FAQ's
The World of Genomic Literature at your Fingertips
FAQs
Mastermind is a comprehensive search and association engine to identify gene, variant, disease, phenotype, and therapy evidence from millions of scientific articles. These data are prioritized based on clinical relevance of the article’s content, and evidence of each citation is provided in the form of contextual sentence fragments from full-text literature.
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.
Sentence fragments are displayed regardless of paywall status. Mastermind provides a link to the publisher’s site to view or purchase the article.
Genomic language processing, or GLP, is the core technology behind Mastermind that normalizes and disambiguates the clinical and genomic information from the entirety of medical literature. Powered by GLP, Mastermind identifies every reference in every article in every way that an author could describe it, analyzes the genomic associations between each concept, and presents the data in an easily understandable interface.
Genomenon’s Genomic Graph (G3) is a Knowledge graph that organizes and connects genomic and biological information from published scientific literature, to help reveal connections and patterns that might otherwise remain hidden.
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/articles?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:
Mastermind indexes and returns articles for mitochondrial and RNA gene searches. We recommend then searching the variant as free-text. This can be done using the Boolean search with the operator OR between multiple variants or different nomenclatures for a single variant.
Mastermind CORE is the free version of the Mastermind PRO platform that provides users a way to explore and discover the features of the PRO edition, but for a limited set of genes. Mastermind CORE gives users access to: • Gene level intrinsic metrics and curated gene-disease relationships • Filters and advanced search criteria (phenotypes, therapies, etc…) • Articles for copy number variants (CNVs) • Curated variant content following ACMG criteria and much more... Mastermind PRO is the licensed version of the product that provides users the above for the entire database of curated and indexed genes and variants.
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 CORE users will only be able to search on phenotypes/diseases for genes included in the Mastermind CORE list.
Therapies are indexed by their unique ingredient identifier (UNII). They can be searched in Mastermind by brand name, generic name, UNII, or investigational name. Mastermind CORE users will only be able to search on therapies for genes included in the Mastermind CORE list.
Yes. Start by entering your first phenotype into the search bar. Enter the second phenotype into the search bar, and identify the desired term from the drop down list of suggestions. To manually add another phenotype to the search, press shift on your keyboard then click the term from the drop down list. You can then apply either “AND” or “OR” as an operator for your list of phenotypes. Click the highlighted operator in the search box to switch between and/or. All searches require Mastermind PRO and Mastermind CORE users to enter a gene/variant to search by phenotype(s)/other association(s). Additionally for Mastermind CORE users, the gene/variant must specifically need to be on the Mastermind CORE list.
Yes. Articles can be sorted by match count, publication date, journal name, or impact factor using the drop down on the top right corner of the Articles list, under Publication History. By default, articles are sorted by Relevance.
Mastermind’s Relevancy score is a set of algorithms used to prioritize articles by their relevance to a search and present the most relevant articles to the user. This incorporates numerous parameters intrinsic to each article itself (such as journal impact factor) and contextual evidence to the search being performed (such as where/how often the variant of interest is being mentioned). The final search results are then prioritized by combining the objective and contextual relevancy scores to list the most clinically relevant articles for your search. Additional information about Relevancy Scores can be found here.
Yes. In the Articles list, first click “Magnifying glass icon” to open the search bar, then you can filter the list of articles by article title, journal name, or author.
Searching for HLA alleles is possible using free-text search. Searching the gene of interest along with the allele as free-text is the recommended workflow. We do not currently index the HLA nomenclatures for use in the context of tissue typing.
If the results of these CNV studies are described in the full-text, they are captured in Mastermind. We are in the process of adding the supplemental data to our CNV indexing process as well. Please contact us at support@genomenon.com to bring to our attention any CNVs that are not captured so that we can address them.
Mastermind allows you to search for evidence pertaining to known fusion pairs (ex – NPM1 and ALK) using multi-parameter gene searching with “and” operator in addition to categorical keywords found under Genetic Mechanism>Fusion Events.
While Mastermind Genomic Search Engine does not itself have pre-categorized Tiers for CNV entries, there are a variety of search features that enable classification. For example – enabling filters under the ACMG Interpretation>Functional category will prioritize papers that discuss consequences of a searched-for CNV.
The default search functionality shows overlapping CNVs with the same effect (if you search a deletion, only overlapping deletions are displayed). If you want to see articles for either, you can perform a Boolean search for both the deletion and amplification, then set the operator between the two to “or”, which will show references citing either the deletion or amplification. The CNV list will also then show all overlapping CNVs of either deletion or amplification types.
We are aware of issues with legacy exon numbering, as we have handled similar issues with variants (such as IVS nomenclature with legacy intron numbering). For now, CNVs are normalized by matching the exon numbers to the longest transcript and mapping that to the GRCh38 reference build.
You can easily see legacy citations using different exon numbers by searching for deletions or amplifications of the entire gene, then sorting the CNV list based on start position to see references using alternate exon numbers. You could then click the legacy exon numbers and sort the article list by publication date to focus on older articles more likely using legacy numbering.
If you are aware of specific genes and examples of this issue, please reach out to support@genomenon.com and let us know so that we can consider incorporating corrections for the genes into our Genomic Language Processing pipeline.
We use GRCh38 by default for normalizing CNV references across different nomenclatures, but lift over coordinates from GRCh37 (hg19) when specified by either an author or user within their nomenclature.
Primarily for normalizing citations using gene-and-exon nomenclatures, we use the longest transcript for a gene mapped to GRCh38 for normalizing the citation to genomic coordinates.
Within Mastermind, a CNV is any structural variant described by authors using any accepted CNV nomenclature or description, including by cytogenetic band, ISCN karyotype notation, genomic coordinates, or genes and exons.
At this time, we are not optimized for trinucleotide repeats or some other types of structural variation. Contact us at support@genomenon.com if you have questions about CNV nomenclature/searching.
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, you can hover over the “information (i) icon to see more details on the Clinvar Record.
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.
All variants in the most recent ClinVar download are available in Mastermind. This includes ClinVar variants where Mastermind has not identified evidence in the literature (zero articles returned).
When referring to the use of Mastermind within a sentence, please use the following text: “Mastermind Genomic Intelligence Platform (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 1,000 genes in Mastermind PRO. A small subset of this content is available in Mastermind CORE.
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.
Disease-Specific Curated Content is a comprehensive and expertly curated set of variants for a gene. The variant data includes a summary of the published evidence, ACMG-based criteria applied to the evidence, and an ACMG-based provisional classification based on the evidence. The curated content also includes gene/transcript information, population data, in silico prediction models, and data intrinsic to the gene.
You can view all standards used at this link
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