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How can I join DECIPHER?
There are two ways of joining DECIPHER, a) register a new project or b) as a member of an already existing project.
How do I join as a new project?
In order to request membership as a new project, visit the Join as a new project page and fill in the form. Membership of DECIPHER is open to academic centres of clinical genetics and research institutions that intend to deposit and share consented patient data with DECIPHER. Membership of DECIPHER is not required for searching/browsing existing anonymous consented information. We require the new project to have at least one senior clinician AND one senior lab scientist and a track record of relevant published research. These two key users are also required to be members of their respective professional bodies (e.g. American Society of Human Genetics). The senior clinician will be expected to assume the role of clinical coordinator for the project.
How do I join an existing project?
To join DECIPHER as part of an existing project, visit the Join an established project page and fill in the form. After receiving the application, DECIPHER will seek authorisation for membership from the coordinator of the centre. The coordinator will then grant read or read/write access to the user to a particular study(s) associated to that centre.
Can I request the creation of a new project if there is already one in my home institution?
We recommend that in this case you liaise with the existing project to explore if you can gain membership of that project. We are happy to consider creation of a new project at the same institution if the purpose or focus of the proposed project is different from the existing one.
What happens when I submit my new user joining form?
Once submitted, every joining form is reviewed by the DECIPHER team and then the coordinator of the project is emailed for authorisation. Once we receive authorisation from the coordinator, we will create an account and instructions for setting up the new account emailed to you directly. The process may take a week or so.
Can a non-clinician be a project clinical coordinator?
We prefer that only clinicians function as the project clincal coordinator. However, we make exceptions in cases where the project is a research study. A senior lab scientist, usually head of lab, can have the role of lab coordinator. Users with this role have the authority to approve new user requests to the project.
Can I access DECIPHER patient data without being a member?
Yes, anonymised genotype and phenotype patient data can be accessed via DECIPHER, Ensembl or UCSC without being a member.
What do I gain by becoming a member of the DECIPHER consortium?
By becoming a member of the DECIPHER Consortium users can:
- Add patient data into the DECIPHER database to make use of the bioinformatics tools provided for interpretation of patient aberration data. There is an implicit commitment that this data should be then shared with the community after obtaining appropriate consent from the patient so that other clinicians may view this patient data and new syndromes may be delineated.
- Access all data - consented and unconsented - from patients belonging to the DECIPHER study to which the user is registered.
- Print patient reports.
- Receive DECIPHER's monthly newsletter informing users of new features and developments.
My account is deactivated, is my data lost?
No. We will never delete any patient data deposited by a DECIPHER user regardless of whether the user still has access to his/her DECIPHER account unless the patient has requested it.
Can I download DECIPHER data for research purposes?
Anonymised consented DECIPHER data can be made available in the form of a downloadable encrypted file from a secure server under a data access agreement. Please see the section on data access agreement on the Data Sharing page.
Can I have DECIPHER data for Display in my own application?
DECIPHER data may be included in visualisation applications under a data display agreement. Please see the data display agreement on the Data Sharing page.
How do I cite DECIPHER for several patients I am using for my publication?
All publications that use data from DECIPHER are bound by our citation policy. Please see the Citing DECIPHER page for more information and guidance.
How many members can join a project?
There is no limit on the number of users per project. However, membership should be restricted to active clinicians and scientists and regularly reviewed by the project coordinator.
How many patients can I add to my project?
There is no limit in terms of the number of patients any project can have. However, since the overall aim of DECIPHER is to make anonymous consented patient data available for aiding collaboration and new findings, we expect most patients added to the project have been consented for sharing.
What is a project?
Projects in DECIPHER are either distinct physical institutions or collaborative efforts with users either in the same location or multiple locations. Each project contains a group of patients managed either at a specific location, under a specific research project or grant. Access to patients and the ability of add patient data is based on the rights each user has in the project.
What level of access is there for any given project?
Users may have different privileges in a study: some can just see the data (read access) and others can access and add patient data (read/write).
What are the different user roles in a project?
DECIPHER users fall into five user roles. These are:
- Clinical coordinator: Generally a senior clinician in the project takes over the role of clinical coordinator. This user is responsible for approving all new user requests to the project they manage. A project should ideally have only one clinical coordinator.
- Lab coordinator: A senior scientist, usually head of lab, who has authority to approve new user requests to the project. A project should ideally have only one lab coordinator
- Clinicians: Users who are consultants or senior clinicians fall in this category. Clinicians are assigned as the responsible contact for a patient record.
- Lab scientists: Any users in the project who are not clinicians but are involved in the generation and analysis of patient genetic data.
- Members: Users who are junior doctors, specialist registrars, nurses, genetic counsellors and others who do not fit into the other categories.
How do I consent a patient?
Once informed consent appropriate to local practices has been obtained, click on the check box that appears in the overview tab. The user must have write access to be able to edit any patient entry.
Are unconsented patients accessible to anyone outside my project?
No. Unconsented patients are completely inaccessible to users who do not have at least read access to the project that patient belongs to. In case the project is part of a consortium within DECIPHER, anonymised patient data plus any variants in that patient that are shared with the consortium will be accessible to other users of that consortium.
What is the effect of consenting a patient?
A consented patient becomes immediately accessible in DECIPHER. Ensembl and UCSC will show these after their scheduled data updates. Any user who searches DECIPHER will be able to see the anonymised entry for this patient. This patient also will appear among the matching patients of any other patient that is being viewed.
