/PRNewswire/ -- A large study from Children's Hospital Boston and the Boston-based Autism Consortium finds that a genetic test that samples the entire genome, known as chromosomal microarray analysis, has about three times the detection rate for genetic changes related to autism spectrum disorders (ASDs) than standard tests. Publishing in the April issue of Pediatrics (and online March 15), the authors urge that CMA become part of the first-line genetic work-up for ASDs.
Expectant parents who have family members with ASDs, as well as families who already have an affected child, often request genetic testing. However, there is still only limited knowledge about actual causative genes. The currently recommended tests (karyotyping to look for chromosomal abnormalities and testing for Fragile X, the single largest known genetic cause of ASDs) often come up negative. Chromosomal microarray analysis (CMA) is a genome-wide assay that examines the chromosomes for tiny, sub-microscopic deletions or duplications of DNA sequences, known as copy-number variants.
CMA offers about 100-fold greater resolution than standard karyotyping. However, since it is new, it is often considered a second-tier test. Depending on where a person lives, or what insurance they have, CMA may not be covered by health insurance. "Based on our findings, CMA should be considered as part of the initial clinical diagnostic evaluation of patients with ASDs," says Bai-Lin Wu, PhD, Director of Children's DNA Diagnostic Lab in the Department of Laboratory Medicine, which has offered CMA to families since 2006.
The research team, led by co-senior authors Wu (heading the Children's team), and David Miller, MD, PhD, of Children's Division of Genetics and Department of Laboratory Medicine (heading the Autism Consortium team), assessed the diagnostic value of CMA in the largest cohort to date - 933 patients with a clinical diagnosis of ASD (by DSM-IV-TR criteria) who received clinical genetic testing in 2006, 2007 and 2008.
Half were Children's patients who had their samples submitted to the hospital's DNA Diagnostic Laboratory, and the others were recruited through the Autism Consortium, a research and clinical collaboration of five Boston-area medical centers. Nearly half of the patients were diagnosed with autistic disorder, nearly half with PDD-NOS (pervasive developmental disorder - not otherwise specified) and about 3 percent with Asperger disorder. Ages ranged from 13 months to 22 years.
Testing included the two currently used tests (G-banded karyotype and fragile X), as well as CMA. When the researchers compared the tests' diagnostic yield, they found:
-- Karyotyping yielded abnormal results in 2.23 percent of patients
-- Fragile X testing was abnormal in 0.46 percent
-- CMA results were judged to be abnormal in 7.3 percent of patients when
the entire length of the chromosomes (the whole genome) was sampled.
Extrapolating from these results, the researchers estimate that without CMA, genetic diagnosis will be missed in at least 5 percent of ASD cases. CMA performed best in certain subgroups, such as girls with autistic disorder, and past studies indicate that it also has a higher yield in patients with intellectual disability (who constituted only 12 percent of this sample).
"CMA clearly detects more abnormalities than other genetic tests that have been the standard of care for many years," says Miller. "We're hoping this evidence will convince insurance companies to cover this testing universally."
In all, roughly 15 percent of people with autism have a known genetic cause. Establishing a clear genetic diagnosis helps families obtain early intervention and services for autism, and helps parents predict the possibility of having another child with autism.
In addition, by pinpointing bits of chromosomes that are deleted or duplicated, CMA can help researchers zero in on specific causative genes within that stretch of DNA. They can also begin to classify patients according to the type of deletion or duplication they have, and try to find specific treatment approaches for each sub-type of autism.
"Just in the last two years, a number of studies have revealed the clinical importance of ever smaller chromosome deletions and duplications found with advanced microarray technology," says Wu. "These new, highly-efficient tests can help in the evaluation or confirmation of autism spectrum disorders and other developmental disorders, leading to early diagnosis and intervention and a significantly improved developmental outcome."
Two known chromosome locations - on chromosome 16 (16p11.2) and chromosome 15 (15q13.2q13.3) accounted for 17 percent of abnormal CMA findings. Both chromosome abnormalities were initially linked with ASDs by Children's Hospital Boston and collaborators in The New England Journal of Medicine and the Journal of Medical Genetics, respectively, in 2008. Children's now offers specific tests targeting both of these "hot spots."
However, the researchers note that most copy-number changes were unique or identified in only a small number of patients, so their implications need further study. Many of them are presumed to be related to ASDs because they involve important genes, cover a large region of the chromosome, or because the child is the first person in that family to have the change.
"Some deletions and duplications are rare and specific to one individual or one family," says Miller. "Learning about them is going to be an evolving process. There won't be one single test that finds all genetic changes related to autism, until we completely understand the entire genome."
The paper's co-first authors were Autism Consortium members Yiping Shen, PhD, of Children's Department of Laboratory Medicine and the Center for Human Genetic Research at Massachusetts General Hospital, and Kira Dies, ScM, LGC, of the Family Research Network of the Autism Consortium and Children's Multi-Disciplinary Tuberous Sclerosis Program. A number of specialists from Children's Departments of Neurology, Developmental Medicine and Clinical Genetics and physicians from other medical centers in greater Boston were also authors on the study. The research was supported by the Nancy Lurie Marks Family Foundation, the Simons Foundation, Autism Speaks and the National Institutes of Health.
