Characterising chromosome rearrangements: Recent technical advances in molecular cytogenetics

Heredity

Volumn 108, Issue 1, 2012, Pages 75-85

  Le Scouarnec, S ^a   Gribble, S M ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

array painting; array CGH; breakpoint mapping; copy number variant; next generation sequencing; structural variant

Indexed keywords

ADVANCED TECHNOLOGY; CHROMOSOME; CYTOGENETICS; GENETIC ANALYSIS; GENETIC VARIATION; GENOME; HERITABILITY; HYBRIDIZATION; MAPPING; MOLECULAR ANALYSIS;

CHROMOSOME ABERRATION; CHROMOSOME BREAKAGE; CHROMOSOME MAP; CHROMOSOME PAINTING; COMPARATIVE GENOMIC HYBRIDIZATION; DNA MICROARRAY; GENETIC ASSOCIATION; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN CHROMOSOME; HUMAN GENOME; NEOPLASM; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM;

CHROMOSOME ABERRATIONS; CHROMOSOME BREAKPOINTS; CHROMOSOME MAPPING; CHROMOSOME PAINTING; CHROMOSOMES, HUMAN; COMPARATIVE GENOMIC HYBRIDIZATION; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 83655201192     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2011.100     Document Type: Review

References (130)

1. Abel HJ, Duncavage EJ, Becker N, Armstrong JR, Magrini VJ, Pfeifer JD(2010).SLOPE: a quick and accurate method for locating non-SNP structural variation from targeted next- generation sequence data. Bioinformatics26: 2684-2688.
2. Abyzov A, Gerstein M (2011). AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision. Bioinfor- matics27: 595-603.
3. Alkan C, Coe BP, Eichler EE (2011a). Genome structural variation discovery and genotyping. Nat Rev Genet 12: 363-376.
4. Alkan C, Kidd JM, Marques-Bonet T, Aksay G, Antonacci F, Hormozdiari F et al. (2009). Personalized copy number and segmental duplication maps using next-generation sequencing. Nat Genet41: 1061-1067.
5. Alkan C, Sajjadian S, Eichler EE (2011b). Limitationsof next-generation genomesequence assembly. Nat Methods 8: 61-65.
6. Andersson R, Bruder CE, Piotrowski A, Menzel U, Nord H, Sandgren J et al. (2008). A segmental maximum a posteriori approach to genome-wide copy number profiling. Bioinformatics24: 751-758. (Pubitemid 351386912)
7. Backx L, Van Esch H, Melotte C, Kosyakova N, Starke H, Frijns JP et al. (2007). Array painting using microdissected chromosomes to map chromosomal breakpoints. Cytogenet Genome Res 116: 158-166. (Pubitemid 46333790)
8. Barrett MT, Scheffer A, Ben-Dor A, Sampas N, Lipson D, Kincaid R et al. (2004). Comparativegenomic hybridization usingoligonucleotide microarraysand total genomic DNA. Proc Natl Acad Sci USA 101: 17765-17770. (Pubitemid 40051961)
9. Bauman JG, Wiegant J, Borst P, van Duijn P (1980). A new method for fluorescence microscopical localization of specific DNA sequences by in situ hybridization of fluorochromelabelled RNA. Exp Cell Res 128: 485-490. (Pubitemid 11210993)
10. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG et al. (2008). Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456: 53-59.
11. Bieche I, Olivi M, Champeme MH, Vidaud D, Lidereau R, Vidaud M (1998). Novel approach to quantitative polymerase chain reaction using real-time detection: application to the detection of gene amplification in breast cancer. Int J Cancer78: 661-666. (Pubitemid 28507194)
12. Bignell GR, Huang J, Greshock J, Watt S, Butler A, West S et al. (2004). High-resolution analysis of DNA copy number using oligonucleotide microarrays. Genome Res 14: 287-295. (Pubitemid 38219842)
13. Brennan C, Zhang Y, Leo C, Feng B, Cauwels C, Aguirre AJ et al. (2004). High-resolution global profiling of genomic alterations with long oligonucleotide microarray Cancer Res 64: 4744-4748. (Pubitemid 38924516)
14. Campbell PJ, Yachida S, Mudie LJ, Stephens PJ, Pleasance ED, Stebbings LA et al. (2010). The patterns and dynamics of genomic instability in metastatic pancreatic cancer. Nature 467: 1109-1113.
