What's new in Genomics Platform!

Below you can read about the newest updates to the Genomics Platform. As always, we welcome your feedback. Please send an email to platform@rd-connect.eu


Release 1.6.0 (2018-04-19)


    Total number of samples in platform:3003

new


  • Matchmaker v1 integration, allowing internal matchmaking (i.e. within RD-Connect alone) and bi-directional external matchmaking (when samples have been confirmed as being matchable) with PhenomeCentral. More external matchmaking nodes will be added in the coming months.
  • Integration of protein-protein interaction data at the gene level from Mentha (https://mentha.uniroma2.it/) in a new Tab.
  • Users can now see who has been querying their samples in the GPAP via logs available in the data-submission interface.


  • improved


  • Updates to Data Submission interface, including allowing bulk metadata submission via TSV.
  • Aligned legacy username-password combinations for PhenoTips and GPAP so each user only has one pairing.




  • Previous Releases

    1.5.0 (2018-02-06)

    Total number of samples in platform:2605

    new


  • RD-Connect Internal variant allele frequencies are now displayed in the results and available to use as a filter.
  • Added an "Analysis Status" tab to allow users to indicate when they have completed their analysis of a particular sample, and add appropriate comments regarding the results of the analysis. This is particularly useful when analysis is being undertaken by more than one individual. There is also a checkbox to show that the sample has been analyed.
  • Pedigree trees, where available in PhenoTips are now directly visible in the Phenotype tab.
  • Added 4 new gene lists: 229 genes associated with leukodystrophy; short list of 1003 genes confirmed to be associated with Intellectual Disability; long list of 1,648 genes confirmed, or suspected to be associated with ID (both from SysID database); 387 genes associated with Pirmary Immune Deficiency, from BRIDGE-PID project.


  • changed


  • Sample selection auto-complete now lists the samples alphabetically.

  • improved


  • Sample selection does not permit the same sample to be selected twice.
  • A variety of small improvements to the GUI.
  • Some significant back-end efficiency improvements.


  • 1.4.0 (2017-11-14)

    Total number of samples in platform:2605

    new


  • Added ability to filter to variants that have been Tagged within the RD-Connect platform.
  • Added "Load" query button, for importing a shared query.
  • Added functionality in Genes, Disorders, and Phenotypes section to search a pathway in order to obtain a list of associated genes to use for filtering.



  • improved


  • Share query feature now returns a simple identifier, to be used when reloading query, rather than long URL previously used.


  • 1.3.0 (2017-10-25)

    Total number of samples in platform:2478

    new


  • Submission platform beta version open to selected testers
  • Added new "Pathways" tab, to the extended results section, displaying the pathways in which the selected genes are involved.
  • Added ability to choose between union and intersection operations for genes in the Genes, Disorders and Phenotypes Tab.
  • Added button in order to import HPO terms from the corresponding Phenotips entry and instantly return all the genes associated with these terms in the Genes, Disorders and Phenotypes Tab.



  • improved


  • Changed the style of the input fields in the Genes, Disorders and Phenotypes tab.
  • Increased the size limit of the "comment" section of the Tagged Variant field to 1,000 characters.


  • 1.2.0 (2017-09-18)

    Total number of samples in platform:2478

    new


  • Added "Clinical status" in Phenotypes tab.



  • changed


  • Upgraded Exomiser to current version (8.0.0).
  • Added horizontal scrollbar in 'Phenotypes' tab.
  • Changed text for various fields and ToolTips to make more self-explanatory.

  • improved


  • Retain indel variants in resultswhen filtering using SNV effect prediction tools e.g. SIFT, PolyPhen.
  • Added ability to remove an uploaded gene list.


  • 1.1.0 (2017-07-26)

    Total number of samples in platform:2124

    new


  • Added new tab "Phenotips" to the results section displaying the phenotypic information for the selected samples.
  • Added ability to upload a BED file of up to 400 regions and filter to these regions - see Chromosome Coordinates Tab.
  • Added ability to upload a file of up to 400 specific co-ordinates and filter to these positions - see Chromosome Coordinates Tab.
  • Added two new gene lists from the Decipher project - a list of genes confirmed to be associated with developmental disorders, and a longer list of both confirmed, and probably associated genes.

  • changed


  • Removed the older musclegenetable.fr gene list from 2015, leaving the 2016 list.


  • 1.0.0 (2017-06-19)

    Total number of samples in platform:2124

    new


  • Added ability to add extra HPO terms for Exomiser in addition to those fetched automatically from the PhenoTips entry.

  • changed


  • The gene name field now provides search results in real-time as you type.



  • improved


  • Users can now select multiple OMIM terms and obtain the genes associated to all of them.
  • Users can now select multiple HPO terms and obtain the genes associated to all of them.


  • 0.13.0 (2017-04-28)

    Total number of samples in platform:2124

    new


  • Integration of the Exomiser application in order to prioritize the candidate causative variants.
  • Added new link from transcript ID to "Human Splicing Finder", an in sillico predictor for mutations leading to splicing defects.



