Clinical pedigree drawing: a pedigree tool for genetic counsellors and clinical geneticists

Short version. Clinical pedigree drawing demands a tool that enforces NSGC 2022 notation, captures three generations efficiently, supports consanguinity loops and pregnancy outcomes, exports in standards-grade formats (GEDCOM, PED, Phenopackets v2, CanRisk), and keeps the boundary between drawing/documentation and clinical-grade risk computation explicit. Evagene addresses this brief from the research-and-education side of that boundary, and routes to canrisk.org for clinical-grade BOADICEA and to the IBIS binary for the official Tyrer-Cuzick.

What clinical pedigree drawing demands of a tool

The clinical pedigree is denser than a genealogy tree. Each individual carries sex assigned at birth, gender identity (where relevant), affected status for each catalogued condition, age at diagnosis, deceased status with cause and age, carrier status, consanguinity links, pregnancy outcomes (live birth, miscarriage, termination, stillbirth) with gestational age, adoption status, and the proband marker. The structural relationships have to encode partner connections, sibship birth order, monozygotic and dizygotic twins, and consanguineous unions drawn as double horizontal lines. Drawing all of this by hand is slow and inconsistent; drawing it in generic diagram software is worse. The tool category emerged because the cognitive load of correct notation outstrips what an unstructured canvas can support.

Specialists evaluating a pedigree-drawing tool typically check the following:

• Notation enforcement. The tool produces NSGC-compliant symbols by default, not as an option, so that the artefact is immediately interpretable by any clinician trained on the standard.
• Three-generation capture. Adding the proband's generation, parents, and grandparents (with sibships, partners, and offspring) is fast and stays visually clean as the family grows.
• Consanguinity, twins, pregnancy outcomes. The tool draws double horizontal lines for consanguinity, distinguishes monozygotic from dizygotic twins, and represents miscarriage / termination / stillbirth with gestational-age annotation.
• Disease annotation against a structured catalogue. Affected-status annotations should resolve against ICD-10, OMIM, HPO, and gene symbols (HGNC), not free text. Free-text disease names break downstream analysis.
• Risk-model implementations. The tool runs published family-history risk-model algorithms directly on the pedigree without re-entry, while being explicit about which computations are illustrative and which are routed off-platform to canonical sources.
• Standards-grade export. GEDCOM 5.5.1, PED, Phenopackets v2, CanRisk, and PDF/PNG/SVG, so that the pedigree leaves the tool in a vendor-neutral form.
• Sensible defaults around data residency. Family-history information involves multiple individuals; a tool that processes pedigrees client-side avoids the question of whether third-party storage is appropriate for teaching, research, or family-documentation use.

NSGC 2022 notation, in practice

The NSGC update published in 2022 is the current reference. It builds on Bennett and colleagues (1995, with subsequent updates) and addresses a long-standing tension in pedigree drawing: the square / circle / diamond convention maps to sex assigned at birth and tracks inheritance through the X and Y chromosomes, but it had sometimes been applied as a statement about gender identity. The 2022 update keeps the structural meaning of the symbols, adds explicit notation for trans and non-binary individuals, and clarifies when separate annotation for sex assigned at birth and gender identity is appropriate. The detail is covered in our NSGC pedigree notation guide and in the broader standard pedigree nomenclature reference.

The core conventions remain stable across the 1995, 2008, and 2022 updates: squares for males, circles for females, diamonds for unknown or unspecified sex; filled (shaded) symbols for affected individuals; a diagonal line for the deceased; an arrow for the proband; horizontal lines for partner connections; double horizontal lines for consanguineous unions; vertical descent lines from the partner line to the sibship; small triangles for miscarriage and termination, with gestational-age annotation; brackets for adoption; central dot or half-fill for carrier status, depending on the carrier convention in use. A clinical pedigree tool encodes all of these as first-class structural elements, not as decorative annotations.

Risk-model implementations: where the boundary sits

Pedigree-based risk-model algorithms originated as research code; some have been wrapped into clinical-grade web applications that the genetics community uses directly. The boundary between an in-tool implementation (suitable for research, teaching, and exploration of published methods) and the canonical clinical-grade computation matters, and Evagene draws that boundary explicitly.

BayesMendel BRCAPRO, MMRpro, PancPRO. Evagene includes implementations of these BayesMendel algorithms running directly on the pedigree. BRCAPRO estimates the probability of carrying a pathogenic BRCA1 or BRCA2 variant from the family-history pattern of breast and ovarian cancer; MMRpro does the analogous calculation for MLH1 / MSH2 / MSH6 / PMS2 in Lynch syndrome; PancPRO addresses familial pancreatic cancer. Outputs are illustrative and intended for research and teaching. The original BayesMendel R packages remain the authoritative source.

