Structural variation in the human genome

Nature Reviews Genetics

Volumn 7, Issue 2, 2006, Pages 85-97

  Feuk, Lars ^a   Carson, Andrew R ^a   Scherer, Stephen W ^a  

^a HOSPITAL FOR SICK CHILDREN   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOME ANALYSIS; CHROMOSOME INVERSION; CHROMOSOME TRANSLOCATION; COMPARATIVE GENOMIC HYBRIDIZATION; FLUORESCENCE IN SITU HYBRIDIZATION; GENE DUPLICATION; GENE INSERTION; GENETIC HETEROGENEITY; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE PHENOTYPE CORRELATION; HETEROCHROMATIN; HUMAN; HUMAN GENOME; KARYOTYPE; LARGE SCALE PRODUCTION; NUCLEOTIDE BINDING SITE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM;

GENOME, HUMAN; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS);

EID: 31144469134     PISSN: 14710056     EISSN: 14710064     Source Type: Journal    
DOI: 10.1038/nrg1767     Document Type: Review

References (113)

1. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
2. Venter, J. C. et al. The sequence of the human genome. Science 291, 1304-1351 (2001).
3. International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 431, 931-945 (2004).
4. Przeworski, M., Hudson, R. R. & Di Rienzo, A. Adjusting the focus on human variation. Trends Genet. 16, 296-302 (2000).
5. Reich, D. E. et al. Human genome sequence variation and the influence of gene history, mutation and recombination. Nature Genet. 32, 135-142 (2002).
6. Jacobs, P. A., Baikie, A. G., Court Brown, W. M. & Strong, J. A. The somatic chromosomes in mongolism. Lancet 1, 710 (1959).
7. Edwards, J. H., Harnden, D. G., Cameron, A. H., Crosse, V. M. & Wolff, O. H. A new trisomic syndrome. Lancet 1, 787-790 (1960).
8. Patau, K., Smith, D. W., Therman, E., Inhorn, S. L. & Wagner, H. P. Multiple congenital anomaly caused by an extra autosome. Lancet 1, 790-793 (1960).
9. Bobrow, M., Joness, L. F. & Clarke, G. A complex chromosomal rearrangement with formation of a ring 4. J. Med. Genet. 8, 235-239 (1971).
10. Jacobs, P. A., Matsuura, J. S., Mayer, M. & Newlands, I. M. A cytogenetic survey of an institution for the mentally retarded: I. Chromosome abnormalities. Clin. Genet. 13, 37-60 (1978).
11. Coco, R. & Penchaszadeh, V. B. Cytogenetic findings in 200 children with mental retardation and multiple congenital anomalies of unknown cause. Am. J. Med. Genet. 12, 155-173 (1982).
12. Warburton, D. De novo balanced chromosome rearrangements and extra marker chromosomes identified at prenatal diagnosis: clinical significance and distribution of breakpoints. Am. J. Hum. Genet. 49, 995-1013 (1991). A comprehensive survey that describes the prevalence of microscopic structural variants and their relevance to clinical diagnostics.
13. Jacobs, P. A., Browne, C., Gregson, N., Joyce, C. & White, H. Estimates of the frequency of chromosome abnormalities detectable in unselected newborns using moderate levels of banding. J. Med. Genet. 29, 103-108 (1992). A landmark study of the frequency of chromosomal abnormalities that affect newborns.
14. Kim, S. S., Jung, S. C., Kim, H. J., Moon, H. R. & Lee, J. S. Chromosome abnormalities in a referred population for suspected chromosomal aberrations: a report of 4117 cases. J. Korean Med. Sci. 14, 373-376 (1999).
15. Benyush, V. A., Luckash, V. G. & Shtannikov, A. V. Quantitative analysis of C-bands based on optical density profiles in human chromosomes. Hum. Genet. 39, 169-175 (1977).
16. Maegenis, R. E., Donlon, T. A. & Wyandt, H. E. Giemsa-11 staining of chromosome 1: a newly described heteromorphism. Science 202, 64-65 (1978).
17. Verma, R. S., Rodriguez, J. & Dosik, H. The clinical significance of pericentric inversion of the human Y chromosome: a rare 'third' type of heteromorphism. J. Hered. 73, 236-238 (1982).
