First full genome sequencing for autism: Promise for future diagnosis, prevention and treatment

July 11, 2013 — A collaborative formed by Autism Speaks, the world’s leading autism science and advocacy organization, has found full genome sequencing examining the entire DNA code of individuals with autism spectrum disorder (ASD) and their family members to provide the definitive look at the wide ranging genetic variations associated with ASD. The study published online today in American Journal of Human Genetics, reports on full genome sequencing on 32 unrelated Canadian individuals with autism and their families, participants in the Autism Speaks Autism Genetic Resource Exchange (AGRE). The results include both inherited as well as spontaneous or de novo, genetic alterations found in one half of the affected families sequenced.This dramatic finding of genetic risk variants associated with clinical manifestation of ASD or accompanying symptoms in 50 percent of the participants tested is promising, as current diagnostic technology has only been able to determine a genetic basis in about 20 percent of individuals with ASD tested. The large proportion of families identified with genetic alterations of concern is in part due to the comprehensive and uniform ability to examine regions of the genome possible with whole genome sequencing missed in other lower resolution genome scanning approaches.”From diagnosis to treatment to prevention, whole genome sequencing efforts like these hold the potential to fundamentally transform the future of medical care for people with autism,” stated Autism Speaks Chief Science Officer and study co-author Robert Ring, Ph.D.The study identified genetic variations associated with risk for ASD including de novo, X-linked and other inherited DNA lesions in four genes not previously recognized for ASD; nine genes previously determined to be associated with ASD risk; and eight candidate ASD risk genes. Some families had a combination of genes involved. In addition, risk alterations were found in genes associated with fragile X or related syndromes (CAPRIN1 and AFF2), social-cognitive deficits (VIP), epilepsy (SCN2A and KCNQ2) as well as NRXN1 and CHD7, which causes ASD-associated CHARGE syndrome.”Whole genome sequencing offers the ultimate tool to advance the understanding of the genetic architecture of autism,” added lead author Dr. Stephen Scherer, senior scientist and director of the Centre for Applied Genomics at The Hospital for Sick Children (SickKids) and director of the McLaughlin Centre at the University of Toronto. “In the future, results from whole genome sequencing could highlight potential molecular targets for pharmacological intervention, and pave the way for individualized therapy in autism. It will also allow for earlier diagnosis of some forms of autism, particularly among siblings of children with autism where recurrence is approximately 18 per cent.”This $1 million collaboration of Autism Speaks, SickKids, BGI and Duke University piloted Autism Speaks’ initiative to generate the world’s largest library of sequenced genomes of individuals with ASD announced in late 2011. “As we continue to test more individuals and their family members from the AGRE cohort, we expect to discover and study additional genetic variants associated with autism. …

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First child born following embryo screening with new genome analysis technique

July 8, 2013 — The first birth has been achieved following the analysis of embryos using a new genome sequencing technique which promises to revolutionise embryo selection for IVF. The technique, which has never before been applied in the screening of embryos, is reported today at the annual meeting of ESHRE by Dr Dagan Wells of the NIHR Biomedical Research Centre at the University of Oxford, UK.The analysis technique is known as “next generation sequencing,” a powerful method capable of decoding entire genomes. Vast quantities of DNA data are produced from each sample tested, simultaneously revealing information on the inheritance of genetic disorders, chromosome abnormalities and mitochondrial mutations. Next generation sequencing (NGS) is already revolutionising many areas of genetic research and diagnostics, said Dr Wells, and, when applied to the assessment of embryos, will allow the concurrent analysis of serious inherited disorders and lethal chromosome abnormalities. “Next generation sequencing provides an unprecedented insight into the biology of embryos,” said Dr Wells.The identification of an embryo destined to implant in the uterus and form a pregnancy remains the holy grail of IVF. On average, only around 30% of embryos currently selected for transfer actually implant. The reason for this high failure rate is unknown, but the prime suspects are unidentified genetic or chromosomal defects. Several genetic screening methods have been introduced over the past decade, but all have been shown to have drawbacks (and have not realised their potential) when tested in randomised clinical trials. This new NGS technique developed by Dr Wells and colleagues, however, seems to overcome the major drawbacks of current methods:Complete chromosome information can be produced revealing abnormalities often responsible for miscarriage Serious gene defects can be identified at the same time The analysis can be completed rapidly (around 16 hours), thus avoiding the need for embryo freezing while awaiting results The test could greatly reduce the costs of embryo screening, which is currently an expensive add-on to IVF. The study described today was designed to test the accuracy and predictability of NGS in embryo selection. …

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