Genome structural variation discovery and genotyping

Nature Reviews Genetics

Volumn 12, Issue 5, 2011, Pages 363-376

  Alkan, Can ^a,b   Coe, Bradley P ^a   Eichler, Evan E ^a,b  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT;

BACTERIAL ARTIFICIAL CHROMOSOME; BASE PAIRING; COMPARATIVE GENOMIC HYBRIDIZATION; COMPUTATIONAL FLUID DYNAMICS; COPY NUMBER VARIATION; DNA SEQUENCE; FLUORESCENCE IN SITU HYBRIDIZATION; GENE SEQUENCE; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE; HETEROZYGOSITY; HUMAN; HUMAN GENOME; KARYOTYPE; MICROARRAY ANALYSIS; MULTIPLEX LIGATION DEPENDENT PROBE AMPLIFICATION; POINT MUTATION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; STRUCTURE ANALYSIS;

DNA COPY NUMBER VARIATIONS; GENETIC VARIATION; GENOME, HUMAN; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 79954672317     PISSN: 14710056     EISSN: 14710064     Source Type: Journal    
DOI: 10.1038/nrg2958     Document Type: Review

References (116)

1. Iafrate, A. J. et al. Detection of large-scale variation in the human genome. Nature Genet. 36, 949-951 (2004). (Pubitemid 39167488)
2. Redon, R. et al. Global variation in copy number in the human genome. Nature 444, 444-454 (2006). (Pubitemid 44809057)
3. Tuzun, E. et al. Fine-scale structural variation of the human genome. Nature Genet 37, 727-732 (2005). (Pubitemid 41754889)
4. Kidd, J. M. et al. Mapping and sequencing of structural variation from eight human genomes. Nature 453, 56-64 (2008). (Pubitemid 351630326)
5. Conrad, D. F. et al. Origins and functional impact of copy number variation in the human genome. Nature 464, 704-712 (2010).
6. Sebat, J. et al. Large-scale copy number polymorphism in the human genome. Science 305, 525-528 (2004). (Pubitemid 38971344)
7. Feuk, L., Carson, A. R. & Scherer, S. W Structural variation in the human genome. Nature Rev Genet. 7, 85-97 (2006). (Pubitemid 43128895)
8. The 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073 (2010).
9. Sebat, J. et al. Strong association of de novo copy number mutations with autism. Science 316, 445-449 (2007). (Pubitemid 46651493)
10. Sharp, A. J. et al. Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome. Nature Genet. 38, 1038-1042 (2006). (Pubitemid 44325929)
11. de Vries, B. B. et al. Diagnostic genome profiling in mental retardation. Am. J. Hum. Genet. 77, 606-616 (2005). (Pubitemid 41361607)
12. Stankiewicz, P. & Lupski, J. R. Genomic architecture, rearrangements and genomic disorders. Trends Genet. 18, 74-82 (2002).
13. Fellermann, K. et al. A chromosome 8 gene-cluster polymorphism with low human ß-defensin 2 gene copy number predisposes to Crohn disease of the colon. Am. J. Hum. Genet. 79, 439-448 (2006). (Pubitemid 44384253)
14. Aitman, T. J. et al. Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans. Nature 439, 851-855 (2006). (Pubitemid 43255703)
15. 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). (Pubitemid 38333794)
16. Itsara, A. et al. Population analysis of large copy number variants and hotspots of human genetic disease. Am. J. Hum. Genet. 84, 148-161 (2009).
17. Snijders, A. M. et al. Assembly of microarrays for genome-wide measurement of DNA copy number Nature Genet. 29, 263-264 (2001). (Pubitemid 33096449)
18. Pinkel, D. et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nature Genet. 20, 207-211 (1998). (Pubitemid 28455458)
19. Park, H. et al. Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing. Nature Genet. 42, 400-405 (2010).
20. McCarroll, S. A. et al. Integrated detection and population-genetic analysis of SNPs and copy number variation. Nature Genet. 40, 1166-1174 (2008).
21. Perry, G. H. et al. The fine-scale and complex architecture of human copy-number variation. Am. J. Hum. Genet. 82, 685-695 (2008).
22. Miller, D. T. et al. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am. J. Hum. Genet. 86, 749-764 (2010).
23. Cooper, G. M., Zerr, T., Kidd, J. M., Eichler, E. E. & Nickerson, D. A. Systematic assessment of copy number variant detection via genome-wide SNP genotyping. Nature Genet. 40, 1199-1203 (2008).
24. Peiffer, D. A. et al. High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. Genome Res. 16, 1136-1148 (2006). (Pubitemid 44320401)
25. Coe, B. P. et al. Resolving the resolution of array CGH. Genomics 89, 647-653 (2007). (Pubitemid 46589944)
