Paired-Duplication Signatures Mark Cryptic Inversions and Other Complex Structural Variation

American Journal of Human Genetics

Volumn 97, Issue 1, 2015, Pages 170-176

  Brand, Harrison ^a,b   Collins, Ryan L ^a   Hanscom, Carrie ^a   Rosenfeld, Jill A ^c   Pillalamarri, Vamsee ^a   Stone, Matthew R ^a   Kelley, Fontina ^d   Mason, Tamara ^d   Margolin, Lauren ^d   Eggert, Stacey ^a   Mitchell, Elyse ^e   Hodge, Jennelle C ^e,f   Gusella, James F ^a,b,d   Sanders, Stephan J ^g   Talkowski, Michael E ^a,b,d  

^a MASSACHUSETTS GENERAL HOSPITAL   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c PERKINELMER INC   (United States)

^d BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^e MAYO CLINIC   (United States)

^f CEDARS SINAI MEDICAL CENTER   (United States)

^g UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTISM; CHROMOSOME; CHROMOSOME REARRANGEMENT; COPY NUMBER VARIATION; CYTOGENETICS; DNA END JOINING REPAIR; GENETIC VARIABILITY; HOMOLOGOUS RECOMBINATION; HUMAN; HUMAN GENOME; KARYOTYPING; MAJOR CLINICAL STUDY; MICROARRAY ANALYSIS; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; TANDEM REPEAT; CHROMOSOME INVERSION; COHORT ANALYSIS; DNA REPAIR; GENE LIBRARY; GENETIC MARKER; GENETICS; SEGMENTAL DUPLICATION;

GENETIC MARKER;

CHILD DEVELOPMENT DISORDERS, PERVASIVE; CHROMOSOME INVERSION; COHORT STUDIES; DNA COPY NUMBER VARIATIONS; DNA REPAIR; GENE LIBRARY; GENETIC MARKERS; HUMANS; SEGMENTAL DUPLICATIONS, GENOMIC;

EID: 84937522527     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2015.05.012     Document Type: Article

References (31)

