Identification of rare noncoding sequence variants in gamma-aminobutyric acid A receptor, alpha 4 subunit in autism spectrum disorder

Neurogenetics - Tập 19 Số 1 - Trang 17-26 - 2018
Griswold, Anthony J.1,2, Van Booven, Derek1, Cuccaro, Michael L.1,2, Haines, Jonathan L.3, Gilbert, John R.1,2, Pericak-Vance, Margaret A.1,2
1John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, USA
2Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, USA
3Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, USA

Tóm tắt

Alterations of the gamma-aminobutyric acid (GABA) signaling system has been strongly linked to the pathophysiology of autism spectrum disorder (ASD). Genetic associations of common variants in GABA receptor subunits, in particular GABRA4 on chromosome 4p12, with ASD have been replicated by several studies. Moreover, molecular investigations have identified altered transcriptional and translational levels of this gene and protein in brains of ASD individuals. Since the genotyped common variants are likely not the functional variants contributing to the molecular consequences or underlying ASD phenotype, this study aims to examine rare sequence variants in GABRA4, including those outside the protein coding regions of the gene. We comprehensively re-sequenced the entire protein coding and noncoding portions of the gene and putative regulatory sequences in 82 ASD individuals and 55 developmentally typical pediatric controls, all homozygous for the most significant previously associated ASD risk allele (G/G at rs1912960). We identified only a single common, coding variant, and no association of any single marker or set of variants with ASD. Functional annotation of noncoding variants identified several rare variants in putative regulatory sites. Finally, a rare variant unique to ASD cases, in an evolutionary conserved site of the 3′UTR, shows a trend toward decreasing gene expression. Hence, GABRA4 rare variants in noncoding DNA may be variants of modest physiological effects in ASD etiology.

Tài liệu tham khảo

citation_title=Diagnostic and Statistical Manual of Mental Disorders; citation_publication_date=2013; citation_id=CR1; citation_publisher=American Psychiatric Publishing

citation_journal_title=MMWR Surveill Summ; citation_title=prevalence of autism spectrum disorder among children aged 8 years—autism and developmental disabilities monitoring network, 11 sites, United States, 2010; citation_author=; citation_volume=63; citation_publication_date=2014; citation_pages=1-21; citation_id=CR2

citation_journal_title=Cytogenet Genome Res; citation_title=The role of rare structural variants in the genetics of autism spectrum disorders; citation_author=M Kusenda, J Sebat; citation_volume=123; citation_issue=1-4; citation_publication_date=2008; citation_pages=36-43; citation_doi=10.1159/000184690; citation_id=CR3

citation_journal_title=Hum Mol Genet; citation_title=Evaluation of copy number variations reveals novel candidate genes in autism spectrum disorder-associated pathways; citation_author=AJ Griswold, D Ma, HN Cukier, LD Nations, MA Schmidt, RH Chung, JM Jaworski, D Salyakina, I Konidari, PL Whitehead, HH Wright, RK Abramson, SM Williams, R Menon, ER Martin, JL Haines, JR Gilbert, ML Cuccaro, MA Pericak-Vance; citation_volume=21; citation_publication_date=2012; citation_pages=3513-3523; citation_doi=10.1093/hmg/dds164; citation_id=CR4

citation_journal_title=Nature; citation_title=Functional impact of global rare copy number variation in autism spectrum disorders; citation_author=D Pinto, AT Pagnamenta, L Klei, R Anney, D Merico, R Regan, J Conroy, TR Magalhaes, C Correia, BS Abrahams, J Almeida, E Bacchelli, GD Bader, AJ Bailey, G Baird, A Battaglia, T Berney, N Bolshakova, S Bolte, PF Bolton, T Bourgeron, S Brennan, J Brian, SE Bryson, AR Carson, G Casallo, J Casey, BH Chung, L Cochrane, C Corsello, EL Crawford, A Crossett, C Cytrynbaum, G Dawson, M Jonge, R Delorme, I Drmic, E Duketis, F Duque, A Estes, P Farrar, BA Fernandez, SE Folstein, E Fombonne, CM Freitag, J Gilbert, C Gillberg, JT Glessner, J Goldberg, A Green, J Green, SJ Guter, H Hakonarson, EA Heron, M Hill, R Holt, JL Howe, G Hughes, V Hus, R Igliozzi, C Kim, SM Klauck, A Kolevzon, O Korvatska, V Kustanovich, CM Lajonchere, JA Lamb, M Laskawiec, M Leboyer, A Couteur, BL Leventhal, AC Lionel, XQ Liu, C Lord, L Lotspeich, SC Lund, E Maestrini, W Mahoney, C Mantoulan, CR Marshall, H McConachie, CJ McDougle, J McGrath, WM McMahon, A Merikangas, O Migita, NJ Minshew, GK Mirza, J Munson, SF Nelson, C Noakes, A Noor, G Nygren, G Oliveira, K Papanikolaou, JR Parr, B Parrini, T Paton, A Pickles, M Pilorge, J Piven, CP Ponting, DJ Posey, A Poustka, F Poustka, A Prasad, J Ragoussis, K Renshaw, J Rickaby, W Roberts, K Roeder, B Roge, ML Rutter, LJ Bierut, JP Rice, J Salt, K Sansom, D Sato, R Segurado, AF Sequeira, L Senman, N Shah, VC Sheffield, L Soorya, I Sousa, O Stein, N Sykes, V Stoppioni, C Strawbridge, R Tancredi, K Tansey, B Thiruvahindrapduram, AP Thompson, S Thomson, A Tryfon, J Tsiantis, H Engeland, JB Vincent, F Volkmar, S Wallace, K Wang, Z Wang, TH Wassink, C Webber, R Weksberg, K Wing, K Wittemeyer, S Wood, J Wu, BL Yaspan, D Zurawiecki, L Zwaigenbaum, JD Buxbaum, RM Cantor, EH Cook, H Coon, ML Cuccaro, B Devlin, S Ennis, L Gallagher, DH Geschwind, M Gill, JL Haines, J Hallmayer, J Miller, AP Monaco, JI Nurnberger, AD Paterson, MA Pericak-Vance, GD Schellenberg, P Szatmari, AM Vicente, VJ Vieland, EM Wijsman, SW Scherer, JS Sutcliffe, C Betancur; citation_volume=466; citation_issue=7304; citation_publication_date=2010; citation_pages=368-372; citation_doi=10.1038/nature09146; citation_id=CR5