15. Campbell PJ, Stephens PJ, Pleasance ED, O'Meara S, Li H, Santarius T et al. (2008). Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet 40: 722-729. (Pubitemid 351748860)
16. Carter NP, Ferguson-Smith MA, Perryman MT, Telenius H, Pelmear AH, Leversha MAet al. (1992). Reverse chromosome painting: a method for the rapid analysis of aberrant chromosomes in clinical cytogenetics. J Med Genet 29: 299-307.
17. Carvalho B, Ouwerkerk E, Meijer GA, Ylstra B (2004). High resolution microarray comparative genomic hybridisation analysis using spotted oligonucleotides. J Clin Pathol57: 644-646. (Pubitemid 38725769)
18. Chen W, Kalscheuer V, Tzschach A, Menzel C, Ullmann R, Schulz MH et al. (2008). Mapping translocation breakpoints by next-generation sequencing. Genome Res 18: 1143-1149. (Pubitemid 351931165)
19. Chen W, Ullmann R, Langnick C, Menzel C, Wotschofsky Z, Hu H et al. (2010). Breakpoint analysis of balanced chromosome rearrangements by next-generation paired-end sequencing. Eur J Hum Genet 18: 539-543.
20. Chiang DY, Getz G, Jaffe DB, O'Kelly MJ, Zhao X, Carter SL et al. (2009). High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods 6: 99-103.
21. Chung YJ, Jonkers J, Kitson H, Fiegler H, Humphray S, Scott C et al. (2004). A whole- genome mouse BAC microarraywith 1-Mb resolution for analysis of DNA copy number changes by array comparative genomic hybridization. Genome Res 14: 188-196. (Pubitemid 38088540)
22. Coffey AJ, Kokocinski F, Calafato MS, Scott CE, Palta P, Drury E et al. (2011). The GENCODE exome: sequencing the complete human exome. Eur J Hum Genet 19: 827-831.
23. Conlin LK, Thiel BD, Bonnemann CG, Medne L, Ernst LM, Zackai EH et al. (2010). Mechanisms of mosaicism, chimerism and uniparental disomy identified by single nucleotide polymorphism array analysis. Hum Mol Genet 19: 1263-1275.
24. Conrad DF, Bird C, Blackburne B, Lindsay S, Mamanova L, Lee C et al. (2010a). Mutation spectrum revealed by breakpoint sequencing of human germline CNVs. Nat Genet42: 385-391.
25. Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Yet al. (2010b). Origins and functional impact of copynumbervariation inthehumangenome. Nature464: 704-712.
26. Cooper GM, Nickerson DA, Eichler EE (2007). Mutational and selective effects on copy- numbervariants inthehumangenome. Nat Genet39: S22-S29. (Pubitemid 47014473)
27. Cooper GM, Zerr T, Kidd JM, Eichler EE, Nickerson DA (2008). Systematic assessment of copy number variant detection via genome-wide SNP genotyping. Nat Genet 40: 1199-1203.
28. Craddock N, Hurles ME, Cardin N, Pearson RD, Plagnol V, Robson S et al. (2010). Genome- wide association study of CNVs in 16000 cases of eight common diseases and 3000 sharedcontrols. Nature 464: 713-720.
29. Cremer T, Lichter P, Borden J, Ward DC, Manuelidis L (1988). Detection of chromosome aberrations in metaphase and interphase tumor cells by in situ hybridization using chromosome-specific libraryprobes. Hum Genet 80: 235-246.
30. Curtis C, Lynch AG, Dunning MJ, Spiteri I, Marioni JC, Hadfield J et al. (2009). The pitfalls of platform comparison: DNA copynumber arraytechnologiesassessed. BMCGenomics 10: 588.
