Chapter 2 - University of British Columbia

75. Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, Nair P, Brothman AR, Stallings
RL: Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase
resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes
Cancer 2005, 44(3):305-319.
76. Zhao X, Li C, Paez JG, Chin K, Janne PA, Chen TH, Girard L, Minna J, Christiani D, Leo
C et al: An integrated view of copy number and allelic alterations in the cancer
genome using single nucleotide polymorphism arrays. Cancer Res 2004,
64(9):3060-3071.
77. Wang TL, Maierhofer C, Speicher MR, Lengauer C, Vogelstein B, Kinzler KW,
Velculescu VE: Digital karyotyping. Proc Natl Acad Sci U S A 2002, 99(25):16156-
16161.
78. 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.
79. Volik S, Raphael BJ, Huang G, Stratton MR, Bignel G, Murnane J, Brebner JH,
Bajsarowicz K, Paris PL, Tao Q et al: Decoding the fine-scale structure of a breast
cancer genome and transcriptome. Genome Res 2006, 16(3):394-404.
80. Volik S, Zhao S, Chin K, Brebner JH, Herndon DR, Tao Q, Kowbel D, Huang G, Lapuk
A, Kuo WL et al: End-sequence profiling: sequence-based analysis of aberrant
genomes. Proc Natl Acad Sci U S A 2003, 100(13):7696-7701.
81. McPherson JD: Next-generation gap. Nat Methods 2009, 6(11 Suppl):S2-5.
82. Alkan C, Kidd JM, Marques-Bonet T, Aksay G, Antonacci F, Hormozdiari F, Kitzman JO,
Baker C, Malig M, Mutlu O et al: Personalized copy number and segmental
duplication maps using next-generation sequencing. Nat Genet 2009, 41(10):1061-
1067.
83. 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.
84. Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews TD,
Barnes C, Campbell P et al: Origins and functional impact of copy number variation
in the human genome. Nature 2009.
85. Fiegler H, Redon R, Andrews D, Scott C, Andrews R, Carder C, Clark R, Dovey O, Ellis
P, Feuk L et al: Accurate and reliable high-throughput detection of copy number
variation in the human genome. Genome Res 2006, 16(12):1566-1574.
86. Jakobsson M, Scholz SW, Scheet P, Gibbs JR, VanLiere JM, Fung HC, Szpiech ZA,
Degnan JH, Wang K, Guerreiro R et al: Genotype, haplotype and copy-number
variation in worldwide human populations. Nature 2008, 451(7181):998-1003.
87. Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N,
Teague B, Alkan C, Antonacci F et al: Mapping and sequencing of structural
variation from eight human genomes. Nature 2008, 453(7191):56-64.
88. McCarroll SA, Kuruvilla FG, Korn JM, Cawley S, Nemesh J, Wysoker A, Shapero MH,
de Bakker PI, Maller JB, Kirby A et al: Integrated detection and population-genetic
analysis of SNPs and copy number variation. Nat Genet 2008, 40(10):1166-1174.
89. Shaikh TH, Gai X, Perin JC, Glessner JT, Xie H, Murphy K, O'Hara R, Casalunovo T,
Conlin LK, D'Arcy M et al: High-resolution mapping and analysis of copy number
variations in the human genome: a data resource for clinical and research
applications. Genome Res 2009, 19(9):1682-1690.
90. Hastings PJ, Ira G, Lupski JR: A microhomology-mediated break-induced
replication model for the origin of human copy number variation. PLoS Genet
2009, 5(1):e1000327.
91. Diskin SJ, Hou C, Glessner JT, Attiyeh EF, Laudenslager M, Bosse K, Cole K, Mosse
YP, Wood A, Lynch JE et al: Copy number variation at 1q21.1 associated with
neuroblastoma. Nature 2009, 459(7249):987-991.
148