18. Hsu, L. Y., Benn, P. A., Tannenbaum, H. L., Perlis, T. E. & Carlson, A. D. Chromosomal polymorphisms of 1, 9, 16, and Y in 4 major ethnic groups: a large prenatal study. Am. J. Med. Genet. 26, 95-101 (1987).
19. Verma, R. S., Dosik, H. & Lubs, H. A. Size and pericentric inversion heteromorphisms of secondary constriction regions (h) of chromosomes 1, 9, and 16 as detected by CBG technique in Caucasians: classification, frequencies, and incidence. Am. J. Med. Genet. 2, 331-339 (1978).
20. Lubs, H. A. A marker X chromosome. Am. J. Hum. Genet. 21, 231-244 (1969).
21. Wright, A. F. in Nature Encyclopedia of the Human Genome 2 959-968 (Nature Publishing Group, London, 2003).
22. Kruglyak, L. & Nickerson, D. A. Variation is the spice of life. Nature Genet. 27, 234-236 (2001).
23. Hinds, D. A. et al. Whole-genome patterns of common DNA variation in three human populations. Science 307, 1072-1079 (2005).
24. The International HapMap Consortium. A haplotype map of the human genome. Nature 437, 1299-1320 (2005).
25. Solinas-Toldo, S. et al. Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer 20, 399-407 (1997).
26. Sebat, J. et al. Large-scale copy number polymorphism in the human genome. Science 305, 525-528 (2004). This and reference 27 were the first papers to describe the global presence and distribution of CNVs in the human genome.
27. Iafrate, A. J. et al. Detection of large-scale variation in the human genome. Nature Genet. 36, 949-951 (2004).
28. Tuzun, E. et al. Fine-scale structural variation of the human genome. Nature Genet 37, 727-732 (2005). The first description of a clone-end sequencing strategy to discover mainly intermediate-sized structural variants in the human genome.
29. Feuk, L. et al. Discovery of human inversion polymorphisms by comparative analysis of human and chimpanzee DNA sequence assemblies. PLoS Genet. 1, e56 (2005).
30. Dhami, P. et al. Exon array CGH: detection of copy-number changes at the resolution of individual exons in the human genome. Am. J. Hum. Genet. 76, 750-762 (2005).
31. Sharp, A. J. et al. Segmental duplications and copy-number variation in the human genome. Am. J. Hum. Genet. 77, 78-88 (2005).
32. Stefansson, H. et al. A common inversion under selection in Europeans. Nature Genet. 37, 129-137 (2005). This reports the discovery and characterization of a 900-kb inversion polymorphism on chromosome 17. This variant was found to be under positive selection in Europeans, as determined by population-based screening.
33. Visser, R. et al. Identification of a 3.0-kb major recombination hotspot in patients with sotos syndrome who carry a common 1.9-Mb microdeletion. Am. J. Hum. Genet. 76, 52-67 (2005).
34. Inoue, K. & Lupski, J. R. Molecular mechanisms for genomic disorders. Annu. Rev. Genomics Hum. Genet. 3, 199-242 (2002). An outstanding review of the mechanisms behind genomic disorders, including their association with segmental duplications, and non-allelic homologous recombination.
35. Gripenberg, U. Size variation and orientation of the human Y chromosome. Chromosoma 15, 618-629 (1964).
36. Nielsen, J. & Sillesen, I. Incidence of chromosome aberrations among 11148 newborn children. Humangenetik 30, 1-12 (1975).
37. Nussbaum, R. L., McInnes, R. R. & Willard, H. F. Thompson & Thompson Genetics in Medicine (W.B. Saunders, 2004).
38. McKinlay Gardner, R. J. & Sutherland, G. R. Chromosome Abnormalities and Genetic Counseling (Oxford Univ. Press, USA, 2003).
39. Barber, J. C. et al. Duplication of 8p23.1: a cytogenetic anomaly with no established clinical significance. J. Med. Genet. 35, 491-496 (1998).
