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German, Iranian Team Combines Linkage, Sequencing to ID 50 New Genes Behind Intellectual Disability


By Julia Karow

An international research team has shed new light on the genetic underpinnings of autosomal recessive intellectual disability that could have diagnostic or treatment implications and may play a role in other neurological disorders.

Intellectual disability is genetically heterogeneous, and to a large extent, the underlying genetic defects are unknown, in particular for autosomal forms of the disease.

Now, a team from the Max Planck Institute for Molecular Genetics in Berlin and the University of Social Welfare and Rehabilitation Sciences in Tehran, Iran, has added 50 new genes to those already implicated in the disease, using a combination of array-based homozygosity mapping and targeted exon sequencing in 136 consanguineous families with autosomal-recessive intellectual disability.

The results, published this month in Nature, have immediate consequences for the affected families, might help diagnose other patients, and can assist in preventing the disease through carrier screening and prenatal diagnostics.

The findings might also be significant for other neurological disorders, such as autism, schizophrenia, and epilepsy, that sometimes co-occur in patients with intellectual disability and can be associated with mutations in the same genes.

Hilger Ropers, a director of the MPI for Molecular Genetics, said that once the genes are validated, he plans to add them to a sequencing-based test for the diagnosis of almost 600 rare childhood disorders that is being developed by his collaborator Stephen Kingsmore and colleagues at Children's Mercy Hospital (CSN 8/9/2011). Ropers said he hopes to introduce the test at the Charité hospital in Berlin, though he did not provide a timeline.

Most severe intellectual disability is caused by gene defects or chromosomal abnormalities, but for practical reasons, most research to date has focused on X-linked forms of the disease, which only account for about 10 percent of cases.

Part of the remaining cases are due to dominant de novo mutations, as demonstrated by a team of Dutch researchers last year, who used exome sequencing of family trios to identify such mutations in a number of patients (IS 11/16/2010).

Until now, little was known about the causes of autosomal recessive intellectual disability, which the German-Iranian team focused on in their study, partly because it requires large, consanguineous families that are rare in Western societies.

For their study, the researchers, led by Ropers, analyzed 136 consanguineous affected families, most of them from Iran. They had previously narrowed down the interval carrying the genetic defect in these families through homozygosity mapping with genotyping arrays. The size of the intervals, which depends on the number of affected family members, averaged about 10 megabases, Ropers said.

They then used custom-made Agilent SureSelect arrays to capture the exons in these regions, followed by sequencing on the Illumina Genome Analyzer.

From the sequence data, they called homozygous candidate mutations, including single nucleotide variants, deletions, and insertions, which they validated by array CGH or Sanger sequencing.

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Candidate genes were filtered against dbSNP, whole genomes from 185 healthy individuals from the 1000 Genomes Project, exomes from 200 Danish individuals, and at least 100 chromosomes from Iranian controls. Also, all candidate mutations co-segregated with intellectual disability in the families in which they were detected.

The researchers observed "plausible causal defects" in 115 of the families, and in 78 of them, they identified a single mutation that is likely disease-causing.

In 26 of these families, the mutation was in known genes for intellectual disability or related disorders. In another 52 families, the researchers identified putative causative mutations in a total of 50 genes that were not previously implicated in the disease.

Functional studies of those mutations and genes are ongoing in order to prove that they are indeed causative, though the authors believe that "the vast majority" of them are probably pathogenic because most of the proteins the candidate genes encode interact with other gene products associated with intellectual disability.

Ropers said that unpublished studies in Drosophila, conducted in collaboration with a group in Vienna, have already confirmed about a third of the mutations as causative.

Interestingly, the majority of the novel genes are not expressed specifically in the brain but have important general cellular functions, such as DNA transcription and translation, protein degradation, mRNA splicing, energy metabolism, and fatty-acid metabolism. That result was "a bit surprising," Ropers said, and the best explanation to date is that the brain is so complex in its development and function "that it's just more dependent on everything going right" than other organs.

Clinical Implications

In at least one family where the researchers identified a causative mutation, the result has immediate treatment implications: That family has a mutation in the folate receptor gene, a known cause of a syndromic form of autosomal recessive intellectual disability that can often be treated by taking folinic acid, Ropers said.

