Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al: Initial sequencing and analysis of the human genome. Nature. 2001, 409 (6822): 860-921. 10.1038/35057062.
Article
CAS
PubMed
Google Scholar
Kruglyak L: Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat Genet. 1999, 22 (2): 139-144. 10.1038/9642.
Article
CAS
PubMed
Google Scholar
A haplotype map of the human genome. Nature. 2005, 437 (7063): 1299-1320. 10.1038/nature04226.
Eichler EE, Nickerson DA, Altshuler D, Bowcock AM, Brooks LD, Carter NP, Church DM, Felsenfeld A, Guyer M, Lee C, et al: Completing the map of human genetic variation. Nature. 2007, 447 (7141): 161-165. 10.1038/447161a.
Article
PubMed Central
CAS
PubMed
Google Scholar
Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C: Detection of large-scale variation in the human genome. Nat Genet. 2004, 36 (9): 949-951. 10.1038/ng1416.
Article
CAS
PubMed
Google Scholar
Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Maner S, Massa H, Walker M, Chi M, et al: Large-scale copy number polymorphism in the human genome. Science. 2004, 305 (5683): 525-528. 10.1126/science.1098918.
Article
CAS
PubMed
Google Scholar
Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, et al: Global variation in copy number in the human genome. Nature. 2006, 444 (7118): 444-454. 10.1038/nature05329.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sharp AJ, Locke DP, McGrath SD, Cheng Z, Bailey JA, Vallente RU, Pertz LM, Clark RA, Schwartz S, Segraves R, et al: Segmental duplications and copy-number variation in the human genome. Am J Hum Genet. 2005, 77 (1): 78-88. 10.1086/431652.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wong KK, deLeeuw RJ, Dosanjh NS, Kimm LR, Cheng Z, Horsman DE, MacAulay C, Ng RT, Brown CJ, Eichler EE, et al: A comprehensive analysis of common copy-number variations in the human genome. Am J Hum Genet. 2007, 80 (1): 91-104. 10.1086/510560.
Article
PubMed Central
CAS
PubMed
Google Scholar
Simon-Sanchez J, Scholz S, Fung HC, Matarin M, Hernandez D, Gibbs JR, Britton A, de Vrieze FW, Peckham E, Gwinn-Hardy K, et al: Genome-wide SNP assay reveals structural genomic variation, extended homozygosity and cell-line induced alterations in normal individuals. Hum Mol Genet. 2007, 16 (1): 1-14. 10.1093/hmg/ddl436.
Article
CAS
PubMed
Google Scholar
Conrad DF, Andrews TD, Carter NP, Hurles ME, Pritchard JK: A high-resolution survey of deletion polymorphism in the human genome. Nat Genet. 2006, 38 (1): 75-81. 10.1038/ng1697.
Article
CAS
PubMed
Google Scholar
Hinds DA, Kloek AP, Jen M, Chen X, Frazer KA: Common deletions and SNPs are in linkage disequilibrium in the human genome. Nat Genet. 2006, 38 (1): 82-85. 10.1038/ng1695.
Article
CAS
PubMed
Google Scholar
Khaja R, Zhang J, MacDonald JR, He Y, Joseph-George AM, Wei J, Rafiq MA, Qian C, Shago M, Pantano L, et al: Genome assembly comparison identifies structural variants in the human genome. Nat Genet. 2006, 38 (12): 1413-1418. 10.1038/ng1921.
Article
PubMed Central
CAS
PubMed
Google Scholar
Locke DP, Sharp AJ, McCarroll SA, McGrath SD, Newman TL, Cheng Z, Schwartz S, Albertson DG, Pinkel D, Altshuler DM, et al: Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome. Am J Hum Genet. 2006, 79 (2): 275-290. 10.1086/505653.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, Pertz LM, Haugen E, Hayden H, Albertson D, Pinkel D, et al: Fine-scale structural variation of the human genome. Nat Genet. 2005, 37 (7): 727-732. 10.1038/ng1562.
Article
CAS
PubMed
Google Scholar
Zogopoulos G, Ha KC, Naqib F, Moore S, Kim H, Montpetit A, Robidoux F, Laflamme P, Cotterchio M, Greenwood C, Scherer SW, Zanke B, Hudson TJ, Bader GD, Gallinger S: Germ-line DNA copy number variation frequencies in a large North American population. Hum Genet. 2007, 122: 345-353. 10.1007/s00439-007-0404-5.
