Sources

What this page is and is not

Varia's V1 catalog currently retains 49 variants across 12 domains. See the Variant Catalog for the full accepted list. The grading pipeline runs through scripts/editorial_grader/, but the product still depends on named outside authorities and named literature sources. This page exists so readers can inspect those sources directly.

This page is not a publication of Varia's database, not a list of every paper cited in the product, and not a roadmap for future findings. It is the compact public index of where Varia looks when it cites external material.

Peer-reviewed literature

Tier 1 anchor journals

The grading code names 7 Tier 1 anchor journals directly, and the wider conventions document expands those anchors into a broader editorial allowlist.

• Nature (Nature): Code-level Tier 1 anchor journal used as part of the direct allowlist that supports high-confidence editorial grading. Last reviewed by Varia: 2026-05-28.
• Cell (Cell): Code-level Tier 1 anchor journal used when Varia checks whether a citation clears the highest editorial source tier. Last reviewed by Varia: 2026-05-28.
• Science (Science): Code-level Tier 1 anchor journal used by the grading pipeline when source-caliber decisions are made. Last reviewed by Varia: 2026-05-28.
• New England Journal of Medicine (NEJM): Code-level Tier 1 anchor journal used for top-tier clinical literature in the editorial grader and source discipline. Last reviewed by Varia: 2026-05-28.
• JAMA (JAMA): Code-level Tier 1 anchor journal that helps define Varia's highest-confidence journal set. Last reviewed by Varia: 2026-05-28.
• Nature Communications (Nat Commun): Code-level Tier 1 anchor journal used to recognize high-caliber translational and population-scale genetics work. Last reviewed by Varia: 2026-05-28.
• Science Translational Medicine (Sci Transl Med): Code-level Tier 1 anchor journal used when translational evidence supports a user-facing editorial claim. Last reviewed by Varia: 2026-05-28.

Tier 2 working set

Tier 2 journals remain citable, but they receive closer editorial review before they are turned into user-facing claims.

• PLOS Genetics (PLOS Genet): Tier 2 journal accepted for citation when the evidence base is solid but not grounded in the Tier 1 anchor set. Last reviewed by Varia: 2026-05-28.
• PLOS Medicine (PLOS Med): Tier 2 journal accepted for clinically relevant literature that still fits Varia's journal standards. Last reviewed by Varia: 2026-05-28.
• PLOS Biology (PLOS Biol): Tier 2 journal accepted for mechanistic work when the conventions allowlist treats it as citable. Last reviewed by Varia: 2026-05-28.
• Genome Medicine (Genome Med): Tier 2 journal used for genomics papers that meet the broader editorial source rules. Last reviewed by Varia: 2026-05-28.
• Genome Biology (Genome Biol): Tier 2 journal accepted for population and methods work relevant to Varia's catalog. Last reviewed by Varia: 2026-05-28.
• Genome Research (Genome Res): Tier 2 journal accepted for genetics and genomics studies that support citable editorial claims. Last reviewed by Varia: 2026-05-28.
• Human Molecular Genetics (Hum Mol Genet): Tier 2 journal used for human genetics literature when the source still clears the conventions allowlist. Last reviewed by Varia: 2026-05-28.
• Neurology (Neurology): Tier 2 journal used for neurology-domain literature that fits Varia's citable source standards. Last reviewed by Varia: 2026-05-28.
• Molecular Neurodegeneration (Mol Neurodegener): Tier 2 journal used for neurodegeneration literature within Varia's editorial review process. Last reviewed by Varia: 2026-05-28.
• Neurobiology of Aging (Neurobiol Aging): Tier 2 journal used for aging and Alzheimer's-adjacent evidence that remains within the allowlist. Last reviewed by Varia: 2026-05-28.
• Translational Psychiatry (Transl Psychiatry): Tier 2 journal used for psychiatry and translational literature that still meets source-caliber rules. Last reviewed by Varia: 2026-05-28.
• Arteriosclerosis, Thrombosis, and Vascular Biology (ATVB): Tier 2 journal used for cardiovascular and vascular-biology evidence in the lipid domain. Last reviewed by Varia: 2026-05-28.
• eLife (eLife): Tier 2 journal used when the conventions file permits its inclusion as citable literature. Last reviewed by Varia: 2026-05-28.
• Atherosclerosis (Atherosclerosis): Tier 2 journal used for cardiovascular lipid evidence that supports user-facing interpretation. Last reviewed by Varia: 2026-05-28.
• Journal of Lipid Research (JLR): Tier 2 journal used for lipid metabolism and transport literature in the cardiovascular domain. Last reviewed by Varia: 2026-05-28.
• Aging Cell (Aging Cell): Tier 2 journal used for longevity and aging biology evidence that remains within the allowlist. Last reviewed by Varia: 2026-05-28.
• Pharmacogenetics and Genomics (Pharmacogenet Genomics): Tier 2 journal used for pharmacogenomic literature that supports medication-response interpretation. Last reviewed by Varia: 2026-05-28.
• Clinical Pharmacology and Therapeutics (CPT): Tier 2 journal used for pharmacogenomic and translational therapeutics evidence in Varia's PGx work. Last reviewed by Varia: 2026-05-28.
• Acta Neuropathologica (Acta Neuropathol): Tier 2 journal used for neuropathology evidence when the conventions allowlist treats it as citable. Last reviewed by Varia: 2026-05-28.