But there is also hope for developing treatments for patients with other genetic defects, he said. The pathogenesis of fragile X syndrome, the most common form of inherited intellectual disability, for example, has now been studied so extensively that researchers know where in the metabolism to intervene to treat it.

"This is really a paradigm for the entire field because it shows that these structural changes you see in the brain … can revert to normal once you normalize metabolism by adding drugs," Ropers said. "So the promise here is [that] these defects are not like a computer that is wrongly wired and won't function and can never be repaired, but there is a flexible structure of the brain."

That is not true, of course, for gross structural changes of the brain, he said, but it appears that many brain changes in patients with non-syndromic intellectual disability are "substructural" and probably reversible to some extent.

The Iranian researchers will also use their results to diagnose and counsel the affected families, he said, allowing them, for example, to undergo prenatal diagnostics.

According to Joris Veltman, an associate professor of genomic disorders at Radboud University Nijmegen Medical Centre in the Netherlands, the results will also help groups like his own diagnose patients with intellectual disability because they increases the number of known disease genes. "If we find a patient with a mutation in the same gene, this will significantly strengthen the diagnostic reporting, because we would be much more convinced that it is indeed linked to the cognitive disorder," he explained.

Veltman cautioned, though, that most of the new genes found in the study only occurred in a single family, and the researchers therefore need to be careful about reporting these back to patients without further validation.

According to Veltman, whose team conducted the family trio exome sequencing study published last year, the new findings are "really impressive" compared to older studies that took a long time and identified fewer causative mutations.

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The new study also complements his own work, he said, which focuses on dominant de novo mutations in mental retardation. "It is different from our hypothesis: we think that a lot of the cognitive disorders that we are looking at are caused by new mutations rather than recessive mutations. Both hypotheses are partly true — both explain part of cognitive disorders."

For both teams, it is now important to extend their work to larger cohorts, he said. "We really need to go in depth and look, perhaps, at 10,000 patients, studying the genomes or the exomes of patients and their parents, and then we will see how much is recessive and how much is dominant."

More Genes to Come…

Though the results of the study have vastly increased the number of genes linked to autosomal recessive intellectual disability, this is likely just the tip of the iceberg.

Based on the number of genes involved in X-linked mental retardation — 105 are known to date — hundreds of genes might play a role in non-syndromic autosomal recessive intellectual disability, and more than a thousand, if not several thousand, in non-syndromic as well as syndromic forms of the disease, Ropers said.

Finding these will be no easy task, and he advised researchers to "find ways that optimize the use of the money" available.

The approach his group took for its study — array-based homozygosity mapping followed by targeted sequencing of exons — differs from the whole-exome sequencing approach favored by many researchers studying genetic diseases these days. Ropers said this was a deliberate choice: "People are a bit too enthusiastic about exome sequencing because you are still likely to drown in this plethora of possible mutations," he said, and separating out the important ones is not trivial.

"It became clear to us that we would be very well advised to take into consideration all the additional information that we could get, be it linkage information or clinical information," he said, prompting them to adopt a more targeted approach.

While the cost difference between exome sequencing and mapping plus targeted sequencing is "marginal," he said, the success rate of their own approach is likely higher because it makes it easier to nail down the causative variant.

Others disagree about that. Veltman said his own group continues to sequence the exomes of patients and their parents, analyzing the data for both dominant de novo and autosomal recessive mutations. Developing targeted sequencing assays for each family is a lot of work, he said, and he therefore believes exome sequencing is a better approach.

In general, Ropers said, studying autosomal-recessive intellectual disability on a family-by-family basis will be more fruitful than genome-wide association studies, "because it is likely that all the families have different causes and you won't find them by these population-wide approaches; you will only find them in these families specifically."

The same approach, he said, can be applied to other neurological diseases like autism, epilepsy, and schizophrenia, where gene defects overlap with those causing intellectual disability.

Have topics you'd like to see covered in Clinical Sequencing News? Contact the editor at jkarow [at] genomeweb [.] com.

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