31. Darai-Ramqvist E, Diaz de Stahl T, Sandlund A, Mantripragada K, Klein G, Dumanski J et al. (2006). Array-CGH and multipoint FISH to decode complex chromosomal rearrangements. BMCGenomics7: 330.
32. Dellinger AE, Saw SM, Goh LK, Seielstad M, Young TL, Li YJ (2010). Comparativeanalyses of seven algorithms for copy number variant identification from single nucleotide polymorphism arrays. Nucleic Acids Res38: e105.
33. Dhami P, Coffey AJ, Abbs S, Vermeesch JR, Dumanski JP, Woodward KJ et al. (2005). 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. (Pubitemid 40563097)
34. Durbin RM, Abecasis GR, Altshuler DL, Auton A, Brooks LD, Durbin RM et al. (2010). A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
35. Fauth C, Gribble SM, Porter KM, Codina-Pascual M, Ng BL, Kraus J et al. (2006). Microarray analysesdecipher exceptional complexfamilial chromosomal rearrangement. Hum Genet 119: 145-153.
36. Feuk L, Carson AR, Scherer SW(2006). Structural variation in thehuman genome. Nat Rev Genet 7: 85-97.
37. Fiegler H, Carr P, Douglas EJ, Burford DC, Hunt S, Scott CE et al. (2003a). DNA microarrays for comparative genomic hybridization based on DOP-PCR amplification of BAC and PAC clones. Genes Chromosomes Cancer36: 361-374. (Pubitemid 36314519)
38. Fiegler H, Geigl JB, Langer S, Rigler D, Porter K, Unger K et al. (2007). High resolution array-CGH analysis of single cells. Nucleic Acids Res 35: e15.
39. Fiegler H, Gribble SM, Burford DC, Carr P, Prigmore E, Porter KM et al. (2003b). Array painting: a method for the rapid analysis of aberrant chromosomes using DNA Microarrays. J Med Genet 40: 664-670. (Pubitemid 37100698)
40. Fitzgerald TW, Larcombe LD, Le Scouarnec S, Clayton S, Rajan D, Carter NP et al. (2011). a CGH\-Spline\-An R package for a CGH dye bias normalisation. Bioinformatics 27: 1195-1200.
41. Greenman CD, Bignell G, Butler A, Edkins S, Hinton J, Beare D et al. (2010). PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data. Biostatistics 11: 164-175.
42. Gribble SM, Fiegler H, Burford DC, Prigmore E, Yang F, Carr P et al. (2004). Applications of combined DNA microarrayand chromosomesortingtechnologies. Chromosome Res 12: 35-43. (Pubitemid 38187083)
43. Gribble SM, Kalaitzopoulos D, Burford DC, Prigmore E, Selzer RR, Ng BL et al. (2007). Ultra-high resolution array painting facilitates breakpoint sequencing. J Med Genet44: 51-58. (Pubitemid 46142839)
44. Gribble SM, Ng BL, Prigmore E, Fitzgerald T, Carter NP (2009). Array painting: a protocol for the rapid analysis of aberrant chromosomes using DNA microarrays. Nat Protoc 4: 1722-1736.
45. Gribble SM, Prigmore E, Burford DC, Porter KM, Ng BL, Douglas EJ et al. (2005). The complex natureof constitutional de novoapparently balanced translocations in patients presentingwith abnormal phenotypes. J Med Genet 42: 8-16. (Pubitemid 40187115)
46. Griffin DK, Robertson LB, Tempest HG, Vignal A, Fillon V, Crooijmans RP et al. (2008). Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution. BMC Genomics9: 168.
47. Gu W, Zhang F, Lupski JR (2008). Mechanisms for human genomic rearrangements. Pathogenetics 1: 4.
48. Guillaud-Bataille M, Valent A, Soularue P, Perot C, Inda MM, Receveur A et al. (2004). Detecting single DNA copy numbervariations in complexgenomes using one nanogram ofstarting DNA and BAC-array CGH. Nucleic Acids Res32: e112.
