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Study Proposes Method to Analyze Exomes for Pathogenic Variants Inherited from Mosaic Parents


NEW YORK (GenomeWeb) — Researchers from the Texas Scottish Rite Hospital for Children and the UT Southwestern Medical Center have published a description of their approach for analyzing exome sequencing data to identify candidate disease-causing mutations inherited by phenotypically normal mosaic parents.

In the study, which appeared earlier this month in the European Journal of Human Genetics, the authors proposed that such analysis could be an alternative or adjunct method for discovering genetic causes of rare human disorders when typical sequencing analysis strategies may fail to identify likely pathogenic variants.

Jonathan Rios, one of the study's two authors, told Clinical Sequencing News in an email this week that he and his colleague Mauricio Delgado set out to use the data from a typical exome sequencing experiment to try to see how many variants they could identify that fit a disease inheritance model in which an affected child inherits a dominant variant from a mosaic, unaffected parent.

While the incidence of such disorders is unknown, and likely very low, Rios wrote that it is possible that some rare unexplained recessive or suspected de novo genetic disorders could be explained by analyzing sequencing data in light of this inheritance model.

"Mosaic mutations, which have recently been described for many overgrowth syndromes, are a little trickier to identify from exome sequence," Rios wrote to CSN. "Compared to inherited mutations that are in every cell in the body … [less-frequent] mosaic mutations may be commonly missed in typical exome sequence analysis since the software programs that are used to identify mutations from exome sequence were modeled after identification of [other types of inherited mutations]."

In their study, Rios and Delgado sequenced the exomes of 13 parent-child trios from seven families and recorded how many candidate genes they were able to identify in each that fulfilled a model of dominant inheritance coupled with parental mosaicism.

They also applied their strategy to a quartet family in which two siblings suffered from hypomyelination with atrophy of the basal ganglia and cerebellum, or HABC, a disorder previously linked to a single de novo variant in the TUBB4A gene.

To look specifically for potential mosaic mutations, the researchers narrowed their exome sequencing analysis to only those SNPs with a low allele fraction in the parent, and thus a likelihood of mosaic status. According to their report, they considered only SNPs with an allele frequency lower than 0.3 in a single parent, as well as a heterozygous genotype in the child with an allele frequency over 0.3.

Rios explained that they did not expect to identify causal mutations in analyzing the 13 parent-child trios because these subjects did not fit a suspected mosaic-dominant inheritance model. Instead, they intended these families to serve as controls, to establish how many candidates this type of analysis would typically uncover.

On average, the authors reported, the strategy identified only about 17 genes per parent-child trio, and after excluding those variants that were annotated in dbSNP, which indicated that they were likely false positives, this narrowed down to about six novel candidate variants on average per trio.

In a separate investigation, Rios and Delgado also applied their approach to a quartet family, with two siblings diagnosed with HABC. This disorder has previously been associated with a single de novo causal missense variant in the TUBB4A gene in six families and three additional patients. It had also been confirmed in a family with a mosaic mother, in which it was passed down to two affected children.

In their analysis, Rios and Delgado hoped to demonstrate that they could also identify the same variant in their subject quartet by analyzing exome sequence data, without the need to consider or identify multiple affected families.

"Obviously if our approach identified the proper gene but also resulted in a couple hundred other genes, investigating the family alone would not have been sufficient," Rios wrote. "As it turns out, the disease gene was one of only a small number of candidates, and was the only candidate when considering both affected siblings. So our study suggests that a single family could be sufficient to identify the disease gene with this type of inheritance pattern."

According to Rios, the fact that the study also demonstrated that the dominant mosaic analysis approach identified only a modest number of candidate genes and variants for each trio, and did so reproducibly across all 13 trios they analyzed, implies that it shouldn't be difficult to add such a strategy to current analysis methods in the context of investigating suspected inherited genetic diseases.

"In this report, we show that [this type of analysis] could possibly be considered without an extreme burden for the investigator. It is important to note, however, that the number of candidate genes could be different depending on the exome capture kit used," Rios added.

In the published study, the researchers used a now outdated Illumina TruSeq exome capture kit, Rios explained. In preliminary analyses for other collaborators who used different capture kits, they have seen different results.

Overall, though, Rios said that he believes the results demonstrate that adding this type of analysis could potentially uncover the genetic cause of additional seemingly recessive or sporadic disorders with little added effort on the part of investigators.

"The literature is biased to 'low-hanging fruit' which typically represents dominant, recessive and de novo diseases because these are technically easy to detect and may result in lower numbers of candidate genes," he wrote. "The diseases with mosaic inheritance are likely to be a minority, but we do not really know … I think this is something else to consider in addition to typical analysis approaches."

Rios said the mosaic inheritance analysis approach has become part of his group's standard approach. "We investigate candidate genes resulting from this analysis along with [those from] dominant/recessive/de novo approaches depending on the suspected model in the family," he wrote.

"So far it has not turned up anything else, but again we do not know how many diseases in the world are caused by mutations that fit this pattern."