citation_journal_title=Nat Genet; citation_title=Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations; citation_author=BJ O’Roak, P Deriziotis, C Lee, L Vives, JJ Schwartz, S Girirajan, E Karakoc, AP Mackenzie, SB Ng, C Baker, MJ Rieder, DA Nickerson, R Bernier, SE Fisher, J Shendure, EE Eichler; citation_volume=43; citation_issue=6; citation_publication_date=2011; citation_pages=585-589; citation_doi=10.1038/ng.835; citation_id=CR6

citation_journal_title=Nature; citation_title=Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations; citation_author=BJ O’Roak, L Vives, S Girirajan, E Karakoc, N Krumm, BP Coe, R Levy, A Ko, C Lee, JD Smith, EH Turner, IB Stanaway, B Vernot, M Malig, C Baker, B Reilly, JM Akey, E Borenstein, MJ Rieder, DA Nickerson, R Bernier, J Shendure, EE Eichler; citation_volume=485; citation_issue=7397; citation_publication_date=2012; citation_pages=246-250; citation_doi=10.1038/nature10989; citation_id=CR7

citation_journal_title=Nature; citation_title=De novo mutations revealed by whole-exome sequencing are strongly associated with autism; citation_author=SJ Sanders, MT Murtha, AR Gupta, JD Murdoch, MJ Raubeson, AJ Willsey, AG Ercan-Sencicek, NM Dilullo, NN Parikshak, JL Stein, MF Walker, GT Ober, NA Teran, Y Song, P El-Fishawy, RC Murtha, M Choi, JD Overton, RD Bjornson, NJ Carriero, KA Meyer, K Bilguvar, SM Mane, N Sestan, RP Lifton, M Gunel, K Roeder, DH Geschwind, B Devlin, MW State; citation_volume=485; citation_issue=7397; citation_publication_date=2012; citation_pages=237-241; citation_doi=10.1038/nature10945; citation_id=CR8

citation_journal_title=Neuron; citation_title=De novo gene disruptions in children on the autistic spectrum; citation_author=I Iossifov, M Ronemus, D Levy, Z Wang, I Hakker, J Rosenbaum, B Yamrom, YH Lee, G Narzisi, A Leotta, J Kendall, E Grabowska, B Ma, S Marks, L Rodgers, A Stepansky, J Troge, P Andrews, M Bekritsky, K Pradhan, E Ghiban, M Kramer, J Parla, R Demeter, LL Fulton, RS Fulton, VJ Magrini, K Ye, JC Darnell, RB Darnell, ER Mardis, RK Wilson, MC Schatz, WR McCombie, M Wigler; citation_volume=74; citation_issue=2; citation_publication_date=2012; citation_pages=285-299; citation_doi=10.1016/j.neuron.2012.04.009; citation_id=CR9

Ma DQ, Salyakina D, Jaworski JM, Konidari I, Whitehead PL, Andersen A, Hoffman JD, Slifer SH, Hedges DJ, Cukier H, Beecham GW, 4d321F92AWright HHA, R.K., Martin ER, Hussman JP, Gilbert JR, Cuccaro ML, Haines JL, Pericak-Vance MA (2009) A genome-wide association study of autism reveals a common novel risk locus at 5p14.1. Ann Hum Genet 73:263–273, 3, DOI:

https://doi.org/10.1111/j.1469-1809.2009.00523.x

Wang K, Zhang H, Ma D, Bucan M, Glessner JT, Abrahams BS, Salyakina D, Imielinski M, Bradfield JP, Sleiman PM, Kim CE, Hou C, Frackelton E, Chiavacci R, Takahashi N, Sakurai T, Rappaport E, Lajonchere CM, Munson J, Estes A, Korvatska O, Piven J, Sonnenblick LI, Alvarez Retuerto AI, Herman EI, Dong H, Hutman T, Sigman M, Ozonoff S, Klin A, Owley T, Sweeney JA, Brune CW, Cantor RM, Bernier R, Gilbert JR, Cuccaro ML, McMahon WM, Miller J, State MW, Wassink TH, Coon H, Levy SE, Schultz RT, Nurnberger JI, Haines JL, Sutcliffe JS, Cook EH, Minshew NJ, Buxbaum JD, Dawson G, Grant SF, Geschwind DH, Pericak-Vance MA, Schellenberg GD, Hakonarson H (2009) Common genetic variants on 5p14.1 associate with autism spectrum disorders. Nature 459:528–533

