FAQ's
The World of Genomic Literature at your Fingertips
FAQs
You can view all standards used at this link
When referring to the use of Mastermind within a sentence, please use the following text: “Mastermind Genomic Search Engine (https://www.genomenon.com/mastermind)”
Population data for curated variants is based on data from gnomAD v2.1.1.
Curated content is available for published variants in the canonical transcript of a curated gene. For variants that are unpublished or for which the published information provides no useful information for classification, curated content may not be available.
Currently, Disease-Specific Curated Content is available for over 230 unique disorders in Mastermind Professional Edition. A small subset of the curated content is available in Mastermind Basic Edition.
Before curated content becomes available in Mastermind, clinical genomic scientists review each article for evidence, ensure that the variant nomenclature is accurate and based on the canonical transcript, and apply ACMG interpretation criteria to the summarized evidence. The curated data then undergoes an extensive secondary QA review process before it is added to the Mastermind database. Our SOP for curated content can be found within the application (Genomenon Sequence Variant Interpretation Standards) or here.
Yes. Click the View in ClinVar button within the ClinVar tab to access the ClinVar record corresponding to the cDNA change of the searched variant.
Yes. In the ClinVar tab, use the drop down next to Select ClinVar Record to see all cDNA changes that map to the protein change in your search.
ClinVar variants can be found in Mastermind by searching the cDNA, protein change, genomic coordinates, or rsID nomenclature. They are displayed in the Variant Info section, and designated with a blue tab when available.
Weekly.
The ClinVar information is from a download copy of the database.
Yes. In the ClinVar tab, use the drop down next to Select ClinVar Record to see all cDNA changes that map to the protein change in your search.
Many. While Mastermind Basic and Mastermind Professional draw from the same source of data, there are important differences between the two versions. High-volume clinical users with more specific analytic needs would benefit from the Professional Edition. With Mastermind Pro, you have access to advanced search capabilities that include: genes, variants, CNVs, diseases, phenotypes, therapies, and user-defined free-text terms. These can be combined to perform multi-parametric searches using AND or OR operators (Boolean search). Pro users can refine their searches by applying Filter Categories, which include ACMG criteria and more. Searches in Mastermind Pro access supplementary data, ensuring a highly sensitive return of evidence. Articles can be sorted by Relevance, a Mastermind-specific scoring system that helps users save time and prioritize articles. In addition to the indexed data, Pro users have access to the entirety of manually curated gene-disease and variant classification information, with new curated data being continually added to the platform. Pro users have unlimited searches, article views, and Alerts. With Mastermind Basic, searches are limited to genes and/or variants only. Advanced search features (CNVs, diseases, phenotypes, therapies, free-text terms) are not available with the Basic edition. Results are not sorted by Relevance and are not filterable using Filter Categories. Articles with matches in the supplemental data will not be displayed to Basic users. While there are some curated data available to Basic users, the vast majority of the curated gene and variant information is only available in the Pro edition. Basic users are limited on the number of articles they can view each week (20), and the number of Alerts they can create in the system (5).
Quite sure. No search engine will ever achieve 100% sensitivity, but we believe Mastermind to be the most comprehensive source of genomic evidence available. By updating weekly, we keep pace with the rate of publication. See how Mastermind’s database compares to resources here.
Yes. You can set up an Alert in Mastermind to receive email notifications when new evidence is available for your gene/variant/disease. To create an alert for a search you’ve just launched, click “Create Alert for search” in the top right corner of the application. Under My Alerts, you can create a single Alert for multiple variants, or optionally include a disease. On the My Alerts page, you can edit/stop/view your Alerts, share Alerts with others at your organization, and set the cadence of notifications (weekly, monthly, quarterly).
Related Variants are displayed in the Variant Info section upon performing a variant search. Related Variants provides quick links to evidence for variants similar to your variant of interest. This is especially useful when little or no evidence is available for the variant you’ve searched. The algorithm that determines “relatedness” is based on a number of factors, including: position, variant type, amino acid properties, domain, and more.