Article
CAS
PubMed
Google Scholar
McCarroll SA, Hadnott TN, Perry GH, Sabeti PC, Zody MC, Barrett JC, Dallaire S, Gabriel SB, Lee C, Daly MJ, et al: Common deletion polymorphisms in the human genome. Nat Genet. 2006, 38 (1): 86-92. 10.1038/ng1696.
Article
CAS
PubMed
Google Scholar
Jakobsson J, Ekstrom L, Inotsume N, Garle M, Lorentzon M, Ohlsson C, Roh HK, Carlstrom K, Rane A: Large differences in testosterone excretion in Korean and Swedish men are strongly associated with a UDP-glucuronosyl transferase 2B17 polymorphism. J Clin Endocrinol Metab. 2006, 91 (2): 687-693. 10.1210/jc.2005-1643.
Article
CAS
PubMed
Google Scholar
Ouahchi K, Lindeman N, Lee C: Copy number variants and pharmacogenomics. Pharmacogenomics. 2006, 7 (1): 25-29. 10.2217/14622416.7.1.25.
Article
CAS
PubMed
Google Scholar
Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, Thorne N, Redon R, Bird CP, de Grassi A, Lee C, et al: Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science. 2007, 315 (5813): 848-853. 10.1126/science.1136678.
Article
PubMed Central
CAS
PubMed
Google Scholar
Gonzalez E, Kulkarni H, Bolivar H, Mangano A, Sanchez R, Catano G, Nibbs RJ, Freedman BI, Quinones MP, Bamshad MJ, et al: The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science. 2005, 307 (5714): 1434-1440. 10.1126/science.1101160.
Article
CAS
PubMed
Google Scholar
Aitman TJ, Dong R, Vyse TJ, Norsworthy PJ, Johnson MD, Smith J, Mangion J, Roberton-Lowe C, Marshall AJ, Petretto E, et al: Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans. Nature. 2006, 439 (7078): 851-855. 10.1038/nature04489.
Article
CAS
PubMed
Google Scholar
Yang Y, Chung EK, Wu YL, Savelli SL, Nagaraja HN, Zhou B, Hebert M, Jones KN, Shu Y, Kitzmiller K, et al: Gene copy-number variation and associated polymorphisms of complement component C4 in human systemic lupus erythematosus (SLE): low copy number is a risk factor for and high copy number is a protective factor against SLE susceptibility in European Americans. Am J Hum Genet. 2007, 80 (6): 1037-1054. 10.1086/518257.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sebat J, Lakshmi B, Malhotra D, Troge J, Lese-Martin C, Walsh T, Yamrom B, Yoon S, Krasnitz A, Kendall J, et al: Strong association of de novo copy number mutations with autism. Science. 2007, 316 (5823): 445-449. 10.1126/science.1138659.
Article
PubMed Central
CAS
PubMed
Google Scholar
Perry GH, Dominy NJ, Claw KG, Lee AS, Fiegler H, Redon R, Werner J, Villanea FA, Mountain JL, Misra R, et al: Diet and the evolution of human amylase gene copy number variation. Nat Genet. 2007, 39 (10): 1256-1260. 10.1038/ng2123.
Article
PubMed Central
CAS
PubMed
Google Scholar
Feuk L, Carson AR, Scherer SW: Structural variation in the human genome. Nat Rev Genet. 2006, 7 (2): 85-97. 10.1038/nrg1767.
Article
CAS
PubMed
Google Scholar
Feuk L, Marshall CR, Wintle RF, Scherer SW: Structural variants: changing the landscape of chromosomes and design of disease studies. Hum Mol Genet. 2006, 15 (Spec No 1): R57-66. 10.1093/hmg/ddl057.
Article
CAS
PubMed
Google Scholar
Inoue K, Lupski JR: Molecular mechanisms for genomic disorders. Annu Rev Genomics Hum Genet. 2002, 3: 199-242. 10.1146/annurev.genom.3.032802.120023.
Article
CAS
PubMed
Google Scholar
Lupski JR, Stankiewicz P: Genomic disorders: molecular mechanisms for rearrangements and conveyed phenotypes. PLoS Genet. 2005, 1 (6): e49-10.1371/journal.pgen.0010049.
Article
PubMed Central
PubMed
Google Scholar
Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L, et al: Paired-end mapping reveals extensive structural variation in the human genome. Science. 2007, 318 (5849): 420-426. 10.1126/science.1149504.
