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In a new study, an international team of researchers used the power of whole genome sequencing to discover a previously hidden type of genetic change associated with autism. They also discovered that these rare structural variations are inherited almost exclusively from fathers – for reasons yet to be discovered.
The report appears today in the journal Science.
“These unexpected findings broaden our appreciation for the enormous diversity of ways that autism develops, and in doing so, hold promise for the development of personalized therapies and services,” says Autism Speaks Chief Science Officer Thomas Frazier. “This study also illustrates the importance of the detailed, comprehensive research made possible through whole genome sequencing.”
The researchers analyzed the complete genomic sequences of 9,274 people in families affected by autism. The vast majority of these people had contributed DNA to the Simons Simplex Collection or the Autism Speaks MSSNG Whole Genome Sequencing Project.
Exploring the genome’s “dark matter”
The researchers linked increased risk for autism to rare structural changes (deleted or duplicated DNA sequences) in the still-mysterious “noncoding” region of the human genome.
This region makes up 98 percent of our DNA. It lies outside the 2 percent of our DNA that makes up our genes. (Genes “code,” or spell-out directions, for creating proteins. Proteins, in turn, control the development and activity of every cell in the body.)
Until recently, researchers largely ignored the noncoding portion of the genome, and some even dubbed it “junk DNA.” We now know that noncoding DNA plays a crucial if incompletely understood role in directing when and where our genes switch on and off. This precise coordination of gene activity is particularly crucial for brain development and function.
Hidden structural variations
Still, a role for non-coding structural variations, like the duplications and deletions identified in the new study, had not been widely investigated until now. This was due, in part, to the difficulty of detecting these variations and their effects.
The research team developed a new method for analyzing whole genome sequences that allowed them to both detect the rare noncoding structural changes and identify which ones disrupt the regulation of gene activity and contribute to autism.
“This represents an important step toward understanding how variation in the ‘switches’ that turn genes on and off influence the development of the brain and risk for autism,” says senior study author Jonathan Sebat, of the University of California San Diego School of Medicine. “Still larger studies could help to identify specific switches that are important and could significantly improve the value of [whole genome] DNA sequencing in the clinic.”
From basic science to applications that improve lives
The goal of clinical genome sequencing for autism is to guide the development of personalized plans to address each person’s needs for treatment and/or support services. This is particularly important for the many subtypes of autism that are accompanied by serious medical problems and cognitive disabilities.
“This kind of analysis can only be done using whole genome sequence data and is, in part, why we created MSSNG,” says study co-author Stephen Scherer. Dr. Scherer is the research director of the Autism Speaks MSSNG program. He also directs the Centre for Applied Genomics at Toronto’s Hospital for Sick Children (SickKids) and the McLaughlin Centre at the University of Toronto.
“Understanding different types of genetic variants is vital to understanding the biochemical pathways that underlie autism,” adds Dean Hartley, Autism Speaks senior director of discovery and translational science. “Once we understand a given pathway, we can design personalized interventions that support or change that pathway to increase a person’s quality of life.”
The Interagency Autism Coordinating Committee (IACC) will hold its next quarterly meeting on April 19, 2018, at the National Institutes of Health in Bethesda, Maryland, with a live webcast. The full-day meeting is open to the public and includes a public comment period. The IACC coordinates federal efforts related to autism.
Autism Speaks encourages members of the autism community to participate and make their views known. Learn more and register to provide public comment here.
Webinars sponsored by the Autism Speaks Autism Treatment Network & the Autism Intervention Research Network on Physical Health
Advances in Autism Research & Care (AARC) is a free, monthly webinar series sponsored by the Autism Intervention Research Network on Physical Health (AIR-P) and the Autism Speaks Autism Treatment Network (ATN). Webinar topics alternate between research reports by ATN/AIR-P investigators and trending topics in autism healthcare. Though aimed primarily at educating healthcare providers, the webinars are open to the public. We extend a special welcome to members of the autism community.
Upcoming webinars for 2018 include:
Advocacy and Autism
Thursday, April 19, from 3 to 4 pm Eastern Register here.
Autism BrainNet (post-mortem tissue donation for autism research)
Wednesday, May 30, from 1 to 2 pm Eastern Register here.