26. Greshock, J. et al. A comparison of DNA copy number profiling platforms. Cancer Res. 67, 10173-10180 (2007). (Pubitemid 350070789)
27. Curtis, C. et al. The pitfalls of platform comparison: DNA copy number array technologies assessed. BMC Genomics 10, 588 (2009).
28. Jakobsson, M. et al. Genotype, haplotype and copy-number variation in worldwide human populations. Nature 451, 998-1003 (2008). (Pubitemid 351301742)
29. Gusev, A. et al. Whole population, genome-wide mapping of hidden relatedness. Genome Res. 19, 318-326 (2009).
30. Winchester, L., Yau, C. & Ragoussis, J. Comparing CNV detection methods for SNP arrays. Brief. Funct. Genomic. Proteomic. 8, 353-366 (2009).
31. Kidd, J. M. et al. Characterization of missing human genome sequences and copy-number polymorphic insertions. Nature Methods 7, 365-371 (2010).
32. Wellcome Trust Case Control Consortium. Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature 464, 713-720 (2010).
33. Paris, P. L. et al. High resolution oligonucleotide CGH using DNA from archived prostate tissue. The Prostate 67, 1447-1455 (2007). (Pubitemid 47435791)
34. Hehir-Kwa, J. Y. et al. Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis. DNA Res. 14, 1-11 (2007).
35. Wicker, N. et al. A new look towards BAC-based array CGH through a comprehensive comparison with oligo-based array CGH. BMC Genomics 8, 84 (2007).
36. van de Wiel, M. A. et al. CGHcall: calling aberrations for array CGH tumor profiles. Bioinformatics (Oxford, England) 23, 892-894 (2007).
37. van Wieringen, W. N., van de Wiel, M. A. & Ylstra, B. Normalized, segmented or called aCGH data? Cancer Inform. 3, 32 1-327 (2007).
38. Wang, K. et al. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res. 17, 1665-1674 (2007). (Pubitemid 350074862)
39. Korn, J. M. et al. Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nature Genet. 40, 1253-1260 (2008).
40. Coe, B. P., Chari, R., MacAulay, C. & Lam, W. L FACADE: a fast and sensitive algorithm for the segmentation and calling of high resolution array CGH data. Nucleic Acids Res. 38, e157 (2010).
41. Dellinger, A. E. et al. Comparative analyses of seven algorithms for copy number variant identification from single nucleotide polymorphism arrays. Nucleic Acids Res. 38, e105 (2010).
42. Church, D. M. et al. Public data archives for genomic structural variation. Nature Genet. 42, 813-814 (2010).
43. Walsh, T. et al. Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science 320, 539-543 (2008). (Pubitemid 351590668)
44. Heinzen, E. L. et al. Rare deletions at 16p13.11 predispose to a diverse spectrum of sporadic epilepsy syndromes. Am. J. Hum. Genet. 86, 707-718 (2010).
45. Bailey, J. A. et al. Recent segmental duplications in the human genome. Science 297, 1003-1007 (2002). (Pubitemid 34856032)
46. Mailman, M. D. et al. The NCBI dbGaP database of genotypes and phenotypes. Nature Genet. 39, 1181-1186 (2007). (Pubitemid 47482671)
47. Trask, B. J. et al. Large multi-chromosomal duplications encompass many members of the olfactory receptor gene family in the human genome. Hum. Mol. Genet 7, 2007-2020 (1998). (Pubitemid 28546408)
48. Schwartz, D. C. et al. Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping. Science 262, 110-114 (1993). (Pubitemid 23338881)
49. Teague, B. et al. High-resolution human genome structure by single-molecule analysis. Proc. Natl Acad. Sci. USA 107, 10848-10853 (2010).
50. Antonacci, F et al. A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease risk. Nature Genet. 42, 745-750 (2010).
51. Das, S. K. et al. Single molecule linear analysis of DNA in nano-channel labeled with sequence specific fluorescent probes. Nucleic Acids Res. 38, e177 (2010).
52. Jo, K. et al. A single-molecule barcoding system using nanoslits for DNA analysis. Proc. Natl Acad. Sci. USA 104, 2673-2678 (2007). (Pubitemid 46327938)
53. Xiao, M. et al. Direct determination of haplotypes from single DNA molecules. Nature Methods 6, 199-201 (2009).
54. Beer, N. R. et al. On-chip, real-time, single-copy polymerase chain reaction in picoliter droplets. Anal. Chem. 79, 8471-8475 (2007). (Pubitemid 350171354)
55. Pushkarev, D., Neff, N. F. & Quake, S. R. Single-molecule sequencing of an individual human genome. Nature Biotech. 27, 847-852 (2009).
56. Wheeler, D. A. et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 452, 872-876 (2008). (Pubitemid 351550870)
