Resolving genomic disorder-associated breakpoints within segmental DNA duplications using massively parallel sequencing

Nature Protocols

Volumn 9, Issue 6, 2014, Pages 1496-1513

  Nuttle, Xander ^a   Itsara, Andy ^a   Shendure, Jay ^a   Eichler, Evan E ^a  

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

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; NUCLEOTIDE; SINGLY UNIQUE NUCLEOTIDE; UNCLASSIFIED DRUG;

ARTICLE; COPY NUMBER VARIATION; CROSSING OVER; GENE SEQUENCE; GENETIC DISORDER; HAPLOTYPE; MASSIVELY PARALLEL SEQUENCING; MEASUREMENT ACCURACY; MOLECULAR INVERSION PROBE; MOLECULAR PROBE; PARALOGY; PRIORITY JOURNAL; SEGMENTAL DUPLICATION; SEQUENCE ANALYSIS; BIOLOGY; CHROMOSOME BREAKAGE; GENE LIBRARY; GENETICS; GENOME; HIGH THROUGHPUT SEQUENCING; HUMAN; PROCEDURES;

CHROMOSOME BREAKPOINTS; COMPUTATIONAL BIOLOGY; GENOME; GENOMIC LIBRARY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; SEGMENTAL DUPLICATIONS, GENOMIC;

EID: 84901820388     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2014.096     Document Type: Article

References (63)