Article
PubMed Central
CAS
PubMed
Google Scholar
Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G, et al: The diploid genome sequence of an individual human. PLoS Biol. 2007, 5 (10): e254-10.1371/journal.pbio.0050254.
Article
PubMed Central
PubMed
Google Scholar
McCarrol SA, Hadnott TN, Perry GH, Sabeti PC, Zody MC, Barrett JC, Dallaire S, Gabriel SB, Lee C, Daly MJ, et al: Common deletion polymorphisms in the human genome. Nat Genet. 2006, 38 (1): 86-92. 10.1038/ng1696.
Article
Google Scholar
Beckmann JS, Estivill X, Antonarakis SE: Copy number variants and genetic traits: closer to the resolution of phenotypic to genotypic variability. Nat Rev Genet. 2007, 8 (8): 639-646. 10.1038/nrg2149.
Article
CAS
PubMed
Google Scholar
Speicher MR, Carter NP: The new cytogenetics: blurring the boundaries with molecular biology. Nat Rev Genet. 2005, 6 (10): 782-792. 10.1038/nrg1692.
Article
CAS
PubMed
Google Scholar
Carson AR, Feuk L, Mohammed M, Scherer SW: Strategies for the detection of copy number and other structural variants in the human genome. Hum Genomics. 2006, 2 (6): 403-414.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lucito R, Healy J, Alexander J, Reiner A, Esposito D, Chi M, Rodgers L, Brady A, Sebat J, Troge J, et al: Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. Genome Res. 2003, 13 (10): 2291-2305. 10.1101/gr.1349003.
Article
PubMed Central
CAS
PubMed
Google Scholar
Komura D, Shen F, Ishikawa S, Fitch KR, Chen W, Zhang J, Liu G, Ihara S, Nakamura H, Hurles ME, et al: Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays. Genome Res. 2006, 16 (12): 1575-1584. 10.1101/gr.5629106.
Article
PubMed Central
CAS
PubMed
Google Scholar
Fujii K, Ishikawa S, Uchikawa H, Komura D, Shapero MH, Shen F, Hung J, Arai H, Tanaka Y, Sasaki K, et al: High-density oligonucleotide array with sub-kilobase resolution reveals breakpoint information of submicroscopic deletions in nevoid basal cell carcinoma syndrome. Hum Genet. 2007, 122 (5): 459-466. 10.1007/s00439-007-0419-y.
Article
CAS
PubMed
Google Scholar
Kennedy GC, Matsuzaki H, Dong S, Liu WM, Huang J, Liu G, Su X, Cao M, Chen W, Zhang J, et al: Large-scale genotyping of complex DNA. Nat Biotechnol. 2003, 21 (10): 1233-1237. 10.1038/nbt869.
Article
CAS
PubMed
Google Scholar
Matsuzaki H, Loi H, Dong S, Tsai YY, Fang J, Law J, Di X, Liu WM, Yang G, Liu G, et al: Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array. Genome Res. 2004, 14 (3): 414-425. 10.1101/gr.2014904.
Article
PubMed Central
CAS
PubMed
Google Scholar
Matsuzaki H, Dong S, Loi H, Di X, Liu G, Hubbell E, Law J, Berntsen T, Chadha M, Hui H, et al: Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays. Nat Methods. 2004, 1 (2): 109-111. 10.1038/nmeth718.
Article
CAS
PubMed
Google Scholar
Gardina PJ, Clark TA, Shimada B, Staples MK, Yang Q, Veitch J, Schweitzer A, Awad T, Sugnet C, Dee S, et al: Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array. BMC Genomics. 2006, 7: 325-10.1186/1471-2164-7-325.
Article
PubMed Central
PubMed
Google Scholar
Fredman D, White SJ, Potter S, Eichler EE, Den Dunnen JT, Brookes AJ: Complex SNP-related sequence variation in segmental genome duplications. Nat Genet. 2004, 36 (8): 861-866. 10.1038/ng1401.
Article
CAS
PubMed
Google Scholar
McCarroll SA, Altshuler DM: Copy-number variation and association studies of human disease. Nat Genet. 2007
Google Scholar
Newman TL, Rieder MJ, Morrison VA, Sharp AJ, Smith JD, Sprague LJ, Kaul R, Carlson CS, Olson MV, Nickerson DA, et al: High-throughput genotyping of intermediate-size structural variation. Hum Mol Genet. 2006, 15 (7): 1159-1167. 10.1093/hmg/ddl031.