What types of variants can I deposit into DECIPHER?
DECIPHER accepts both copy-number variants (CNV) and sequence variant data with associated phenotypes. For depositing CNV data, you will require at minimum the following information - chromosome, start, end, mean ratio (or choose appropriate category from deposition form). For depositing sequence variants, you will require at least the following items - chromosome, start, reference allele, alternate allele and transcript identifiers.
How do I deposit sequence variants?
Please see the following short guide on help on depositing sequence variants.
I have many patient records to deposit, is there another way of doing this than one at a time?
Certainly! You can choose to use the bulk upload option. This will allow you to upload a large comma-separated value file or Excel spreadsheet with the patient information. Please download the templates files from the "Bulk Upload" section of your project overview page. Please choose the correct template based on the data you will be uploading.
What is the definition of copy-number variant and sequence variant in DECIPHER?
Variants that are less than 50bp are considered to be sequence variants while those exceeding this size are dealt with as copy-number variants. It is difficult to define the transition from one to the other since variation is a continuous spectrum and the decision is based on reasons of performance.
How can I search DECIPHER?
Users can search DECIPHER by location (e.g. 10:1-1000000), by phenotype (e.g. cleft palate), by band (e.g. 1q13), by gene (e.g. shank3) by entering the search terms into the search box accessible from all DECIPHER pages. A search using a combination of phenotypes and/or gene symbols is also possible. Please see "Search Examples" on the search box for ways to search DECIPHER. Please also see the following tutorial.
Can I search for my unconsented patient data?
Yes, but only if you are logged in and only for project you have access to. Search results will include results from your project(s) under a separate tab "Patients within your projects". All consented patients (including yours) will be under "Consented Patients". If you are not logged in, only the "Consented Patients" tabs will appear.
Can I visualize search results in the karyotype?
Yes, just click on the karyotype tab.
What are haploinsufficiency scores?
High ranks (e.g. 0-10%) indicate a gene which is more likely to exhibit the features of haploinsufficient genes, low ranks (e.g. 90-100%) indicate a gene is more likely to NOT exhibit haploinsufficiency. The manuscript describing the generation and validation of these haploinsufficiency predictions (Huang et al) is published in PLoS Genetics. Updated predictions of haploinsufficiency can be downloaded from our data download page.
How can I get hold of the haploinsufficiency scores used by DECIPHER?
An updated copy of the HI scores may be downloaded from the Data Downloads page.
What human genome assemblies does DECIPHER support?
DECIPHER currently supports only GRCh37. To convert to GRCh37 from your assembly, please use the NCBI Remap facility or UCSC LiftOver.
How are genes displayed in DECIPHER?
DECIPHER maintains a regularly updated list of known genes from HGNC with location information derived from Ensembl and UCSC. In addition DECIPHER also maintains a list of associated cross-references for these genes including OMIM and OMIM Morbid identifiers, among others.
What are DECIPHER syndromes?
A syndrome is the association of several clinically recognizable symptoms that often occur together. DECIPHER Syndromes are a collection of syndromes known to be caused by microdeletion or microduplication of regions of the genome.
Why is my syndrome of interest not included in DECIPHER?
DECIPHER syndromes are updated irregularly. We are actively working on improving our ability to keep DECIPHER syndromes current and exploring mechanisms to ensure they remain up to date. If you would like us to incorporate a new syndrome in DECIPHER, please email us with details of the syndrome you would like included along with a publication reference.
How do I contact the responsible clinician for a deposited patient?
From search results or matching patients click on the contact icon for the patient you are interested in getting more information about. Alternatively, from a patient page you can click on the "Contacts" tab to initiate contact with the depositing clinician.
I can't see the responsible clinician who deposited the patient. What am I doing wrong?
Depositing clinician emails are masked in DECIPHER for security reasons. If you are a registered user then you will be able to see the names of the clinicians but not their email addresses. Contact requests from unregistered users are facilitated by members of the DECIPHER team.
Are there courses for DECIPHER?
While we do not run specific DECIPHER couses, we welcome requests for members of the team to give seminars and teach on courses. Members of the team are usually represented at major genetics and clinical conferences around the world.
How can I contact DECIPHER team for reporting a bug or support?
Please email email@example.com or fill in the "Feedback" form on our website. We will endeavour to respond to your message within one working day of receipt of your message.
Is there a list of contributing centres?
A list of contributing projects in DECIPHER is available from our Statistics page.
I have a suggestion for improvement?
We welcome all suggestions for improvement! Please write to us at firstname.lastname@example.org or use the "Feedback" form on our website with your suggestions for improvement.
What is DDD?
DDD (Deciphering Developmental Disorders) is a UK-wide initiative aiming at analysing 12,000 patients affected with developmental disorders and their parents, using high resolution arrays and Next Generation Sequencing. The results will provide a unique, on-line catalogue (via DECIPHER) of genetic changes linked to phenotypes that will enable clinicians to diagnose developmental disorders.
Are DDD patients accessible via the DECIPHER?
DDD patients will be accessible via the DECIPHER interface in a similar way as consented patients and will in no way be identifiable as DDD patients. The DDD project periodically releases anonymised data for sharing based on their internal release criteria.
Can I join DDD?
DDD is an UK-based project recruiting only through UK NHS clinical genetics services and cannot accept samples from outside of the UK.
How can I know more about the DDD?
Please see the DDD UK website or email email@example.com.