17 March 2007. Two major studies on the genetic causes of autism suggest that copy number variations play an unexpectedly important role in the risk for the disease. These sub-microscopic deletions or insertions in the genome were recently shown to contribute much of the variation among people (see SRF related news story), and are the subject of intense study as the source of a number of diseases.
The autism studies, the largest linkage analysis carried out in families with autism to date and a fine dissection of genome-wide copy number variation, find no single smoking gun. Instead, the results suggest that potentially hundreds of genes play a role in the disease. One of the studies points to genes involved in glutamate signaling, which has also been implicated in the pathology of schizophrenia. If these studies, one in the February 18 issue of Nature Genetics online, and the other in this week’s Science, are any indication, then researchers probing the genetics of other complex disorders, such as schizophrenia, had better have plenty of stamina, funding, and a taste for surprises.
Like schizophrenia, autism is a complex neurodevelopmental disorder, encompassing a spectrum of behavioral symptoms. Genetics clearly play a role in autism since the condition runs in families. At the same time, most cases appear as isolated occurrences, and many families have just one affected child. Previous single nucleotide polymorphism (SNP) linkage studies have suggested risk genes on multiple chromosomes. In addition, researchers have found chromosomal abnormalities in up to 5 percent of cases. However, no specific genes that cause autism have been identified.
To remedy that situation, researchers formed the Autism Genome Project Consortium in 2002. With funding from private and government sources, researchers from 50 institutions pooled samples and expertise to perform large-scale analysis of genetic variation in autism spectrum disorders. The Nature Genetics report is their first, a preliminary analysis of SNP linkage data from more than 8,000 people in 1,400 families.
The consortium researchers chose to analyze only families with more than one affected member, reasoning that taking families with a strong genetic tendency to autism would boost the chances of finding common gene variants on a heterogeneous background. After mapping 10,000 SNPs, they further probed the data for a gain or loss of signal intensity at individual SNP positions to detect copy number variations (CNVs). Because of the large sample size, the investigators were also able to analyze associations of SNPs independent of CNVs, and break the sample into subgroups (e.g., families with only females or only males affected, and narrow vs. broad diagnosis) for linkage analysis.
By the SNP results, one region (11p12-p13) showed a suggestive linkage with autism across all the families. In some subsets, they confirmed the 11p12-p13 result and found additional suggestive linkages, including one on chromosome 15, which had been noted in previous studies. While none of the detected linkages were statistically significant, the authors conclude that the results call for a thorough fine mapping of 11p12-p13, which has been previously linked to autism but not extensively studied.
The analysis of CNVs based on the SNP results revealed a higher frequency of disease-associated changes than expected. Depending on the method of analysis, about 8 to 11 percent of families showed chromosomal abnormalities that were shared among affected family members. Some of the changes occurred in regions linked to other neurodevelopmental diseases. One deletion, which the investigators found in two sisters, removed coding regions of the neurexin gene. Rare mutations in the neurexin gene have been reported to increase risk for autism and mental retardation, and neurexin’s binding partners, the neuroligins, have also been implicated in autism. Together, the proteins regulate glutamatergic synaptogenesis, and their involvement fits with the hypothesis that aberrant glutamatergic transmission underlies the developmental defects that give rise to autism.
The Other Autism
The second study, a genome-wide scan for sub-microscopic copy number variation, also demonstrated a high level of disease-related changes, but in a different group of patients. That work, from Jonathan Sebat and Michael Wigler at the Cold Spring Harbor Laboratory in New York, appears in this week’s online issue of Science.
For some diseases, a cytogenetic search for de novo chromosomal abnormalities in affected children has led researchers to important causative mutations. Sebat, Wigler, and a bevy of collaborators from the U.S., the U.K., and Finland, took that idea one step further. They replaced the low-resolution microscopic analysis of chromosome structure with a high-resolution array-based search for micro-deletions and insertions. Since they were hunting for de novo mutations, the investigators probed 118 families with a single affected child (simplex families), and compared them to 47 with multiple affected children (multiplex families, like the group in the consortium study), plus 99 control families.
They found that children with autism frequently showed de novo gene copy number changes, which were far more common in children from families with sporadic disease. In the simplex families, the researchers found that 10 percent of children with autism or a related disorder showed copy number changes that were not seen in their parents. This compared to only 2 percent in children in the multiplex families and 1 percent in controls.
