FAQ's

The World of Genomic Literature at your Fingertips

A person on a laptop using Mastermind to conduct research for genes and variants.

FAQs

What is the Mastermind Genomic Intelligence Platform?

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.

Mastermind Overview
What is the source of evidence for Mastermind?

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).

How often is the Mastermind database updated?

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.

Can results change from day to day on the same search in Mastermind?

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.

Are genes and variants cited in the tables and figures of full text searches included in the Mastermind database?

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.

What browsers are currently supported by Mastermind?

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.

What happens if an article is behind a paywall?

Sentence fragments are displayed regardless of paywall status. Mastermind provides a link to the publisher’s site to view or purchase the article.

What is Genomic Language Processing?

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.

What is Genomenon's Genomic Graph

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.

Variant Nomenclature
Which types of variants can be searched in Mastermind?

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.

What variant formats and nomenclatures are supported in Mastermind?

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”

How do I search for SNVs/indels by genomic positions?

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.

See table here

How are insertions and deletions, nonsense, frameshift, and non-coding variants displayed in Mastermind?

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:

How and why does Mastermind group non-coding 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:

Can I search for mitochondrial variants or RNA variants in Mastermind?

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 Details
What are the differences between Mastermind CORE and Mastermind PRO?

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.

How sure can I be that a zero result means there are no articles that mention the variant I searched?

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.

Can I be notified if new articles are published that mention my gene/variant of interest?

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).

What are Related Variants?

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.

Does Mastermind take HPO terms as an input for phenotype search?

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.

How can therapies be searched in Mastermind?

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.

Can I include multiple phenotypes or other associations in a single search?

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.

Can the Articles list be sorted by date?

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.

How is Relevance determined?

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.

Can you search for titles and/or authors?

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.

CNV Searching
Can you search for HLA alleles including the HLA nomenclature for a high resolution HLA NGS data, including specific phenotypes?

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.

Does the Mastermind capture those CNVs from the large scale cancer genomics projects?

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.

Does Mastermind also work for fusions, inversions, and translocations?

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.

In addition to the CNV feature, is it possible to search according to the Tier classification for somatic variants?

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.

If I search for a deletion in a certain region, would it also show any duplication associated with that region?

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.

Do you index articles based on legacy exon numbering, as well as systematic versus custom exon numbering?

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.

How did you solve the problem which is caused by changes in the reference genome (different genome coordinates)?

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.

How are various transcripts accounted for in CNV search?

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.

How do you define a CNV?

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.

Can you search for other types of structural variations?

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.

ClinVar Integration
Can I link out to ClinVar from Mastermind?

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.

Does Mastermind match all cDNA changes for a specific protein change?

Yes, you can hover over the “information (i) icon to see more details on the Clinvar Record.

How do I find ClinVar variants in Mastermind?

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.

How often will ClinVar information be updated in Mastermind?

Weekly.

Does Mastermind index the current live version of the ClinVar database or a downloaded copy?

The ClinVar information is from a download copy of the database.

What ClinVar variants are included in the new Mastermind integration?

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).

Disease-Specific Curated Content
How should I cite Mastermind in my paper?

When referring to the use of Mastermind within a sentence, please use the following text: “Mastermind Genomic Intelligence Platform (https://www.genomenon.com/mastermind)”

Where does your population data come from?

Population data for curated variants is based on data from gnomAD v2.1.1.

Does Mastermind have curated content for every variant for a curated gene?

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.

Which variants have curated content?

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.

What part of the content is curated by humans?

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.

What is Disease-Specific Curated Content?

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.

Gene-Disease Relationships
What standards are used to assess Gene-Disease Relationships on the Gene Information Page?

You can view all standards used at this link

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How does Mastermind Compare

Mastermind
HGMD
ClinVar
Genes
19,332
18,959
17,570
Variants
24,108,330
541,457
2,602,372
Germline Variants
Yes
Yes
Yes
Somatic Variants
Yes
No
Yes
Journals
37,369
3,100
4,176*
Full-Text Articles Indexed
10,359,887
72,987
121,862*
Supplemental Datasets Indexed
3,362,377
N/A
N/A
Update Schedule
Weekly
Quarterly
Weekly
Free Version Content
Up to Date
3 Years Old
Up to Date
Interpretation Criteria
ACMG/AMP
Own Criteria
ACMG/AMP
ACMG Gene Curation Parameters
Yes
No
No
Clinical Exome Genes Curated based on ClinGen recommendations
Yes
No
No

Mastermind Plans

Mastermind CORE
Mastermind CORE - Freemium version of the Mastermind PRO Platform
Search 30M+ papers by gene and/or variant
Prioritize results by clinical relevance, date, & impact
See highlighted genes and variants in context
Sign Up Free
Mastermind PRO
Ideal for Clinical Decision Support
Prioritize results by relevance
Curated content for thousands of GDRs and variants
All the features of Basic, PLUS
Refine search results by ACMG criteria
Powerful advanced search capability
Unlimited searches, alerts, & article views
Export bibliographic search results
Go Pro
Data Licensing
Enabling Automation Services
Integrate into your pipeline for streamlined analyses
Access causative association between genes and diseases
Get variant level curated insights, following ACMG guidelines
Automated, real-time updates on highly sensitive data for every published variant
Available via flat data files and our API
Learn More

*Stats as of January 2025