1. J. Sebat, B. Lakshmi, D. Malhotra, J. Troge, C. Lese-Martin, T. Walsh, B. Yamrom, S. Yoon, A. Krasnitz, J. Kendall, and et al. Strong association of de novo copy number mutations with autism Science 316 2007 445 449
2. J.T. Glessner, K. Wang, G. Cai, O. Korvatska, C.E. Kim, S. Wood, H. Zhang, A. Estes, C.W. Brune, J.P. Bradfield, and et al. Autism genome-wide copy number variation reveals ubiquitin and neuronal genes Nature 459 2009 569 573
3. S. Girirajan, R.L. Johnson, F. Tassone, J. Balciuniene, N. Katiyar, K. Fox, C. Baker, A. Srikanth, K.H. Yeoh, S.J. Khoo, and et al. Global increases in both common and rare copy number load associated with autism Hum. Mol. Genet. 22 2013 2870 2880
4. D. Pinto, A.T. Pagnamenta, L. Klei, R. Anney, D. Merico, R. Regan, J. Conroy, T.R. Magalhaes, C. Correia, B.S. Abrahams, and et al. Functional impact of global rare copy number variation in autism spectrum disorders Nature 466 2010 368 372
5. R.E. Mills, K. Walter, C. Stewart, R.E. Handsaker, K. Chen, C. Alkan, A. Abyzov, S.C. Yoon, K. Ye, R.K. Cheetham 1000 Genomes Project Mapping copy number variation by population-scale genome sequencing Nature 470 2011 59 65
6. D.T. Miller, M.P. Adam, S. Aradhya, L.G. Biesecker, A.R. Brothman, N.P. Carter, D.M. Church, J.A. Crolla, E.E. Eichler, C.J. Epstein, and 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 2010 749 764
7. American College of Obstetricians and Gynecologists Committee on Genetics Committee Opinion No. 581: the use of chromosomal microarray analysis in prenatal diagnosis Obstet. Gynecol. 122 2013 1374 1377
8. H. Brand, V. Pillalamarri, R.L. Collins, S. Eggert, C. O'Dushlaine, E.B. Braaten, M.R. Stone, K. Chambert, N.D. Doty, C. Hanscom, and et al. Cryptic and complex chromosomal aberrations in early-onset neuropsychiatric disorders Am. J. Hum. Genet. 95 2014 454 461
9. J. Drabova, M. Trkova, M. Hancarova, D. Novotna, M. Hejtmankova, M. Havlovicova, and Z. Sedlacek A 15 Mb large paracentric chromosome 21 inversion identified in Czech population through a pair of flanking duplications Mol. Cytogenet. 7 2014 51
10. S. Newman, K.E. Hermetz, B. Weckselblatt, and M.K. Rudd Next-generation sequencing of duplication CNVs reveals that most are tandem and some create fusion genes at breakpoints Am. J. Hum. Genet. 96 2015 208 220
11. J.O. Korbel, A.E. Urban, J.P. Affourtit, B. Godwin, F. Grubert, J.F. Simons, P.M. Kim, D. Palejev, N.J. Carriero, L. Du, and et al. Paired-end mapping reveals extensive structural variation in the human genome Science 318 2007 420 426
12. G.D. Fischbach, and C. Lord The Simons Simplex Collection: a resource for identification of autism genetic risk factors Neuron 68 2010 192 195
13. S.J. Sanders, A.G. Ercan-Sencicek, V. Hus, R. Luo, M.T. Murtha, D. Moreno-De-Luca, S.H. Chu, M.P. Moreau, A.R. Gupta, S.A. Thomson, and et al. Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism Neuron 70 2011 863 885
14. M.E. Talkowski, C. Ernst, A. Heilbut, C. Chiang, C. Hanscom, A. Lindgren, A. Kirby, S. Liu, B. Muddukrishna, T.K. Ohsumi, and et al. Next-generation sequencing strategies enable routine detection of balanced chromosome rearrangements for clinical diagnostics and genetic research Am. J. Hum. Genet. 88 2011 469 481
15. M.E. Talkowski, Z. Ordulu, V. Pillalamarri, C.B. Benson, I. Blumenthal, S. Connolly, C. Hanscom, N. Hussain, S. Pereira, J. Picker, and et al. Clinical diagnosis by whole-genome sequencing of a prenatal sample N. Engl. J. Med. 367 2012 2226 2232
16. M.E. Talkowski, J.A. Rosenfeld, I. Blumenthal, V. Pillalamarri, C. Chiang, A. Heilbut, C. Ernst, C. Hanscom, E. Rossin, A.M. Lindgren, and et al. Sequencing chromosomal abnormalities reveals neurodevelopmental loci that confer risk across diagnostic boundaries Cell 149 2012 525 537
17. C. Chiang, J.C. Jacobsen, C. Ernst, C. Hanscom, A. Heilbut, I. Blumenthal, R.E. Mills, A. Kirby, A.M. Lindgren, S.R. Rudiger, and et al. Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration Nat. Genet. 44 2012 390 397 S1
18. C. Hanscom, and M. Talkowski Design of large-insert jumping libraries for structural variant detection using illumina sequencing Curr. Protoc. Hum. Genet. 80 2014 1 9
19. R.M. Layer, C. Chiang, A.R. Quinlan, and I.M. Hall LUMPY: a probabilistic framework for structural variant discovery Genome Biol. 15 2014 R84
20. G. Klambauer, K. Schwarzbauer, A. Mayr, D.A. Clevert, A. Mitterecker, U. Bodenhofer, and S. Hochreiter cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate Nucleic Acids Res. 40 2012 e69
21. G.P. Schroth, and P.S. Ho Occurrence of potential cruciform and H-DNA forming sequences in genomic DNA Nucleic Acids Res. 23 1995 1977 1983
22. P.J. Hastings, G. Ira, and J.R. Lupski A microhomology-mediated break-induced replication model for the origin of human copy number variation PLoS Genet. 5 2009 e1000327
23. F. Zhang, M. Khajavi, A.M. Connolly, C.F. Towne, S.D. Batish, and J.R. Lupski The DNA replication FoSTeS/MMBIR mechanism can generate genomic, genic and exonic complex rearrangements in humans Nat. Genet. 41 2009 849 853
24. W. Gu, F. Zhang, and J.R. Lupski Mechanisms for human genomic rearrangements PathoGenetics 1 2008 4
25. S. De Rubeis, X. He, A.P. Goldberg, C.S. Poultney, K. Samocha, A.E. Cicek, Y. Kou, L. Liu, M. Fromer, S. Walker DDD Study Homozygosity Mapping Collaborative for Autism UK10K Consortium Synaptic, transcriptional and chromatin genes disrupted in autism Nature 515 2014 209 215
26. I. Iossifov, B.J. O'Roak, S.J. Sanders, M. Ronemus, N. Krumm, D. Levy, H.A. Stessman, K.T. Witherspoon, L. Vives, K.E. Patterson, and et al. The contribution of de novo coding mutations to autism spectrum disorder Nature 515 2014 216 221
27. G.T. Consortium GTEx Consortium The Genotype-Tissue Expression (GTEx) project Nat. Genet. 45 2013 580 585
28. B. Bakkaloglu, B.J. O'Roak, A. Louvi, A.R. Gupta, J.F. Abelson, T.M. Morgan, K. Chawarska, A. Klin, A.G. Ercan-Sencicek, A.A. Stillman, and et al. Molecular cytogenetic analysis and resequencing of contactin associated protein-like 2 in autism spectrum disorders Am. J. Hum. Genet. 82 2008 165 173
29. R. Sultana, C.E. Yu, J. Yu, J. Munson, D. Chen, W. Hua, A. Estes, F. Cortes, F. de la Barra, D. Yu, and et al. Identification of a novel gene on chromosome 7q11.2 interrupted by a translocation breakpoint in a pair of autistic twins Genomics 80 2002 129 134
30. G. Beunders, E. Voorhoeve, C. Golzio, L.M. Pardo, J.A. Rosenfeld, M.E. Talkowski, I. Simonic, A.C. Lionel, S. Vergult, R.E. Pyatt, and et al. Exonic deletions in AUTS2 cause a syndromic form of intellectual disability and suggest a critical role for the C terminus Am. J. Hum. Genet. 92 2013 210 220
31. R.J. Wapner, C.L. Martin, B. Levy, B.C. Ballif, C.M. Eng, J.M. Zachary, M. Savage, L.D. Platt, D. Saltzman, W.A. Grobman, and et al. Chromosomal microarray versus karyotyping for prenatal diagnosis N. Engl. J. Med. 367 2012 2175 2184