citation_journal_title=Hum Mol Genet; citation_title=A genome-wide scan for common alleles affecting risk for autism; citation_author=R Anney, L Klei, D Pinto, R Regan, J Conroy, TR Magalhaes, C Correia, BS Abrahams, N Sykes, AT Pagnamenta, J Almeida, E Bacchelli, AJ Bailey, G Baird, A Battaglia, T Berney, N Bolshakova, S Bolte, PF Bolton, T Bourgeron, S Brennan, J Brian, AR Carson, G Casallo, J Casey, SH Chu, L Cochrane, C Corsello, EL Crawford, A Crossett, G Dawson, M Jonge, R Delorme, I Drmic, E Duketis, F Duque, A Estes, P Farrar, BA Fernandez, SE Folstein, E Fombonne, CM Freitag, J Gilbert, C Gillberg, JT Glessner, J Goldberg, J Green, SJ Guter, H Hakonarson, EA Heron, M Hill, R Holt, JL Howe, G Hughes, V Hus, R Igliozzi, C Kim, SM Klauck, A Kolevzon, O Korvatska, V Kustanovich, CM Lajonchere, JA Lamb, M Laskawiec, M Leboyer, A Couteur, BL Leventhal, AC Lionel, XQ Liu, C Lord, L Lotspeich, SC Lund, E Maestrini, W Mahoney, C Mantoulan, CR Marshall, H McConachie, CJ McDougle, J McGrath, WM McMahon, NM Melhem, A Merikangas, O Migita, NJ Minshew, GK Mirza, J Munson, SF Nelson, C Noakes, A Noor, G Nygren, G Oliveira, K Papanikolaou, JR Parr, B Parrini, T Paton, A Pickles, J Piven, DJ Posey, A Poustka, F Poustka, A Prasad, J Ragoussis, K Renshaw, J Rickaby, W Roberts, K Roeder, B Roge, ML Rutter, LJ Bierut, JP Rice, J Salt, K Sansom, D Sato, R Segurado, L Senman, N Shah, VC Sheffield, L Soorya, I Sousa, V Stoppioni, C Strawbridge, R Tancredi, K Tansey, B Thiruvahindrapduram, AP Thompson, S Thomson, A Tryfon, J Tsiantis, H Engeland, JB Vincent, F Volkmar, S Wallace, K Wang, Z Wang, TH Wassink, K Wing, K Wittemeyer, S Wood, BL Yaspan, D Zurawiecki, L Zwaigenbaum, C Betancur, JD Buxbaum, RM Cantor, EH Cook, H Coon, ML Cuccaro, L Gallagher, DH Geschwind, M Gill, JL Haines, J Miller, AP Monaco, JI Nurnberger, AD Paterson, MA Pericak-Vance, GD Schellenberg, SW Scherer, JS Sutcliffe, P Szatmari, AM Vicente, VJ Vieland, EM Wijsman, B Devlin, S Ennis, J Hallmayer; citation_volume=19; citation_issue=20; citation_publication_date=2010; citation_pages=4072-4082; citation_doi=10.1093/hmg/ddq307; citation_id=CR12

Weiss LA, Arking DE, Gene Discovery Project of Johns Hopkins & the Autism Consortium, Daly MJ, Chakravarti A (2009) A genome-wide linkage and association scan reveals novel loci for autism. Nature 461:802–808

citation_journal_title=Brain Res; citation_title=Etiological heterogeneity in autism spectrum disorders: more than 100 genetic and genomic disorders and still counting; citation_author=C Betancur; citation_volume=1380; citation_publication_date=2011; citation_pages=42-77; citation_doi=10.1016/j.brainres.2010.11.078; citation_id=CR14

citation_journal_title=Annu Rev Med; citation_title=Genome-wide association studies: results from the first few years and potential implications for clinical medicine; citation_author=JN Hirschhorn, ZK Gajdos; citation_volume=62; citation_issue=1; citation_publication_date=2011; citation_pages=11-24; citation_doi=10.1146/annurev.med.091708.162036; citation_id=CR15

citation_title=GABA emerges as a developmental signal during neurogenesis of the rat central nervous system; citation_inbook_title=GABA in the nervous system: the view at fifty years; citation_publication_date=2000; citation_pages=245-263; citation_id=CR16; citation_author=JL Barker; citation_author=TN Behar; citation_author=W Ma; citation_author=D Maric; citation_author=I Maric; citation_publisher=Lippincott Williams and Wilkins

citation_journal_title=J Autism Dev Disord; citation_title=Suppressed GABAergic inhibition as a common factor in suspected etiologies of autism; citation_author=JP Hussman; citation_volume=31; citation_issue=2; citation_publication_date=2001; citation_pages=247-248; citation_doi=10.1023/A:1010715619091; citation_id=CR17

citation_journal_title=J Autism Dev Disord; citation_title=Density and distribution of hippocampal neurotransmitter receptors in autism: an autoradiographic study; citation_author=GJ Blatt, CM Fitzgerald, JT Guptill, AB Booker, TL Kemper, ML Bauman; citation_volume=31; citation_issue=6; citation_publication_date=2001; citation_pages=537-543; citation_doi=10.1023/A:1013238809666; citation_id=CR18

citation_journal_title=Dev Med Child Neurol; citation_title=Duplication of the 15q11-13 region in a patient with autism, epilepsy and ataxia; citation_author=S Bundey, C Hardy, S Vickers, MW Kilpatrick, JA Corbett; citation_volume=36; citation_issue=8; citation_publication_date=1994; citation_pages=736-742; citation_doi=10.1111/j.1469-8749.1994.tb11916.x; citation_id=CR19

citation_journal_title=J Autism Dev Disord; citation_title=Duplication of chromosome 15q11-13 in two additional individuals with autistic disorder; citation_author=P Baker, J Piven, S Schwartz, S Patil; citation_volume=24; citation_issue=4; citation_publication_date=1994; citation_pages=529-535; citation_doi=10.1007/BF02172133; citation_id=CR20

citation_journal_title=Am J Med Genet; citation_title=Interstitial duplications of chromosome region 15q11q13: clinical and molecular characterization; citation_author=GM Repetto, LM White, PJ Bader, D Johnson, JH Knoll; citation_volume=79; citation_issue=2; citation_publication_date=1998; citation_pages=82-89; citation_doi=10.1002/(SICI)1096-8628(19980901)79:2<82::AID-AJMG2>3.0.CO;2-P; citation_id=CR21

citation_journal_title=Am J Med Genet; citation_title=Analysis of linkage disequilibrium in gamma-aminobutyric acid receptor subunit genes in autistic disorder; citation_author=ER Martin, MM Menold, CM Wolpert, MP Bass, SL Donnelly, SA Ravan, A Zimmerman, JR Gilbert, JM Vance, LO Maddox, HH Wright, RK Abramson, GR DeLong, ML Cuccaro, MA Pericak-Vance; citation_volume=96; citation_issue=1; citation_publication_date=2000; citation_pages=43-48; citation_doi=10.1002/(SICI)1096-8628(20000207)96:1<43::AID-AJMG9>3.0.CO;2-3; citation_id=CR22

