What Is New in This Research Area, and What Have We Learned in the Past Two Years?

Several advances have been made in developing infrastructure for autism research over the past two years, including increased data sharing and availability of DNA samples for study. Surveillance efforts have continued and are expanding in scope, and investments in the autism research workforce have been made to ensure continued development in the field.

Data Sharing

Most public and private funders of autism research have now made data sharing with the autism research data repository funded by the National Institutes of Health (NIH), the National Database for Autism Research (NDAR), an integral part of funding new research projects, which will in turn make future data available to other researchers. In addition, the Autism Speaks-supported Autism Genetic Resource Exchange (AGRE) and Autism Tissue Program (ATP), as well as the Interactive Autism Network (IAN), supported by NIH, Autism Speaks, Simons Foundation, and the Kennedy Krieger Institute, are now linked with NDAR. Collectively, this means that data from more than 40,000 consenting de-identified research participants are available for secondary analysis by other scientific researchers. Data sharing requires a global universal identifier (GUID) to track subjects in different studies, and to date, more than 78,000 research participants have been registered with such an identifier. All data within NDAR is harmonized (e.g., uses the same names for each piece of data collected) and validated (e.g., reported values are consistent with other projects) to a community-established common data definition. At the NIH, 80% of newly awarded human subject grants related to autism have an expectation for data sharing.¹ By 2015, virtually all NIH-funded human subjects research is expected to include these terms.

Biobanking

The loss in June 2012 of frozen samples from 55 brains that were part of the ATP collection after a freezer malfunction at the Harvard Brain Tissue Resource Center was a tragic blow to the slowly developing ASD biobank effort, as nearly one-third of the largest autism brain repository was destroyed or compromised in this accident. Quality investigations following the accident showed that while the affected tissue will no longer be able to be used for general research purposes, the tissue integrity and genetic material are adequate for some specialized research uses. The loss will lead to delays in research due to extremely limited availability of samples for some time to come.

Progress is being made in other aspects of brain banking efforts. The ATP has developed a donor registry in which 5,976 individuals have registered to donate brain tissue and carry a card designating their wishes. In the last two years, the program has received 15 brains and 278 individuals have been added to the registry. Brains that are donated to the ATP are analyzed and the data are made available through the ATP informatics portal, which now has 297 neuropathology reports on donor brains (Autism Tissue Program Informatics Portal website). These data are central to the ATP Brain Atlas Project, which began 13 years ago to create a three-dimensional map of the autistic brain that integrates anatomic and gene expression data throughout the adult human brain. Brain repositories contributed 40 brain hemispheres to the original project, and an additional 53 hemispheres have now been processed. During the past two years, the final 10 brain hemispheres were analyzed.

Autism Speaks, the Simons Foundation, and several academic leaders in the field have developed a network model to bring together several existing biobanks and to centralize and standardize brain banking efforts. The network model is focused on enhanced outreach to promote brain donation and use of refined operating procedures for brain and other tissue acquisition, processing, and access.

In parallel, the NIH has also been addressing the need for more coordination and networking in biobanking by creating the NIH Neurobiobank, a federation linking NIH-supported brain banks via a centralized data management system. The project was launched in October 2012. The accompanying NIH Neurobiobank Information Technology (IT) Portal will provide information about brain and tissue donation for research to the public, disease advocates, and researchers, including links to brain banks and their consent policies and other information.

Genetics

As noted in Question 2, whole genome and whole exome sequencing, in which an organism's entire genome or the entire coding portion of their DNA is sequenced at one time, have emerged as high-throughput approaches to accelerate gene discovery. The existing infrastructure of stored DNA samples has enabled both the NIH-funded Autism Sequencing Consortium's exome sequencing efforts (with 7,600 DNA samples from unrelated ASD patients) and several whole genome sequencing initiatives, including the collaboration between Beijing Genomics Institute and Autism Speaks. Additionally, Autism Speaks, the Simons Foundation, and the NIH developed partnerships to increase the amount and diversity of genetic data available through AGRE and NDAR by co-funding the phenotype and DNA collection on several unique cohorts. Newly established cohorts for collecting DNA include those funded by Autism Speaks and the NIH, such as the Autism Speaks Autism Treatment Network (ATN) Biorepository, high-risk infant cohort, and Infant Brain Imaging Study (IBIS) high-risk infant cohort. These cohorts are expected to accrue an estimated 456,775 and 1,360 DNA samples, respectively (by 2014 for the Biorepository and 2015 for the others). Additionally, Autism Speaks and the Simons Foundation jointly fund the Baby Siblings Research Consortium, with an estimated 1,780 DNA samples expected by 2015.

