The genetics underlying the autism spectrum disorders (ASDs) is complex and remains poorly understood. Previous work has demonstrated an important role for structural variation in a subset of cases, but has lacked the resolution necessary to move beyond detection of large regions of potential interest to identification of individual genes. To pinpoint genes likely to contribute to ASD etiology, we performed high density genotyping in 912 multiplex families from the Autism Genetics Resource Exchange (AGRE) collection and contrasted results to those obtained for 1,488 healthy controls. Through prioritization of exonic deletions (eDels), exonic duplications (eDups), and whole gene duplication events (gDups), we identified more than 150 loci harboring rare variants in multiple unrelated probands, but no controls. Importantly, 27 of these were confirmed on examination of an independent replication cohort comprised of 859 cases and an additional 1,051 controls. Rare variants at known loci, including exonic deletions at NRXN1 and whole gene duplications encompassing UBE3A and several other genes in the 15q11–q13 region, were observed in the course of these analyses. Strong support was likewise observed for previously unreported genes such as BZRAP1, an adaptor molecule known to regulate synaptic transmission, with eDels or eDups observed in twelve unrelated cases but no controls (p = 2.3×10？5). Less is known about MDGA2, likewise observed to be case-specific (p = 1.3×10？4). But, it is notable that the encoded protein shows an unexpectedly high similarity to Contactin 4 (BLAST E-value = 3×10？39), which has also been linked to disease. That hundreds of distinct rare variants were each seen only once further highlights complexity in the ASDs and points to the continued need for larger cohorts.
References
[1]
Abrahams BS, Geschwind DH (2008) Advances in autism genetics: on the threshold of a new neurobiology. Nat Rev Genet 9: 341–355.
[2]
Bailey A, Le Couteur A, Gottesman I, Bolton P, Simonoff E, et al. (1995) Autism as a strongly genetic disorder: evidence from a British twin study. Psychol Med 25: 63–77.
[3]
Steffenburg S, Gillberg C, Hellgren L, Andersson L, Gillberg IC, et al. (1989) A twin study of autism in Denmark, Finland, Iceland, Norway and Sweden. J Child Psychol Psychiatry 30: 405–416.
[4]
Cantor RM, Kono N, Duvall JA, Alvarez-Retuerto A, Stone JL, et al. (2005) Replication of autism linkage: fine-mapping peak at 17q21. Am J Hum Genet 76: 1050–1056.
[5]
Vorstman JA, Staal WG, van Daalen E, van Engeland H, Hochstenbach PF, et al. (2006) Identification of novel autism candidate regions through analysis of reported cytogenetic abnormalities associated with autism. Mol Psychiatry 11: 1.18–28
[6]
Szatmari P, Paterson AD, Zwaigenbaum L, Roberts W, Brian J, et al. (2007) Mapping autism risk loci using genetic linkage and chromosomal rearrangements. Nat Genet 39: 319–328.
[7]
Sebat J, Lakshmi B, Malhotra D, Troge J, Lese-Martin C, et al. (2007) Strong association of de novo copy number mutations with autism. Science 316: 445–449.
[8]
Marshall CR, Noor A, Vincent JB, Lionel AC, Feuk L, et al. (2008) Structural variation of chromosomes in autism spectrum disorder. Am J Hum Genet 82: 477–488.
[9]
Jacquemont ML, Sanlaville D, Redon R, Raoul O, Cormier-Daire V, et al. (2006) Array-based comparative genomic hybridisation identifies high frequency of cryptic chromosomal rearrangements in patients with syndromic autism spectrum disorders. J Med Genet 43: 843–849.
Weiss LA, Shen Y, Korn JM, Arking DE, Miller DT, et al. (2008) Association between Microdeletion and Microduplication at 16p11.2 and Autism. N Engl J Med.
[12]
Sharp AJ, Mefford HC, Li K, Baker C, Skinner C, et al. (2008) A recurrent 15q13.3 microdeletion syndrome associated with mental retardation and seizures. Nat Genet 40: 322–328.
[13]
Mefford HC, Sharp AJ, Baker C, Itsara A, Jiang Z, et al. (2008) Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypes. N Engl J Med 359: 1685–1699.
[14]
Alarcon M, Abrahams BS, Stone JL, Duvall JA, Perederiy JV, et al. (2008) Linkage, Association, and Gene-Expression Analyses Identify CNTNAP2 as an Autism-Susceptibility Gene. Am J Hum Genet 82: 150–159.
[15]
Kim HG, Kishikawa S, Higgins AW, Seong IS, Donovan DJ, et al. (2008) Disruption of neurexin 1 associated with autism spectrum disorder. Am J Hum Genet 82: 199–207.
