Common Gene Variants Account for Most of the Genetic Risk for Autism
Heritability trumps spontaneous glitches, environment
Nearly 60 percent of the risk of developing autism is genetic and most of that risk is caused by inherited variant genes that are common in the population and present in individuals without the disorder, according to a study led by researchers at the Icahn School of Medicine at Mount Sinai and published in the July 20 edition of Nature Genetics.
“We show very clearly that inherited common variants comprise the bulk of the risk that sets up susceptibility to autism,” says Joseph D. Buxbaum, PhD, the study’s lead investigator and Director of the Seaver Autism Center for Research and Treatment and Professor of Psychiatry, Neuroscience and Genetics and Genomic Sciences at the Icahn School of Medicine at Mount Sinai. “But while families can be genetically loaded for autism risk, it may take additional rare genetic factors to actually produce the disorder in a particular family member.”
Dr. Buxbaum and colleagues of the Population-Based Autism Genetics and Environment Study (PAGES) Consortium conducted a rigorous analysis of DNA sequence variations from an ongoing, comprehensive study of autism in Sweden.
Although autism is thought to be caused by an interplay of genetic and other factors, there has been no consensus on their relative contributions and the nature of its genetic architecture. Recently, evidence has been mounting that genomes of people with autism are prone to harboring de novo mutations - rare, spontaneous mutations that exert strong effects and can largely account for particular cases of the disorder.
Specifically, the current study found that about 52.4 percent of autism was traced to common and rare inherited variations, with spontaneous mutations contributing a modest 2.6 percent of the total risk.
“Many people have been focusing on de novo mutations, such as the ones that can occur in the sperm of an older father,” explains Dr. Buxbaum. “While we find these mutations are also key contributors, it is important to know that there is underlying risk in the family genetic architecture itself.”
Gauging the collective impact on autism risk of variations in the genetic code shared by most people, individually much subtler in effect, has proven to be even more challenging. Limitations in sample size and composition have made it difficult to detect these effects and to estimate the relative influence of such common, rare inherited and rare, spontaneous de novo variation. Differences in methods and statistical models have also resulted in estimates of autism heritability ranging from 17 to 50 percent.
Meanwhile, recent genome-wide studies of schizophrenia have achieved large enough sample sizes to reveal involvement of well over 100 common gene variants in that disorder. These promise improved understanding of the underlying biology – and even development of risk-scores, which could help predict who might benefit from early interventions to nip psychotic episodes in the bud.
With their new study, autism genetics is beginning to catch up, say the researchers. The PAGES study was made possible by Sweden’s universal health registry, which allowed investigators to compare very large samples (n~3000 in the current study) of people with autism with matched controls. Researchers also employed new statistical methods that allowed them to more reliably sort out the heritability of the disorder. In addition, they were able to compare their results with a parallel family-based study in the Swedish population, which took into account data from twins, cousins and factors such as age of the father at birth and parents’ psychiatric history.
“This is a different kind of analysis than employed in previous studies,” says Thomas Lehner, PhD, Chief of the National Institute of Mental Health’s (NIMH) Genomics Research Branch. “Data from genome-wide association studies was used to identify a genetic model instead of focusing on just pinpointing genetic risk factors. The researchers were able to pick from all cases of illness within a population-based registry.”
Now that the genetic architecture is better understood, the researchers are identifying specific genetic risk factors detected in the sample, such as deletions and duplications in genetic material and spontaneous mutations. Even though such rare spontaneous mutations accounted for only a small fraction of autism risk, the potentially large effects of these glitches makes them important clues to understanding the molecular underpinnings of the disorder, say the researchers.
“Within a given family, a de novo mutation could be a critical determinant that leads to the manifestation of autism spectrum disorder in a particular family member,” says Dr. Buxbaum. “If the family has a common variation that puts it at risk, an added de novo mutation could push an individual over the edge and result in that person developing the disorder.”
This study was supported by NIMH Grants MH057881 and MH097849, in part by the Seaver Foundation and through the computational resources and staff expertise provided by the Scientific Computing Facility at the Icahn School of Medicine at Mount Sinai.
Researchers from Carnegie Mellon University, the University of Pittsburgh School of Medicine, the University of California, San Francisco, Yale University School of Medicine, Massachusetts General Hospital and the Karolinska Institute in Stockholm, Sweden contributed to the study.
About the Seaver Autism Center for Research and Treatment at Mount Sinai:
The Seaver Autism Center for Research and Treatment at Mount Sinai conducts progressive research studies aimed at understanding the multiple causes of autism spectrum disorders (ASD). The multidisciplinary team is comprised of experts in the fields of genetics, molecular biology, model systems, neuroimaging, and experimental therapeutics who are dedicated to discovering the biological causes of ASD. The Center strives to develop innovative diagnostics and treatments for integration into the provision of personalized, comprehensive assessment and care for people with ASD. The Seaver Autism Center was founded through the generous support of the Beatrice and Samuel A. Seaver Foundation. For more information, visit www.seaverautismcenter.org.
About the Mount Sinai Health System
The Mount Sinai Health System is New York City's largest integrated delivery system, encompassing eight hospitals, a leading medical school, and a vast network of ambulatory practices throughout the greater New York region. Mount Sinai's vision is to produce the safest care, the highest quality, the highest satisfaction, the best access and the best value of any health system in the nation. The Health System includes approximately 7,480 primary and specialty care physicians; 11 joint-venture ambulatory surgery centers; more than 410 ambulatory practices throughout the five boroughs of New York City, Westchester, Long Island, and Florida; and 31 affiliated community health centers. The Icahn School of Medicine is one of three medical schools that have earned distinction by multiple indicators: ranked in the top 20 by U.S. News & World Report's "Best Medical Schools", aligned with a U.S. News & World Report's "Honor Roll" Hospital, No. 12 in the nation for National Institutes of Health funding, and among the top 10 most innovative research institutions as ranked by the journal Nature in its Nature Innovation Index. This reflects a special level of excellence in education, clinical practice, and research. The Mount Sinai Hospital is ranked No. 18 on U.S. News & World Report's "Honor Roll" of top U.S. hospitals; it is one of the nation's top 20 hospitals in Cardiology/Heart Surgery, Gastroenterology/GI Surgery, Geriatrics, Nephrology, and Neurology/Neurosurgery, and in the top 50 in six other specialties in the 2018-2019 "Best Hospitals" issue. Mount Sinai's Kravis Children's Hospital also is ranked nationally in five out of ten pediatric specialties by U.S. News & World Report. The New York Eye and Ear Infirmary of Mount Sinai is ranked 11th nationally for Ophthalmology and 44th for Ear, Nose, and Throat. Mount Sinai Beth Israel, Mount Sinai St. Luke's, Mount Sinai West, and South Nassau Communities Hospital are ranked regionally.