Variant catalogs and population frequencies

These reference datasets anchor variant lookup, population frequency context, and citation cross-checking:

• dbSNP (dbSNP): Reference SNP registry used to normalize rsID identity across source papers, scanner logic, and public-facing copy. Last reviewed by Varia: 2026-05-28.
• ClinVar (ClinVar): Clinical variant archive used for pathogenicity surfacing, review-status interpretation, and weekly change detection. Last reviewed by Varia: 2026-05-28.
• gnomAD (gnomAD): Population frequency reference used when Varia needs ancestry and allele-frequency context for variant interpretation. Last reviewed by Varia: 2026-05-28.
• 1000 Genomes Project (1000 Genomes): Population reference panel used as a named catalog in the public source list and broader genetics context. Last reviewed by Varia: 2026-05-28.

Clinical guidelines and authority bodies

Varia does not re-grade authorities that already publish their own clinical framework. Instead, it cites them directly and routes their outputs to the relevant product surfaces.

• ClinPGx (ClinPGx): Successor platform for CPIC and PharmGKB data after the March 2026 migration. Varia queries CPIC guideline levels and PharmGKB clinical annotations via api.clinpgx.org and watches github.com/clinpgx/clinpgx-data/releases for schema and content updates. Last reviewed by Varia: 2026-05-28.
• Clinical Pharmacogenetics Implementation Consortium (CPIC): Pharmacogenomic guideline authority; content and API access now route through ClinPGx (clinpgx.org, api.clinpgx.org). Legacy cpicpgx.org redirects. Last reviewed by Varia: 2026-05-28.
• PharmGKB (PharmGKB): Pharmacogenomics knowledge base; clinical annotation levels queried via ClinPGx API post-migration. Last reviewed by Varia: 2026-05-28.
• PharmVar (PharmVar): Star-allele nomenclature authority; event-driven release detection via RSS plus monthly fallback poll. Last reviewed by Varia: 2026-05-28.
• FDA Table of Pharmacogenomic Biomarkers in Drug Labeling (FDA PGx Table): Named U.S. regulatory source used on the sources page when Varia explains its pharmacogenomic authority chain. Last reviewed by Varia: 2026-05-28.
• HUGO Gene Nomenclature Committee (HGNC): Gene-symbol authority used when Varia needs canonical naming and symbol-drift correction in editorial tooling. Last reviewed by Varia: 2026-05-28.

ACMG Secondary Findings

Varia tracks the ACMG Secondary Findings (SF) gene list as both an authority reference and a change-detection source. The current list is ACMG SF v3.2 (Miller et al. 2023, Genetics in Medicine, DOI 10.1016/j.gim.2023.100866). Updates publish in Genetics in Medicine; Varia's ACMG SF detector subscribes to the journal RSS feed with an annual fallback poll per VEGS § 10.

• ACMG (ACMG SF v3.2): Secondary Findings recommendations list used for pathogenic-class surfacing context. Last reviewed by Varia: 2026-05-28.

Domain-specific consortia

Varia also relies on large collaborative programs that publish trait-level association data or maintain cross-study evidence infrastructure in focused domains.

• GWAS Catalog at EMBL-EBI (GWAS Catalog): Association catalog used by the algorithmic grader for cohort counts, effect direction, and genome-wide-significance context. Last reviewed by Varia: 2026-05-28.
• Alzheimer's Disease Genetics Consortium (ADGC): Named Alzheimer's consortium listed on the public sources page as part of Varia's domain-specific evidence stack. Last reviewed by Varia: 2026-05-28.
• International Genomics of Alzheimer's Project (IGAP): Named Alzheimer's consortium listed because Varia cites major collaborative evidence rather than single-lab prominence alone. Last reviewed by Varia: 2026-05-28.
• Global Lipids Genetics Consortium (GLGC): Named lipid consortium listed to show where large-scale cardiovascular association signals are aggregated and maintained. Last reviewed by Varia: 2026-05-28.

Build-time tooling

Some sources matter because they make the editorial workflow reproducible. These tools support lookup, normalization, and build reconciliation in the scripts layer.

• NCBI E-utilities (NCBI eutils): Build-time lookup tool used for PubMed verification, ClinVar support, and other reproducible editorial fetches. Last reviewed by Varia: 2026-05-28.
• UCSC liftOver (UCSC liftOver): Build-time coordinate-mapping tool used when Varia reconciles genome builds in scanner and editorial workflows. Last reviewed by Varia: 2026-05-28.

Closing note

This page is a named reference list, not a curation roadmap. Varia still applies its own public editorial discipline on top of these sources, and the rules for that discipline live on the Editorial Standards page. The operational details of how those sources feed the product live on the Methodology page.