A whole-genome DNA analysis, using sensitive new research tools to thoroughly examine the chromosomes of more than 3,000 people, reveals a section of chromosome 16 that is deleted or duplicated in some people with autism spectrum disorders (ASDs). The findings were released Online First by The New England Journal of Medicine on January 9, 2008.
The analysis--representing the largest, most complete genome scan for ASDs to date--was completed in October using three independent data sources. One analysis, using stored DNA samples from a national research repository known as the Autism Genome Research Exchange (AGRE), was conducted by the Autism Consortium, a collaboration involving 14 leading universities and medical centers, including Children's Hospital Boston.
An independent analysis at Children's Hospital Boston, using clinical samples from its own patients, provided real-world validation and extended the findings. Findings were also replicated by deCODE Genetics, Inc. in Iceland.
The Autism Consortium researchers scanned DNA samples from more than 3,000 children and families, of whom 1,441 were diagnosed with an ASD. Five individuals with ASDs had a chromosome 16 deletion. The deCODE team found the same deletion in three of 299 people.
The Children's researchers, using a high-resolution genomic copy-number variant analysis technique, designed by the hospital's laboratory team for clinical use, tested close to 1,000 patient samples and found five more instances of the deletion among 512 patients referred for developmental delay and/or suspected ASDs.
In addition, the Children's team identified four patients with a duplication, rather than a deletion, of the chromosome 16 region, a seeming paradox that is not uncommon in genetics.
"Genes may need to be expressed at exactly the right level within particular tissues," says David Miller, MD, PhD, assistant director of the Genetics Diagnostic Laboratory at Children's and a coauthor on the paper. "Expressing them at half of the normal amount within the cells, or twice the normal amount, can throw things out of balance within a cell, especially if they're involved in a complicated network where they're interacting with other genes."
The chromosome 16 deletion/duplication accounts for an estimated 1 percent of autism cases, adding to the roughly 15 percent of cases of autism with known genetic causes, says Miller, who is also a clinical geneticist and a member of the Consortium.
"I don't think we're going to find one cause that explains 50 percent of autism," Miller notes. "It's going to be an incremental process. Even if it's 1 percent at a time, that's still progress. And we'll eventually get to the point where we can figure out what's going on in each particular family, and help them figure out their chances of having another child affected with autism."
Bai-Lin Wu, PhD, director of Children's Genetics Diagnostic Laboratory, one of the two senior authors on the study, and a Consortium member, notes that the findings have direct and immediate application in evaluating children for developmental delay and autism. "We are gratified that our research observations have jumped the gap to the clinic and become part of the diagnostic testing we offer to patients," he says.
ASDs are diagnosed in as many as 1 in 150 children under the age of three. Symptoms can range from mild to severe and can include social, cognitive and behavioral deficits. Genetic causes have been difficult to identify for many reasons. ASDs are difficult to diagnose accurately, published studies use different criteria for defining them, and ASDs are complex conditions with many potential genetic causes, making it hard to pinpoint any single one.
The Children's team used a high-resolution genomic copy-number variant analysis to identify the chromosome 16 deletion/duplication. Very high-resolution microarrays such as this one, capable of spotting very small missing or extra pieces of DNA, have only become available within the past 6 to 8 months.
Other research teams have identified chromosome 16 deletions in patients with autism, but the new study is largest to date; confirmed its findings independently in three populations, including a group of current patients that can be studied further; identified patients with both duplications and deletions; and provides the most precise genetic information, identifying a very narrow region of chromosome 16 that is altered.
The chromosome 16 region that is missing or duplicated contains some 25 genes whose function is not yet known. But it is small enough that researchers at Children's can go back and study their nine patients more thoroughly, in hopes of understanding the role of that stretch of DNA and how its deletion or duplication affects brain function. Similar studies are planned by other Consortium members.
"We don't know from this study which of those genes is the critical one, or whether abnormalities in more than one of the genes are causing autism," says Christopher Walsh, MD, PhD, chief of Genetics at Children's, chair of the Autism Consortium Advisory Board, and consortium member, and a coauthor on the study. "Since these children are in our backyard, we can go back and ask them more questions and learn more about them."
"It is rare to have the opportunity to take information from a large database such as AGRE and then be able to quickly verify your findings among a group of children under clinical care at an affiliated hospital which has state-of-the art technology," says study leader Mark J. Daly, PhD, an Autism Consortium member with the Center for Human Genetic Research and the Department of Medicine at Massachusetts General Hospital and a senior associate member of the Broad Institute of Massachusetts Institute of Technology and Harvard.
In the majority of cases the chromosome 16--deletion occurred de novo, meaning that it was not inherited from a parent, but instead occurred during embryonic development. This information is helpful in counseling families because it suggests that the chances of another child in the family having autism are small, perhaps five percent rather than 50 percent if the trait is inherited from parent, Miller says. "We would need to have more data from more individuals before we could give families an exact number," he adds.
The discovery of the chromosome 16 abnormality was made possible by new, highly sensitive chromosome scanning technology based on microarrays from Affymetrix (NASDAQ: AFFX) and Agilent Technologies (NYSE: A). "The ability to do these very high-resolution microarrays to look for very small missing or extra pieces of DNA is very new," says Wu.
"The resolution has evolved to the point that we can find such small pieces and find them reliably just within the last six to eight months," adds coauthor Yiping Shen, PhD, director of R&D at the Children's Genetics Diagnostic Lab.