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Archive of posts filed under the NGS category.

Non-coding variant interpretation using GeneTalk

Variants in noncoding regions are always difficult to interpret on a genomic level . In a recently published article in Human Mutation entitled “Rare Noncoding Mutations Extend the Mutational Spectrum in the PGAP3 Subtype of HPMRS“ we present an approach for filtering pathogenic nonconding variants and explain how to interpret the implications of the variants [...]

39 novel pathogenic mutations for Usher Syndrome

It took us quite a while, but finally we got our paper accepted. That means 39 variants of unknown clinical significance can now be regarded as disease causing. You will find all annotations in GeneTalk, as well as in CinVar in one of the next releases.

comprehensive review about NGS data analysis in clinical context

Lyon and Wang wrote a very informative review about identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress in Genome Medicine .

From genetic privacy to open consent

In this article, we would like to tell you more about the three different levels of consent we currently support in GeneTalk. We think that a community creates its ethical values when informed individuals debate. Therefore, we would like to invite you to join our discussion! Personal consent Concerning your own genetic information, we take [...]

Artefact Blacklist

Nope, you don’t have to call a Code Blue!! This is not a life threatening fungal infection, it is just an artefact from static electricity on the imaging plate. Well, not only in radiography technical artefacts can make life miserable. In NGS data sets we know at least about 7 million commonly detected artefacts that we would like to [...]

1000 genomes is so yesterday

Genotypes frequencies of the popultation are the most powerfull filter for rare mutations, we all know that. That’s also why we had the genotype frequency filter that was based on the 1000 genomes data right from the beginning. If you set this filter to let’s say 0.5 you reduced your vcf file to genotypes that [...]