Annotation Sources 🗄️

Genome Nexus aggregates variant annotation from various sources. There are two types:

  1. Small sized annotations are stored as static data in the mongo database

    directly. See the genome-nexus-importer repo if you want to

    update/change this data.

  2. For larger annotation services/databases we either run the full annotation

    service ourselves or the program pulls on the fly from other APIs and caches

    the result in the mongo database.

For a list of all supported variant annotation sources see this Google Sheet:

https://docs.google.com/spreadsheets/d/1xML949NWzJGcvltjlquwSRIv79o13C_sfrVPAU5ci9Q/edit#gid=258442188

Versions

The static annotation sources are either stored directly in the mongo database or we run the annotation service ourselves. In both cases the version is guaranteed. For the dynamic annotion sources an external API is called and responses are cached on a per request basis. Given that the external API is outside of our control, no particular version is guaranteed, but we provide links to documentation of those APIs to find the currently live version.

Static annotation sources

Algorithm

URL

Version

VEP

https://grch37.ensembl.org/info/docs/tools/vep/index.html

grch37

Cancer Hotspots

https://www.cancerhotspots.org

From paper

3D Hotspots

https://www.3dhotspots.org/#/home

From paper

VEP includes various other annotations:

Source

Version (GRCh38)

Version (GRCh37)

Ensembl database version

97

97

Genome assembly

GRCh38.p12

GRCh37.p13

GENCODE

31

19

RefSeq

2019-01-30 (interim_GRCh38.p12_top_level_2019-01-25.gff3)

2015-01

Regulatory build

1.0

1.0

PolyPhen

2.2.2

2.2.2

SIFT

5.2.2

5.2.2

dbSNP

151

151

COSMIC

88

86

HGMD-PUBLIC

2018.4

2017.4

ClinVar

2019-04

2018-10

1000 Genomes

Phase 3 (remapped)

Phase 3

NHLBI-ESP

V2-SSA137 (remapped)

V2-SSA137

gnomAD

r2.1, exomes only (remapped)

r2.1, exomes only

Dynamic annotation sources

These annotation sources are pulled on the fly. The version number is not guaranteed given that the data is cached in the mongo database.

API

URL

Note

My Variant Info

https://myvariant.info

Includes many annotation sources, see https://docs.myvariant.info/en/latest/doc/data.html

Mutation Assessor

http://mutationassessor.org/r3/