Families interested in scheduling an appointment at Children's may call the Developmental Medicine Center (617-355-7025) or the Department of Neurology (617-355-2711).
Citation: Shen Y; et al. Clinical genetic testing for patients with autism spectrum disorders. Pediatrics 2010 Apr; 125(4):e1-e17. (Published online March 15)
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Monday, March 15, 2010
A Better Genetic Test for Autism
Thursday, October 30, 2008
Breakthrough Mapping of Alzheimer's Genome Helps ID Four New Suspect Genes
PRNewswire-USNewswire/ -- Four novel genes that may significantly increase the risk of the most common form of late-onset Alzheimer's have been identified by researchers at Massachusetts General Hospital and Harvard Medical School, as reported in the November 7th issue of American Journal of Human Genetics. The findings, part of a larger "Alzheimer's Genome Project" (AGP) established three years ago to identify the full set of Alzheimer's disease genetic risk factors, may lead to more aggressive therapeutic interventions to slow, stop or even reverse the effects of the disease. These new therapies would differ from current treatments that only address the symptoms of the disease.
Dr. Rudolph Tanzi, chairman of the Cure Alzheimer's Fund Research Consortium and the Joseph P. and Rose F. Kennedy Professor of Neurology at Harvard Medical School, completed the largest family-based genome-wide association screen conducted to date. More than 400 families affected by Alzheimer's disease were screened to determine genetic variants associated with the inheritance of Alzheimer's. The four genes discovered in the family study are described in the article.
Technological advances are improving the understanding of the genetic mechanism that governs Alzheimer's disease and are making it feasible to identify the complete set of genes influencing risk for Alzheimer's disease, Dr. Tanzi said.
In addition to the genome-wide association screen, Dr. Tanzi and Dr. Lars Bertram of Harvard Medical School have been analyzing Alzheimer's genetics literature to determine which of the hundreds of proposed Alzheimer's candidate genes are genuine disease genetic risk factors. These summarized findings, implicating 30 gene candidates, are updated regularly at http://alzgene.org/ (a public Web site sponsored by the Cure Alzheimer's Fund). Tanzi and Bertram highlighted 10 of the most interesting of these genes in the current issue of Nature Reviews Neuroscience. Ultimately, the goal is to combine the results of the Alzheimer's family-based genome-wide association screen with the bioinformatics results of AlzGene.org.
The combined efforts of the family-based genome-wide association screen and AlzGene.org studies have led to the identification of 70 genes containing variants that either confer risk for, or protect against, Alzheimer's, making up the most comprehensive genetic map of the disease.
"This project is the most complete and comprehensive search for the genes that cause Alzheimer's disease published to date," Tanzi said. "Our hope is to use this new information to not only better diagnose and someday predict risk for Alzheimer's but to also learn from these genes the biological causes of Alzheimer's. The knowledge gained from understanding the Alzheimer's-associated defects in these genes will almost certainly accelerate the development of novel therapeutics and hopefully lead to a potential cure for this devastating disease."
The current understanding of the causes and pathological progression of Alzheimer's disease have been made possible by studies of four Alzheimer's genes discovered between 1987 and 1995, three of which were co-discovered by Tanzi. Since these genes account for only 30 percent of the genetic basis of Alzheimer's disease, three years ago Cure Alzheimer's Fund initiated the Alzheimer's Genome Project aimed at determining the remaining 70 percent of the genetic basis of Alzheimer's disease. Taking advantage of major technological and analytical breakthroughs in human genetic studies, the project was able to reach this milestone with a limited budget, led by a contribution of $3 million from Cure Alzheimer's Fund.
"We are on the cusp of a rare 'science moment' that could alter the way we diagnose, treat and prevent Alzheimer's disease," said Tanzi. "Ultimately, the combined results of the family-based genome-wide screen and AlzGene.org will allow for the reliable prediction of Alzheimer's disease while also guiding the development of therapies."
Alzheimer's disease is the most common cause of dementia in the elderly and a burgeoning unmet medical need that only will worsen as individuals continue to live longer. The Alzheimer's Association estimates that as many as 5.2 million Americans are living with Alzheimer's disease, including between 200,000 and 500,000 people under age 65 with young-onset Alzheimer's disease or other dementias. Experts predict that, by 2010, nearly a half million new cases of Alzheimer's disease will occur each year; and by 2050, nearly a million new cases will occur annually.
Cure Alzheimer's Fund has no endowment and passes funds raised directly to selected research as determined by the Cure Alzheimer's Research Consortium. The Foundation has no financial or intellectual property interest in the research funded, and will make known the results of all funded research as soon as possible. At a time when the federal government investment for Alzheimer's research and education is decreasing, Cure Alzheimer's Fund has raised more than $10 million, investing all of it directly into research.
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