With version 1.10, Mastermind now features a free text variant search field. Mastermind users can enter flexible variant nomenclatures including cDNA changes for both coding and non-coding variants in their search.
Searching and filtering by cDNA variant names for variants further streamlines user workflow for tertiary analysis, and allow for greater confidence in search accuracy and relevancy.
Several example searches for protein-coding changes including missense variants, frameshift variants, nonsense variants 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 are also included in hyperlinks to Google Scholar searches for each variant searched in Mastermind.
To date, Mastermind has indexed over 5.5 million full-text genomic articles cataloging the genetic relationships to human diseases. We are continuously improving Mastermind in our quest to revolutionize NGS analysis and connect patients’ DNA data with evidence from the scientific literature. Please let us know if you have any questions or suggestions as you continue to use Mastermind.
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Happy New Year to all. We at Genomenon are looking forward to many breakthroughs in 2018!