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Gene Panel Sequencing Uncovers Role for Somatic, Mosaic Mutations in Brain Malformations

NEW YORK (GenomeWeb) – In a study appearing online last night in the New England Journal of Medicine, researchers based at Boston Children's Hospital and elsewhere described a suite of mosaic somatic mutations they detected in individuals with unexplained brain malformations.

The team used targeted, high-throughput sequencing to assess a few dozen genes with known or suspected roles in brain development in white blood cell DNA from 158 individuals with a range of brain malformations. The deep sequencing analysis — combined with follow-up validation testing — uncovered brain malformation-causing mutations in 27 of the patients.

Nearly one-third of those were somatic mutations affecting just a subset of cells in affected individuals, they noted, supporting the notion that such changes can be picked up by sequencing in a diagnostic setting.

"We were (pleasantly) surprised that somatic mutations represent a significant portion of identified mutations in undiagnosed brain malformations," first author Saumya Jamuar, a clinical fellow in pediatrics at Boston Children's Hospital, told GenomeWeb Daily News in an email message.

"Routine methods of Sanger sequencing and whole-exome sequencing are not designed to detect somatic mutations and systematically miss them," Jamuar added, noting that such genetic glitches are likely under-represented in past studies based on those techniques.

Somatic mosaicism is best documented in cancer samples, Jamuar and his colleagues explained. But glitches that occur during development and affect just a subset of an individual's cells are increasingly being implicated in the development or inheritance of other conditions, too.

In a study published in the American Journal of Human Genetics recently, for example, a Baylor College of Medicine-led team used long-range PCR to track down mutations in individuals with rare genomic conditions that had been passed on from an unaffected parent carrying a mosaic form of the same alteration.

For the current study, researchers focused on 158 individuals who had forms of brain malformation such as double-cortex syndrome, megaloencephaly, or pachygyria diagnosed by magnetic resonance imaging.

Using custom Illumina TruSeq kits, they captured genes from one of two genes panels from white blood cell DNA for each patient.

One of the gene sets was used to target 14 genes in individuals with brain malformations such as double-cortex, periventricular nodular heterotopia, polymicrogyria , or megalencephaly, Jamuar explained, while a gene panel composed of 54 genes was used to screen individuals for a brain condition called pachygyria.

After using Illumina's MiSeq to deep sequence these gene sets, the researchers began sorting through these sequences for signs of mutations that might explain each participant's brain condition.

All told, the team tracked down causal mutations in 27 of the cases, including germline glitches in the DYNC1H1, KIF5C, KIF7, KIF1A, and KIF26A genes that had not previously been linked to brain malformation.

Eight of those cases seemed to stem from somatic rather than germline alterations. Such mosaicism appeared somewhat more common in individuals affected by double-cortex syndrome, the study's authors noted. In that patient group, one-fifth of the mutations identified by sequencing the 14-gene panel were somatic, mosaic changes.

In general, the apparently pathogenic somatic mutations fell in and around the DCX, LIS1, TUBB2B, or FLNA genes and included at least three mutations that have been implicated in brain malformation in the past.

Not surprisingly, the ability to detect such mosaicism hinged on sufficient sequencing depths, since somatic mutations seemed capable of causing disease when present in as few as one-tenth of an individual's blood cells. Consequently, the study's authors argued that both Sanger sequencing and low-coverage exome sequencing would have missed many of the mosaic mutations.

"Until whole-exome sequencing with very high coverage is routinely available," they concluded, "gene panels permit a higher depth of coverage and cost-efficient detection of somatic variants."

Along with its implications for understanding the genetic basis of brain malformations, the current work is expected to impact the way future studies of other conditions are done.

In particular, Jamuar noted that somatic mosaicism may play an under-appreciated role in conditions marked by frequent de novo mutations such epilepsy and neuropsychiatric conditions including autism and schizophrenia.

Indeed, the authors of the current analysis hope to get a better sense of somatic mutation prevalence in such conditions in the future. They are also keen to begin translating findings from the brain malformation study to develop a diagnostic approach that complements existing sequencing tests based on Sanger or whole exome/genome sequencing.

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