49. Gunderson KL, Steemers FJ, Lee G, Mendoza LG, Chee MS (2005). A genome-wide scalable SNP genotyping assay using microarray technology. Nat Genet37: 549-554. (Pubitemid 40617286)
50. Hedges DJ, Guettouche T, Yang S, Bademci G, Diaz A, Andersen A et al. (2011). Comparison of threetargeted enrichment strategies on the SOLi D sequencing platform. PLo S One 6: e18595.
51. Heiskanen MA, Bittner ML, Chen Y, Khan J, Adler KE, Trent JM et al. (2000). Detection of gene amplification by genomic hybridization to c DNA microarrays. Cancer Res 60: 799-802. (Pubitemid 30129504)
52. Heng HH, Squire J, Tsui LC (1992). High-resolution mapping of mammalian genes by in situ hybridization to free chromatin. Proc Natl Acad Sci USA 89: 9509-9513.
53. Howarth KD, Blood KA, Ng BL, Beavis JC, Chua Y, Cooke SL et al. (2008). Array painting reveals a high frequencyof balancedtranslocations in breastcancer cell linesthat break in cancer-relevant genes. Oncogene 27: 3345-3359. (Pubitemid 351733393)
54. Howarth KD, Pole JC, Beavis JC, Batty EM, Newman S, Bignell GR et al. (2011). Large duplications at reciprocal translocation breakpoints that might be the counterpart of largedeletionsandcould arisefrom stalled replication bubbles. Genome Res21: 525-534.
55. Huang J, Wei W, Zhang J, Liu G, Bignell GR, Stratton MR et al. (2004). Wholegenome DNA copy number changes identified by high density oligonucleotide arrays. Hum Genomics 1: 287-299.
56. Huang N, Lee I, Marcotte EM, Hurles ME (2010). Characterising and predicting haploin- sufficiency in the human genome. PLo S Genet6: e1001154.
57. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK,Qi Yet al.(2004). Detection of large-scale variation in the human genome. Nat Genet36: 949-951. (Pubitemid 39167488)
58. Ishkanian AS, Malloff CA, Watson SK, De Leeuw RJ, Chi B, Coe BP et al. (2004). A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet 36: 299-303. (Pubitemid 38282757)
59. Kallioniemi A, Kallioniemi OP, Sudar D, Rutovitz D, Gray JW, Waldman F et al. (1992). Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258: 818-821.
60. Kennedy GC, Matsuzaki H, Dong S, Liu WM, Huang J, Liu G et al. (2003). Large-scale genotyping of complex DNA. Nat Biotechnol 21: 1233-1237. (Pubitemid 37186182)
61. Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T et al. (2008). Mapping and sequencing of structural variation from eight human genomes. Nature 453: 56-64. (Pubitemid 351630326)
62. Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF et al. (2007). Pairedend mapping reveals extensive structural variation in the human genome. Science318: 420-426. (Pubitemid 47614521)
63. La Framboise T (2009). Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances. Nucleic Acids Res 37: 4181-4193.
64. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J et al. (2001). Initial sequencing and analysis of the human genome. Nature 409: 860-921. (Pubitemid 32165345)
65. Le Caignec C, Spits C, Sermon K, De Rycke M, Thienpont B, Debrock S et al. (2006). Single-cell chromosomal imbalances detection by array CGH. Nucleic Acids Res 34: e68.
66. Li H, Ruan J, Durbin R (2008). Mappingshort DNA sequencing reads and callingvariants using mapping quality scores. Genome Res 18: 1851-1858.
67. Lichter P, Cremer T, Borden J, Manuelidis L, Ward DC (1988). Delineation of individual human chromosomes in metaphase and interphase cells by in situ suppression hybridization using recombinant DNA libraries. Hum Genet80: 224-234.
