Genomics & Variant Research

DeepCog's Genomics & Variant Research pipeline turns raw sequencing output into clinically-interpretable insight. GenomicLLM-7B ingests VCF files, annotates variants against reference knowledge bases, and applies ACMG/AMP classification criteria to produce structured, citation-backed interpretation reports — compressing what typically takes a molecular pathologist hours into minutes, with every call traceable to its evidence.

• VCF annotation — end-to-end ingestion of single-sample and joint-called VCFs, with functional annotation, population-frequency lookup (gnomAD), and transcript-level consequence prediction.
• ACMG/AMP classification — automated application of the ACMG 2015 criteria (PVS1, PS1-4, PM1-6, PP1-5, and benign counterparts) to classify variants as Pathogenic, Likely Pathogenic, VUS, Likely Benign, or Benign.
• VUS resolution — targeted evidence-gathering for variants of uncertain significance, surfacing in-silico predictions, segregation data, and functional-study references to help reclassify borderline calls.
• Phenotype-genotype correlation — links observed variants to associated conditions and inheritance patterns using OMIM, ClinVar, and HPO term mapping.
• ClinVar-ready reporting — generates structured interpretation reports formatted for clinical sign-out and ClinVar submission, with full citation trails.
• Multi-panel & exome scale — handles targeted gene panels through whole-exome datasets, prioritizing clinically-relevant variants for review.

• Live knowledge-base sync — annotation draws on regularly-refreshed ClinVar, gnomAD, and OMIM releases so classifications reflect the latest evidence.
• Reclassification alerts — flags previously-reported variants whose classification may change as new evidence enters the public databases.
• Full auditability — every classification decision is traceable to the specific ACMG criteria invoked and the source evidence that triggered them.