Yes. Phenotypes including HPO terms can be used as search parameters for filtering and prioritization.
Mastermind can be used to search for coding variants including: missense variants; insertion, deletion, and indel variants; nonsense variants; frameshift variants; and copy number variations (CNVs). Mastermind will also search for non-coding variants affecting 5’- and 3’-untranslated regions (UTRs), splice donor/acceptor sites, splice regions, introns, as well as intergenic variants up- and down-stream of neighboring genes.
Mastermind recognizes variant information provided as cDNA, protein, genomic coordinates, rsID, legacy, and IVS nomenclature. Mastermind uses genomic language processing (GLP) to search the literature for all nomenclatures – standardized or not – and provides a highly sensitive return of references regardless of how individual authors might describe a variant in an article. For data display, variants in the Variants Table are shown as protein changes (ex – p.G1355D) to make it easier to find and interact with relevant articles. Mastermind also supports copy number variation (CNV) searching by karyotype, array nomenclature, genomic coordinates, and more. The system assumes coordinates are provided in GRCh38, however we accept coordinates in older builds by simply specifying that build (ex – hg18, hg19) at the end of the search. Deletion events are displayed in the search bar and CNV table as “del” and can be searched as: deletion of __________ del __________ loss of __________ Amplification events are displayed in the search bar and CNV table as “amp” and can be described as: amplification of __________ amp __________ duplication of __________ dup __________ gain of __________ Here are some examples of CNV below: ISCN karyotype – “46,XX,del(5)(q13)” or “dup(1)(p36p11)” Array – “arr[hg19] 7q36.3(158,583,829-159,119,707)x3” Genomic coordinates – “deletion chr11:1918222-1977026 hg18” Cytogenetic band – “del 11q23” or “loss of 11q23” Intragenic CNVs – “dup KMT2A exons 2-6” or “amp KMT2A exons 2-6” or “gain of KMT2A exons 2-6”
Mastermind recognizes variant information provided as cDNA, protein, genomic coordinates, rsID, legacy, and IVS nomenclature. Mastermind uses genomic language processing (GLP) to search the literature for all nomenclatures – standardized or not – and provides a highly sensitive return of references regardless of how individual authors might describe a variant in an article. For data display, variants in the Variants Table are shown as protein changes (ex – p.G1355D) to make it easier to find and interact with relevant articles.
Mastermind also supports copy number variation (CNV) searching by karyotype, array nomenclature, genomic coordinates, and more. The system assumes coordinates are provided in GRCh38, however we accept coordinates in older builds by simply specifying that build (ex – hg18, hg19) at the end of the search.
Deletion events are displayed in the search bar and CNV table as “del” and can be searched as:
- deletion of __________
- del __________
- loss of __________
Amplification events are displayed in the search bar and CNV table as “amp” and can be described as:
- amplification of __________
- amp __________
- duplication of __________
- dup __________
- gain of __________
Here are some examples of CNV below:
- ISCN karyotype – “46,XX,del(5)(q13)” or “dup(1)(p36p11)”
- Array – “arr[hg19] 7q36.3(158,583,829-159,119,707)x3”
- Genomic coordinates – “deletion chr11:1918222-1977026 hg18”
- Cytogenetic band – “del 11q23” or “loss of 11q23”
- Intragenic CNVs – “dup KMT2A exons 2-6” or “amp KMT2A exons 2-6” or “gain of KMT2A exons 2-6”
Mastermind supports GRCh37 and GRCh38 searches for SNVs/indels. Variants can be entered directly in the search box as shown below in GRCh37 and GRCh38, respectively:
NC_000001.10:g.94508323G>A
NC_000001.11:g.94042767G>A
To search for genomic coordinates in Mastermind, enter them in the search bar with the appropriate sequence identifier or modify the URL directly as in the example link below.
https://mastermind.genomenon.com/detail?mutation=(add chromosome here):g.94508323G>A
where (add chromosome here) can be taken from the list below and substituted into the URL.
