Challenges and standards in integrating surveys of structural variation (original) (raw)
Feuk, L., Carson, A.R. & Scherer, S.W. Structural variation in the human genome. Nat. Rev. Genet.7, 85–97 (2006). ArticleCAS Google Scholar
Freeman, J.L. et al. Copy number variation: new insights in genome diversity. Genome Res.16, 949–961 (2006). ArticleCAS Google Scholar
Sharp, A.J., Cheng, Z. & Eichler, E.E. Structural variation of the human genome. Annu. Rev. Genomics Hum. Genet.7, 407–442 (2006). ArticleCAS Google Scholar
Iafrate, A.J. et al. Detection of large-scale variation in the human genome. Nat. Genet.36, 949–951 (2004). ArticleCAS Google Scholar
Sebat, J. et al. Large-scale copy number polymorphism in the human genome. Science305, 525–528 (2004). ArticleCAS Google Scholar
Tuzun, E. et al. Fine-scale structural variation of the human genome. Nat. Genet.37, 727–732 (2005). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
Hinds, D.A., Kloek, A.P., Jen, M., Chen, X. & Frazer, K.A. Common deletions and SNPs are in linkage disequilibrium in the human genome. Nat. Genet.38, 82–85 (2006). ArticleCAS Google Scholar
Locke, D.P. et al. Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome. Am. J. Hum. Genet.79, 275–290 (2006). ArticleCAS Google Scholar
McCarroll, S.A. et al. Common deletion polymorphisms in the human genome. Nat. Genet.38, 86–92 (2006). ArticleCAS Google Scholar
Redon, R. et al. Global variation in copy number in the human genome. Nature444, 444–454 (2006). ArticleCAS Google Scholar
Simon-Sanchez, J. et al. Genome-wide SNP assay reveals structural genomic variation, extended homozygosity and cell-line induced alterations in normal individuals. Hum. Mol. Genet.16, 1–14 (2007). ArticleCAS Google Scholar
Vissers, L.E. et al. Array-based comparative genomic hybridization for the genomewide detection of submicroscopic chromosomal abnormalities. Am. J. Hum. Genet.73, 1261–1270 (2003). ArticleCAS Google Scholar
Locke, D.P. et al. BAC microarray analysis of 15q11-q13 rearrangements and the impact of segmental duplications. J. Med. Genet.41, 175–182 (2004). ArticleCAS Google Scholar
Shaw-Smith, C. et al. Microarray based comparative genomic hybridisation (array-CGH) detects submicroscopic chromosomal deletions and duplications in patients with learning disability/mental retardation and dysmorphic features. J. Med. Genet.41, 241–248 (2004). ArticleCAS Google Scholar
de Vries, B.B. et al. Diagnostic genome profiling in mental retardation. Am. J. Hum. Genet.77, 606–616 (2005). ArticleCAS Google Scholar
Koolen, D.A. et al. A new chromosome 17q21.31 microdeletion syndrome associated with a common inversion polymorphism. Nat. Genet.38, 999–1001 (2006). ArticleCAS Google Scholar
Sharp, A.J. et al. Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome. Nat. Genet.38, 1038–1042 (2006). ArticleCAS Google Scholar
Shaw-Smith, C. et al. Microdeletion encompassing MAPT at chromosome 17q21.3 is associated with developmental delay and learning disability. Nat. Genet.38, 1032–1037 (2006). ArticleCAS Google Scholar
Urban, A.E. et al. High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. Proc. Natl. Acad. Sci. USA103, 4534–4539 (2006). ArticleCAS Google Scholar
Szatmari, P. et al. Mapping autism risk loci using genetic linkage and chromosomal rearrangements. Nat. Genet.39, 319–328 (2007). ArticleCAS Google Scholar
Zhang, J., Feuk, L., Duggan, G.E., Khaja, R. & Scherer, S.W. Development of bioinformatics resources for display and analysis of copy number and other structural variants in the human genome. Cytogenet. Genome Res.115, 205–214 (2006). ArticleCAS Google Scholar
Cooper, G.M., Nickerson, D.A. & Eichler, E.E. Mutational and selective effects on copy-number variants in the human genome. Nat. Genet.39, S22–S29 (2007). ArticleCAS Google Scholar