citation_journal_title=Am J Hum Gen; citation_title=Evidence for linkage but not association to teh GABR3 region of chromosome 15 in a subset of autistic disorder (AutD) families characterized by an increase in restricted and repetitive behaviors; citation_author=MM Menold, Y Shao, SJ Kim, CM Wolpert, SL Donnelly, SA Ravan, RK Abramson, HH Wright, GR DeLong, ML Cuccaro, MA Pericak-Vance, JR Gilbert; citation_volume=71; citation_publication_date=2002; citation_pages=488; citation_id=CR23

citation_journal_title=Mol Psychiatry; citation_title=Association between a GABRB3 polymorphism and autism; citation_author=JD Buxbaum, JM Silverman, CJ Smith, DA Greenberg, M Kilifarski, J Reichert, EH Cook, Y Fang, CY Song, R Vitale; citation_volume=7; citation_issue=3; citation_publication_date=2002; citation_pages=311-316; citation_doi=10.1038/sj.mp.4001011; citation_id=CR24

citation_journal_title=Am J Hum Genet; citation_title=Identification of significant association and gene-gene interaction of GABA receptor subunit genes in autism; citation_author=DQ Ma, PL Whitehead, MM Menold, ER Martin, AE Ashley-Koch, H Mei, MD Ritchie, GR DeLong, RK Abramson, HH Wright, ML Cuccaro, JP Hussman, JR Gilbert, MA Pericak-Vance; citation_volume=77; citation_issue=3; citation_publication_date=2005; citation_pages=377-388; citation_doi=10.1086/433195; citation_id=CR25

Collins AL, Ma DQ, Whitehead PL, Martin ER, Wright HH, Abramson RK, Hussman JP, Gilbert JR, Cuccaro ML, Pericak-Vance MA (2005) Association of GABRA4 and GABRB1 in African American autism families. American Society of Human Genetics 55th Annual Meeting, Salt Lake City, Utah

citation_journal_title=Neurogenetics; citation_title=Investigation of autism and GABA receptor subunit genes in multiple ethnic groups; citation_author=AL Collins, D Ma, PL Whitehead, ER Martin, HH Wright, RK Abramson, JP Hussman, JL Haines, ML Cuccaro, JR Gilbert, MA Pericak-Vance; citation_volume=7; citation_issue=3; citation_publication_date=2006; citation_pages=167-174; citation_doi=10.1007/s10048-006-0045-1; citation_id=CR27

citation_journal_title=Cerebellum; citation_title=Expression of GABA(B) receptors is altered in brains of subjects with autism; citation_author=SH Fatemi, TD Folsom, TJ Reutiman, PD Thuras; citation_volume=8; citation_issue=1; citation_publication_date=2009; citation_pages=64-69; citation_doi=10.1007/s12311-008-0075-3; citation_id=CR28

citation_journal_title=J Autism Dev Disord; citation_title=GABA(A) receptor downregulation in brains of subjects with autism; citation_author=SH Fatemi, TJ Reutiman, TD Folsom, PD Thuras; citation_volume=39; citation_issue=2; citation_publication_date=2009; citation_pages=223-230; citation_doi=10.1007/s10803-008-0646-7; citation_id=CR29

citation_journal_title=J Autism Dev Disord; citation_title=mRNA and protein levels for GABAAalpha4, alpha5, beta1 and GABABR1 receptors are altered in brains from subjects with autism; citation_author=SH Fatemi, TJ Reutiman, TD Folsom, RJ Rooney, DH Patel, PD Thuras; citation_volume=40; citation_issue=6; citation_publication_date=2010; citation_pages=743-750; citation_doi=10.1007/s10803-009-0924-z; citation_id=CR30

citation_title=Social Communication Questionnaire (SCQ); citation_publication_date=2003; citation_id=CR31; citation_author=M Rutter; citation_author=A Bailey; citation_author=SK Berument; citation_author=A LeCouteur; citation_author=C Lord; citation_author=A Pickles; citation_publisher=Western Psychological Services

citation_journal_title=Bioinformatics; citation_title=Enhancements and modifications of primer design program Primer3; citation_author=T Koressaar, M Remm; citation_volume=23; citation_issue=10; citation_publication_date=2007; citation_pages=1289-1291; citation_doi=10.1093/bioinformatics/btm091; citation_id=CR32

citation_journal_title=Nucleic Acids Res; citation_title=Primer3—new capabilities and interfaces; citation_author=A Untergasser, I Cutcutache, T Koressaar, J Ye, BC Faircloth, M Remm, SG Rozen; citation_volume=40; citation_issue=15; citation_publication_date=2012; citation_doi=10.1093/nar/gks596; citation_id=CR33

citation_journal_title=Bioinformatics; citation_title=Fast and accurate long-read alignment with Burrows-Wheeler transform; citation_author=H Li, R Durbin; citation_volume=26; citation_issue=5; citation_publication_date=2010; citation_pages=589-595; citation_doi=10.1093/bioinformatics/btp698; citation_id=CR34

citation_journal_title=Genome Res; citation_title=The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data; citation_author=A McKenna, M Hanna, E Banks, A Sivachenko, K Cibulskis, A Kernytsky, K Garimella, D Altshuler, S Gabriel, M Daly, MA DePristo; citation_volume=20; citation_issue=9; citation_publication_date=2010; citation_pages=1297-1303; citation_doi=10.1101/gr.107524.110; citation_id=CR35

citation_journal_title=Nucleic Acids Res; citation_title=ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data; citation_author=K Wang, M Li, H Hakonarson; citation_volume=38; citation_issue=16; citation_publication_date=2010; citation_doi=10.1093/nar/gkq603; citation_id=CR36