Furthermore, AGRE expanded its Multiplex Family Collection by more than 28% by making DNA available for an additional 383 families (including 653 probands, or individuals with ASD). The total DNA available from AGRE includes 1,736 families with a documented pedigree, or ancestry. The total number of probands in the collection is 3,348, while the number of fraternal twins is 204 and the number of identical twins is 118. The National Institute of Mental Health (NIMH)-funded Center for Collaborative Genomics Studies on Mental Disorders (CCGSMD) at Rutgers University, a resource center that provides biological samples, data, and data access tools to researchers, has recently increased the number of autism-related samples available to researchers. This makes it possible to conduct studies with increased statistical power, allowing the detection of rarer genetic causes of autism. The CCGSMD currently distributes samples for autism-related research from almost 11,500 children with autism and their families.

Induced Pluripotent Stem Cells (iPSCs)

A major advance in ASD research has been the development of iPSC technology, including the proof-of-principle that iPSC lines can be derived from somatic cells of patients with syndromic forms of autism (i.e., fragile X, Rett, and Timothy syndromes) (Kim et al., 2012). To date, more than 50 fibroblast lines have been collected from people with ASD for iPSC derivation.

Clinical Trials

Two new networks have been established for clinical trials. First, the Network for Excellence in Neuroscience Clinical Trials (NeuroNEXT) was created to conduct treatment studies (Phase 2 or biomarker studies) through partnerships with academia, private foundations, and industry. The network is designed to expand the National Institute of Neurological Disorders and Stroke's (NINDS) capability to test therapies, increase the efficiency of clinical trials before embarking on larger studies, and respond quickly as opportunities arise to test treatments. Second, the NIMH launched the Fast Fail Trials in Autism Spectrum Disorder (FAST-AS), a contract-based initiative that uses an experimental medicine paradigm to quickly test pharmacologic treatments and rule out ineffective ones, enabling more rapid identification of promising therapeutic approaches.

Autism Speaks convened two workgroups composed of academic and industry leaders, as well as representatives from Autism Speaks and the Simons Foundation, to evaluate existing outcome measures and support the development of medicines to improve social communication, repetitive behaviors, and anxiety associated with autism. The workgroups met with the Food and Drug Administration (FDA) to help develop consensus around appropriate outcome measures for autism clinical trials, and papers summarizing the outcome are in preparation.

In 2012, the Innovative Medicines Initiative (IMI) launched a major new effort in Europe called the European Autism Interventions - A Multicentre Study for Developing New Medications (EU-AIMS), investing $55 million over five years to accelerate the discovery and development of medicines for ASD.

Surveillance

Updated estimates from the Centers for Disease Control and Prevention's (CDC) Autism and Developmental Disabilities Monitoring (ADDM) Network—based on a cohort of children who were eight years old in 2008—confirmed that just over 1% of children (1 in 88) in the U.S. are identified as having ASD (CDC, 2012). This figure ranged from 4.8 to 21.2 per 1,000 children across ADDM collection sites. Of particular concern is the average increase in ASD prevalence of 78% from 2002 to 2008 in multiple areas of the U.S. covered by the ADDM Network. While some of the increase was attributed to improved identification of particular subgroups, a true increase in the number of individuals affected is possible. In concert with recommendations from a workshop on factors contributing to the increasing ASD prevalence held by CDC and Autism Speaks in 2011 (CDC, 2011), several studies have highlighted the role of changes in identification (Keyes et al., 2012; Miller et al., 2012) as well as the limited role of some perinatal risk factors on changes in ASD prevalence (Schieve et al., 2011).