  • improved


  • Upgrade to elasticsearch version 2.4 and play2 framework 2.5.
  • Upgrade to ALFA release2 (ALFA2) which includes new fields: phastCons_mean_score, phyloP_mean_score, nearest_gene, nearest_transcript, nearest_transcript_bp.


  • 0.12.0 (2017-04-05)

    Total number of samples in platform:1955

    new


  • Added ability to filter by ClinVar classification.
  • Added ability to filter by transcript biotype.
  • Added ability to pre-select global stringency filtering (HIGH, MEDIUM, LOW).
  • Added ability to pre-select global ClinVar filtering.
  • Added new link from variant position to VarSome.
  • Added new link from variant position to ClinVar.
  • Added new column to the sample tab (called "User ID") with the external ID of each sample that links out to the Phenotips entry.

  • changed


  • The scroll of filter section has been simplified.



  • improved


  • We have increased the maximal number of samples to export results.


  • 0.11.0 (2017-03-07)

    Total number of samples in platform:1466

    new


  • Added functionality in Genes, Disorders, and Phenotypes section to search OMIM by ID, or disease name, in order to obtain a list of associated genes to use for filtering.
  • Added functionality in Genes, Disorders, and Phenotypes section to search HPO by ID, or phenotype, in order to obtain a list of associated genes to use for filtering.
  • Users can now see how many samples they have access to, how many they own, how many have been shared with them, and how many are visible to all registered users in the Sample Selection section.
  • Added 3 new pre-defined Gene Lists - Digenic genes, imprinted genes (confirmed), imprinted genes (suspected).

  • changed


  • The ExAC column in the results section now displays NA (instead of 0) if there is no ExAC annotation available. Currently this indicates that either ExAC did not cover this region OR that they filtered out the calls at that co-ordinate. In a future release we will include the frequency and an indication that the position was filtered.



  • improved


  • When adding a filter and rerunning a query, the platform now returns the user to the top of the first page of their results.


  • 0.10.0 (2017-02-14)

    Total number of samples in platform:1466

    new


  • Added ability to filter for variants occurring in an apparent Run Of Homozygosity in the "Chromosome Coordinates" Filter tab. Particularly useful if you suspect the case is the offspring of a consanguineous pairing.
  • Added "Share" button, which will generate a URL that you can share with collaborators that they can paste into the address bar, when logged-in to the platform, and see exactly the same filtration results that you saw.
  • Added ClinVar classification annotations to the main results section (November, 2016 release). In the near future we will also allow for filtering by ClinVar classification.
  • Added 3 new pre-defined Gene Lists - ACMG actionable, Medically Interpretable Genome, MitoCarta Version 2.0.

  • changed


  • We have updated our mapping and variant calling pipeline, following GATKs Best Practices, including indel-realignment and BQSR, using GATK version 3.6.
  • We have removed the Ensembl Gene Biotype filter, as this was not particularly useful, and will add the ability to filter by transcript biotype filter in an upcoming release.
  • As a result of the new annotation pipeline (see also below), we have changed a few of the fields in the "Functional" tab, incorporating some HGVS nomenclature where appropriate.

  • improved


  • We have updated our Annotation Pipeline to SnpEff 4.3 "ANN" annotations. In particular this adds variants identified as being involved in intra- or inter-protein interactions. Changes at such positions are always considered of HIGH impact, so you may see a handful more HIGH impact variants than previously when undertaking priortisaion. (see http://snpeff.sourceforge.net/SnpEff_manual.html) for more.
  • We have moved a few filters into more appropriate tabs e.g. SNV/INDEL selection is now within Variant Type.


  • 0.9.0

    new


  • Added new link from gene to "genome Aggregation Database"(gnomAD)
  • Added a feature that will return a list of all available samples which have a particular type of variant, in a particular gene or genes

  • changed


  • Links out to corresponding entries in Phenotips are now loaded automatically without having to run a filtration query

  • improved


  • Added a "gene" field into the flag-variant feature, allowing the researcher to select for which gene they believe a variant to be important when there is more than one possible option




  • 0.8.0

    new


  • Users can now search for samples using their own internal centre ID as well as the unique RD-Connect ID
  • Users are now prevented from accidentally selecting the same sample twice
  • Username is now shown in the header

  • changed


  • The musclegenetable.fr gene list has been updated to the current version

  • improved


  • We have reorganised the user-interface to make it more elegant and intuitive to use, with a more compact and responsive design that increases the number of filtered results that are displayed on screen




  • 0.7.7

    new


  • Data version and platform GUI version displayed on platform and associated to download
  • This What's New page
  • Added quick-view tab: Links to show which remote resources have information for a particular variant

  • changed


  • When return is pressed on the keyboard, this will now run a query, rather than resetting query settings

  • improved


  • Link added from Gene Name to PubMed
  • Link added from Position to GA4GH Beacon of Beacons