citation_journal_title=J Med Genet; citation_title=wANNOVAR: annotating genetic variants for personal genomes via the web; citation_author=X Chang, K Wang; citation_volume=49; citation_issue=7; citation_publication_date=2012; citation_pages=433-436; citation_doi=10.1136/jmedgenet-2012-100918; citation_id=CR37

citation_journal_title=Nature; citation_title=An integrated encyclopedia of DNA elements in the human genome; citation_author=ENCODE Project Consortium, I Dunham, A Kundaje, SF Aldred, PJ Collins, CA Davis, F Doyle, CB Epstein, S Frietze, J Harrow, R Kaul, J Khatun, BR Lajoie, SG Landt, BK Lee, F Pauli, KR Rosenbloom, P Sabo, A Safi, A Sanyal, N Shoresh, JM Simon, L Song, ND Trinklein, RC Altshuler, E Birney, JB Brown, C Cheng, S Djebali, X Dong, I Dunham, J Ernst, TS Furey, M Gerstein, B Giardine, M Greven, RC Hardison, RS Harris, J Herrero, MM Hoffman, S Iyer, M Kelllis, J Khatun, P Kheradpour, A Kundaje, T Lassman, Q Li, X Lin, GK Marinov, A Merkel, A Mortazavi, SC Parker, TE Reddy, J Rozowsky, F Schlesinger, RE Thurman, J Wang, LD Ward, TW Whitfield, SP Wilder, W Wu, HS Xi, KY Yip, J Zhuang, BE Bernstein, E Birney, I Dunham, ED Green, C Gunter, M Snyder, MJ Pazin, RF Lowdon, LA Dillon, LB Adams, CJ Kelly, J Zhang, JR Wexler, ED Green, PJ Good, EA Feingold, BE Bernstein, E Birney, GE Crawford, J Dekker, L Elinitski, PJ Farnham, M Gerstein, MC Giddings, TR Gingeras, ED Green, R Guigo, RC Hardison, TJ Hubbard, M Kellis, WJ Kent, JD Lieb, EH Margulies, RM Myers, M Snyder, JA Starnatoyannopoulos, SA Tennebaum, Z Weng, KP White, B Wold, J Khatun, Y Yu, J Wrobel, BA Risk, HP Gunawardena, HC Kuiper, CW Maier, L Xie, X Chen, MC Giddings, BE Bernstein, CB Epstein, N Shoresh, J Ernst, P Kheradpour, TS Mikkelsen, S Gillespie, A Goren, O Ram, X Zhang, L Wang, R Issner, MJ Coyne, T Durham, M Ku, T Truong, LD Ward, RC Altshuler, ML Eaton, M Kellis, S Djebali, CA Davis, A Merkel, A Dobin, T Lassmann, A Mortazavi, A Tanzer, J Lagarde, W Lin, F Schlesinger, C Xue, GK Marinov, J Khatun, BA Williams, C Zaleski, J Rozowsky, M Roder, F Kokocinski, RF Abdelhamid, T Alioto, I Antoshechkin, MT Baer, P Batut, I Bell, K Bell, S Chakrabortty, X Chen, J Chrast, J Curado, T Derrien, J Drenkow, E Dumais, J Dumais, R Duttagupta, M Fastuca, K Fejes-Toth, P Ferreira, S Foissac, MJ Fullwood, H Gao, D Gonzalez, A Gordon, HP Gunawardena, C Howald, S Jha, R Johnson, P Kapranov, B King, C Kingswood, G Li, OJ Luo, E Park, JB Preall, K Presaud, P Ribeca, BA Risk, D Robyr, X Ruan, M Sammeth, KS Sandu, L Schaeffer, LH See, A Shahab, J Skancke, AM Suzuki, H Takahashi, H Tilgner, D Trout, N Walters, H Wang, J Wrobel, Y Yu, Y Hayashizaki, J Harrow, M Gerstein, TJ Hubbard, A Reymond, SE Antonarakis, GJ Hannon, MC Giddings, Y Ruan, B Wold, P Carninci, R Guigo, TR Gingeras, KR Rosenbloom, CA Sloan, K Learned, VS Malladi, MC Wong, GP Barber, MS Cline, TR Dreszer, SG Heitner, D Karolchik, WJ Kent, VM Kirkup, LR Meyer, JC Long, M Maddren, BJ Raney, TS Furey, L Song, LL Grasfeder, PG Giresi, BK Lee, A Battenhouse, NC Sheffield, JM Simon, KA Showers, A Safi, D London, AA Bhinge, C Shestak, MR Schaner, SK Kim, ZZ Zhang, PA Mieczkowski, JO Mieczkowska, Z Liu, RM McDaniell, Y Ni, NU Rashid, MJ Kim, S Adar, Z Zhang, T Wang, D Winter, D Keefe, E Birney, VR Iyer, JD Lieb, GE Crawford, G Li, KS Sandhu, M Zheng, P Wang, OJ Luo, A Shahab, MJ Fullwood, X Ruan, Y Ruan, RM Myers, F Pauli, BA Williams, J Gertz, GK Marinov, TE Reddy, J Vielmetter, EC Partridge, D Trout, KE Varley, C Gasper, A Bansal, S Pepke, P Jain, H