Article
CAS
PubMed
Google Scholar
Pinto D, Marshall C, Feuk L, Scherer SW: Copy-number variation in control population cohorts. Hum Mol Genet. 2007, 16 (Spec No 2): R168-173. 10.1093/hmg/ddm241.
Article
CAS
PubMed
Google Scholar
McCarroll SA, Altshuler DM: Copy-number variation and association studies of human disease. Nat Genet. 2007, 39 (7 Suppl): S37-42. 10.1038/ng2080.
Article
CAS
PubMed
Google Scholar
Scherer SW, Lee C, Birney E, Altshuler DM, Eichler EE, Carter NP, Hurles ME, Feuk L: Challenges and standards in integrating surveys of structural variation. Nat Genet. 2007, 39 (7 Suppl): S7-15. 10.1038/ng2093.
Article
PubMed Central
CAS
PubMed
Google Scholar
Irizarry RA, Wu Z, Jaffee HA: Comparison of Affymetrix GeneChip expression measures. Bioinformatics. 2006, 22 (7): 789-794. 10.1093/bioinformatics/btk046.
Article
CAS
PubMed
Google Scholar
Komura D, Nishimura K, Ishikawa S, Panda B, Huang J, Nakamura H, Ihara S, Hirose M, Jones KW, Aburatani H: Noise reduction from genotyping microarrays using probe level information. In Silico Biol. 2006, 6 (1–2): 79-92.
CAS
PubMed
Google Scholar
Huang J, Wei W, Chen J, Zhang J, Liu G, Di X, Mei R, Ishikawa S, Aburatani H, Jones KW, et al: CARAT: a novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays. BMC Bioinformatics. 2006, 7: 83-10.1186/1471-2105-7-83.
Article
PubMed Central
PubMed
Google Scholar
Nannya Y, Sanada M, Nakazaki K, Hosoya N, Wang L, Hangaishi A, Kurokawa M, Chiba S, Bailey DK, Kennedy GC, et al: A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays. Cancer Res. 2005, 65 (14): 6071-6079. 10.1158/0008-5472.CAN-05-0465.
Article
CAS
PubMed
Google Scholar
Price TS, Regan R, Mott R, Hedman A, Honey B, Daniels RJ, Smith L, Greenfield A, Tiganescu A, Buckle V, et al: SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data. Nucleic Acids Res. 2005, 33 (11): 3455-3464. 10.1093/nar/gki643.
Article
PubMed Central
CAS
PubMed
Google Scholar
Olshen AB, Venkatraman ES, Lucito R, Wigler M: Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics. 2004, 5 (4): 557-572. 10.1093/biostatistics/kxh008.
Article
PubMed
Google Scholar
Carter NP: Methods and strategies for analyzing copy number variation using DNA microarrays. Nat Genet. 2007, 39 (7 Suppl): S16-21. 10.1038/ng2028.
Article
PubMed Central
CAS
PubMed
Google Scholar
Fodor SP, Rava RP, Huang XC, Pease AC, Holmes CP, Adams CL: Multiplexed biochemical assays with biological chips. Nature. 1993, 364 (6437): 555-556. 10.1038/364555a0.
Article
CAS
PubMed
Google Scholar
Fodor SP, Read JL, Pirrung MC, Stryer L, Lu AT, Solas D: Light-directed, spatially addressable parallel chemical synthesis. Science. 1991, 251 (4995): 767-773. 10.1126/science.1990438.
Article
CAS
PubMed
Google Scholar
Pease AC, Solas D, Sullivan EJ, Cronin MT, Holmes CP, Fodor SP: Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc Natl Acad Sci USA. 1994, 91 (11): 5022-5026. 10.1073/pnas.91.11.5022.
Article
PubMed Central
CAS
PubMed
Google Scholar
Scherer SW, Lee C, Birney E, Altshuler DM, Eichler EE, Carter NP, Hurles ME, Feuk L: Challenges and standards in integrating surveys of structural variation. Nat Genet. 2007, 39 (7 Suppl): S7-15. 10.1038/ng2093.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sharp AJ, Cheng Z, Eichler EE: Structural variation of the human genome. Annu Rev Genomics Hum Genet. 2006, 7: 407-442. 10.1146/annurev.genom.7.080505.115618.