The CDC's ADDM Network infrastructure has now been expanded to include six sites evaluating prevalence among younger children. One ADDM site, funded by Autism Speaks, will include direct population-based screening and evaluation to compare to records-based surveillance. Additionally, CDC, Autism Speaks, and NIH are co-funding a project that is underway to determine the prevalence of ASD among Somali children in Minneapolis, Minnesota. Other surveillance programs also have made progress over the last two years, yielding results that have informed further autism initiatives. For example, findings from CDC and the U.S. Health Resources and Services Administration’s National Survey of Children's Health (NSCH) led to the development of the Pathways to Diagnosis and Services Survey, a population-based study of the diagnostic and service experiences of children with autism (CDC, 2012).

Communication and Dissemination

Direct studies of family involvement in autism research shows participation still lags behind that for other diseases. Results from a 2005 national online survey of the general population (not specific to autism) reported that only 15% of adults have had the opportunity to participate in a clinical research study (Gullo, 2005). Similar results were found in a 2007 market research survey on autism research attitudes and behavior, where only 14% of respondents reported having participated in an autism-related research study, though 90% reported that they would like to participate (Patchwork Consulting LLC, 2004). Unfortunately, 2012 data from IAN continues to corroborate that finding, reporting that only 16% of respondents say they have participated in autism research (IAN Data Explorer website ).

Research Workforce Development and Support

As the ASD research effort has expanded in recent years, so too has investment in the ASD research workforce. For instance, in 2011, the NIH supported 27 individual postdoctoral trainee awards (in addition to the large number of postdoctoral researchers funded through larger grants awarded to Principal Investigators), compared to 15 in 2010. Autism Speaks and the Autism Science Foundation have also launched support for post-doctoral training, collectively supporting 16 new trainees in 2011 and 2012. All of the Autism Science Foundation fellows and 73% of the Autism Speaks fellows reported that the award was their first autism research grant, and more than 90% of the fellows reported that they planned to stay in the field.

The American Recovery and Reinvestment Act (ARRA), enacted by Congress in February 2009, included funds that were awarded to autism research grantees during a 2-year period from 2009 to 2010. During that time period, ARRA provided $123,916,638, or 22%, of Federal funds for autism research. Now that ARRA funding has ended, even with an unchanged NIH budget appropriation, autism research funding will experience a real decline.

What Gaps Have Emerged in the Past Two Years?

Data Sharing and Databases

The NDAR program has identified several critical data sharing issues that must be addressed as the field continues to move forward:

• Timeliness – Researchers are currently expected to share data updates every six months and full results at the time of publication. However, this process is frequently delayed, which is an issue that must be remedied.
• Data Quality – While provisions have been made to include the cost to share data within a project's budget, further support is needed to ensure data are professionally maintained and shared throughout the life of a project.
• Culture – Offering funding opportunities for secondary use of existing data is needed to demonstrate and improve the utility of the investment made in data sharing infrastructure.
• Data Storage and Computational Approaches – Costs associated with the storage and processing of data may overwhelm the existing infrastructure. Establishing the mechanisms for efficient data storage and use of available emerging computational pipelines is recommended.

In this era of "big data," there are emerging opportunities for large datasets that can be used for secondary analyses. The first manuscript from the NIH-funded Autism Health Outcomes Study, with claims data from one large commercial insurance company on 33,000 individuals with ASD, nearly 100,000 of their family members, and over 100,000 controls, is expected to be published in 2013. The Mental Health Research Network, a consortium of public-domain research centers based in large not-for-profit healthcare systems with 11 million patients, including nearly 24,000 children with an ASD diagnosis, could also be a useful resource. Additionally, claims data from Medicaid, the single largest healthcare insurer of children in the United States and the largest insurer of individuals with disabilities, could provide data on more than 75,000 individuals with ASD each year for secondary data analyses. Linking these large datasets to environmental data would provide another untapped resource for future research.