Amrhein, KM Bowling, M Anaya, MK Cross, B King, MA Muratet, I Antoshechkin, KM Newberry, K McCue, AS Nesmith, KI Fisher-Aylor, B Pusey, G DeSalvo, SL Parker, S Balasubramanian, NS Davis, SK Meadows, T Eggleston, C Gunter, JS Newberry, SE Levy, DM Absher, A Mortazavi, WH Wong, B Wold, MJ Blow, A Visel, LA Pennachio, L Elnitski, EH Margulies, SC Parker, HM Petrykowska, A Abyzov, B Aken, D Barrell, G Barson, A Berry, A Bignell, V Boychenko, G Bussotti, J Chrast, C Davidson, T Derrien, G Despacio-Reyes, M Diekhans, I Ezkurdia, A Frankish, J Gilbert, JM Gonzalez, E Griffiths, R Harte, DA Hendrix, C Howald, T Hunt, I Jungreis, M Kay, E Khurana, F Kokocinski, J Leng, MF Lin, J Loveland, Z Lu, D Manthravadi, M Mariotti, J Mudge, G Mukherjee, C Notredame, B Pei, JM Rodriguez, G Saunders, A Sboner, S Searle, C Sisu, C Snow, C Steward, A Tanzer, E Tapanan, ML Tress, MJ Baren, N Walters, S Washieti, L Wilming, A Zadissa, Z Zhengdong, M Brent, D Haussler, M Kellis, A Valencia, M Gerstein, A Raymond, R Guigo, J Harrow, TJ Hubbard, SG Landt, S Frietze, A Abyzov, N Addleman, RP Alexander, RK Auerbach, S Balasubramanian, K Bettinger, N Bhardwaj, AP Boyle, AR Cao, P Cayting, A Charos, Y Cheng, C Cheng, C Eastman, G Euskirchen, JD Fleming, F Grubert, L Habegger, M Hariharan, A Harmanci, S Iyenger, VX Jin, KJ Karczewski, M Kasowski, P Lacroute, H Lam, N Larnarre-Vincent, J Leng, J Lian, M Lindahl-Allen, R Min, B Miotto, H Monahan, Z Moqtaderi, XJ Mu, H O’Geen, Z Ouyang, D Patacsil, B Pei, D Raha, L Ramirez, B Reed, J Rozowsky, A Sboner, M Shi, C Sisu, T Slifer, H Witt, L Wu, X Xu, KK Yan, X Yang, KY Yip, Z Zhang, K Struhl, SM Weissman, M Gerstein, PJ Farnham, M Snyder, SA Tenebaum, LO Penalva, F Doyle, S Karmakar, SG Landt, RR Bhanvadia, A Choudhury, M Domanus, L Ma, J Moran, D Patacsil, T Slifer, A Victorsen, X Yang, M Snyder, KP White, T Auer, L Centarin, M Eichenlaub, F Gruhl, S Heerman, B Hoeckendorf, D Inoue, T Kellner, S Kirchmaier, C Mueller, R Reinhardt, L Schertel, S Schneider, R Sinn, B Wittbrodt, J Wittbrodt, Z Weng, TW Whitfield, J Wang, PJ Collins, SF Aldred, ND Trinklein, EC Partridge, RM Myers, J Dekker, G Jain, BR Lajoie, A Sanyal, G Balasundaram, DL Bates, R Byron, TK Canfield, MJ Diegel, D Dunn, AK Ebersol, AK Ebersol, T Frum, K Garg, E Gist, RS Hansen, L Boatman, E Haugen, R Humbert, G Jain, AK Johnson, EM Johnson, TM Kutyavin, BR Lajoie, K Lee, D Lotakis, MT Maurano, SJ Neph, FV Neri, ED Nguyen, H Qu, AP Reynolds, V Roach, E Rynes, P Sabo, ME Sanchez, RS Sandstrom, A Sanyal, AO Shafer, AB Stergachis, S Thomas, RE Thurman, B Vernot, J Vierstra, S Vong, H Wang, MA Weaver, Y Yan, M Zhang, JA Akey, M Bender, MO Dorschner, M Groudine, MJ MacCoss, P Navas, G Stamatoyannopoulos, R Kaul, J Dekker, JA Stamatoyannopoulos, I Dunham, K Beal, A Brazma, P Flicek, J Herrero, N Johnson, D Keefe, M Lukk, NM Luscombe, D Sobral, JM Vaquerizas, SP Wilder, S Batzoglou, A Sidow, N Hussami, S Kyriazopoulou-Panagiotopoulou, MW Libbrecht, MA Schaub, A Kundaje, RC Hardison, W Miller, B Giardine, RS Harris, W Wu, PJ Bickel, B Banfai, NP Boley, JB Brown, H Huang, Q Li, JJ Li, WS Noble, JA Bilmes, OJ Buske, MM Hoffman, AO Sahu, PV Kharchenko, PJ Park, D Baker, J Taylor, Z Weng, S Iyer, X Dong, M Greven, X Lin, J Wang, HS Xi, J Zhuang, M Gerstein, RP Alexander, S Balasubramanian, C Cheng, A Harmanci, L Lochovsky, R Min, XJ Mu, J Rozowsky, KK Yan, KY Yip, E Birney; citation_volume=489; citation_publication_date=2012; citation_pages=57-74; citation_doi=10.1038/nature11247; citation_id=CR38