68. Linardopoulou EV, Williams EM, Fan Y, Friedman C, Young JM, Trask BJ (2005). Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication. Nature 437: 94-100. (Pubitemid 41613430)
69. Maher CA, Kumar-Sinha C, Cao X, Kalyana-Sundaram S, Han B, Jing X et al. (2009). Transcriptome sequencing to detect gene fusions in cancer. Nature 458: 97-101.
70. Mani RS, Chinnaiyan AM (2010). Triggers for genomic rearrangements: insights into genomic, cellular and environmental influences. Nat Rev Genet 11: 819-829.
71. Mantripragada KK, Tapia-Paez I, Blennow E, Nilsson P, Wedell A, Dumanski JP (2004). 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.
72. Mardis ER, Ding L, Dooling DJ, Larson DE, Mc Lellan MD, Chen K et al. (2009). Recurring mutationsfound bysequencinganacutemyeloid leukemiagenome. NEngl JMed361: 1058-1066.
73. Marioni JC, Thorne NP, Valsesia A, Fitzgerald T, Redon R, Fiegler H et al. (2007). Breaking the waves: improved detection of copy number variation from microarray-based com- parative genomic hybridization. Genome Biol8: R228.
74. Mc Carroll SA, Kuruvilla FG, Korn JM, Cawley S, Nemesh J, Wysoker A et al. (2008). Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet 40: 1166-1174.
75. Medvedev P, Stanciu M, Brudno M (2009). Computational methods for discovering structural variation with next-generation sequencing. Nat Methods 6: S13-S20.
76. Mefford HC, Eichler EE (2009). Duplication hotspots, rare genomic disorders, and common disease. Curr Opin Genet Dev 19: 196-204.
77. Metzker ML (2010). Sequencing technologies\-the next generation. Nat Rev Genet 11: 31-46.
78. Meyerson M, Gabriel S, Getz G (2010). Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet 11: 685-696.
79. Michalet X, Ekong R, Fougerousse F, Rousseaux S, Schurra C, Hornigold N et al. (1997). Dynamic molecular combing: stretching the whole human genome for high-resolution studies. Science277: 1518-1523. (Pubitemid 27449242)
80. Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP et al. (2010). 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.
81. Mills RE, Luttig CT, Larkins CE, Beauchamp A, Tsui C, Pittard WS et al. (2006). An initial map of insertion and deletion (INDEL)variation in the human genome. Genome Res 16: 1182-1190. (Pubitemid 44320405)
82. Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C et al. (2011). Mappingcopy number variation by population-scale genome sequencing. Nature 470: 59-65.
83. Nuwaysir EF, Huang W, Albert TJ, Singh J, Nuwaysir K, Pitas A et al. (2002). Gene expression analysis using oligonucleotide arrays produced by maskless photolithogra- phy. Genome Res 12: 1749-1755. (Pubitemid 35363679)
84. Olshen AB, Venkatraman ES, Lucito R, Wigler M (2004). Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics5: 557-572. (Pubitemid 41180205)
85. Ou Z, Stankiewicz P, Xia Z, Breman AM, Dawson B, Wiszniewska J et al. (2011). Observation and prediction of recurrent human translocations mediated by NAHR between nonhomologous chromosomes. Genome Res 21: 33-46.
86. Pang AW, Mac Donald JR, Pinto D, Wei J, Rafiq MA, Conrad DF et al. (2010). Towards a com- prehensivestructural variation mapof an individual human genome. Genome Biol11: R52.
87. Parameswaran P, Jalili R, Tao L, Shokralla S, Gharizadeh B, Ronaghi M et al. (2007). A pyrosequencing-tailored nucleotide barcodedesign unveils opportunities for large-scale sample multiplexing. Nucleic Acids Res 35: e130.
88. Park H, Kim JI, Ju YS, Gokcumen O, Mills RE, Kim S et al. (2010). Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing. Nat Genet 42: 400-405.