40. Babu, A. & Verma, R. S. Heteromorphic variants of human chromosome 4. Cytogenet. Cell Genet. 41, 60-61 (1986).
41. Verma, R. S. Heterochromatin: Molecular and Structural Aspects (Cambridge Univ. Press, New York, 1988).
42. Starke, H. et al. Homologous sequences at human chromosome 9 bands p12 and q13-21.1 are involved in different patterns of pericentric rearrangements, Eur. J. Hum. Genet. 10, 790-800 (2002).
43. Wyandt, H. E. & Tonk, V. S. Atlas of Human Chromosome Heteromorphisms (Kluwer Academic, Netherlands, 2004).
44. Barber, J. C. Directly transmitted unbalanced chromosome abnormalities and euchromatic variants. J. Med. Genet. 42, 609-629 (2005).
45. Speicher, M. R. & Carter, N. P. The new cytogenetics: blurring the boundaries with molecular biology. Nature Rev. Genet. 6, 782-792 (2005).
46. 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).
47. Vissers, L. E., Veltman, J. A., van Kessel, A. G. & Brunner, H. G. Identification of disease genes by whole genome CGH arrays. Hum. Mol. Genet. 14 (Suppl. 2), R215-R223 (2005).
48. Mantripragada, K. K. et al. DNA copy-number analysis of the 22q11 deletion-syndrome region using array-CGH with genomic and PCR-based targets. Int. J. Mol. Med. 13, 273-279 (2004).
49. Lucito, R. et al. Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. Genome Res. 13, 2291-2305 (2003).
50. Pollack, J. R. et al. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nature Genet. 23, 41-46 (1999).
51. Barrett, M. T. et al. Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proc. Natl Acad. Sci. USA 101, 17765-17770 (2004).
52. Brennan, C. et al. High-resolution global profiling of genomic alterations with long oligonucleotide microarray. Cancer Res. 64, 4744-4748 (2004).
53. Zhao, X. et al. An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Res. 64, 3060-3071 (2004).
54. Heid, C. A., Stevens, J., Livak, K. J. & Williams, P. M. Real time quantitative PCR. Genome Res. 6, 986-994 (1996).
55. Bieche, I. et al. Novel approach to quantitative polymerase chain reaction using real-time detection: application to the detection of gene amplification in breast cancer. Int. J. Cancer 78, 661-666 (1998).
56. Charbonnier, F. et al. Detection of exon deletions and duplications of the mismatch repair genes in hereditary nonpolyposis colorectal cancer families using multiplex polymerase chain reaction of short fluorescent fragments. Cancer Res. 60, 2760-2763 (2000).
57. Armour, J. A., Sismani, C., Patsalis, P. C. & Cross, G. Measurement of locus copy number by hybridisation with amplifiable probes. Nucleic Acids Res. 28, 605-609 (2000).
58. Hollox, E. J., Akrami, S. M. & Armour, J. A. DNA copy number analysis by MAPH: molecular diagnostic applications. Expert Rev. Mol. Diagn. 2, 370-378 (2002).
59. Schouten, J. P. et al. Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res. 30, e57 (2002).
60. White, S. J. et al. Two-color multiplex ligation-dependent probe amplification: detecting genomic rearrangements in hereditary multiple exostoses. Hum. Mutat. 24, 86-92 (2004).
61. Pinkel, D. et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nature Genet. 20, 207-211 (1998).
62. Kennedy, G. C. et al. Large-scale genotyping of complex DNA. Nature Biotechnol. 21, 1233-1237 (2003).
63. Slater, S. R. et al. High-resolution identification of chromosomal abnormalities using oligonucleotide arrays containing 116,204 SNPs. Am. J. Hum. Genet. 77, 709-726 (2005).
64. Huang, J. et al. Whole genome DNA copy number changes identified by high density oligonucleotide arrays. Hum. Genomics 1, 287-299 (2004).
65. Bignell, G. R. et al. High-resolution analysis of DNA copy number using oligonucleotide microarrays. Genome Res. 14, 287-295 (2004).
66. Lindblad-Toh, K. et al. Loss-of-heterozygosity analysis of small-cell lung carcinomas using single-nucleotide polymorphism arrays. Nature Biotechnol. 18, 1001-1005 (2000).
