OMICS: Variant Interpretation as a Teaching Tool
Dexter Hadley, MD/PhD (Penn) · CANONIC Foundation
title: OMICS: Variant Interpretation as a Teaching Tool date: 2026-05-12 author: Dexter Hadley, MD/PhD (Penn) · CANONIC Foundation tags: [nex, abopm, omicsnex, variant-interpretation, multi-omics, all-tracks] scope: BLOGS _generated: true generator: gen-nex-fleet-doc (do_not_edit) — _generated by gen-nex-fleet-doc
Reading the reasoning, not just the verdict. A genetics fellow at Mount Sinai opens her laptop one afternoon in May 2026. She types in a missense change in BRCA1 that came back on a 39-year-old patient's panel that morning. The screen returns not a verdict but a paragraph: the 5 ACMG criteria that apply, the ClinVar entries the call is anchored to, the relevant CPIC guideline because the variant has pharmacogenomic implications, and the name of the board-certified geneticist who signed the interpretations she is reading across the seven omics layers her board certification will cover. The conventional read is that a variant call is a verdict — pathogenic, benign, uncertain. The actual rule is that the verdict is the easy part; the reasoning behind it is the part a candidate is expected to learn, defend, and pass on.
What the App Is
OMICS is variant interpretation built for teaching. Every interpretation is authored by a board-certified clinical geneticist, signed, and anchored to the public resources a candidate is expected to know on examination day — ClinVar for the variant, CPIC for the drug response, the ACMG criteria for the classification rules. The fellow does not just learn what the call is. She sees how the call was made.
OMICS covers seven layers of omics — the genome, the transcriptome, the proteome, the epigenome, the metabolome, the microbiome, and the exposome. Each layer is built in partnership with a laboratory that handles that kind of data in clinical practice. Each layer carries its own running record of interpretations so a reader can trace any call back to its anchors.
For a candidate preparing for the precision-medicine board, OMICS is the closest thing available to looking over a credentialled geneticist's shoulder.
ANKI, CASE, ONCO, and OMICS are the four apps a candidate uses to prepare for board certification in precision medicine. The figure is rebuilt from the same source files that drive the apps themselves.
Who Built It
Board-certified clinical geneticists author the interpretations. Authoring partnerships with laboratories across the seven omics layers are in place or pending.
What Is Verified About the Content
Every interpretation is signed by a credentialed geneticist and anchored to ClinVar and the ACMG variant-classification criteria. Pharmacogenomic implications cite CPIC. An interpretation without the anchors does not publish.
Where It Fits in Board Certification
OMICS contributes to every track of the ABOPM Foundation curriculum — molecular pathology, oncology, pharmacogenomics, genetic counseling, and Caribbean governance. The tracks are described in the chapters on each track inside the ABOPM book.
- Caribbean Governance (Ch. 15)
- Genetic Counseling (Ch. 14)
- Molecular Pathology (Ch. 11)
- Oncology (Ch. 12)
- Pharmacogenomics (Ch. 13)
What It Costs and How to Use It
Reading is free. Authoring is open to board-certified clinical geneticists. The first credentialed interpretation is expected to be published by the end of 2026.
Laboratory Partners
The seven omics layers are built with laboratory partners. Authoring partnerships are expected to be closed by 2026-07-27.
| Laboratory partner | Omics layer | Where the conversation stands |
|---|---|---|
| EPOCH | epigenome | Drafted; under negotiation |
| GENOVA | metabolome | Drafted; under negotiation |
| ILLUMINA | genome | Drafted; under negotiation |
| MOLECULAR_U | proteome | Terms agreed; signature pending |
| ORAL_DNA | microbiome | Drafted; under negotiation |
| PROGENEDX | transcriptome | Drafted; under negotiation |
| VIBRANT_WELLNESS | exposome | Drafted; under negotiation |
What Is Next
Open for reading now. The first credentialed variant interpretation is expected by December 2026.
The Real Variant Call
The real variant call is not the label at the top of the report. The real call is the paragraph that follows — the criteria invoked, the ClinVar entries anchored, the CPIC guideline cross-referenced. Reading the reasoning is what turns a verdict into a teaching tool.
The Wider Picture
ANKI, CASE, ONCO, and OMICS share one permanent record. A flashcard, a case, a tumor-board thread, and a variant interpretation all sit on the same trail of evidence a candidate, a reviewer, or a board member can audit. For the full architecture, see Chapter 16 — Four Apps for Board Preparation.
OMICS is the closest thing a candidate has to reading variant interpretation over a credentialed geneticist's shoulder.
Sources
| Claim | Source | Ref |
|---|---|---|
| ACMG/AMP variant-classification standards are the canonical framework for clinical variant interpretation | Richards et al. — ACMG/AMP variant interpretation standards (Genetics in Medicine) | pubmed.ncbi.nlm.nih.gov |
| ClinVar is the NIH public archive of clinical variant interpretations | ClinVar (NCBI) | www.ncbi.nlm.nih.gov |
| CPIC publishes pharmacogenomic guidelines mapping variant genotype to drug response | CPIC Guidelines | cpicpgx.org |
| BRCA1 missense interpretation draws on functional and population evidence curated in the BRCA Exchange | BRCA Exchange | brcaexchange.org |
| The exposome concept — non-genetic environmental exposures — is governed in the National Academies framework | National Academies — Exposome and Exposomics report | nap.nationalacademies.org |
| Illumina, the founding genome-layer laboratory partner, anchors sequencing-platform conventions for OMICS | Illumina | www.illumina.com |
| ABOPM Foundation curriculum tracks for molecular pathology, oncology, pharmacogenomics, genetic counseling, and Caribbean governance govern the OMICS scope | ABOPM book (CANONIC) | hadleylab.org |
OMICS | GENOMICS | ABOPM | BLOGS