citation_journal_title=Bioinformatics; citation_title=BEDTools: a flexible suite of utilities for comparing genomic features; citation_author=AR Quinlan, IM Hall; citation_volume=26; citation_issue=6; citation_publication_date=2010; citation_pages=841-842; citation_doi=10.1093/bioinformatics/btq033; citation_id=CR39

citation_journal_title=Am J Hum Genet; citation_title=PLINK: a tool set for whole-genome association and population-based linkage analyses; citation_author=S Purcell, B Neale, K Todd-Brown, L Thomas, MA Ferreira, D Bender, J Maller, P Sklar, PI Bakker, MJ Daly, PC Sham; citation_volume=81; citation_issue=3; citation_publication_date=2007; citation_pages=559-575; citation_doi=10.1086/519795; citation_id=CR40

Johnson JL, Abecasis GR (2017) GAS Power Calculator: web-based power calculator for genetic association studies. bioRxiv. doi:

https://doi.org/10.1101/164343

citation_journal_title=Nat Genet; citation_title=Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies; citation_author=AD Skol, LJ Scott, GR Abecasis, M Boehnke; citation_volume=38; citation_issue=2; citation_publication_date=2006; citation_pages=209-213; citation_doi=10.1038/ng1706; citation_id=CR42

citation_journal_title=Am J Hum Genet; citation_title=Rare-variant association testing for sequencing data with the sequence kernel association test; citation_author=MC Wu, S Lee, T Cai, Y Li, M Boehnke, X Lin; citation_volume=89; citation_issue=1; citation_publication_date=2011; citation_pages=82-93; citation_doi=10.1016/j.ajhg.2011.05.029; citation_id=CR43

citation_journal_title=Am J Hum Genet; citation_title=Optimal unified approach for rare-variant association testing with application to small-sample case-control whole-exome sequencing studies; citation_author=; citation_volume=91; citation_publication_date=2012; citation_pages=224-237; citation_doi=10.1016/j.ajhg.2012.06.007; citation_id=CR44

citation_journal_title=Genome Res; citation_title=Most mammalian mRNAs are conserved targets of microRNAs; citation_author=RC Friedman, KK Farh, CB Burge, DP Bartel; citation_volume=19; citation_issue=1; citation_publication_date=2009; citation_pages=92-105; citation_doi=10.1101/gr.082701.108; citation_id=CR45

citation_journal_title=Hum Mutat; citation_title=MicroSNiPer: a web tool for prediction of SNP effects on putative microRNA targets; citation_author=M Barenboim, BJ Zoltick, Y Guo, DR Weinberger; citation_volume=31; citation_issue=11; citation_publication_date=2010; citation_pages=1223-1232; citation_doi=10.1002/humu.21349; citation_id=CR46

citation_journal_title=Nat Biotechnol; citation_title=Next-generation DNA sequencing; citation_author=J Shendure, H Ji; citation_volume=26; citation_issue=10; citation_publication_date=2008; citation_pages=1135-1145; citation_doi=10.1038/nbt1486; citation_id=CR47

citation_journal_title=Nat Rev Genet; citation_title=Uncovering the roles of rare variants in common disease through whole-genome sequencing; citation_author=ET Cirulli, DB Goldstein; citation_volume=11; citation_issue=6; citation_publication_date=2010; citation_pages=415-425; citation_doi=10.1038/nrg2779; citation_id=CR48

citation_journal_title=Hum Genet; citation_title=Comprehensive resequence analysis of a 97 kb region of chromosome 10q11.2 containing the MSMB gene associated with prostate cancer; citation_author=M Yeager, Z Deng, J Boland, C Matthews, J Bacior, V Lonsberry, A Hutchinson, LA Burdett, L Qi, KB Jacobs, J Gonzalez-Bosquet, SI Berndt, RB Hayes, RN Hoover, G Thomas, DJ Hunter, M Dean, SJ Chanock; citation_volume=126; citation_issue=6; citation_publication_date=2009; citation_pages=743-750; citation_doi=10.1007/s00439-009-0723-9; citation_id=CR49

citation_journal_title=Nat Genet; citation_title=A rare variant in MYH6 is associated with high risk of sick sinus syndrome; citation_author=H Holm, DF Gudbjartsson, P Sulem, G Masson, HT Helgadottir, C Zanon, OT Magnusson, A Helgason, J Saemundsdottir, A Gylfason, H Stefansdottir, S Gretarsdottir, SE Matthiasson, GM Thorgeirsson, A Jonasdottir, A Sigurdsson, H Stefansson, T Werge, T Rafnar, LA Kiemeney, B Parvez, R Muhammad, DM Roden, D Darbar, G Thorleifsson, GB Walters, A Kong, U Thorsteinsdottir, DO Arnar, K Stefansson; citation_volume=43; citation_issue=4; citation_publication_date=2011; citation_pages=316-320; citation_doi=10.1038/ng.781; citation_id=CR50

citation_journal_title=Schizophr Res; citation_title=ADAMTSL3 as a candidate gene for schizophrenia: gene sequencing and ultra-high density association analysis by imputation; citation_author=DJ Dow, J Huxley-Jones, JM Hall, C Francks, PR Maycox, JN Kew, IS Gloger, NA Mehta, FM Kelly, P Muglia, G Breen, S Jugurnauth, I Pederoso, D St Clair, D Rujescu, MR Barnes; citation_volume=127; citation_issue=1-3; citation_publication_date=2011; citation_pages=28-34; citation_doi=10.1016/j.schres.2010.12.009; citation_id=CR51

citation_journal_title=Nature; citation_title=The contribution of de novo coding mutations to autism spectrum disorder; citation_author=I Iossifov, BJ O’Roak, SJ Sanders, M Ronemus, N Krumm, D Levy, HA Stessman, KT Witherspoon, L Vives, KE Patterson, JD Smith, B Paeper, DA Nickerson, J Dea, S Dong, LE Gonzalez, JD Mandell, SM Mane, MT Murtha, CA Sullivan, MF Walker, Z Waqar, L Wei, AJ Willsey, B Yamrom, YH Lee, E Grabowska, E Dalkic, Z Wang, S Marks, P Andrews, A Leotta, J Kendall, I Hakker, J Rosenbaum, B Ma, L Rodgers, J Troge, G Narzisi, S Yoon, MC Schatz, K Ye, WR McCombie, J Shendure, EE Eichler, MW State, M Wigler; citation_volume=515; citation_issue=7526; citation_publication_date=2014; citation_pages=216-221; citation_doi=10.1038/nature13908; citation_id=CR52

