Mastermind Version 1.10 – Free Text Variant Search

Mastermind has been updated to version 1.10 and now features the ability to enter flexible variant nomenclatures including cDNA changes for both coding and non-coding variants in your search.

Searching and filtering by cDNA variant names for variants will further streamline user workflow for tertiary analysis and allow for greater confidence in search accuracy and relevancy.

Several example searches for protein coding changes including missense, frameshift, nonsense and deletion variants as well as non-coding changes are listed below. Splice acceptor changes and splice donor changes affecting the first or second nucleotides from the exon-intron junction are labeled as “sa” and “sd” based on the nearest protein position to the affected intron. Similarly, other intronic changes three or more nucleotides from this boundary are labeled “int” as below. This simplified query capability will ease identification of clinically relevant genomic articles using Mastermind.

Type of Variant Gene User-defined Search Mastermind Result
Missense BRAF V600E V600E
Missense BRAF p.Val600Glu V600E
Missense BRAF c.1799T>A V600E
Missense BRAF T1799A V600E
Frameshift CFTR K684Nfs K684fs
Frameshift CFTR K684Nfs*38 K684fs
Frameshift CFTR p.Lys684Asnfs K684fs
Frameshift CFTR Lys684Serfs K684fs
Nonsense CFTR G542X G452X
Nonsense CTFR p.G542* G452X
Deletion CFTR F508del F508del
Deletion CFTR p.Phe508del F508del
Deletion CFTR delF508 F508del
Deletion CFTR p.Phe508del F508del
Splice donor PAH c.441+5G>T P147sd
Splice acceptor PAH 442-1G>A P147sa
Intronic PAH c.441+47C>T P147int

These alternate variant nomenclatures will also be included in hyperlinks to Google Scholar searches for each variant searched in Mastermind.

Screen Shot 2018-01-04 at 11.59.24 AM

To date, Mastermind comprises over five and a half million full text genomic articles cataloguing the genetic relationships to human diseases. Mastermind is a continually improving tool that is revolutionizing tertiary NGS analysis. Please let us know if you have any questions or suggestions as you continue to use Mastermind.

Happy New Year to all. We at Genomenon are looking forward to many breakthroughs in 2018!

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