Frequency and Complexity of de Novo Structural Mutation in Autism

American Journal of Human Genetics

Volumn 98, Issue 4, 2016, Pages 667-679

  Brandler, William M ^a,b,c   Antaki, Danny ^a,b,c   Gujral, Madhusudan ^a,b,c   Noor, Amina ^a,b,c   Rosanio, Gabriel ^a,b,c   Chapman, Timothy R ^a,b,c   Barrera, Daniel J ^a,b,c   Lin, Guan Ning ^b   Malhotra, Dheeraj ^a,b,c   Watts, Amanda C ^a   Wong, Lawrence C ^d   Estabillo, Jasper A ^d   Gadomski, Therese E ^a,b,c   Hong, Oanh ^a,b,c   Fajardo, Karin V Fuentes ^a,b,c   Bhandari, Abhishek ^a,b,c   Owen, Renius ^e   Baughn, Michael ^a   Yuan, Jeffrey ^a   Solomon, Terry ^a   Moyzis, Alexandra G ^a   Maile, Michelle S ^a,b,c   Sanders, Stephan J ^f   Reiner, Gail E ^g   Vaux, Keith K ^g   Strom, Charles M ^e   Zhang, Kang ^a   Muotri, Alysson R ^c   Akshoomoff, Natacha ^d   Leal, Suzanne M ^h   Pierce, Karen ⁱ   Courchesne, Eric ⁱ   Iakoucheva, Lilia M ^b   Corsello, Christina ^d   Sebat, Jonathan ^a,b,c   more..

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d RADY CHILDREN'S HOSPITAL   (United States)

^e QUEST DIAGNOSTICS NICHOLS INSTITUTE   (United States)

^f UNIVERSITY OF CALIFORNIA   (United States)

^g UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^h BAYLOR COLLEGE OF MEDICINE   (United States)

ⁱ UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTISM; CONTROLLED STUDY; GENE LOCUS; GENE MUTATION; GENE REARRANGEMENT; GENE SEQUENCE; GENETIC RISK; GENETIC VARIABILITY; GENOTYPE; HUMAN; MAJOR CLINICAL STUDY; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; ALLELE; AMINO ACID SEQUENCE; CASE CONTROL STUDY; CHILD; COPY NUMBER VARIATION; FEMALE; GENE DELETION; GENE DUPLICATION; GENE FREQUENCY; GENETICS; GENOTYPING TECHNIQUE; HUMAN GENOME; INDEL MUTATION; MALE; MICROARRAY ANALYSIS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PEDIGREE; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY;

ALLELES; AMINO ACID SEQUENCE; AUTISM SPECTRUM DISORDER; BASE SEQUENCE; CASE-CONTROL STUDIES; CHILD; DNA COPY NUMBER VARIATIONS; FEMALE; GENE DELETION; GENE DUPLICATION; GENE FREQUENCY; GENE REARRANGEMENT; GENETIC LOCI; GENOME, HUMAN; GENOTYPING TECHNIQUES; HUMANS; INDEL MUTATION; MALE; MICROARRAY ANALYSIS; MOLECULAR SEQUENCE DATA; PEDIGREE; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY;

EID: 84964800573     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2016.02.018     Document Type: Article

References (44)