De Rubeis S, He X, Goldberg AP, Poultney CS, Samocha K, Cicek AE, Kou Y, Liu L, Fromer M, Walker S, Singh T, Klei L, Kosmicki J, Shih-Chen F, Aleksic B, Biscaldi M, Bolton PF, Brownfeld JM, Cai J, Campbell NG, Carracedo A, Chahrour MH, Chiocchetti AG, Coon H, Crawford EL, Curran SR, Dawson G, Duketis E, Fernandez BA, Gallagher L, Geller E, Guter SJ, Hill RS, Ionita-Laza J, Jimenz Gonzalez P, Kilpinen H, Klauck SM, Kolevzon A, Lee I, Lei I, Lei J, Lehtimaki T, Lin CF, Ma’ayan A, Marshall CR, McInnes AL, Neale B, Owen MJ, Ozaki N, Parellada M, Parr JR, Purcell S, Puura K, Rajagopalan D, Rehnstrom K, Reichenberg A, Sabo A, Sachse M, Sanders SJ, Schafer C, Schulte-Ruther M, Skuse D, Stevens C, Szatmari P, Tammimies K, Valladares O, Voran A, Li-San W, Weiss LA, Willsey AJ, Yu TW, Yuen RK, DDD Study, Homozygosity Mapping Collaborative for Autism, UK10K Consortium, Cook EH, Freitag CM, Gill M, Hultman CM, Lehner T, Palotie A, Schellenberg GD, Sklar P, State MW, Sutcliffe JS, Walsh CA, Scherer SW, Zwick ME, Barett JC, Cutler DJ, Roeder K, Devlin B, Daly MJ, Buxbaum JD (2014) Synaptic, transcriptional and chromatin genes disrupted in autism. Nature 515:209–215

Sanders SJ, He X, Willsey AJ, Ercan-Sencicek AG, Samocha KE, Cicek AE, Murtha MT, Bal VH, Bishop SL, Dong S, Goldberg AP, Jinlu C, Keaney JF,3rd, Klei L, Mandell JD, Moreno-De-Luca D, Poultney CS, Robinson EB, Smith L, Solli-Nowlan T, Su MY, Teran NA, Walker MF, Werling DM, Beaudet AL, Cantor RM, Fombonne E, Geschwind DH, Grice DE, Lord C, Lowe JK, Mane SM, Martin DM, Morrow EM, Talkowski ME, Sutcliffe JS, Walsh CA, Yu TW, Autism Sequencing Consortium, Ledbetter DH, Martin CL, Cook EH, Buxbaum JD, Daly MJ, Devlin B, Roeder K, State MW (2015) Insights into autism spectrum disorder genomic architecture and biology from 71 risk loci. Neuron 87:1215–1233

citation_journal_title=Nat Med; citation_title=Whole-genome sequencing of quartet families with autism spectrum disorder; citation_author=RK Yuen, B Thiruvahindrapuram, D Merico, S Walker, K Tammimies, N Hoang, C Chrysler, T Nalpathamkalam, G Pellecchia, Y Liu, MJ Gazzellone, L D’Abate, E Deneault, JL Howe, RS Liu, A Thompson, M Zarrei, M Uddin, CR Marshall, RH Ring, L Zwaigenbaum, PN Ray, R Weksberg, MT Carter, BA Fernandez, W Roberts, P Szatmari, SW Scherer; citation_volume=21; citation_issue=2; citation_publication_date=2015; citation_pages=185-191; citation_doi=10.1038/nm.3792; citation_id=CR55

C Yuen RK, Merico D, Bookman M, L Howe J, Thiruvahindrapuram B, Patel RV, Whitney J, Deflaux N, Bingham J, Wang Z, Pellecchia G, Buchanan JA, Walker S, Marshall CR, Uddin M, Zarrei M, Deneault E, D’Abate L, Chan AJ, Koyanagi S, Paton T, Pereira SL, Hoang N, Engchuan W, Higginbotham EJ, Ho K, Lamoureux S, Li W, MacDonald JR, Nalpathamkalam T, Sung WW, Tsoi FJ, Wei J, Xu L, Tasse AM, Kirby E, Van Etten W, Twigger S, Roberts W, Drmic I, Jilderda S, Modi BM, Kellam B, Szego M, Cytrynbaum C, Weksberg R, Zwaigenbaum L, Woodbury-Smith M, Brian J, Senman L, Iaboni A, Doyle-Thomas K, Thompson A, Chrysler C, Leef J, Savion-Lemieux T, Smith IM, Liu X, Nicolson R, Seifer V, Fedele A, Cook EH, Dager S, Estes A, Gallagher L, Malow BA, Parr JR, Spence SJ, Vorstman J, Frey BJ, Robinson JT, Strug LJ, Fernandez BA, Elsabbagh M, Carter MT, Hallmayer J, Knoppers BM, Anagnostou E, Szatmari P, Ring RH, Glazer D, Pletcher MT, Scherer SW (2017) Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder. Nat Neurosci 20:602–611, 4, DOI:

https://doi.org/10.1038/nn.4524

citation_journal_title=Nature; citation_title=Dysfunction in GABA signalling mediates autism-like stereotypies and Rett syndrome phenotypes; citation_author=HT Chao, H Chen, RC Samaco, M Xue, M Chahrour, J Yoo, JL Neul, S Gong, HC Lu, N Heintz, M Ekker, JL Rubenstein, JL Noebels, C Rosenmund, HY Zoghbi; citation_volume=468; citation_issue=7321; citation_publication_date=2010; citation_pages=263-269; citation_doi=10.1038/nature09582; citation_id=CR57

citation_journal_title=J Neurochem; citation_title=Decreased GABA(B) receptors in the cingulate cortex and fusiform gyrus in autism; citation_author=AL Oblak, TT Gibbs, GJ Blatt; citation_volume=114; citation_issue=5; citation_publication_date=2010; citation_pages=1414-1423; citation_id=CR58

citation_journal_title=Nucleic Acids Res; citation_title=Targeted resequencing of candidate genes using selector probes; citation_author=H Johansson, M Isaksson, EF Sorqvist, F Roos, J Stenberg, T Sjoblom, J Botling, P Micke, K Edlund, S Fredriksson, HG Kultima, O Ericsson, M Nilsson; citation_volume=39; citation_issue=2; citation_publication_date=2011; citation_doi=10.1093/nar/gkq1005; citation_id=CR59

Steinberg KM, Ramachandran D, Patel VC, Shetty AC, Cutler DJ, Zwick ME (2012) Identification of rare X-linked neuroligin variants by massively parallel sequencing in males with autism spectrum disorder. Mol Autism 3:8-2392-3-8

Thông tin
Thông tin xuất bản

Neurogenetics

Tập 19 Số 1

17-26

Thông tin tác giả