Lee, C., Iafrate, A.J. & Brothman, A.R. Copy number variations and clinical cytogenetic diagnosis of constitutional disorders. Nat. Genet.39, S48–S54 (2007). ArticleCAS Google Scholar
McCarroll, S.A. & Altshuler, D.M. Copy-number variation and association studies of human disease. Nat. Genet.39, S37–S42 (2007). ArticleCAS Google Scholar
Eichler, E.E. et al. Completing the map of human genetic variation. Nature447, 161–165 (2007). ArticleCAS Google Scholar
Shendure, J., Mitra, R.D., Varma, C. & Church, G.M. Advanced sequencing technologies: methods and goals. Nat. Rev. Genet.5, 335–344 (2004). ArticleCAS Google Scholar
Bennett, S.T., Barnes, C., Cox, A., Davies, L. & Brown, C. Toward the $1,000 human genome. Pharmacogenomics6, 373–382 (2005). ArticleCAS Google Scholar
Service, R.F. Gene sequencing. The race for the $1000 genome. Science311, 1544–1546 (2006). ArticleCAS Google Scholar
Altshuler, D. et al. An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature407, 513–516 (2000). ArticleCAS Google Scholar
Mullikin, J.C. et al. An SNP map of human chromosome 22. Nature407, 516–520 (2000). ArticleCAS Google Scholar
Sachidanandam, R. et al. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature409, 928–933 (2001). ArticleCAS Google Scholar
Report of the Standing Committee on Human Cytogenetic Nomenclature, ISCN 1985. An International System for Human Cytogenetic Nomenclature. Birth Defects Orig. Artic. Ser.21, 1–117 (1985).
Heim, S. Genetic nomenclature: ISCN and ISGN. Pediatr. Hematol. Oncol.13, iii (1996). ArticleCAS Google Scholar
den Dunnen, J.T. & Antonarakis, S.E. Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion. Hum. Mutat.15, 7–12 (2000). ArticleCAS Google Scholar
Eichler, E.E. Widening the spectrum of human genetic variation. Nat. Genet.38, 9–11 (2006). ArticleCAS Google Scholar
Istrail, S. et al. Whole-genome shotgun assembly and comparison of human genome assemblies. Proc. Natl. Acad. Sci. USA101, 1916–1921 (2004). ArticleCAS Google Scholar
Khaja, R. et al. Genome assembly comparison identifies structural variants in the human genome. Nat. Genet.38, 1413–1418 (2006). ArticleCAS Google Scholar
Sharp, A.J. et al. Segmental duplications and copy-number variation in the human genome. Am. J. Hum. Genet.77, 78–88 (2005). ArticleCAS Google Scholar
Wong, K.K. et al. A comprehensive analysis of common copy-number variations in the human genome. Am. J. Hum. Genet.80, 91–104 (2007). ArticleCAS Google Scholar
Mills, R.E. et al. An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res.16, 1182–1190 (2006). ArticleCAS Google Scholar
Carter, N.P. Methods and strategies for analyzing copy number variation using DNA microarrays. Nat. Genet.39, S16–S21 (2007). ArticleCAS Google Scholar
Cheung, J. et al. Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence. Genome Biol.4, R25 (2003). Article Google Scholar
Bailey, J.A. & Eichler, E.E. Primate segmental duplications: crucibles of evolution, diversity and disease. Nat. Rev. Genet.7, 552–564 (2006). ArticleCAS Google Scholar
Risin, S., Hopwood, V.L. & Pathak, S. Trisomy 12 in Epstein-Barr virus-transformed lymphoblastoid cell lines of normal individuals and patients with nonhematologic malignancies. Cancer Genet. Cytogenet.60, 164–169 (1992). ArticleCAS Google Scholar
Carson, A.R., Feuk, L., Mohammed, M. & Scherer, S.W. Strategies for the detection of copy number and other structural variants in the human genome. Hum. Genomics2, 403–414 (2006). ArticleCAS Google Scholar
Burgoon, L.D. The need for standards, not guidelines, in biological data reporting and sharing. Nat. Biotechnol.24, 1369–1373 (2006). ArticleCAS Google Scholar
Brazma, A. et al. Minimum information about a microarray experiment (MIAME)—toward standards for microarray data. Nat. Genet.29, 365–371 (2001). ArticleCAS Google Scholar