89. Parra I, Windle B (1993). High resolution visual mapping of stretched DNA byfluorescent hybridization. Nat Genet5: 17-21. (Pubitemid 23261512)
90. Peiffer DA, Le JM, Steemers FJ, Chang W, Jenniges T, Garcia F et al. (2006). High- resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. Genome Res16: 1136-1148. (Pubitemid 44320401)
91. Pinkel D, Landegent J, Collins C, Fuscoe J, Segraves R, Lucas J et al. (1988). Fluorescence insituhybridization with human chromosome-specific libraries: detection oftrisomy21 and translocations of chromosome 4. Proc Natl Acad Sci USA 85: 9138-9142. (Pubitemid 19001853)
92. Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D et al. (1998). High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet20: 207-211. (Pubitemid 28455458)
93. Pinto D, Darvishi K, Shi X, Rajan D, Rigler D, Fitzgerald Tet al. (2011). Comprehensive assessment of array-based platforms and calling algorithms for detection of copy numbervariants. Nat Biotechnol 29: 512-520.
94. Pique-Regi R, Monso-Varona J, Ortega A, Seeger RC, Triche TJ, Asgharzadeh S (2008). Sparse representation and Bayesian detection of genome copy number alterations from microarray data. Bioinformatics24: 309-318. (Pubitemid 351189005)
95. Pleasance ED, Cheetham RK, Stephens PJ, Mc Bride DJ, Humphray SJ, Greenman CD et al. (2010). A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 463: 191-196.
96. Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF et al. (1999). Genome-wide analysis of DNA copy-number changes using c DNA microarrays. Nat Genet23: 41-46. (Pubitemid 29418785)
97. Price TS, Regan R, Mott R, Hedman A, Honey B, Daniels RJ et al. (2005). 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 33: 3455-3464. (Pubitemid 41430569)
98. Przybytkowski E, Ferrario C, Basik M(2011).Theuseofultra-densearray CGHanalysisfor the discoveryof micro-copy number alterationsand gene fusions in the cancer genome. BMC Med Genomics 4: 16.
99. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD et al. (2006). Global variation in copy number in the human genome. Nature 444: 444-454. (Pubitemid 44809057)
100. Scherer SW, Lee C, Birney E, Altshuler DM, Eichler EE, Carter NP et al. (2007). Challenges and standards in integrating surveys of structural variation. Nat Genet39: S7-15.
101. Schouten JP, Mc Elgunn CJ, Waaijer R, Zwijnenburg D, Diepvens F, Pals G (2002). Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res30: e57.
102. Schrock E, du Manoir S, Veldman T, Schoell B, Wienberg J, Ferguson-Smith MAet al. (1996). Multicolor spectral karyotyping of human chromosomes. Science 273: 494-497. (Pubitemid 26286449)
103. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P et al. (2004). Large-scalecopy number polymorphism in the human genome. Science305: 525-528. (Pubitemid 38971344)
104. Sharp AJ, Itsara A, Cheng Z, Alkan C, Schwartz S, Eichler EE (2007). Optimal design of oligonucleotide microarrays for measurement of DNA copy-number. Hum Mol Genet 16: 2770-2779. (Pubitemid 350018519)
105. Sharp AJ, Locke DP, Mc Grath SD, Cheng Z, Bailey JA, Vallente RU et al. (2005). Segmental duplications and copy-number variation in the human genome. Am J Hum Genet 77: 78-88. (Pubitemid 40848038)
106. Shendure J, Porreca GJ, Reppas NB, Lin X, Mc Cutcheon JP, Rosenbaum AM et al. (2005). Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309: 1728-1732. (Pubitemid 41285943)
107. Simonis M, Klous P, Homminga I, Galjaard RJ, Rijkers EJ, Grosveld F et al. (2009). High- resolution identification of balanced and complex chromosomal rearrangements by 4C technology. Nat Methods 6: 837-842.
108. Skinner BM, Robertson LB, Tempest HG, Langley EJ, Ioannou D, Fowler KE et al. (2009). Comparative genomics in chicken and Pekin duck using FISH mapping and microarray analysis. BMC Genomics 10: 357.
109. Slade I, Stephens P, Douglas J, Barker K, Stebbings L, Abbaszadeh F et al. (2010). Constitutional translocation breakpoint mapping by genome-wide paired-end sequencing identifies HACE1 as a putative Wilmstumoursusceptibilitygene. J Med Genet47: 342-347.