67. Mei, R. et al. Genome-wide detection of allelic imbalance using human SNPs and high-density DNA arrays. Genome Res. 10, 1126-1137 (2000).
68. Altug-Teber, O. et al. A rapid microarray based whole genome analysis for detection of uniparental disomy. Hum. Mutat. 26, 153-159 (2005).
69. Raghavan, M. et al. Genome-wide single nucleotide polymorphism analysis reveals frequent partial uniparental disomy due to somatic recombination in acute myeloid leukemias. Cancer Res. 65, 375-378 (2005).
70. Bruce, S. K. et al. Global analysis of uniparental disomy using high-density genotyping arrays. J. Med. Genet. 42, 847-851 (2005).
71. Ponchel, F. et al. Real-time PCR based on SYBR-Green I fluorescence: An alternative to the TaqMan assay for a relative quantification of gene rearrangements, gene amplifications and micro gene deletions. BMC Biotechnol 3, 18 (2003).
72. Fredman, D. et al. Complex SNP-related sequence variation in segmental genome duplications. Nature Genet. 36, 861-866 (2004).
73. Estivill, X. et al. Chromosomal regions containing high-density and ambiguously mapped putative single nucleotide polymorphisms (SNPs) correlate with segmental duplications in the human genome. Hum. Mol. Genet. 11, 1987-1995 (2002).
74. Istrail, S. et al. Whole-genome shotgun assembly and comparison of human genome assemblies. Proc. Natl Acad. Sci. USA 101, 1916-1921 (2004).
75. Scherer, S. W. et al. Human chromosome 7: DNA sequence and biology. Science 300, 767-772 (2003).
76. Scherer, S. W. & Green, E. D. Human chromosome 7 circa 2004: a model for structural and functional studies of the human genome. Hum. Mol. Genet. 13 (Spec. No. 2), R303-R313 (2004).
77. Hillier, L. W. et al. The DNA sequence of human chromosome 7. Nature 424, 157-164 (2003).
78. Beck, S. & Trowsdale, J. The human major histocompatability complex: lessons from the DNA sequence. Annu. Rev. Genomics Hum. Genet. 1, 117-137 (2000).
79. Bailey, J. A. et al. Recent segmental duplications in the human genome. Science 297, 1003-1007 (2002). The first global map of segmental duplications in the human genome, including an analysis of their relationship to genes and genetic diseases.
80. An International System for Human Cytogenetic Nomenclature ISCN 1985. Report of the Standing Committee on Human Cytogenetic Nomenclature. Birth Defects Orig. Artic. Ser. 21, 1-117 (1985).
81. 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).
82. Cheung, J. et al. Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence. Genome Biol. 4, R25 (2003).
83. Eichler, E. E., Clark, R. A. & She, X. An assessment of the sequence gaps: unfinished business in a finished human genome. Nature Rev. Genet. 5, 345-354 (2004).
84. Robledo, R. et al. A 9.1 -kb gap in the genome reference map is shown to be a stable deletion/insertion polymorphism of ancestral origin. Genomics 80, 585-592 (2002).
85. Ghanem, N. et al. Polymorphism of MHC class III genes: definition of restriction fragment linkage groups and evidence for frequent deletions and duplications. Hum. Genet. 79, 209-218 (1988).
86. Groot, P. C., Mager, W. H. & Frants, R. R. Interpretation of polymorphic DNA patterns in the human α-amylase multigene family. Genomics 10, 779-785 (1991).
87. Buckland, P. R. Polymorphically duplicated genes: their relevance to phenotypic variation in humans. Ann. Med. 35, 308-315 (2003).
88. Hollox, E. J., Armour, J. A. & Barber, J. C. Extensive normal copy number variation of a β-defensin antimicrobial-gene cluster. Am. J. Hum. Genet. 73, 591-600 (2003).
89. Knight, S. J. & Flint, J. Perfect endings: a review of subtelomeric probes and their use in clinical diagnosis. J. Med. Genet. 37, 401-409 (2000).
90. Barber, J. C. et al. Duplications and copy number variants of 8p23.1 are cytogenetically indistinguishable but distinct at the molecular level. Eur. J. Hum. Genet. 13, 1131-1136 (2005).