Article
CAS
PubMed
Google Scholar
Pinto D, Marshall C, Feuk L, Scherer SW: Copy-number variation in control population cohorts. Hum Mol Genet. 2007, 16 (Spec No 2): R168-173. 10.1093/hmg/ddm241.
Article
CAS
PubMed
Google Scholar
Carter NP: Methods and strategies for analyzing copy number variation using DNA microarrays. Nat Genet. 2007, 39 (7 Suppl): S16-21. 10.1038/ng2028.
Article
PubMed Central
CAS
PubMed
Google Scholar
Affymetrix. [http://www.affymetrix.com]
Fujii K, Ishikawa S, Uchikawa H, Komura D, Shapero MH, Shen F, Hung J, Arai H, Tanaka Y, Sasaki K, et al: High-density oligonucleotide array with sub-kilobase resolution reveals breakpoint information of submicroscopic deletions in nevoid basal cell carcinoma syndrome. Hum Genet. 2007
Google Scholar
Lee C, Iafrate AJ, Brothman AR: Copy number variations and clinical cytogenetic diagnosis of constitutional disorders. Nat Genet. 2007, 39 (7 Suppl): S48-54. 10.1038/ng2092.
Article
CAS
PubMed
Google Scholar
Mei R, Hubbell E, Bekiranov S, Mittmann M, Christians FC, Shen MM, Lu G, Fang J, Liu WM, Ryder T, et al: Probe selection for high-density oligonucleotide arrays. Proc Natl Acad Sci USA. 2003, 100 (20): 11237-11242. 10.1073/pnas.1534744100.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ishikawa S, Komura D, Tsuji S, Nishimura K, Yamamoto S, Panda B, Huang J, Fukayama M, Jones KW, Aburatani H: Allelic dosage analysis with genotyping microarrays. Biochem Biophys Res Commun. 2005, 333 (4): 1309-1314. 10.1016/j.bbrc.2005.06.040.
Article
CAS
PubMed
Google Scholar
dbSNP. [http://www.ncbi.nlm.nih.gov/SNP]
Li WC, Brown M, Liu XS: xMAN: extreme Mapping of OligoNucleotides. BMC Genomics. 2008, 9 (Suppl 1): S20-10.1186/1471-2164-9-S1-S20.
Article
PubMed Central
PubMed
Google Scholar
Wu Z, Irizarry R, Gentleman R, Martinez-Murillo F, Spencer F: A model based background adjustment for oligonucleotide expression arrays. J Amer Stat Assoc. 2004, 99: 909-917. 10.1198/016214504000000683.
Article
Google Scholar
Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M, Liu XS: Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci USA. 2006, 103 (33): 12457-12462. 10.1073/pnas.0601180103.
Article
PubMed Central
CAS
PubMed
Google Scholar
Carvalho B, Bengtsson H, Speed TP, Irizarry RA: Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics. 2007, 8 (2): 485-499. 10.1093/biostatistics/kxl042.
Article
PubMed
Google Scholar
Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP: Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 2003, 31 (4): e15-10.1093/nar/gng015.
Article
PubMed Central
PubMed
Google Scholar
Abecasis G, Tam PK, Bustamante CD, Ostrander EA, Scherer SW, Chanock SJ, Kwok PY, Brookes AJ: Human Genome Variation 2006: emerging views on structural variation and large-scale SNP analysis. Nat Genet. 2007, 39 (2): 153-155. 10.1038/ng0207-153.
Article
CAS
PubMed
Google Scholar
Breiman L, Friedman J, Olshen R, Stone C: Classification and Regression Trees. 1984, Chapman & Hall, New York
Google Scholar
Benjamini Y, Hochberg Y: Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society. 1995, 57 (1): 289-300.
Google Scholar
Hochberg Y, Benjamini Y: More powerful procedures for multiple significance testing. Stat Med. 1990, 9 (7): 811-818. 10.1002/sim.4780090710.
Article
CAS
PubMed
Google Scholar
Di X, Matsuzaki H, Webster TA, Hubbell E, Liu G, Dong S, Bartell D, Huang J, Chiles R, Yang G, et al: Dynamic model based algorithms for screening and genotyping over 100 K SNPs on oligonucleotide microarrays. Bioinformatics. 2005, 21 (9): 1958-1963. 10.1093/bioinformatics/bti275.
Article
CAS
PubMed
Google Scholar
Gene Expression Omnibus. [http://www.ncbi.nlm.nih.gov/geo/]
Segmental duplication data source. [http://projects.tcag.ca/humandup/segmental_b35]