Lander, E. & Kruglyak, L. Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results. Nat. Genet.11, 241–247 (1995). ArticleCAS Google Scholar
Barrett, T. et al. NCBI GEO: mining tens of millions of expression profiles–database and tools update. Nucleic Acids Res.35, D760–D765 (2007). ArticleCAS Google Scholar
Parkinson, H. et al. ArrayExpress–a public database of microarray experiments and gene expression profiles. Nucleic Acids Res.35, D747–D750 (2007). ArticleCAS Google Scholar
Ikeo, K., Ishi-i, J., Tamura, T., Gojobori, T. & Tateno, Y. CIBEX: center for information biology gene expression database. C. R. Biol.326, 1079–1082 (2003). ArticleCAS Google Scholar
Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B (Methodological)57, 289–300 (1995). Google Scholar
Feuk, L., Marshall, C.R., Wintle, R.F. & Scherer, S.W. Structural variants: changing the landscape of chromosomes and design of disease studies. Hum. Mol. Genet.15 (special no. 1), R57–R66 (2006). ArticleCAS Google Scholar
Lee, J.A. & Lupski, J.R. Genomic rearrangements and gene copy-number alterations as a cause of nervous system disorders. Neuron52, 103–121 (2006). ArticleCAS Google Scholar
Lupski, J.R. et al. DNA duplication associated with Charcot-Marie-Tooth disease type 1A. Cell66, 219–232 (1991). ArticleCAS Google Scholar
Ewart, A.K. et al. Hemizygosity at the elastin locus in a developmental disorder, Williams syndrome. Nat. Genet.5, 11–16 (1993). ArticleCAS Google Scholar
Chance, P.F. et al. Two autosomal dominant neuropathies result from reciprocal DNA duplication/deletion of a region on chromosome 17. Hum. Mol. Genet.3, 223–228 (1994). ArticleCAS Google Scholar
Chen, K.S. et al. Homologous recombination of a flanking repeat gene cluster is a mechanism for a common contiguous gene deletion syndrome. Nat. Genet.17, 154–163 (1997). ArticleCAS Google Scholar
Small, K., Iber, J. & Warren, S.T. Emerin deletion reveals a common X-chromosome inversion mediated by inverted repeats. Nat. Genet.16, 96–99 (1997). ArticleCAS Google Scholar
Potocki, L. et al. Molecular mechanism for duplication 17p11.2— the homologous recombination reciprocal of the Smith-Magenis microdeletion. Nat. Genet.24, 84–87 (2000). ArticleCAS Google Scholar
Kurotaki, N. et al. Haploinsufficiency of NSD1 causes Sotos syndrome. Nat. Genet.30, 365–366 (2002). ArticleCAS Google Scholar
Bailey, J.A., Yavor, A.M., Massa, H.F., Trask, B.J. & Eichler, E.E. Segmental duplications: organization and impact within the current human genome project assembly. Genome Res.11, 1005–1017 (2001). ArticleCAS Google Scholar
Bailey, J.A. et al. Recent segmental duplications in the human genome. Science297, 1003–1007 (2002). ArticleCAS Google Scholar
International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature431, 931–945 (2004).
Budarf, M.L. & Emanuel, B.S. Progress in the autosomal segmental aneusomy syndromes (SASs): single or multi-locus disorders? Hum. Mol. Genet.6, 1657–1665 (1997). ArticleCAS Google Scholar
Fiegler, H. et al. Accurate and reliable high-throughput detection of copy number variation in the human genome. Genome Res.16, 1566–1574 (2006). ArticleCAS Google Scholar
Komura, D. et al. Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays. Genome Res.16, 1575–1584 (2006). ArticleCAS Google Scholar
Lin, M. et al. dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data. Bioinformatics20, 1233–1240 (2004). ArticleCAS Google Scholar
Nannya, Y. et al. A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays. Cancer Res.65, 6071–6079 (2005). ArticleCAS Google Scholar
Colella, S. et al. QuantiSNP: an objective Bayes hidden-Markov model to detect and accurately map copy number variation using SNP genotyping data. Nucleic Acids Res.35, 2013–2025 (2007). ArticleCAS Google Scholar
Conrad, D.F. & Hurles, M.E. The population genetics of structural variation. Nat. Genet.39, S30–S36 (2007). ArticleCAS Google Scholar