1. Inoue, K. & Lupski, J.R. Molecular mechanisms for genomic disorders. Annu. Rev. Genomics Hum. Genet. 3, 199-242 (2002).
2. Stankiewicz, P. & Lupski, J.R. Genome architecture, rearrangements and genomic disorders. Trends Genet. 18, 74-82 (2002).
3. 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).
4. Stankiewicz, P. & Lupski, J.R. Structural variation in the human genome and its role in disease. Annu. Rev. Med. 61, 437-455 (2010).
5. Lupski, J.R. et al. DNA duplication associated with Charcot-Marie-Tooth disease type 1A. Cell 66, 219-232 (1991).
6. Pinkel, D. et al. GH (CGH). US Patent 5,976,790 (1999).
7. Wang, N.J. et al. High-resolution molecular characterization of 15q11-q13 rearrangements by array CGH (array CGH) with detection of gene dosage. Am. J. Hum. Genet. 75, 267-281 (2004).
8. Sahoo, T. et al. Prader-Willi phenotype caused by paternal deficiency for the HBII-85 C/D box small nucleolar RNA cluster. Nat. Genet. 40, 719-721 (2008).
9. Korbel, J.O. et al. Paired-end mapping reveals extensive structural variation in the human genome. Science 318, 420-426 (2007).
10. Mills, R.E. et al. Mapping copy number variation by population-scale genome sequencing. Nature 470, 59-65 (2011).
11. Sharp, A.J. et al. Segmental duplications and copy number variation in the human genome. Am. J. Hum. Genet. 77, 78-88 (2005).
12. Zody, M.C. et al. Evolutionary toggling of the MAPT 17q21.31 inversion region. Nat. Genet. 40, 1076-1083 (2008).
13. Girirajan, S. & Eichler, E.E. Phenotypic variability and genetic susceptibility to genomic disorders. Hum. Mol. Genet. 19, R176-R187 (2010).
14. Itsara, A. et al. Resolving the breakpoints of the 17q21.31 microdeletion syndrome with next-generation sequencing. Am. J. Hum. Genet. 90, 599-613 (2012).
15. Highsmith, W.E., Meyer, K.J., Marley, V.M. & Jenkins, R.B. Conversion technology for the separation of maternal and paternal copies of any autosomal chromosome in somatic cell hybrids. Curr. Prot. Hum. Genet. 3, 3-6 (2007).
16. van den Ijssel, P. & Ylstra, B. Oligonucleotide array CGH. in Methods in Molecular Biology vol. 396: Comparative Genomics, Volume 2 (ed. Bergman N.H.) 207-221 (Humana Press, 2007).
17. Horvath, J.E., Schwartz, S. & Eichler, E.E. The mosaic structure of human pericentromeric DNA: a strategy for characterizing complex regions of the human genome. Genome Res. 10, 839-852 (2000).
18. Saxena, R. et al. Four DAZ genes in two clusters found in the AZFc region of the human Y chromosome. Genomics 67, 256-267 (2000).
19. Tilford, C.A. et al. A physical map of the human Y chromosome. Nature 409, 943-945 (2001).
20. 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).
21. Fredman, D. et al. Complex SNP-related sequence variation in segmental genome duplications. Nat Genet. 36, 861-866 (2004).
22. Sudmant, P.H. et al. Diversity of human copy number variation and multicopy genes. Science 330, 641-646 (2010).
23. Nuttle, X. et al. Rapid and accurate large-scale genotyping of duplicated genes and discovery of interlocus gene conversions. Nat. Methods 10, 903-909 (2013).
24. Dennis, M.Y. et al. Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication. Cell 149, 912-922 (2012).
25. Bovee, D. et al. Closing gaps in the human genome with fosmid resources generated from multiple individuals. Nat. Genet. 40, 96-101 (2008).
26. Inoue, K. & Lupski, J.R. Molecular mechanisms for genomic disorders. Annu. Rev. Genomics Hum. Genet. 3, 199-242 (2002).
27. Stankiewicz, P. & Lupski, J.R. Genome architecture, rearrangements and genomic disorders. Trends Genet. 18, 74-82 (2002).
28. 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).
29. Stankiewicz, P. & Lupski, J.R. Structural variation in the human genome and its role in disease. Annu. Rev. Med. 61, 437-455 (2010).
30. Lupski, J.R. et al. DNA duplication associated with Charcot-Marie-Tooth disease type 1A. Cell 66, 219-232 (1991).
31. Pinkel, D. et al. GH (CGH). US Patent 5,976,790 (1999).
32. Wang, N.J. et al. High-resolution molecular characterization of 15q11-q13 rearrangements by array CGH (array CGH) with detection of gene dosage. Am. J. Hum. Genet. 75, 267-281 (2004).
33. Sahoo, T. et al. Prader-Willi phenotype caused by paternal deficiency for the HBII-85 C/D box small nucleolar RNA cluster. Nat. Genet. 40, 719-721 (2008).
34. Korbel, J.O. et al. Paired-end mapping reveals extensive structural variation in the human genome. Science 318, 420-426 (2007).
35. Mills, R.E. et al. Mapping copy number variation by population-scale genome sequencing. Nature 470, 59-65 (2011).
36. Sharp, A.J. et al. Segmental duplications and copy number variation in the human genome. Am. J. Hum. Genet. 77, 78-88 (2005).
37. Zody, M.C. et al. Evolutionary toggling of the MAPT 17q21.31 inversion region. Nat. Genet. 40, 1076-1083 (2008).
38. Girirajan, S. & Eichler, E.E. Phenotypic variability and genetic susceptibility to genomic disorders. Hum. Mol. Genet. 19, R176-R187 (2010).
39. Itsara, A. et al. Resolving the breakpoints of the 17q21.31 microdeletion syndrome with next-generation sequencing. Am. J. Hum. Genet. 90, 599-613 (2012).
40. Highsmith, W.E., Meyer, K.J., Marley, V.M. & Jenkins, R.B. Conversion technology for the separation of maternal and paternal copies of any autosomal chromosome in somatic cell hybrids. Curr. Prot. Hum. Genet. 3, 3.6 (2007).
41. van den Ijssel, P. & Ylstra, B. Oligonucleotide array CGH. in Methods in Molecular Biology vol. 396: Comparative Genomics, Volume 2 (ed. Bergman N.H.) 207-221 (Humana Press, 2007).
42. Horvath, J.E., Schwartz, S. & Eichler, E.E. The mosaic structure of human pericentromeric DNA: a strategy for characterizing complex regions of the human genome. Genome Res. 10, 839-852 (2000).
43. Saxena, R. et al. Four DAZ genes in two clusters found in the AZFc region of the human Y chromosome. Genomics 67, 256-267 (2000).
44. Tilford, C.A. et al. A physical map of the human Y chromosome. Nature 409, 943-945 (2001).
45. 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).
46. Fredman, D. et al. Complex SNP-related sequence variation in segmental genome duplications. Nat Genet. 36, 861-866 (2004).
47. Sudmant, P.H. et al. Diversity of human copy number variation and multicopy genes. Science 330, 641-646 (2010).
48. Nuttle, X. et al. Rapid and accurate large-scale genotyping of duplicated genes and discovery of interlocus gene conversions. Nat. Methods 10, 903-909 (2013).
49. Dennis, M.Y. et al. Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication. Cell 149, 912-922 (2012).
50. Bovee, D. et al. Closing gaps in the human genome with fosmid resources generated from multiple individuals. Nat. Genet. 40, 96-101 (2008).
51. Genovese, G. et al. Using population admixture to help complete maps of the human genome. Nat. Genet. 45, 406-414 (2013).
52. Carlson, C. et al. Molecular definition of 22q11 deletions in 151 velo-cardio-facial syndrome patients. Am. J. Hum. Genet. 61, 620-629 (1997).
53. Kitzman, J.O. et al. Haplotype-resolved genome sequencing of a Gujarati Indian individual. Nat. Biotechnol. 29, 59-63 (2011).
54. Peters, B.A. et al. Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells. Nature 487, 190-195 (2012).
55. Porreca, G.J. et al. Multiplex amplification of large sets of human exons. Nat. Methods 4, 931-936 (2007).
56. Turner, E.H. et al. Massively parallel exon capture and library-free resequencing across 16 genomes. Nat. Methods 6, 315-316 (2009).
57. O'Roak, B.J. et al. Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders. Science 338, 1619-1622 (2012).
58. Renshaw, M.A., Giresi, M. & Adams, J.O. Microsatellite fragment analysis using the ABI PRISM 377 DNA sequencer. in Methods in Molecular Biology, vol. 1006: Microsatellites (ed. Kantartzi, S.K.) 181-196 (Humana Press, 2013).
59. Broman, K.W., Murray, J.C., Sheffield, V.C., White, R.L. & Weber, J.L. Comprehensive human genetic maps: individual and sex-specific variation in recombination. Am. J. Hum. Genet. 63, 861-869 (1998).
60. Alkan, C. et al. Personalized copy number and segmental duplication maps using next-generation sequencing. Nat. Genet. 41, 1061-1067 (2009).
61. Tuzun, E., Bailey, J.A. & Eichler, E.E. Recent segmental duplications in the working draft assembly of the brown Norway rat. Genome Res. 14, 493-506 (2004).
62. Kidd, J.M. et al. Characterization of missing human genome sequences and copy number polymorphic insertions. Nat. Methods 7, 365-371 (2010).
63. Chin, C.S. et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10, 563-569 (2013).