Variantyx Posts

Spotlight on Fragile X syndrome

fragile x syndrome

Fragile X syndrome (FXS) is one of the most common heritable forms of intellectual disability, occurring in approximately 1 in 4,000 males and 1 in 8,000 females. In nearly all cases, the causative mutation is an expansion of the unstable CGG repeat sequence present in the 5’ UTR of the FMR1 gene.

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Six variant interpretation strategies for NGS data analysis

variant interpretation

We’ve spoken frequently about variant detection, but variant interpretation is just as important to providing useful genetic testing results. Particularly in the case of whole exome (WES) and whole genome (WGS) analyses which identify thousands of variants. Here we focus on six key variant interpretation strategies that geneticists reviewing a case should have access to.

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Why 30X WGS beats 100X WES for variant coverage

variant coverage

We’re often asked why whole genome sequencing (WGS) is only performed at 30X coverage while whole exome sequencing (WES) is typically performed at 100X coverage. Isn’t 100X better than 30X? If we’re comparing apples to apples, the answer would logically be yes. But in reality we’re comparing apples to oranges, so the answer is not so intuitively no. Here’s why.

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Detecting large structural variants using WGS

structural variants

In this week’s post we’re taking a closer look at large (>50bp) structural variants, including copy number variants (CNVs). Previously, we’ve noted how whole genome sequencing (WGS) technology provides unique opportunities for detection of CNVs. But we’re often asked what specific types of structural variants are detected by WGS.

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In silico panels: An effective tool for performing targeted, outcome-driven analyses of WGS data

in silico panels

In our last post, we talked about the importance of periodically reanalyzing whole exome (WES) and whole genome sequencing (WGS) data for unsolved cases. An additional benefit of reanalysis of WGS data is that there’s no need to worry about coverage and changing pull-down kits as knowledge of exonic and regulatory regions of emerging importance grows. The full genomic sequence is already available. Which leads us to consider another related strength of WGS technology in this post: support for in silico panels.

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Periodic data reanalysis leads to higher diagnostic yield

data reanalysis

A case came to us in early 2017. The patient was an adult male with symptoms of muscle weakness along with limb girdle and distal inclusion body myopathy, with a suspicion of autosomal dominant inheritance. We process new cases all the time, sequencing the whole genome to obtain the most comprehensive coverage of variants possible. And for the subset that don’t receive a diagnosis following interpretation, we routinely subject them to periodic reanalysis. But this particular case was a data reprocessing project from the very beginning …

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