Category Archives: Clinical genetics

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 »

Case Study: iTARGET Autism Project

Dr. Suzanne Lewis is a Clinical Professor in the Department of Medical Genetics at University of British Columbia (UBC) and Senior Investigator at British Columbia Children’s Hospital Research Institute (BCCHR), Vancouver, Canada. She is also the Chair of the iTARGET Autism Project and Vice-Chair of Autism Canada Chief Medical Officer and VP Research of Pacific Autism Family Network. She and… Read more »

Clinical Workflows Webcast Q&A

Workflows in VarSeq

In case you missed our live event yesterday, I wanted to share the Q&A session and a link to the webcast recording: An Exploration of Clinical Workflows in VarSeq. Question:You mentioned saving projects as templates, will it save GenomeBrowse plots in the project template or do you have to replot the data when opening the software? Answer: Yes, if you save your… Read more »