Send us your topic suggestions:
We would love your input on topics and presenters for our autism healthcare and research series. Our goal is to identify relevant topics and broaden our audience – starting with you. We are excited to collaborate and hear about your various research interests. If you have an autism-related topic that you want to learn more about, please fill out this short survey. Find links to all our past webinars here.
On December 14, 2017, Autism Speaks Chief Science Officer Tom Frazier and Chief Program and Marketing Officer Lisa Goring discussed Autism Speaks’ newly released Strategic Plan for Science 2018-2020 and took your questions.
The federal Interagency Autism Coordinating Committee (IACC) holds quarterly meetings at the National Institutes of Health in Bethesda, Maryland. The full-day meeting is open to the public and includes a public comment period. It can also be viewed via live webcast from 9 am to 5 pm. The IACC is charged with overseeing and coordinating autism-related research and services across federal agencies and departments within the National Institutes of Health. Autism Speaks encourages members of the autism community to participate in the meeting and make their views known.
Register to attend here.
Find meeting agendas here.
View archived webcasts here.
On Feb. 22nd, Donna Murray, Autism Speaks vice president for clinical programs and head of our Autism Treatment Network, hosted a Facebook Live chat, answering questions related to "Improving healthcare for people on the autism spectrum." You can view the archived webchat below or by clickinghere. Check out the comment section for related resources and links.
On Jan. 25, Autism Speaks VP for Genomic Discovery Mat Pletcher hosted a Facebook Live chat about the Autism Speaks research program. View the archived chat - including an extended question and answer session below.
A new U.S. Food and Drug Administration (FDA) report, “The Voice of the Patient: Autism,” distills the input the agency received from members of the autism community during a 2017 public meeting and panel discussion on Patient-Focused Drug Development in Autism.
The public meeting and report are part of a broader FDA initiative to make patient priorities an integral part of drug development.
The FDA’s most familiar role is as the arbiter of whether a new medicine is safe and effective for public use. The agency also plays a crucial role in guiding the early design of studies that aim to bring new treatments to market. It is in this second role that the agency has promised to represent patient priorities and perspectives.
For instance, the new FDA report on the autism community’s priorities includes emphasizes a desire for therapies that “alleviate our discomforts rather than … take away our unique gifts.”
It also notes a community consensus on prioritizing treatments for the many health conditions that frequently accompany autism. These include epilepsy, GI disorders, disrupted sleep, medication-related obesity and mental health challenges including anxiety, attention deficit and hyperactivity disorder (ADHD) and depression. (To learn more, see Autism and Health: A Special Report by Autism Speaks.)
By contrast, participating members of the autism community expressed relatively low interest in medicines or other therapies that decrease sensory-related repetitive behaviors such as flapping and spinning. So in using that feedback, the FDA might discourage researchers from making “decreased repetitive behaviors” a primary goal in a study evaluating the benefits of a new medicine or other treatment.
Read the full FDA report here.
Click here to read a Q&A with meeting participants Stuart Spielman, Autism Speaks’ senior policy advisor and counsel, and Thomas Frazier, Autism Speaks’ chief science officer. They attended as parents of children who have autism, and Dr. Frazier also participated as a panelist.
Autism Speaks, with generous support from the Royal Arch Masons International, is pleased to announce two new funding opportunities for research focused on improving understanding, evaluation and treatment of auditory processing disorders among people who have autism and related conditions.
The goal is to increase quality of life, with an emphasis on personalizing interventions.
Since the 1970s, the Royal Arch Masons International have ranked among the leading philanthropies helping children with auditory processing disorders, also known as central auditory processing disorders. This includes a range of conditions affecting the way individuals process the information they hear. Many people with autism have related challenges that can include difficulty using and comprehending speech and/or paying attention to and remembering spoken information.
The new research grant opportunities include
one pilot research award, up to $60,000
one predoctoral fellowship award, up to $40,000.
Autism Speaks seeks proposals for research that will
* increase understanding of the relationship between auditory processes and neurobehavioral function;
* lead to improved treatments for auditory processing challenges and related brain function and behavioral challenges;
* improve healthcare guidelines for identifying, evaluating and treating central auditory processing disorders;
* hold the potential to increase quality of life for people who have differences in brain development.