Mastermind uses shorthand identifiers to represent different types of variants, which are displayed and searchable within the Variants table. The shorthands used by Mastermind are as follows:
- Insertions: “ins” — e.g. V600ins
- Deletions: “del” — e.g. V600del
- Indels: “delins” — e.g. V600delins
- Nonsense: “X” — e.g. V600X
- Frameshift: “fs” — e.g. V600fs
- Untranslated regions: “UTR” — e.g. 5’UTR or 3’UTR. Some genes contain introns within the untranslated regions; therefore a variant might belong to both the “UTR” and “int” groups simultaneously – e.g. 5’UTRint.
- Splice donor: “sd” — e.g. V168sd; these are variants affecting the 2-base region at the 5′ side of the intron. In the protein space, these are mapped to the nearest amino acid in the nearest coding neighbor at the 5′ side of the intron.
- Splice acceptor: “sa” — e.g. N581sa; these are variants affecting the 2-base region at the 3′ side of the intron. In the protein space, these are mapped to the nearest amino acid in the nearest coding neighbor at the 3′ side of the intron.
- Intronic: “int” — e.g. E46int; these are variants affecting any of the bases within the intron between the splice acceptor and splice donor sites. In the protein space, these are mapped to the nearest amino acid in the nearest coding neighbor.
- Intronic donor and acceptor sides: “intd” and “inta” — e.g. N581intd or N581inta; these are variants that occur in either the donor half or the acceptor half of the Intronic “int” variant region between the splice donor and splice acceptor sites. These are more specific sub-divisions of the “int” category, and so variants in either the “intd” or “inta” categories will appear in the “int” category as well.
- Splice regions: “srd” and “sra” — e.g. N581srd or N581sra; these are variants surrounding the splice sites, from 1 to 3 bases into the exon and from 3 to 8 bases into the intron. The intronic part of the splice regions overlap the intronic “int” classification as well, so splice region variants within the intron will also appear in the “int” and either the “intd” or “inta” categories as well.
- Upstream genetic variant: “ugv” — these are variants affecting the region of 5,000 bases upstream of the 5′ side of the gene.
- Downstream genetic variant: “dgv” — these are variants affecting the region of 5,000 bases downstream of the 3′ side of the gene.
- Extensions: “ext” — e.g. M1ext; these are variants extending the reference amino acid sequence at the N- or C-terminal end with one or more amino acids.
The graphic below shows the different regions for these groups of variants:
Mastermind group types of non-coding variants together to provide a highly sensitive return of evidence. Articles with an exact nucleotide-level match are prioritized on the list and designated with a crosshairs/target symbol, shown below:
PubMed – Full Text and Supplemental data. We index the titles, abstracts, and other PubMed meta-data for all articles, along with the full text and supplemental data of articles relevant to genomics and Mendelian disease. We have also integrated ClinVar as an additional source of evidence. Variants that have been submitted to ClinVar are available in Mastermind. This includes ClinVar variants where Mastermind has not identified evidence in the literature (zero articles returned).
Weekly. Mastermind performs weekly updates to its database by identifying the new content that has been published in the preceding week through PubMed and prioritizing this content for indexing.
Yes. Because Mastermind data is updated on a weekly cadence and genomic data indexing is ongoing, new data can be added to the search results as new articles are indexed.
Yes. Mastermind indexes the entirety of the full text in its search, including tables and figure captions. If data is contained directly in images, Mastermind does not index it. These instances tend to be rare and occur more often with much older articles.
Google Chrome is the preferred browser. We also offer a Chrome plugin called Mastermind Search Companion, which can be installed from the Chrome Web Store: https://chrome.google.com/webstore/detail/mastermind-search-compani/afjaifocdahgfpfgepaniahacjjoeeli If you do not have Google Chrome installed, you can download it by following the instructions here: https://www.google.com/chrome/. Mastermind is also accessible via Firefox, Safari, Internet Explorer, and Microsoft Edge – though some features may be limited.
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