110. Snijders AM, Nowak N, Segraves R, Blackwood S, Brown N, Conroy J et al. (2001). Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet29: 263-264. (Pubitemid 33096449)
111. Solinas-Toldo S, Lampel S, Stilgenbauer S, Nickolenko J, Benner A, Dohner H et al. (1997). Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer20: 399-407. (Pubitemid 27520090)
112. Speicher MR, Carter NP (2005). The new cytogenetics: blurring the boundaries with molecular biology. Nat Rev Genet 6: 782-792. (Pubitemid 41400836)
113. Speicher MR, Gwyn Ballard S, Ward DC (1996). Karyotyping human chromosomes by combinatorial multi-fluor FISH. Nat Genet 12: 368-375. (Pubitemid 26105926)
114. Stankiewicz P, Lupski JR (2010). Structural variation in the human genome and its role in disease. Annu Rev Med61: 437-455.
115. Stephens PJ, Greenman CD, Fu B, Yang F, Bignell GR, Mudie LJ et al. (2011). Massive genomic rearrangement acquired in a single catastrophic event during cancer develop- ment. Cell 144: 27-40.
116. Stephens PJ, Mc Bride DJ, Lin ML, Varela I, Pleasance ED, Simpson JT et al. (2009). Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature 462: 1005-1010.
117. Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A et al. (2010). Diversity of human copy number variation and multicopy genes. Science 330: 641-646.
118. Talseth-Palmer BA, Bowden NA, Hill A, Meldrum C, Scott RJ (2008). Whole genome amplification and its impact on CGH array profiles. BMC Res Notes 1: 56.
119. Telenius H, Carter NP, Bebb CE, Nordenskjold M, Ponder BA, Tunnacliffe A (1992). Degenerateoligonucleotide-primed PCR: general amplification oftarget DNA bya single degenerate primer. Genomics 13: 718-725.
120. The International Hap Map Consortium (2003). The International Hap Map Project. Nature 426: 789-796.
121. Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, Pertz LM et al. (2005). Fine-scale structural variation of the human genome. Nat Genet37: 727-732. (Pubitemid 41754889)
122. Tzschach A, Bisgaard AM, Kirchhoff M, Graul-Neumann LM, Neitzel H, Page S et al. (2010). Chromosome aberrations involving 10q22: report of three overlapping inter- stitial deletions and a balanced translocation disrupting C10orf11. Eur J Hum Genet 18: 291-295.
123. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG et al. (2001). Thesequence ofthehumangenome. Science291: 1304-1351.
124. Volker M, Backstrom N, Skinner BM, Langley EJ, Bunzey SK, Ellegren H et al. (2010). Copy number variation, chromosome rearrangement, and their association with recom- binationduringavianevolution. Genome Res20: 503-511.
125. Wiegant J, Kalle W, Mullenders L, Brookes S, Hoovers JM, Dauwerse JG et al. (1992). High-resolution in situ hybridization using DNA halo preparations. Hum Mol Genet 1: 587-591.
126. Winchester L, Yau C, Ragoussis J (2009). Comparing CNV detection methods for SNP arrays. Brief Funct Genomic Proteomic8: 353-366.
127. Yamada NA, Rector LS, Tsang P, Carr E, Scheffer A, Sederberg MC et al. (2011). Visualization of fine-scale genomic structure by oligonucleotide-based high-resolution FISH. Cytogenet Genome Res 132: 248-254.
128. Yamazawa K, Ogata T, Ferguson-Smith AC (2010). Uniparental disomyand human disease: an overview. Am J Med Genet C Semin Med Genet 154C: 329-334.
129. Ye K, Schulz MH, Long Q, Apweiler R, Ning Z (2009). Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end shortreads. Bioinformatics25: 2865-2871.
130. Yoon S, Xuan Z, Makarov V, Ye K, Sebat J (2009). Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res 19: 1586-1592.