Find more information and instructions for applying in this Request For Applications.
Autism Speaks is pleased to announce its annual selection of the ten studies that most-powerfully advanced the field of autism research to enhance lives today and accelerate a spectrum of solutions for tomorrow.
The Autism Speaks Medical and Scientific Advisory Board and the Autism Speaks science leadership team selected the annual Top Ten from more than 4,000 peer-reviewed research reports published in scientific journals this year.
“These studies exemplify the noteworthy advances we’re witnessing across the field – from research into the causes and biology of autism to the evaluation of new methods for earlier identification and intervention,” says Autism Speaks Chief Science Officer Thomas Frazier. “Their results are helping children today and laying the foundation for more-effective, personalized treatments and support services across the lifespan.”
The selections listed below include commentary by science staff and advisors with related expertise. (Autism Speaks funding noted where applicable)
Harnessing the power of parent participation in early intervention
Randomised trial of a parent-mediated intervention for infants at high risk for autism: longitudinal outcomes to age 3 years. Green, J, Pickles, A, Pasco, G, et al. J Child Psychol Psychiatr. 2017 Dec;58(12):1330-40. [Autism Speaks research grants 7773 and 1292]
Longitudinal follow-up of academic achievement in children with autism from age 2 to 18. Kim SH, Bal VH, Lord C. J Child Psychol Psychiatr. 2017 Sept 26 Epub
“These two studies stand out in demonstrating the benefits of parent participation in early intervention for autism. The study led by Jonathan Green, at the University of Manchester, is the first to show long-term benefits – milder autism features and increased social interaction – from a very early intervention that teaches parents how to interact with infants at high risk for autism. (Read more about this study here.)
The research led by So Hyun Kim, at Weill Cornell Medicine, focuses on the understudied topic of what influences academic achievement in children and youth on the autism spectrum. I find it particularly interesting that the study identified parent participation in early intervention by age 3 to be a significant predictor of academic achievement, in addition to cognitive abilities.”
- Stelios Georgiades, Ph.D., member of the Autism Speaks Medical and Scientific Advisory Board and co-director of the McMaster Autism Research Team, at McMaster University & Hamilton Health Sciences, in Hamilton, Ontario
Advances and insights in autism genomics
Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder. Yuen RK, Merico D, Bookman M, et al. Nat Neurosci. 2017 Apr;20(4):602-11. [Autism Speaks research grants 9767, 9365, 7907]
Polygenic transmission disequilibrium confirms that common and rare variation act additively to create risk for autism spectrum disorders. Weiner DJ, Wigdor EM, Ripke S, et al. Nat Genet. 2017 Jul;49(7):978-985.
Meta-analysis of GWAS of over 16,000 individuals with autism spectrum disorder highlights a novel locus at 10q24.32 and a significant overlap with schizophrenia. Autism Spectrum Disorders Working Group of the Psychiatric Genomics Consortium. Mol Autism. 2017 May 22;8:21.
“These studies highlight how far we’ve come and how fast we’re moving in understanding the complex genetics of autism, though they were not alone in doing so. (Also see Turner 2017, Werling 2017 and Grove 2017.)
Previously, genetic studies focused almost exclusively on genes, which contain instructions, or coding, for making proteins in our body. But they didn’t look closely at other parts of the genome, such as the less-understood “non-coding” regions. We’re just beginning to understand the role of non-coding DNA changes in autism. The next step is to combine the results of these and still more genomic studies. Only then will we be able to understand how different types of genetic – and environmental – risks interact with each other.
- Joseph Buxbaum, Ph.D., member of the Autism Speaks Medical and Scientific Advisory Board and director of the Seaver Autism Center, Icahn School of Medicine at Mount Sinai, in New York City
Deciphering early differences in infant behavior and brain development
Infant viewing of social scenes is under genetic control and is atypical in autism. Constantino JN, Kennon-McGill S, Weichselbaum C, et al. Nature. 2017 Jul 20;547(7663):340-344.
Early brain development in infants at high risk for autism spectrum disorder. Hazlett HC, Gu H, Munsell BC, et al. Nature. 2017;542:348-51. [Autism Speaks research grant 6020]
“These two studies are important for revealing new early predictors of autism and its severity. Such predictors can help us identify infants who may benefit from early interventions before the outward signs of autism develop. The study findings also give us insights into autism’s underlying biology, which can help us develop better treatments and support services.
