Autism and single nucleotide variants

Disease-causing mutations can be incredibly subtle: Sometimes a single-letter change in a gene or a so-called somatic mutation (affecting only some of the body’s cells) can be enough. Researchers report this week in Neuron that both kinds of mutations — easily missed on standard blood and saliva testing — play a role in autism spectrum disorder (ASD).

Scientists have suspected a role for these mutations in brain disorders, but the technology to find them has only recently come online. Sampling brain tissue is the most likely way to find them, but brain biopsies aren’t something you do every day.

In their study, a team led by Christopher Walsh, MD, PhD, and Alissa D’Gama, of Boston Children’s Hospital and Harvard Medical School, tapped several brain banks — the NIH’s NeuroBioBank, the Oxford (U.K.) Brain Bank and Autism BrainNet — to gather brain tissue from more than 100 deceased individuals, some neurotypical and some with ASD.

Using deep sequencing methods, the researchers then looked for single-letter changes (known as single-nucleotide variants or SNVs) and somatic mutations. To narrow their search, they looked only at 78 genes previously linked to autism. To detect as many rare, subtle mutations as possible, they amplified the DNA sequences and read them multiple times — 547 reads per sequence, on average. These techniques found quite a few genetic variants in the ASD and control groups. The majority of these were completely harmless, but the ASD group had significantly more biologically meaningful mutations: 26 of the 55 ASD brains had mutations that altered proteins (versus just 12 of the 50 neurotypical brains), 16 had clearly damaging mutations (versus 5 controls) and 6 had mutations that completely disabled the protein (versus 0 controls).

At least two people with ASD had protein-altering variants identifiable as somatic, in the SETD2 and SCN1A genes; none were found in the controls. Some genes had more than one kind of variant, and some individuals harbored multiple variants. One individual had both an SNV and a somatic mutation. “These cases underscore the complex genetic architecture of ASD,” the researchers write. Since their sample size was small and only 78 genes were tested, the researchers had a limited ability to detect somatic mutations, but believe they could be important in autism and that some may interact with inherited mutations.

The likelihood that somatic mutations contribute to autism does raise questions about diagnostic testing. “Understanding that some mutations can occur late in development and only be present in the brain has important implications for clinical genetic testing, as studying the blood will miss the somatic mutations present only in brain,” says D’Gama.

http://vector.childrenshospital.org/2015/12/brain-samples-show-a-wealth-of-single-letter-and-somatic-mutations-in-autism/

D'Gama AM, Pochareddy S, Li M, Jamuar SS, Reiff RE, Lam AT, Sestan N, Walsh
CA. Targeted DNA Sequencing from Autism Spectrum Disorder Brains Implicates
Multiple Genetic Mechanisms. Neuron. 2015 Dec 2;88(5):910-7.

Abstract

Single nucleotide variants (SNVs), particularly loss-of-function mutations, are significant contributors to autism spectrum disorder (ASD) risk. Here we report the first systematic deep sequencing study of 55 postmortem ASD brains for SNVs in 78 known ASD candidate genes. Remarkably, even without parental samples, we find more ASD brains with mutations that are protein-altering (26/55 cases versus 12/50 controls, p = 0.015), deleterious (16/55 versus 5/50, p = 0.016), or loss-of-function (6/55 versus 0/50, p = 0.028) compared to controls, with recurrent deleterious mutations in ARID1B, SCN1A, SCN2A, and SETD2, suggesting these mutations contribute to ASD risk. In several cases, the identified mutations and medical records suggest syndromic ASD diagnoses. Two ASD and one Fragile X premutation case showed deleterious somatic mutations, providing evidence that somatic mutations occur in ASD cases, and supporting a model in which a combination of germline and/or somatic mutations may contribute to ASD risk on a case-by-case basis.