Frequently Asked Questions (FAQs)


1
What is the purpose of GeneMatcher?

To connect patients, their families, researchers, and clinicians around a shared goal - to identify novel disease genes and better understand rare diseases.


2
Who can be a part of the GeneMatcher community?

  1. Researchers
  2. Clinicians/Counselors/Other health care providers
  3. Patients and their families


3
How does GeneMatcher work?

GeneMatcher is a freely accessible web site developed with support from the Baylor-Hopkins Center for Mendelian Genomics as part of the Centers for Mendelian Genomics network.

GeneMatcher is designed to enable connections between patients, their families, clinicians and researchers from around the world who share an interest in the same gene or genes. The principal goal for making GeneMatcher available is to help solve 'unsolved' exomes. This may be done with cases from research or clinical sources.

The site allows individuals to post a gene (or genes) of interest and will connect individuals who post the same gene. Users create an account and submit gene(s) of interest (by gene symbol or base pair position). Users have the option, though are not required, to provide a variant (or variants) (by base pair position), diagnosis based upon OMIM® number, as well as to submit clinical features of the patient/family and add that to the matching criteria. The match is done automatically. When a match occurs, the submitters will automatically receive email notification. Follow-up is at the discretion of the submitters. It is also possible to query other Matchmakers (see MatchmakerExchange.org) to see if they contain matches. Upon entry to the site, the submitter will be prompted to select the database(s) and matching criteria.

If a match is not identified at the time of submission, the genes of interest will continue to be queried by new entries. Genes or gene lists may also be left on the site even after a match has been identified.

GeneMatcher adheres to strict safety and privacy protocols. Users must register to use the site. The database is not searchable and does not collect identifiable data. Submitters have access to their own data and full control over the contents including the options to edit or delete it at any time. Users may not access the full database, and may only search or view the data linked to their own account.


4
How are features matched?

Features are matched between submissions using the matching algorithm described in this paper:

Wang JZ, Du Z, Payattakool R, Yu PS, Chen CF. A new method to measure the semantic similarity of GO terms. Bioinformatics. 2007 May 15;23(10):1274-81. Epub 2007 Mar 7. PubMed: 17344234.


5
What does it mean to "match"?

A "match" occurs when a user finds another user with interest on the same gene or on phenotypically similar features. Users can choose to match any of the following or a combination of them:

  1. MIM number
  2. Gene Symbol
  3. Genomic Location
  4. Phenotypic Features


6
What happens after a user saves the submission?

Users will receive an email informing them of the presence or absence of a match in the database.

If there is currently no match in the database, the user will be notified and the submission will be stored in the database unless or until it is deleted by the user. In the future, if another user creates a submission that matches, both users will be notified of the match simultaneously.

If there is an instant match or the match takes place in the future, all the users involved in the match will be simultaneously notified. The email about the match includes the information that matched and the email contact of the users involved. The users can contact each other if they wish and ex-change more information about the gene, variant, mode of inheritance, phenotype, features, etc...


7
What does a positive match on a Gene Symbol mean?

If you match another user based of the Gene Symbol or any other information by itself, this is just the first step. The patients do not always have the same phenotypic features or the disease may not follow the same mode of inheritance. The next step is contacting the other users and exchanging more information. This is crucial to define if this is a complete match that can generate a new disease gene/phenotype association.


8
What is the next step if there is not a "match" based on the other information exchanged?

Users' entries will remain in the database for future matches that may solve their case. If a user determines that the entry does not represent the gene or variant causing the phenotype that the user is investigating, they may choose to remove or delete the submission.


9
What information is required to participate on GeneMatcher?

At least one of the following pieces of information is required:

  1. MIM number. This information can be updated in the Genetic Disorder section. Please add only one MIM number per entry.
  2. Gene Symbol. This information can be updated in the Results section. It is possible to add multiple Gene Symbols, however, please note that very few genes are the final candidates for each phenotype.
  3. Genomic Location. This information can be updated in the Results section as chromosome, start position and end position.
  4. Features. This information can be updated in the Family Members section by creating at least one family member, and then selecting the edit/add features link.


10
Important steps for patients to take before using GeneMatcher?

  1. Check to make sure the gene of interest is not already associated with a phenotype that is similar to the phenotype of interest by checking OMIM: https://omim.org. GeneMatcher is intended to match individuals with interest in the same novel disease gene candidate.
  2. Patients or family members should confirm that a health care provider (including the clinical laboratory that performed the test) did not already create a submission with the same novel disease gene candidate or with the phenotypic features of the same patient which may result in a match on the same patient.


11
What are Matchmaker Exchange repositories?

Matchmaker Exchange (MME) repositories are databases for genomic and phenotypic data related to novel diseases. Users are able to query these databases by using data received from GeneMatcher to conduct a match or search process in another database. As of today, the MME repositories do not accept a query directly from the patient. If you are a patient or family member and wish to query the other MME repositories, please contact a health care provider to create a submission and initiate the query.


12
Additional resources for patients and their families to connect with others with interest in the same gene(s) and/or phenotype(s) related to novel diseases.

13
How should I cite GeneMatcher?

Please use this citation:

Sobreira N, Schiettecatte F, Valle D, Hamosh A. GeneMatcher: A Matching Tool for Connecting Investigators with an Interest in the Same Gene. Hum Mutat. 2015 Jul 29. doi: 10.1002/humu.22844. PubMed: 26220891.

Another paper that discusses GeneMatcher is:

Sobreira N, Schiettecatte F, Boehm C, Valle D, Hamosh A. New tools for Mendelian disease gene identification: PhenoDB variant analysis module; and GeneMatcher, a web-based tool for linking investigators with an interest in the same gene. Hum Mutat. 2015 Apr;36(4):425-31. doi: 10.1002/humu.22769. PubMed: 25684268.