Because autism tends to run in families, both studies enrolled the baby siblings of children already diagnosed with the condition. Heather Hazlett’s team identified an increase in brain surface volume before 12 months in babies who later developed autism. During the second year of life, their overall brain size increased at the same time as their behavioral symptoms appeared. And the babies with the largest brain overgrowth developed the most-severe symptoms.
John Constantino’s team followed up on their previous discovery that, as babies, children who later developed autism were already paying less attention to socially important features of faces – the eyes and mouth. The team’s new study confirmed this finding and found that the preference for looking at eyes and mouths is strongly controlled by genetics across the general population. This implies that a strong genetic influence leads to differences in how a young child begins to experience and draw information from the social world. Such insights hold promise for guiding the development of interventions that support very early social development and communication in babies and toddlers at risk for autism. This includes any baby who shows warning signs. (See “Learn the signs of autism”)
- Edwin Cook, M.D., member of the Autism Speaks Medical and Scientific Advisory Board and director of the Laboratory of Developmental Neuroscience, University of Illinois, Chicago
New insights into predictors and possible contributors to autism
Increased extra-axial cerebrospinal fluid in high-risk infants who later develop autism. Shen MD, Kim SH, McKinstry RC, et al. Biol Psychiatry. 2017 Aug 1;82(3):186-193. [Autism Speaks research grant 6020]
Association between serotonergic antidepressant use during pregnancy and autism spectrum disorder in children. Brown HK, Ray JG, Wilton AS, et al. JAMA. 2017 Apr 18;317(15):1544-1552.
“The large study led by Mark Shen involved 343 infants and confirmed the unexpected results of a smaller 2013 study that found increased cerebrospinal fluid overlying the brain in babies who are later diagnosed with autism. This discovery represents more than an early biomarker of autism risk. It may lead to a better understanding of the neurodevelopmental processes that contribute to autism. For example, we now need to understand whether fundamental problems with the production or control of cerebrospinal fluid contribute to autism. Or perhaps the increased fluid stems from an underlying factor such as inflammation.
The report by Hilary Brown and colleagues is one of the best in a flurry of studies suggesting that serotonin antidepressants taken during pregnancy do not increase risk for autism. Some earlier studies suggested such a risk. But we know that autism occurs at higher rates in families affected by depression, anxiety or obsessive-compulsive disorder – the conditions commonly treated with these medicines. The new study found no difference in autism rates between siblings whose mothers took such a medication during one pregnancy but not the other.
This illustrates the need for exquisite control for differences in study populations when identifying risk factors for autism. The results also offer crucial guidance to expectant mothers who want to balance a medicine’s potential risk to a future child against the known risks of leaving a serious medical condition such as depression untreated.”
- Jeremy Veenstra-VanderWeele, M.D., member of the Autism Speaks Medical and Science Advisory Committee and director of Division of Child and Adolescent Psychiatry, Columbia University College of Physicians and Surgeons, in New York City
Functional neuroimaging of high-risk 6-month-old infants predicts a diagnosis of autism at 24 months of age. Emerson RW, Adams C, Nishino T, et al. Sci Transl Med. 2017 Jun 7;9(393). [Autism Speaks research grant 6020]
“Earlier identification of autism is crucial for earlier intervention with its great potential to improve outcomes. To that end, Robert Emerson and colleagues showed that, at 6 months of age, differences in brain activity patterns (e.g. functional brain connections) can predict a later diagnosis of autism. This discovery is consistent with those of previous studies that identified tell-tale differences in anatomical, or structural, brain connections in babies who later developed autism. Together, this body of research reinforces the idea that the brain changes leading to autism begin very early in life.
However, this year’s study involved just 59 infants at high risk for autism (because they were born into families already affected by the condition). It’s important to confirm its results with a larger group of babies. If the findings prove true – and these brain-imaging methods become practical for use outside of research studies – we may gain an important new tool for detecting autism and intervening earlier in babies at high risk for the condition.”
- Autism Speaks Chief Science Officer Thomas Frazier, Ph.D.
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