Category Archives: Clinical genetics

Variant Interpretation with VSClinical: Evaluation of an X-linked recessive mutation

Overview VSClinical enables users to evaluate variants according to the ACMG guidelines in a high-throughput fashion and obtain consistent results and accurate variant interpretations. This feature is tightly integrated into our VarSeq platform as well, and when paired together, users can evaluate NGS data and obtain clinical reports all in one suite. Coupled with the ability to find novel or… Read more »

Variant Interpretation with VSClinical: Clinical Example for Congenital Indifference to Pain

VSClinical provides a rapid-fire way to investigate any variant’s impact by following the ACMG Guidelines process for classification. We will be demonstrating this by looking at interesting examples of rare disorders and showcasing some evaluation steps users may deploy in their analysis. Our first example in this blog series is for a patient who has an indifference to pain, while… Read more »

Clinical Variant Interpretation: Part VI

VSClinical algorithm

Functional Predictions and Conservation Scores in VSClinical Several algorithms have been developed to predict the impact of amino acid substitutions on protein function and quantify conservation of nucleotide positions. These methods provide vital supporting evidence to clinicians when interpreting variants in accordance with the ACMG guidelines. The two most popular functional prediction algorithms are SIFT and PolyPhen2, while the most… Read more »

Using GRCh38 for Clinical Interpretation: Now Possible with Our Custom LiftOver Tracks

There are many good reasons why the pursuit of the highest quality genomic interpretation would lead you to the latest human reference. It is more complete and fixes incorrect or partially missing genes that have known implications for human disease. While most major projects cataloging human populations have plans to re-do all their genomic alignments to the new human reference… Read more »

Revisiting the Five Splice Site Algorithms used in Clinical Genetics

Interpretation of variants in accordance with the ACMG guidelines requires that variants near canonical splice boundaries be evaluated for their potential to disrupt gene splicing [1]. The five most common tools for splice site detection are NNSplice, MaxEntScan, GeneSplicer, HumanSplicingFinder, and SpliceSiteFinder-like. Because these algorithms have been made easily accessible in the bioinformatics tool Alamut, they have been canonized for… Read more »