modelscope·@de-grave/OneKGP
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Natural language access to 1000 Genomes Project dataset, hosted online in Dnaerys variant store
Dataset is sequenced & aligned to GRCh38 by New York Genome Center
real-time access to 138 044 724 unique variants and about 442 billion individual genotypes in 3202 samples
variant, sample, and genotype selection based on coordinates, annotations, zygosity
filtering by VEP, ClinVar, gnomAD AF and AlphaMissense annotations
filtering by inheritance model (de novo, heterozygous dominant, homozygous recessive)
Remote MCP service is available online via Streamable HTTP:
For local build with stdio transport see details below
MCP Server is implemented as a Java EE service, accessing 1KGP dataset via gRPC calls to public Dnaerys variant store service.
Answers below are from Sonnet 4.5: some from multi-agent Research system, some with extended thinking mode, and some from a single-agent system in normal mode.
Identify potential modifier variants for well-known pathogenic alleles in TTN - variants that consistently co-occur in the same haplotype block with pathogenic alleles and may alter severity or penetrance. Conduct research forpathogenic alleles documented in the literature.Use KGP dataset of healthy individuals to find potential modifier variants. Start with 100kb for "the same haplotype block" definition, then extend if required. Evaluate statistical significance for the best modifier candidates found. No initial constraints for modifier types.
Which variants in the HBB gene are unexpectedly tolerated in the KGP dataset with at least several annotation sources in agreement with regard to their expected pathogenicity ?
Which regions in POLR2A are most likely disease-critical, with strong purifying selection, based on available variation patterns across functional domains in KGP ? Do statistical evaluation.
In what cardiac related genes, e.g. ion channels, variants in KGP dataset near catalytic residues or ligand-binding pockets show strong depletion compared to flanking residues (20 amino acids) ?
Retrieve all variants in KGP dataset in the voltage-gated sodium channel gene family (SCN1A, SCN2A, SCN5A) currently classified as 'VUS' in ClinVar. Correlate their 'Likely Pathogenic' AlphaMissense classification with their frequency in this healthy cohort. Synthesize a reasoned argument to reclassify a subset of these as 'Likely Benign' based on the logic that pathogenic predictions by AlphaMissense are incompatible with the observed allele frequency in this healthy population.