57. Bentley, D. R. et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53-59 (2008).
58. McKernan, K. J. et al. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res. 19, 1527-1541 (2009).
59. Korbel, J. O. et al. Paired-end mapping reveals extensive structural variation in the human genome. Science 318, 420-426 (2007). (Pubitemid 47614521)
60. Volik, S. et al. End-sequence profiling: sequence-based analysis of aberrant genomes. Proc. Natl Acad. Sci. USA 100, 7696-7701 (2003). (Pubitemid 36760032)
61. Medvedev, P., Stanciu, M. & Brudno, M. Computational methods for discovering structural variation with next-generation sequencing. Nature Methods 6, S13-S20 (2009).
62. Mills, R. E. et al. Mapping copy number variation at fine scale by population scale genome sequencing. Nature 470, 59-65 (2011).
63. Kidd, J. M. et al. A human genome structural variation sequencing resource reveals insights into mutational mechanisms. Cell 143, 837-847 (2010).
64. Korbel, J. O. et al. PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol. 10, R23 (2009).
65. Hormozdiari, F., Alkan, C, Eichler, E. E. & Sahinalp, S. C. Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res. 19, 1270-1278 (2009).
66. Hormozdiari, F et al. Next-generation Variation Hunter: combinatorial algorithms for transposon insertion discovery. Bioinformatics (Oxford, England) 26, i350-i357 (2010).
67. Hormozdiari, F, Hajirasouliha, I., A., M., Eichler, E. E. & Sahinalp, S. C. Simultaneous structural variation discovery in multiple paired-end sequenced genomes. Proc. RECOMB 201 1 (in the press).
68. Chen, K. et al. Break Dancer: an algorithm for high-resolution mapping of genomic structural variation. Nature Methods 6, 677-681 (2009).
69. Lee, S., Hormozdiari, F, Alkan, C. & Brudno, M. MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions. Nature Methods 6, 473-474 (2009).
70. Lee, S., Xing, E. & Brudno, M. MoGUL: detecting common insertions and deletions in a population. Proc. RECOMB 2010 6044, 357-368 (2010).
71. Quinlan, A. R. et al. Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. Genome Res. 20, 623-635 (2010).
72. Campbell, P. J. et al. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nature Genet 40, 722-729 (2008). (Pubitemid 351748860)
73. Chiang, D. Y. et al. High-resolution mapping of copy-number alterations with massively parallel sequencing. Nature Methods 6, 99-103 (2009).
74. Alkan, C. et al. Personalized copy number and segmental duplication maps using next-generation sequencing. Nature Genet. 41, 1061-1067 (2009).
75. Sudmant, P. H. et al. Diversity of human copy number variation and multicopy genes. Science 330, 641-646 (2010).
76. Yoon, S., Xuan, Z., Makarov, V, Ye, K. & Sebat, J. Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res. 19, 1586-1592 (2009).
77. Abyzov, A., Urban, A. E., Snyder, M. & Gerstein, M. CNVnator: an approach to discover, genotype and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res. 7 Feb 2011 (doi:10.1101/gr.114876.110).
78. Mills, R. E. et al. An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res. 16, 1182-1190 (2006). (Pubitemid 44320405)
79. Ye, K., Schulz, M. H., Long, Q., Apweiler, R. & Ning, Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics (Oxford, England) 25, 2865-2871 (2009).
80. Levy, S. et al. The diploid genome sequence of an individual human. PLoS Biol. 5, e254 (2007).
81. Xing, J. et al. Mobile elements create structural variation: analysis of a complete human genome. Genome Res. 19, 1516-1526 (2009).
82. Pang, A. W. et al. Towards a comprehensive structural variation map of an individual human genome. Genome Biol. 11, R52 (2010).
83. Chaisson, M. J., Brinza, D. & Pevzner, P. A. De novo fragment assembly with short mate-paired reads: does the read length matter? Genome Res. 19, 336-346 (2009).
84. Simpson, J. T. et al. ABySS: a parallel assembler for short read sequence data. Genome Res. 19, 1117-1123 (2009).
85. Li, R. et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265-272 (2009).
86. Gnerre, S. et al. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc. Natl Acad. Sci. USA 108, 1513-1518 (2011).
87. Hajirasouliha, I. et al. Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. Bioinformatics (Oxford, England) 26, 1277-1283 (2010).
