Online Services - Low Latency Genome Variant Store

1000 Genomes Project Dataset

The 1000 Genomes 30x on GRCh38 dataset (sequenced & aligned by the New York Genome Center) is available for real-time querying.

Connection Endpoints:

Protocol	Non-TLS (Port 80)	TLS (Port 443)
gRPC	`http://db.dnaerys.org`	`https://db.dnaerys.org`
gRPC-web	`http://db.dnaerys.org`	`https://db.dnaerys.org`
MCP	`http://db.dnaerys.org/mcp`	`https://db.dnaerys.org/mcp`

Dataset Composition: The cluster hosts 3,202 samples with 138,044,723 unique variants. This includes 2,504 unrelated samples from the Phase 3 panel and 698 related samples (1,598 males, 1,604 females total).

Data Annotations and Attribution

This dataset was annotated by:

Ensembl Variant Effect Predictor (VEP) software, developed by the Ensembl project at EMBL-EBI and the Wellcome Sanger Institute. Annotated with GENCODE Primary set. Data was used as provided.
AlphaMissense annotations, developed by Google DeepMind and EMBL-EBI, licensed under the Creative Commons Attribution 4.0 International License. Data was used as provided.
gnomAD AF annotations, derived from the Genome Aggregation Database, developed by the gnomAD consortium and the Broad Institute. Data have been used as provided in VEP cache in accordance with their terms of use (CC0 Public Domain Dedication).
ClinVar annotations, derived from public archive of interpretations of clinically relevant variants maintained by the National Center for Biotechnology Information (NCBI). The information is publicly available for use without restriction, as provided by the NCBI's data use policy. Data was used as provided.
Sequence Ontology variant consequence terms from the Sequence Ontology (SO), which are available under the permissive CC BY 4.0 license. The SO is developed as an open source project for the genomics community. Data was used as provided.
Annotation versions:
- VEP="v115.2"
  - cache="115_GRCh38" ensembl=115.266b84d ensembl-compara=115.ae48a7a ensembl-funcgen=115.57f7061 ensembl-io=115.25061d3 ensembl-variation=115.b7c2637 1000genomes="phase3" ClinVar="202502" assembly="GRCh38.p14" gencode="GENCODE 49" genebuild="GENCODE49" gnomADe="v4.1" gnomADg="v4.1"
- AlphaMissense thresholds
  - 'Likely benign' if score < 0.34, 'Likely pathogenic' if score > 0.564, 'ambiguous' otherwise;
  - see doi.org/10.1126/science.adg7492

Note

db.dnaerys.org is located Down Under. Please account for geographic latency.

Model Context Protocol

OneKGPd provides real-time access for LLMs to the 1000 Genomes Project Dataset.

Documentation, Source & Installation: github.com/dnaerys/onekgpd-mcp
Remote Service (Streamable HTTP): https://db.dnaerys.org/mcp

gRPC Queries

The following examples utilize gRPCurl. API is defined in dnaerys_1.17.4.proto file which needs to be available locally.

Query by Coordinates

homozygous & heterozygous variants from TP53 from all samples, limiting response by 10 variants

grpcurl \
  -proto dnaerys_1.17.4.proto \
  -d '{"chr":"17", "start":"7661779", "end":"7687546", "hom":"true", "het":"true", "limit":"10", "assembly":"GRCh38"}' \
  db.dnaerys.org:443 \
  org.dnaerys.cluster.grpc.DnaerysService/SelectVariantsInRegion

Query by annotations

pathogenic variants in TP53

grpcurl \
  -proto dnaerys_1.17.4.proto \
  -d '{"chr":"17", "start":"7661779", "end":"7687546", "hom":"true", "het":"true", "ann": {"clinsgn":"PATHOGENIC"}, "assembly":"GRCh38"}' \
  db.dnaerys.org:443 \
  org.dnaerys.cluster.grpc.DnaerysService/SelectVariantsInRegion

high impact heterozygous variants in transcripts in TP53

grpcurl \
  -proto dnaerys_1.17.4.proto \
  -d '{"chr":"17", "start":"7661779", "end":"7687546", "het":"true", "ann": {"feature_type":["TRANSCRIPT"], "impact":["HIGH"]}, "assembly":"GRCh38"}' \
  db.dnaerys.org:443 \
  org.dnaerys.cluster.grpc.DnaerysService/SelectVariantsInRegion

pathogenic heterozygous variants in sample (NA10842) in TP53

grpcurl \
  -proto dnaerys_1.17.4.proto \
  -d '{"chr":"17", "start":"7661779", "end":"7687546", "het":"true", "samples":"NA10842", "ann": {"clinsgn":["PATHOGENIC"]}, "assembly":"GRCh38"}' \
  db.dnaerys.org:443 \
  org.dnaerys.cluster.grpc.DnaerysService/SelectVariantsInRegionInSamples

Sample Selection

Select samples with pathogenic heterozygous variants in transcripts in TP53 with gnomAD exomes AF < 0.0001

grpcurl \
  -proto dnaerys_1.17.4.proto \
  -d '{"chr":"17", "start":"7661779", "end":"7687546", "het":"true", "ann": {"feature_type":"TRANSCRIPT", "clinsgn":"PATHOGENIC", "gnomad_exomes_af_lt":"0.0001"}, "assembly":"GRCh38"}' \
  db.dnaerys.org:443 \
  org.dnaerys.cluster.grpc.DnaerysService/SelectSamplesInRegion

Inheritance Model

De Novo: All de novo variants in chromosome 1 in a trio classified as likely pathogenic by AlphaMissense

grpcurl \
  -proto dnaerys_1.17.4.proto \
  -d '{"parent1":"HG00418", "parent2":"HG00419", "proband":"HG00420", "chr":"1", "start":"1", "end":"248956422", "ann": {"am_class":"AM_LIKELY_PATHOGENIC"}}' \
  db.dnaerys.org:443 \
  org.dnaerys.cluster.grpc.DnaerysService/SelectDeNovo

Homozygous Recessive: All homozygous recessive variants in chromosome 1 in a trio classified as likely pathogenic by AlphaMissense

grpcurl \
  -proto dnaerys_1.17.4.proto \
  -d '{"unaffected_parent1":"HG00418", "unaffected_parent2":"HG00419", "affected_child":"HG00420", "chr":"1", "start":"1", "end":"248956422", "ann": {"am_class":"AM_LIKELY_PATHOGENIC"}}' \
  db.dnaerys.org:443 \
  org.dnaerys.cluster.grpc.DnaerysService/SelectHomRecessive

Heterozygous Dominant: All heterozygous dominant variants in chromosome 1 in a trio classified as likely pathogenic by AlphaMissense

grpcurl \
  -proto dnaerys_1.17.4.proto \
  -d '{"affected_parent":"HG00418", "unaffected_parent":"HG00419", "affected_child":"HG00420", "chr":"1", "start":"1", "end":"248956422", "ann": {"am_class":"AM_LIKELY_PATHOGENIC"}}' \
  db.dnaerys.org:443 \
  org.dnaerys.cluster.grpc.DnaerysService/SelectHetDominant

References

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