Biobanking

The continued limited supply of available brain tissue for research from donors with ASD and from those with co-occurring conditions and disorders, such as epilepsy, as well as from unaffected ‘control' donors, continues to be one of the great challenges for research on the neurobiology of ASD, intensified by the loss of tissue caused by the 2012 freezer failure. Tissue donation recruitment programs would benefit from enlisting parent advisors who would be able to be sensitive to patient perspectives and responsive to the expectations of this unique group of advocates who wish to support research in this most personal way.

Genetics

The scale and volume of data being generated (~1 terabyte/genome) could easily overwhelm even the most robust computational storage and analytic systems. There are three emerging major gaps that must be addressed: (1) adequate facilities to store data, (2) the means to effectively disseminate this resource to the broader scientific community, and (3) cost-effective computational resources that the research community can use to easily access and analyze the dataset. None of these issues are unique to ASD research, and all are being addressed by the broad genomics community.

Infrastructure Support

The amount of tissue that has been collected and data that have been generated has increased in recent years. In order to ensure continued integrity of the tissue and data, both physical and virtual backup support methodology and systems must be built into the collection and storage processes. Physical hardware and virtual software systems must be developed to protect and ensure the integrity and longevity of the samples.

Induced Pluripotent Stem Cells (iPSCs)

The development of iPSC technology has created both new research opportunities and new research needs. Among the needs is standardization of methodology and generation of a variety of fibroblast lines from patients with different diagnoses in order to understand the heterogeneity and natural history of ASD.

Clinical Trials

Support continues to be needed for clinical trials of treatments for core symptoms of autism and co-occurring conditions such as sleep disturbances, as well as for comparative effectiveness trials. Difficulty in recruiting research participants restricts progress; therefore, access to large, well-characterized patient populations must be addressed, and a centralized registry for re-contact of patients for further research would assist in this endeavor. Collection of data with well-characterized populations should be systematic and standardized (tissue samples, blood, microarray data analysis, etc.). For trials to be successful, there should be an infrastructure for supporting small- and large-scale ASD trials throughout the process, from pre-clinical studies to clinical trials and data analysis.

Surveillance

Recent findings demonstrate the need for enhanced surveillance and monitoring of ASD prevalence among younger children and the incorporation of direct screening (screening based on parent questionnaires and follow-up assessment with research participants) and case confirmation components into the current ADDM methodology to analyze ASD prevalence estimates and improve understanding of the identified disparities. It will be important to investigate the impact of changes to ASD diagnostic criteria in the fifth edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-5). Continued support for international surveillance activities and epidemiologic research is important because it enables the comparison of prevalence estimates and characteristics across countries. Further, surveillance among adults (including needs assessments), ethnic minorities, and underserved populations will be critically important in understanding risk factors (including environmental exposures) and barriers to services in these groups.

Communication and Dissemination

At present, research productivity is often measured by the number of publications produced. However, there is a need to develop new measures that focus on valued outcomes such as improvement in quality of life. In order to boost participation in research studies, new outreach approaches to effectively disseminate information about the types of trials and research studies available for participation, and to encourage participation, must also be considered. Finally, information about the prevalence of autism and the methods used to collect prevalence data need to be expressed to the stakeholder community in clear, lay language in order to raise awareness and promote understanding of the meaning and limitations of the data.

Research Workforce Development and Support

Continued focus on developing a diverse research workforce through investment in young investigators at levels of predoctoral and postdoctoral training is a high priority. Similarly, there is a need to focus on developing a funding mechanism to support early-career investigators in order to bridge the gap between postdoctoral training and assistant professorship. Retention of investigators in active research and investment in vital ongoing autism research efforts will be affected by the loss of ARRA funding. These and other potential impacts will need to be monitored. The decline in Federal spending post-ARRA has raised significant concerns about the sustainability of research progress and the possible loss of well-trained, productive autism researchers. Active efforts must be made to maintain and continue enhancing the research workforce needed to address the many research needs and challenges presented by ASD.

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