[16]
Morrow EM, Yoo SY, Flavell SW, Kim TK, Lin Y, et al. (2008) Identifying autism loci and genes by tracing recent shared ancestry. Science 321: 218–223.
[17]
Glessner JT, Wang K, Cai G, Korvatska O, Kim CE, et al. (2009) Autism genome-wide copy number variation reveals ubiquitin and neuronal genes. Nature.
[18]
Geschwind DH, Sowinski J, Lord C, Iversen P, Shestack J, et al. (2001) The autism genetic resource exchange: a resource for the study of autism and related neuropsychiatric conditions. Am J Hum Genet 69: 463–466.
[19]
Nalls MA, Simon-Sanchez J, Gibbs JR, Paisan-Ruiz C, Bras JT, et al. (2009) Measures of autozygosity in decline: globalization, urbanization, and its implications for medical genetics. PLoS Genet 5: e1000415. doi:10.1371/journal.pgen.1000415.
[20]
Wang K, Li M, Hadley D, Liu R, Glessner J, et al. (2007) PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res 17: 1665–1674.
[21]
Christian SL, Brune CW, Sudi J, Kumar RA, Liu S, et al. (2008) Novel submicroscopic chromosomal abnormalities detected in autism spectrum disorder. Biol Psychiatry 63: 1111–1117.
[22]
Cai G, Edelmann L, Goldsmith JE, Cohen N, Nakamine A, et al. (2008) Multiplex ligation-dependent probe amplification for genetic screening in autism spectrum disorders: Efficient identification of known microduplications and identification of a novel microduplication in ASMT. BMC Med Genomics 1: 50.
[23]
Martin CL, Duvall JA, Ilkin Y, Simon JS, Arreaza MG, et al. (2007) Cytogenetic and molecular characterization of A2BP1/FOX1 as a candidate gene for autism. Am J Med Genet B Neuropsychiatr Genet 144: 869–876.
[24]
Bond J, Roberts E, Mochida GH, Hampshire DJ, Scott S, et al. (2002) ASPM is a major determinant of cerebral cortical size. Nat Genet 32: 316–320.
[25]
Bakkaloglu B, O'Roak BJ, Louvi A, Gupta AR, Abelson JF, et al. (2008) Molecular Cytogenetic Analysis and Resequencing of Contactin Associated Protein-Like 2 in Autism Spectrum Disorders. Am J Hum Genet 82: 165–173.
[26]
Strauss KA, Puffenberger EG, Huentelman MJ, Gottlieb S, Dobrin SE, et al. (2006) Recessive symptomatic focal epilepsy and mutant contactin-associated protein-like 2. N Engl J Med 354: 1370–1377.
[27]
Feng J, Schroer R, Yan J, Song W, Yang C, et al. (2006) High frequency of neurexin 1beta signal peptide structural variants in patients with autism. Neurosci Lett 409: 10–13.
[28]
Yan J, Noltner K, Feng J, Li W, Schroer R, et al. (2008) Neurexin 1alpha structural variants associated with autism. Neurosci Lett 438: 368–370.
[29]
Jamain S, Quach H, Betancur C, Rastam M, Colineaux C, et al. (2003) Mutations of the X-linked genes encoding neuroligins NLGN3 and NLGN4 are associated with autism. Nat Genet 34: 27–29.
[30]
Comoletti D, De Jaco A, Jennings LL, Flynn RE, Gaietta G, et al. (2004) The Arg451Cys-neuroligin-3 mutation associated with autism reveals a defect in protein processing. J Neurosci 24: 4889–4893.
[31]
Laumonnier F, Bonnet-Brilhault F, Gomot M, Blanc R, David A, et al. (2004) X-linked mental retardation and autism are associated with a mutation in the NLGN4 gene, a member of the neuroligin family. Am J Hum Genet 74: 552–557.
[32]
Yan J, Oliveira G, Coutinho A, Yang C, Feng J, et al. (2005) Analysis of the neuroligin 3 and 4 genes in autism and other neuropsychiatric patients. Mol Psychiatry 10: 329–332.
[33]
Scheiffele P, Fan J, Choih J, Fetter R, Serafini T (2000) Neuroligin expressed in nonneuronal cells triggers presynaptic development in contacting axons. Cell 101: 657–669.
[34]
Graf ER, Zhang X, Jin SX, Linhoff MW, Craig AM (2004) Neurexins induce differentiation of GABA and glutamate postsynaptic specializations via neuroligins. Cell 119: 1013–1026.