88. She, X. et al. Shotgun sequence assembly and recent segmental duplications within the human genome. Nature 431, 927-930 (2004). (Pubitemid 39434408)
89. Alkan, C, Sajjadian, S. & Eichler, E. E. Limitations of next-generation genome sequence assembly. Nature Methods 8, 61-65 (2011).
90. Medvedev, P., Fiume, M., Dzamba, M., Smith, T. & Brudno, M. Detecting copy number variation with mated short reads. Genome Res. 20, 1613-1622 (2010).
91. Handsaker, R. E., Korn, J. M., Nemesh, J. & McCarroll, S. A. Discovery and genotyping of genome structural polymorphism by sequencing on a population scale. Nature Genet. 13 Feb 2011 (doi:10.1038/ng.768).
92. Schatz, M. C, Delcher, A. L. & Salzberg, S. L. Assembly of large genomes using second-generation sequencing. Genome Res. 20, 1165-1173 (2010).
93. Human genome: genomes by the thousand. Nature 467, 1026-1027 (2010).
94. Weksberg, R. et al. A method for accurate detection of genomic microdeletions using real-time quantitative PCR. BMC Genomics 6, 180 (2005).
95. Schaeffeler, E., Schwab, M., Eichelbaum, M. & Zanger, U. M. CYP2D6 genotyping strategy based on gene copy number determination by TaqMan real-time PCR. Hum. Mutation 22, 476-485 (2003). (Pubitemid 38009951)
96. Gomez-Curet, I. et al. Robust quantification of the SMN gene copy number by real-time TaqMan PCR. Neurogenetics 8, 271-278 (2007). (Pubitemid 47624450)
97. 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). (Pubitemid 30058002)
98. Kumps, C. et al. Multiplex amplicon quantification (MAQ), a fast and efficient method for the simultaneous detection of copy number alterations in neuroblastoma. BMC Genomics 11, 298 (2010).
99. Schouten, J. P. et al. Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res. 30, e57 (2002).
100. Fan, H. C, Blumenfeld, Y J., El-Sayed, Y Y., Chueh, J. & Quake, S. R. Microfluidic digital PCR enables rapid prenatal diagnosis of fetal aneuploidy. Am. J. Obstet. Gynecol. 200, 543.e1-543.e7 (2009).
101. Shen, F, Du, W., Kreutz, J. E., Fok, A. & Ismagilov, R. F Digital PCR on a SlipChip. Lab Chip 10, 2666-2672 (2010).
102. Diehl, F et al. BEAMing: single-molecule PCR on microparticles in water-in-oil emulsions. Nature Methods 3, 551-559 (2006). (Pubitemid 43941774)
103. Weaver, S. et al. Taking qPCR to a higher level: analysis of CNV reveals the power of high throughput qPCR to enhance quantitative resolution. Methods (San Diego, California) 50, 271-276 (2010).
104. Mefford, H. C. et al. A method for rapid, targeted CNV genotyping identifies rare variants associated with neurocognitive disease. Genome Res. 19, 1579-1585 (2009).
105. Zerr, T., Cooper, G. M., Eichler, E. E. & Nickerson, D. A. Targeted interrogation of copy number variation using SCIMMkit. Bioinformatics (Oxford, England) 26, 120-122 (2010).
106. Lam, H. Y. et al. Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nature Biotech. 28, 47-55 (2010).
107. Waszak, S. M. et al. Systematic inference of copy-number genotypes from personal genome sequencing data reveals extensive olfactory receptor gene content diversity. PLoS Comput. Biol. 6, e1000988 (2010).
108. Conrad, D. F et al. Mutation spectrum revealed by breakpoint sequencing of human germline CNVs. Nature Genet. 42, 385-391 (2010).
109. Itsara, A. et al. De novo rates and selection of large copy number variation. Genome Res. 20, 1469-1481 (2010).
110. Zody, M. C. et al. Evolutionary toggling of the MAPT 17q21.31 inversion region. Nature Genet. 40, 1076-1083 (2008).
111. Kitzman, J. O. et al. Haplotype-resolved genome sequencing of a Gujarati Indian individual. Nature Biotech. 29, 59-63 (2011).
112. Oostlander, A. E., Meijer, G. A. & Ylstra, B. Microarray-based comparative genomic hybridization and its applications in human genetics. Clin. Genet. 66, 488-495 (2004). (Pubitemid 39562010)
113. Conlin, L. K. et al. Mechanisms of mosaicism, chimerism and uniparental disomy identified by single nucleotide polymorphism array analysis. Hum. Mol. Genet. 19, 1263-1275 (2010).
114. Rodriguez-Santiago, B. et al. Mosaic uniparental disomies and aneuploidies as large structural variants of the human genome. Am. J Hum. Genet. 87, 129-138 (2010).
115. Zerbino, D. R. & Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821-829 (2008). (Pubitemid 351645072)
116. Perry, G. H. et al. Diet and the evolution of human amylase gene copy number variation. Nature Genet. 39, 1256-1260 (2007). (Pubitemid 47482688)