Over the past five years, sequencing studies of individuals with autism and their families have led to the discovery of about 100 high-confidence autism risk genes — a remarkable step forward in understanding the genetic basis of the condition. These studies have successfully gleaned many of the mutations most prominently involved in autism: the ones that, though rare, appear frequently enough to have made their role in autism unmistakable. Yet researchers estimate that 300 to 1,000 genes may confer risk for autism. To shake out these additional genes, the Simons Foundation Autism Research Initiative (SFARI) is pursuing a wide range of approaches.
One approach is simply to sequence more families. ‘Whole-exome’ sequencing — sequencing the protein-coding regions of the genome — remains an effective way to identify new autism risk genes and strengthen evidence for existing candidate genes, says Louis Reichardt, SFARI’s director. “It works, and there’s a lot more to be discovered there.”
To date, researchers supported by SFARI and other institutions have carried out whole-exome sequencing on about 6,000 families. A SFARI initiative called SPARK, or Simons Foundation Powering Autism Research for Knowledge, aims to raise that number to 50,000. “It’s a certainty that SPARK will enable new risk-gene discovery in autism,” says Wendy Chung, the initiative’s principal investigator.
Collecting genetic data from 50,000 families should not only reveal new rare autism mutations, but also jump-start the search for the common gene variants that affect autism risk — variants that, by definition, appear in at least 1 percent of the general population. These common variants are often harmless but can be damaging when joined with just the right combination of other common variants. “We know that collectively they impart a significant risk for autism, but for the most part we don’t know which ones they are yet,” Reichardt says.
Searching for common variants requires tens of thousands of samples. “If we get to 50,000, that dramatically changes what can be done,” Reichardt says. “To date we have not been able to find out much about common variants, but our knowledge is going to accelerate over the next year or so.”
Between 5 and 10 percent of children with ‘simplex’ autism may have somatic mutations.
Although sequencing tens of thousands of SPARK families is expected to be a key driver of future discoveries, there’s still a lot to learn from the roughly 2,600 families in the Simons Simplex Collection (SSC), a data repository launched by the Simons Foundation in 2007. Many of the early sequencing studies of the SSC focused on the exome, where it is most straightforward to find direct links between mutations and autism, but the exome represents only about 1.5 percent of the human genome’s 3 billion nucleotides. With support from SFARI, the New York Genome Center has completed whole-genome sequencing of the families in the SSC. Researchers hope this sequencing data will illuminate how the non-protein-coding regions of the genome — such as regulatory regions, which control where and how much a given gene is expressed — affect autism risk.
Researchers supported by the Simons Foundation are also taking a closer look at ‘synonymous’ mutations among individuals in the SSC — mutations that, by definition, don’t change the sequence of amino acids in the coded protein. It might seem, at first glance, that these mutations should not confer heightened autism risk, because they don’t change which protein gets created. Yet these mutations do sometimes affect either the ‘splicing’ or the amount of turnover of the messenger RNA molecules that carry the gene’s instructions to the ribosomes, the cell’s protein factories. These changes can in turn affect the amount of protein that gets created. “It’s important to try to find as many of these mutations as we can,” says Alan Packer, a senior scientist at SFARI.
Searching for somatic mutations
SFARI is also supporting research into ‘somatic’ mutations — ones that occur during development rather than at or before fertilization, and so appear in only a fraction of an individual’s cells. Several papers in the past year indicate that somatic mutations contribute significantly to autism risk.
Between 5 and 10 percent of children with ‘simplex’ autism — autism that affects no one else in their family — may have one of these somatic mutations, says Brian O’Roak of Oregon Health and Science University in Portland, whose team, with support from SFARI, has been combing the SSC for somatic mutations. So far, his research group has uncovered somatic mutations both in known autism risk genes and in novel genes that had not previously been connected to autism, but that are involved in biological pathways linked to the disorder.
Although somatic mutations may sound more benign than mutations that appear in every single cell, it’s possible the reverse is true. “Some of the somatic mutations we’re finding might be so bad that if they were in every cell, that would not be compatible with life,” O’Roak says. Sequencing SPARK families should clarify the role of these mutations, he says.
All told, the mutations identified so far by all methods explain about 20 to 25 percent of simplex autism, Packer says. “It’s fair to say that this number will only grow, and probably fairly rapidly.”