Ben Kremer - Technical Application

Clinvitae

Running live at: https://ben-kremer-clinvitae.herokuapp.com/

Clinvitae is a genomic variant web application that allows a user to search for genomic variants based on a gene name and display the results in a table.

To run this project locally

1. Clone repo
2. which python3
3. mkvirtualenv ben_kremer_clinvitae --python=<result from step 2>
4. cd ben_kremer_clinvitae
5. pip install -r requirements.txt
6. python3 manage.py migrate
7. Download variant_results.tsv file and place in management/data directory http://clinvitae.invitae.com/download
8. python3 manage.py loadtsvdata genomic_variants/management/data/variant_results.tsv
9. python3 manage.py runserver

Features

There are two components to the Clinvitae application, web UI access and API access (described below).

Clinvitae API V1 WIKI

The Clinvitae REST API provides simple access to read data in JSON format via HTTP GET/POST requests over http(s).

Endpoints

Genomic Variant List [GET]

Example: Genomic Variant List [GET]

https://ben-kremer-clinvitae.herokuapp.com/api/v1/variants/

Response

Paginated list of Genomic Variants, as described below

Genomic Variant Detail [GET]

Response

Single Genomic Variant object with the following properties:

Example: Genomic Variant Detail [GET]

https://ben-kremer-clinvitae.herokuapp.com/api/v1/variants/2/

{
    id: 2,
    gene: 2
    nucleotide_change: "NM_000018.3:c.1182+1G>A",
    protein_change: "",
    other_mappings: "NM_000018.3:c.1182+1G>A,NG_007975.1:g.8405G>A,NC_000017.11:g.7223238G>A,NC_000017.10:g.7126557G>A,NM_000018.2:c.1182+1G>A",
    alias: "",
    transcripts: "NM_000018.3,NG_007975.1,NC_000017.11,NC_000017.10,NM_000018.2",
    region: "NM_000018.3:IVS11",
    reported_classification: "Pathogenic",
    inferred_classification: "Pathogenic",
    source: "ClinVar",
    last_evaluated: "2014-05-15T00:00:00Z",
    last_updated: "2017-09-14T00:00:00Z",
    url: "https://www.ncbi.nlm.nih.gov/clinvar/RCV000077901",
    submitter_comment: "",
    assembly: "GRCh37",
    chr: "17",
    genomic_start: "7126556",
    genomic_stop: "7126557",
    ref: "G",
    alt: "A",
    accession: "NC_000017.10",
    reported_ref: "G",
    reported_alt: "A",
}

Gene Name suggests [GET]

Request Query Parameters

Example: Suggested Gene names [GET]

https://ben-kremer-clinvitae.herokuapp.com/api/v1/gene/suggest/?name=a

{
    results: [{
            id: "3142",
            text: "A1BG-AS1"
        },
        {
            id: "2927",
            text: "A1CF"
        },
        {
            id: "44",
            text: "AADAC"
        },
        {
            id: "2914",
            text: "AADACL2-AS1"
        },
    ],
    pagination: {
        more: true
    }
}