91. Lakich, D., Kazazian, H. H. Jr, Antonarakis, S. E. & Gitschier, J. Inversions disrupting the factor VIII gene are a common cause of severe haemophilia A. Nature Genet. 5, 236-41 (1993).
92. Bondeson, M. L. et al. Inversion of the IDS gene resulting from recombination with IDS-related sequences is a common cause of the Hunter syndrome. Hum. Mol. Genet. 4, 615-621 (1995).
93. Small, K., Iber, J. & Warren, S. T. Emerin deletion reveals a common X-chromosome inversion mediated by inverted repeats. Nature Genet. 16, 96-99 (1997).
94. Osborne, L. R. et al. A 1.5 million-base pair inversion polymorphism in families with Williams-Beuren syndrome. Nature Genet. 29, 321-5 (2001). A study of structural variants at the Williams-Beuren locus, describing a 1.5-Mb polymorphic micro-inversion that predisposes to subsequent disease-causing deletions.
95. Gimelli, G. et al. Genomic inversions of human chromosome 15q11-q13 in mothers of Angelman syndrome patients with class II (BP2/3) deletions. Hum. Mol. Genet. 12, 849-858 (2003).
96. Kurotaki, N. et al. Fifty microdeletions among 112 cases of Sotos syndrome: low copy repeats possibly mediate the common deletion. Hum. Mutat. 22, 378-387 (2003).
97. Giglio, S. et al. Olfactory receptor-gene clusters, genomic-inversion polymorphisms, and common chromosome rearrangements. Am. J. Hum. Genet. 68, 874-883 (2001).
98. Giglio, S. et al. Heterozygous submicroscopic inversions involving olfactory receptor-gene clusters mediate the recurrent t(4;8)(p16;p23) translocation. Am. J. Hum. Genet. 71, 276-285 (2002).
99. Nobrega, M. A., Zhu, Y., Plajzer-Frick, I., Afzal, V. & Rubin, E. M. Megabase deletions of gene deserts result in viable mice. Nature 431, 988-993 (2004).
100. Ravnan, J. B. et al. Subtelomere FISH analysis of 11,688 cases: An evaluation of the frequency and pattern of subtelomere rearrangements in individuals with developmental disabilities. J. Med. Genet. 30 September 2005 (doi:10.1136/jmg.2005.036350).
101. Yu, C. E. et al. Presence of large deletions in kindreds with autism. Am. J. Hum. Genet. 71, 100-115 (2002). A thorough analysis of microsatellite markers behaving in a non-Mendelian manner in autism kindreds, which led to the discovery of novel microdeletions.
102. Gribble, S. M. et al. The complex nature of constitutional de novo apparently balanced translocations in patients presenting with abnormal phenotypes. J. Med. Genet. 42, 8-16 (2005).
103. Gonzalez, E. et al. The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science 307, 1434-1440 (2005).
104. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437, 69-87 (2005).
105. Cheng, Z. et al. A genome-wide comparison of recent chimpanzee and human segmental duplications. Nature 437, 88-93 (2005).
106. Aston, C., Mishra, B. & Schwartz, D. C. Optical mapping and its potential for large-scale sequencing projects. Trends Biotechnol. 17, 297-302 (1999).
107. 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. Nature Genet. 38, 82-85 (2006).
108. 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. Nature Genet. 38, 75-81 (2006).
109. McCarroll, S. A. et al. Common deletion polymorphisms in the human genome. Nature. Genet. 38, 86-92 (2006).
110. Le Caignec, C. et al. Detection of genomic imbalances by array based comparative genomic hybridisation in fetuses with multiple malformations. J. Med. Genet. 42, 121-128 (2005).
111. Jobanputra, V. et al. Application of ROMA (representational oligonucleotide microarray analysis) to patients with cytogenetic rearrangements. Genet. Med. 7, 111-118 (2005).
112. Bejjani, B. A. et al. Use of targeted array-based CGH for the clinical diagnosis of chromosomal imbalance: is less more? Am. J. Med. Genet. A 134, 259-267 (2005).
113. van Ommen, G. J. Frequency of new copy number variation in humans. Nature Genet. 37, 333-334 (2005).