kremerben / clinvitae

Technical Assessment for Invitae - invitae.com

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

URL	Description	HTTP
api/v1/variants/	Genomic Variant List	GET
api/v1/variants/:variant_id	Genomic Variant Details by Variant Id	GET
api/v1/gene/suggest/	Suggested Autocomplete search based on name argument	GET/POST

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:

Name	Type	Description
gene	integer	ID of related Gene.
id	integer	ID of Genomic Variant.
nucleotide_change	string	nucleotide change.
protein_change	string	protein change.
other_mappings	string	additional mappings.
alias	string	alias.
transcripts	string	transcripts.
region	string	region.
reported_classification	string	reported classification.
inferred_classification	string	inferred classification.
source	string	source.
last_evaluated	datetime	last evaluated datetime.
last_updated	datetime	last updated datetime.
url	string	html url.
submitter_comment	string	submitter comment.
assembly	string	assembly.
chr	string	chr.
genomic_start	string	genomic start.
genomic_stop	string	genomic stop.
ref	string	ref.
alt	string	alt.
accession	string	accession.
reported_ref	string	reported ref.
reported_alt	string	reported alt.

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

Name	Format	Description
name	string	Retrieve Gene's beginning with this string

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
    }
}