1. D. Malhotra, and J. Sebat CNVs: harbingers of a rare variant revolution in psychiatric genetics Cell 148 2012 1223 1241
2. 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
3. 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
4. S.J. Sanders, X. He, A.J. Willsey, A.G. Ercan-Sencicek, K.E. Samocha, A.E. Cicek, M.T. Murtha, V.H. Bal, S.L. Bishop, S. Dong, et al. Autism Sequencing Consortium Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci Neuron 87 2015 1215 1233
5. B.J. O'Roak, L. Vives, S. Girirajan, E. Karakoc, N. Krumm, B.P. Coe, R. Levy, A. Ko, C. Lee, J.D. Smith, and et al. Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations Nature 485 2012 246 250
6. H. Brand, R.L. Collins, C. Hanscom, J.A. Rosenfeld, V. Pillalamarri, M.R. Stone, F. Kelley, T. Mason, L. Margolin, S. Eggert, and et al. Paired-Duplication Signatures Mark Cryptic Inversions and Other Complex Structural Variation Am. J. Hum. Genet. 97 2015 170 176
7. P.H. Sudmant, T. Rausch, E.J. Gardner, R.E. Handsaker, A. Abyzov, J. Huddleston, Y. Zhang, K. Ye, G. Jun, M. Hsi-Yang Fritz, et al. 1000 Genomes Project Consortium An integrated map of structural variation in 2,504 human genomes Nature 526 2015 75 81
8. W.P. Kloosterman, L.C. Francioli, F. Hormozdiari, T. Marschall, J.Y. Hehir-Kwa, A. Abdellaoui, E.W. Lameijer, M.H. Moed, V. Koval, I. Renkens, et al. Genome of Netherlands Consortium Characteristics of de novo structural changes in the human genome Genome Res. 25 2015 792 801
9. R.K. Yuen, B. Thiruvahindrapuram, D. Merico, S. Walker, K. Tammimies, N. Hoang, C. Chrysler, T. Nalpathamkalam, G. Pellecchia, Y. Liu, and et al. Whole-genome sequencing of quartet families with autism spectrum disorder Nat. Med. 21 2015 185 191
10. C. Gilissen, J.Y. Hehir-Kwa, D.T. Thung, M. van de Vorst, B.W. van Bon, M.H. Willemsen, M. Kwint, I.M. Janssen, A. Hoischen, A. Schenck, and et al. Genome sequencing identifies major causes of severe intellectual disability Nature 511 2014 344 347
11. C. Lord, S. Risi, L. Lambrecht, E.H. Cook Jr., B.L. Leventhal, P.C. DiLavore, A. Pickles, and M. Rutter The autism diagnostic observation schedule-generic: a standard measure of social and communication deficits associated with the spectrum of autism J. Autism Dev. Disord. 30 2000 205 223
12. J.J. Michaelson, Y. Shi, M. Gujral, H. Zheng, D. Malhotra, X. Jin, M. Jian, G. Liu, D. Greer, A. Bhandari, and et al. Whole-genome sequencing in autism identifies hot spots for de novo germline mutation Cell 151 2012 1431 1442
13. H. Li, and R. Durbin Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics 25 2009 1754 1760
14. H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin 1000 Genome Project Data Processing Subgroup The Sequence Alignment/Map format and SAMtools Bioinformatics 25 2009 2078 2079
15. A. McKenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis, A. Kernytsky, K. Garimella, D. Altshuler, S. Gabriel, M. Daly, and M.A. DePristo The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data Genome Res. 20 2010 1297 1303
16. M.A. DePristo, E. Banks, R. Poplin, K.V. Garimella, J.R. Maguire, C. Hartl, A.A. Philippakis, G. del Angel, M.A. Rivas, M. Hanna, and et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data Nat. Genet. 43 2011 491 498
17. J.J. Michaelson, and J. Sebat forestSV: structural variant discovery through statistical learning Nat. Methods 9 2012 819 821
18. C. Chiang, R.M. Layer, G.G. Faust, M.R. Lindberg, D.B. Rose, E.P. Garrison, G.T. Marth, A.R. Quinlan, and I.M. Hall SpeedSeq: ultra-fast personal genome analysis and interpretation Nat. Methods 12 2015 966 968
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. D.T. Thung, J. de Ligt, L.E. Vissers, M. Steehouwer, M. Kroon, P. de Vries, E.P. Slagboom, K. Ye, J.A. Veltman, and J.Y. Hehir-Kwa Mobster: accurate detection of mobile element insertions in next generation sequencing data Genome Biol. 15 2014 488
21. P.H. Sudmant, S. Mallick, B.J. Nelson, F. Hormozdiari, N. Krumm, J. Huddleston, B.P. Coe, C. Baker, S. Nordenfelt, M. Bamshad, and et al. Global diversity, population stratification, and selection of human copy-number variation Science 349 2015 aab3761
22. A. Abraham, F. Pedregosa, M. Eickenberg, P. Gervais, A. Mueller, J. Kossaifi, A. Gramfort, B. Thirion, and G. Varoquaux Machine learning for neuroimaging with scikit-learn Front. Neuroinform. 8 2014 14
