Sci U S A. 103(21): 8006-8011. [PubMed]
Perry, G. H., et al. 2008. Copy number variation and evolution in humans and chimpanzees. Genome Res. 18(11): 1698-1710. [PubMed]
Pinkel, D., et al. 1998. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet. 20(2): 207-211. [PubMed]
Qi, J., et al. 2010. inGAP: an integrated next-generation genome analysis pipeline. Bioinformatics. 26(1): 127-129. [PubMed]
Queller, D. C., et al. 1993. Microsatellites and kinship. Trends Ecol Evol. 8(8): 285-288. [PubMed]
Redon, R., et al. 2006. Global variation in copy number in the human genome. Nature. 444(7118): 444-454. [PubMed]
Saiki, R. K., et al. 1985. Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science. 230(4732): 1350-1354. [PubMed]
Saxena, R., et al. 2007. Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science. 316(5829): 1331-1336. [PubMed]
Schuster, S. C. 2008. Next-generation sequencing transforms today's biology. Nat Methods. 5(1): 16-18. [PubMed]
Sebat, J., et al. 2004. Large-scale copy number polymorphism in the human genome. Science. 305(5683): 525-528. [PubMed]
She, X., et al. 2008. Mouse segmental duplication and copy number variation. Nat Genet. 40(7): 909-914. [PubMed]
Shendure, J. 2008. The beginning of the end for microarrays? Nat Methods. 5(7): 585-587. [PubMed]
Smith, D. R., et al. 2008. Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res. 18(10): 1638-1642. [PubMed]
Solinas-Toldo, S., et al. 1997. Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer. 20(4): 399-407. [PubMed]
Stankiewicz, P. and J. R. Lupski. 2002. Genome architecture, rearrangements and genomic disorders. Trends Genet. 18(2): 74-82. [PubMed]
Stankiewicz, P. and J. R. Lupski. 2010. Structural variation in the human genome and its role in disease. Annu Rev Med. 61: 437-455. [PubMed]
Stephens, J. C., et al. 2001. Haplotype variation and linkage disequilibrium in 313 human genes. Science. 293(5529): 489-493. [PubMed]
Stranger, B. E., et al. 2007. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science. 315(5813): 848-853. [PubMed]
Stuber, F., et al. 1996. A genomic polymorphism within the tumor necrosis factor locus influences plasma tumor necrosis factor-alpha concentrations and outcome of patients with severe sepsis. Crit Care Med. 24(3): 381-384. [PubMed]
The International HapMap Consortium. 2005. A haplotype map of the human genome. Nature. 437(7063): 1299-1320. [PubMed]
Tuzun, E., et al. 2005. Fine-scale structural variation of the human genome. Nat Genet. 37(7): 727-732. [PubMed]
van Ommen, G. J. 2005. Frequency of new copy number variation in humans. Nat Genet. 37(4): 333-334. [PubMed]
Vignal, A., et al. 2002. A review on SNP and other types of molecular markers and their use in animal genetics. Genet Sel Evol. 34(3): 275-305. [PubMed]
Wang, D. G., et al. 1998. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science. 280(5366): 1077-1082. [PubMed]
Wang, J., et al. 2008. The diploid genome sequence of an Asian individual. Nature. 456(7218): 60-65. [PubMed]
Warren, S. T., et al. 1987. The fragile X site in somatic cell hybrids: an approach for molecular cloning of fragile sites. Science. 237(4813): 420-423. [PubMed]
Wicks, S. R., et al. 2001. Rapid gene mapping in Caenorhabditis elegans using a high density polymorphism map. Nat Genet. 28(2): 160-164. [PubMed]
Xie, C. and M. T. Tammi. 2009. CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics. 10: 80. [PubMed]
Ye, K., et al. 2009. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics. 25(21): 2865-2871. [PubMed]
Yoon, S., et al. 2009. Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res. 19(9): 1586-1592. [PubMed]
Zhang, K., et al. 2004. Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies. Genome Res. 14(5): 908-916. [PubMed]