An association of de novo CNVs with autism spectrum disorders does not prove they cause the disease, the authors point out. Establishing causation will require pinpointing the genes involved and studying variation in additional patients and their families. Five of the 16 confirmed changes involved single genes, each of which makes a good candidate for further genetic and biological studies. While some overlapping deletions were detected, the CNVs occurred on eight different chromosomes among the 14 affected children. This suggests that rare changes at many loci could contribute to autism spectrum disorders, and might explain why previous work has failed to find common heritable variants with a major effect on disease risk, the authors write.
The enrichment for CNVs in the simplex families suggests that there may be two genetically distinct forms of autism. The idiopathic or sporadic cases make up one class, while the less common, inherited cases make up another. The two may be related, and the authors speculate that a high rate of spontaneous mutations in autism could account for heritable disease. If new mutations have incomplete penetrance, then apparently unaffected parents could pass damaged genes on to their children who might be the first to manifest the disease.
The findings likely represent the tip of the iceberg. The limited resolution of current genomic CNV scans probably results in a severe underestimate of the prevalence of genetic changes. “As technology for discovering spontaneous germline mutations in children improves, the proportion of autism cases with detectable events is bound to rise,” the authors write.
“The implications of this for future research are that different genetic approaches should be used for sporadic disease, and it is very important to initiate the recruitment efforts that focus on sporadic cases,” lead author Jonathan Sebat told SRF. “As a result of our study, a private foundation has begun to organize a consortium of several sites to recruit well-characterized simplex families,” he said.—Pat McCaffrey.
The Autism Genome Project Consortium; Szatmari P, Paterson AD, Zwaigenbaum L, Roberts W, Brian J, Liu XQ, Vincent JB, Skaug JL, Thompson AP, Senman L, Feuk L, Qian C, Bryson SE, Jones MB, Marshall CR, Scherer SW, Vieland VJ, Bartlett C, Mangin LV, Goedken R, Segre A, Pericak-Vance MA, Cuccaro ML, Gilbert JR, Wright HH, Abramson RK, Betancur C, Bourgeron T, Gillberg C, Leboyer M, Buxbaum JD, Davis KL, Hollander E, Silverman JM, Hallmayer J, Lotspeich L, Sutcliffe JS, Haines JL, Folstein SE, Piven J, Wassink TH, Sheffield V, Geschwind DH, Bucan M, Brown WT, Cantor RM, Constantino JN, Gilliam TC, Herbert M, Lajonchere C, Ledbetter DH, Lese-Martin C, Miller J, Nelson S, Samango-Sprouse CA, Spence S, State M, Tanzi RE, Coon H, Dawson G, Devlin B, Estes A, Flodman P, Klei L, McMahon WM, Minshew N, Munson J, Korvatska E, Rodier PM, Schellenberg GD, Smith M, Spence MA, Stodgell C, Tepper PG, Wijsman EM, Yu CE, Roge B, Mantoulan C, Wittemeyer K, Poustka A, Felder B, Klauck SM, Schuster C, Poustka F, Bolte S, Feineis-Matthews S, Herbrecht E, Schmotzer G, Tsiantis J, Papanikolaou K, Maestrini E, Bacchelli E, Blasi F, Carone S, Toma C, Van Engeland H, de Jonge M, Kemner C, Koop F, Langemeijer M, Hijimans C, Staal WG, Baird G, Bolton PF, Rutter ML, Weisblatt E, Green J, Aldred C, Wilkinson JA, Pickles A, Le Couteur A, Berney T, McConachie H, Bailey AJ, Francis K, Honeyman G, Hutchinson A, Parr JR, Wallace S, Monaco AP, Barnby G, Kobayashi K, Lamb JA, Sousa I, Sykes N, Cook EH, Guter SJ, Leventhal BL, Salt J, Lord C, Corsello C, Hus V, Weeks DE, Volkmar F, Tauber M, Fombonne E, Shih A. Mapping autism risk loci using genetic linkage and chromosomal rearrangements. Nat Genet. 2007 Mar;39(3):319-28. Epub 2007 Feb 18. Abstract
Sebat J, Lakshmi B, Malhotra D, Lese-Martin C, Troge J, Walsh T, Yamrom B, Yoon S, Krasnitz A, Kendall J, Leotta A, Pai D, Zhang R, Lee Y, Hicks J, Spence SJ, Lee AT, Puura K, Lehtimäki T, Ledbetter D, Gregersen PK, Bregman J, Sutcliffe JS, Jobanputra J, Chung W, Warburton D, King M-C, Skuse D, Geschwind DH, Gilliam TC, Ye K, Wigler M. Strong association of de novo copy number mutations with autism. Science. 2007 March 15 [Epub ahead of print] Abstract