23. T.F. Wu, C.J. Lin, and R.C. Weng Probability estimates for multi-class classification by pairwise coupling J. Mach. Learn. Res. 5 2004 975 1005
24. K. Wang, M. Li, D. Hadley, R. Liu, J. Glessner, S.F. Grant, H. Hakonarson, and M. Bucan PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data Genome Res. 17 2007 1665 1674
25. D.R. Zerbino, and E. Birney Velvet: algorithms for de novo short read assembly using de Bruijn graphs Genome Res. 18 2008 821 829
26. S. Purcell, B. Neale, K. Todd-Brown, L. Thomas, M.A. Ferreira, D. Bender, J. Maller, P. Sklar, P.I. de Bakker, M.J. Daly, and P.C. Sham PLINK: a tool set for whole-genome association and population-based linkage analyses Am. J. Hum. Genet. 81 2007 559 575
27. A.R. Quinlan, and I.M. Hall BEDTools: a flexible suite of utilities for comparing genomic features Bioinformatics 26 2010 841 842
28. B.P. Coe, K. Witherspoon, J.A. Rosenfeld, B.W. van Bon, A.T. Vulto-van Silfhout, P. Bosco, K.L. Friend, C. Baker, S. Buono, L.E. Vissers, and et al. Refining analyses of copy number variation identifies specific genes associated with developmental delay Nat. Genet. 46 2014 1063 1071
29. D. Pinto, E. Delaby, D. Merico, M. Barbosa, A. Merikangas, L. Klei, B. Thiruvahindrapuram, X. Xu, R. Ziman, Z. Wang, and et al. Convergence of genes and cellular pathways dysregulated in autism spectrum disorders Am. J. Hum. Genet. 94 2014 677 694
30. G. Narzisi, J.A. O'Rawe, I. Iossifov, H. Fang, Y.H. Lee, Z. Wang, Y. Wu, G.J. Lyon, M. Wigler, and M.C. Schatz Accurate de novo and transmitted indel detection in exome-capture data using microassembly Nat. Methods 11 2014 1033 1036
31. A. Rimmer, H. Phan, I. Mathieson, Z. Iqbal, S.R. Twigg, A.O. Wilkie, G. McVean, G. Lunter WGS500 Consortium Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications Nat. Genet. 46 2014 912 918
32. R. Chen, Q. Wei, X. Zhan, X. Zhong, J.S. Sutcliffe, N.J. Cox, E.H. Cook, C. Li, W. Chen, and B. Li A haplotype-based framework for group-wise transmission/disequilibrium tests for rare variant association analysis Bioinformatics 31 2015 1452 1459
33. P.J. Hastings, J.R. Lupski, S.M. Rosenberg, and G. Ira Mechanisms of change in gene copy number Nat. Rev. Genet. 10 2009 551 564
34. A.T. Pagnamenta, H. Khan, S. Walker, D. Gerrelli, K. Wing, M.C. Bonaglia, R. Giorda, T. Berney, E. Mani, M. Molteni, and et al. Rare familial 16q21 microdeletions under a linkage peak implicate cadherin 8 (CDH8) in susceptibility to autism and learning disability J. Med. Genet. 48 2011 48 54
35. J. Xu, L. Zwaigenbaum, P. Szatmari, and S.W. Scherer Molecular Cytogenetics of Autism Curr. Genomics 5 2004 347 364
36. B.S. Abrahams, D.E. Arking, D.B. Campbell, H.C. Mefford, E.M. Morrow, L.A. Weiss, I. Menashe, T. Wadkins, S. Banerjee-Basu, and A. Packer SFARI Gene 2.0: a community-driven knowledgebase for the autism spectrum disorders (ASDs) Mol. Autism 4 2013 36
37. A.T. Pagnamenta, R. Holt, M. Yusuf, D. Pinto, K. Wing, C. Betancur, S.W. Scherer, E.V. Volpi, and A.P. Monaco A family with autism and rare copy number variants disrupting the Duchenne/Becker muscular dystrophy gene DMD and TRPM3 J. Neurodev. Disord. 3 2011 124 131
38. Y.H. Jiang, R.K. Yuen, X. Jin, M. Wang, N. Chen, X. Wu, J. Ju, J. Mei, Y. Shi, M. He, and et al. Detection of clinically relevant genetic variants in autism spectrum disorder by whole-genome sequencing Am. J. Hum. Genet. 93 2013 249 263
39. 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
40. 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
41. S. De Rubeis, X. He, A.P. Goldberg, C.S. Poultney, K. Samocha, A.E. Cicek, Y. Kou, L. Liu, M. Fromer, S. Walker, et al. DDD Study Homozygosity Mapping Collaborative for Autism UK10K Consortium Synaptic, transcriptional and chromatin genes disrupted in autism Nature 515 2014 209 215
42. A. Deem, A. Keszthelyi, T. Blackgrove, A. Vayl, B. Coffey, R. Mathur, A. Chabes, and A. Malkova Break-induced replication is highly inaccurate PLoS Biol. 9 2011 e1000594
43. A. Abyzov, S. Li, D.R. Kim, M. Mohiyuddin, A.M. Stütz, N.F. Parrish, X.J. Mu, W. Clark, K. Chen, M. Hurles, and et al. Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms Nat. Commun. 6 2015 7256
44. E.L. van Dijk, H. Auger, Y. Jaszczyszyn, and C. Thermes Ten years of next-generation sequencing technology Trends Genet. 30 2014 418 426