Autism is a developmental disorder that affects how people perceive the world and interact with others. Autism is technically known as Autism Spectrum Disorder (ASD) as it includes a wide range of different symptoms and levels of disability ^1.
Currently, there is a limited understanding of the causes of ASD, with no cure and limited treatments. This is compounded by the fact that it is actually a spectrum of disorders and therefore it is likely there are many different causes and genetic risk factors. Increasing evidence suggests that genetics and heritability play a very important role in ASD susceptibility. Many organisations and charities are supporting multiple different types of research into causes and cures of ASD.
Findings have repeatedly and unequivocally determined that heritable variation in DNA plays a substantial role in the etiology of autism and ASD^2.
At Reposititve we aim to support research into whether there are any genetics risk factors or genes that might cause ASD, by curating a specific collection of human genomic datasets that has relevance to Autism research.
Autism data on Repositive
On Repositive we are releasing a new collection of all the Autism data we have on the platform. This currently includes over 6,500 datasets from over 9 different data sources.
Whole exome sequencing data from Autism patients
The majority of the ASD related data on Repositive is whole exome sequencing data found in SRA (Browse). Of this SRA data, most is from a major, multi-institute, ASD study known as ARRA. This is a partnership between expert large-scale sequencing centres at the Baylor College of Medicine and the Broad Institute of MIT and Harvard, and a collaborative network of research labs focused on the genetics of autism brought together by the Autism Genome Project and the Autism Consortium.
"The goal is to conclusively identify which genes harbor individual or collections of rare DNA variants that predispose to autism, and thus translate the abstract heritability into solid biological clues about disease pathogenesis that can be studied molecularly and approached therapeutically."
They are preforming whole exome sequencing on thousands of autism families collected by the autism research groups and being provided with phenotype data by NIMH repositories, which together will form a cornerstone of autism genetic research for the future ^3.
The role of microRNAs in Autism
The 34 miRNA-Seq datasets related to ASD on Repositive (Browse) particularly caught my eye as research into the roles of microRNA were still a relatively new, unexplored, and poorly understood topic when I started my PhD (less 6 years ago). Therefore, I was intrigued that miRNA analysis had been applied to the study of ASD.
MicroRNAs were only discovered in 1993. Their main role, which is epigenetic, is to inhibit protein synthesis of protein-coding genes and has been known of for less than 10 years ^4. Only in last couple of years have researchers started studying miRNA in Autism, with the first major study in 2008 ^5. It is now thought that the dysregulation of microRNAs may have a role in ASD pathophysiology ^6.
The samples on Repositive relate to a study that has tried to establish if microRNA detected in the saliva can be used as a biomarker for the diagnosis of ASD ^7.
Autism and gut microbiota
In a previous blog post I discuss why studying the human microbiome is important. However, I did not go into depth about the phenomenon known as the microtiota-gut-brain (MGB) axis which is the term used to refer to the relationship between the gut microbiota and the brain. There is increasing evidence that the gut microbiota not only regulate function and health of the intestine but also the immune and nervous systems.
Many studies have shown that children with ASD have gastrointestinal problems and altered gut flora ^8. This has now been associated with the inflammation of microglia, the immune cells that reside within the brain.
Children with autism have unusual species or imbalances of gut bacteria^9.
Image by Abigail Goh, from Spectrum News
On Repositive we have over 150 datasets from gut microbiota samples from individuals involved in ASD studies. This can include individuals suffering from ASD or healthy controls. For example, 103 of the samples (Browse) are from the Autism gut targeted loci study, which is a comparison of the gut microbiota of children with ASD and their neurotypical siblings using 16S rRNA gene sequencing. These samples were recruited through the Simons Simplex Community at the Interactive Autism Network ^10.
The American gut project, which can also be found in the Repositive Autism collection (Browse), is a crowdsourced citizen science project with samples collected from thousands of participants, resulting in the largest human microbiome cohort in existence. By gaining detailed information on health, lifestyle and diet researchers how to find associations between the microbiome and diseases such as ASD.
^10: JS Son et al. Comparison of Fecal Microbiota in Children with Autism Spectrum Disorders and Neurotypical Siblings in the Simons Simplex Collection. PLoS One 2015 | doi: 10.1371/journal.pone.0137725