[35]
Sadakata T, Washida M, Iwayama Y, Shoji S, Sato Y, et al. (2007) Autistic-like phenotypes in Cadps2-knockout mice and aberrant CADPS2 splicing in autistic patients. J Clin Invest 117: 931–943.
[36]
Walsh T, McClellan JM, McCarthy SE, Addington AM, Pierce SB, et al. (2008) Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science 320: 539–543.
[37]
Wang Y, Sugita S, Sudhof TC (2000) The RIM/NIM family of neuronal C2 domain proteins. Interactions with Rab3 and a new class of Src homology 3 domain proteins. J Biol Chem 275: 20033–20044.
[38]
Zoghbi HY (2003) Postnatal neurodevelopmental disorders: meeting at the synapse? Science 302: 826–830.
[39]
Litwack ED, Babey R, Buser R, Gesemann M, O'Leary DD (2004) Identification and characterization of two novel brain-derived immunoglobulin superfamily members with a unique structural organization. Mol Cell Neurosci 25: 263–274.
[40]
Fernandez T, Morgan T, Davis N, Klin A, Morris A, et al. (2004) Disruption of contactin 4 (CNTN4) results in developmental delay and other features of 3p deletion syndrome. Am J Hum Genet 74: 1286–1293.
[41]
Roohi J, Montagna C, Tegay DH, Palmer LE, DeVincent C, et al. (2009) Disruption of contactin 4 in three subjects with autism spectrum disorder. J Med Genet 46: 176–182.
[42]
Wang K, Zhang H, Ma D, Bucan M, Glessner JT, et al. (2009) Common genetic variants on 5p14.1 associate with autism spectrum disorders. Nature.
[43]
Cook EH Jr, Lindgren V, Leventhal BL, Courchesne R, Lincoln A, et al. (1997) Autism or atypical autism in maternally but not paternally derived proximal 15q duplication. Am J Hum Genet 60: 928–934.
[44]
Potocki L, Bi W, Treadwell-Deering D, Carvalho CM, Eifert A, et al. (2007) Characterization of Potocki-Lupski syndrome (dup(17)(p11.2p11.2)) and delineation of a dosage-sensitive critical interval that can convey an autism phenotype. Am J Hum Genet 80: 633–649.
[45]
(1993) Identification and characterization of the tuberous sclerosis gene on chromosome 16. Cell 75: 1305–1315.
[46]
Slager RE, Newton TL, Vlangos CN, Finucane B, Elsea SH (2003) Mutations in RAI1 associated with Smith-Magenis syndrome. Nat Genet 33: 466–468.
[47]
Bolton P, Macdonald H, Pickles A, Rios P, Goode S, et al. (1994) A case-control family history study of autism. J Child Psychol Psychiatry 35: 877–900.
[48]
Bishop DV, Maybery M, Maley A, Wong D, Hill W, et al. (2004) Using self-report to identify the broad phenotype in parents of children with autistic spectrum disorders: a study using the Autism-Spectrum Quotient. J Child Psychol Psychiatry 45: 1431–1436.
[49]
Millar JK, Wilson-Annan JC, Anderson S, Christie S, Taylor MS, et al. (2000) Disruption of two novel genes by a translocation co-segregating with schizophrenia. Hum Mol Genet 9: 1415–1423.
[50]
Sachs NA, Sawa A, Holmes SE, Ross CA, DeLisi LE, et al. (2005) A frameshift mutation in Disrupted in Schizophrenia 1 in an American family with schizophrenia and schizoaffective disorder. Mol Psychiatry 10: 758–764.
[51]
Risch N, Spiker D, Lotspeich L, Nouri N, Hinds D, et al. (1999) A genomic screen of autism: evidence for a multilocus etiology. Am J Hum Genet 65: 493–507.
[52]
Rzhetsky A, Wajngurt D, Park N, Zheng T (2007) Probing genetic overlap among complex human phenotypes. Proc Natl Acad Sci U S A 104: 11694–11699.
[53]
Bodmer W, Bonilla C (2008) Common and rare variants in multifactorial susceptibility to common diseases. Nat Genet 40: 695–701.
[54]
Yang S, Wang K, Gregory B, Berrettini W, Wang LS, et al. (2009) Genomic landscape of a three-generation pedigree segregating affective disorder. PLoS ONE 4: e4474. doi:10.1371/journal.pone.0004474.
[55]
Ji W, Foo JN, O'Roak BJ, Zhao H, Larson MG, et al. (2008) Rare independent mutations in renal salt handling genes contribute to blood pressure variation. Nat Genet 40: 592–599.
[56]
Dennis G Jr, Sherman BT, Hosack DA, Yang J, Gao W, et al. (2003) DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 4: P3.