Tyrer-Cuzick approximation. Evagene's Tyrer-Cuzick implementation is an IBIS-style approximation of the published Tyrer / Duffy / Cuzick 2004 algorithm. The official IBIS Breast Cancer Risk Evaluator binary — whose full coefficients are not public — is the authoritative implementation, and it is the appropriate tool when a Tyrer-Cuzick computation is needed for clinical purposes. We label this on every page that mentions the model.

BOADICEA via CanRisk export. BOADICEA is licensed by the University of Cambridge and is not bundled in Evagene. Evagene exports a ##CanRisk 2.0 pedigree file that the user uploads at canrisk.org for the canonical computation. The off-platform pattern is positive evidence of architectural separation between pedigree drawing / documentation and clinical-grade computation, and it is the canonical workflow when BOADICEA output is needed.

Mendelian inheritance and family-history scoring. Evagene includes Mendelian inheritance calculators (autosomal dominant, autosomal recessive, X-linked dominant, X-linked recessive, Y-linked, mitochondrial) and a set of family-history scoring tools described in published literature (Manchester scoring, Amsterdam II, revised Bethesda, NICE CG164 / NG101 referral criteria as illustrative thresholds). All outputs are framed as illustrative descriptions of what the published algorithm produces from the family-history pattern; they are not platform recommendations.

Detailed worked examples for each model are available in hereditary cancer risk assessment and the Mendelian inheritance calculator page; for the BOADICEA bridge specifically, see CanRisk vs Evagene.

Three-generation capture and consanguinity

The minimum effective family-history record is a three-generation pedigree from the proband. Evagene's gesture-based drawing mode is designed to make three-generation capture fast in real time during a teaching session, a research-data review, or an alpha-tester walkthrough; partners, parents, siblings, aunts, uncles, and first cousins can be added with a small number of consistent gestures, and the tool maintains a clean layout as the family grows.

Consanguinity loops are a notable test case for any pedigree tool. A double-horizontal-line union between cousins, plus the resulting offspring with their carrier-state implications, has to render correctly without manual intervention; Wright's coefficient of inbreeding is then computable directly from the structure. Evagene includes consanguinity detection with Wright's coefficient as part of its standard family-structure analysis. Where a closed loop produces ambiguous descent, the tool flags it for the user to resolve rather than rendering an incorrect structure silently.

Disease annotation against the catalogue

Affected status by itself is not enough; specialists need to know which condition. Evagene annotates affected individuals against a curated catalogue of more than 200 monogenic, complex, and polygenic conditions, mapped to ICD-10, OMIM, and HPO codes; the broader help-catalogue extends to over 1,900 entries across diseases, traits, allergies, clinical tests, markers / genes, and treatments, with cross-references to LOINC, NCBI Gene, ClinVar, RxNorm, BNF, and DrugBank. Annotation against a structured catalogue is what enables downstream analysis; free-text disease labels break batch family-history risk screening, inheritance-pattern identification, and any computation that depends on knowing the condition's expected inheritance.

The catalogue is browseable at evagene.net/help. For a research view of how it covers complex/polygenic conditions, see complex-disease pedigree software.

Standards-grade interoperability

A clinical pedigree should never be locked into a single tool. Evagene supports interchange in both directions:

• GEDCOM 5.5.1 import and export — the de facto interchange format for family-structure data.
• PED for linkage and population-genetics workflows.
• Phenopackets v2 (GA4GH) for phenotype-aware exchange — see phenopackets and pedigree data.
• HL7 FHIR FamilyMemberHistory for downstream consumption by systems that choose to receive structured family-history data — see HL7 FHIR and pedigree data. This is a static export pattern; Evagene does not present itself as a clinical-workflow integration.
• CanRisk 2.0 for the off-platform BOADICEA bridge.
• 23andMe import as a structured starting point for trait and ancestry context — see 23andMe pedigree import.
• Pedigree OCR for reconstructing structured pedigrees from a hand-drawn or scanned pedigree image — see pedigree OCR.
• PDF, PNG, SVG exports for printable artefacts and inclusion in slides, teaching materials, and research notes.

The REST API and the Model Context Protocol server provide programmatic access for research and tooling-integration use cases.

Outputs: what Evagene generates and what it does not

Evagene produces educational and research artefacts:

• A printable pedigree (PDF, PNG, SVG) with full NSGC-compliant notation.
• A structured family-history record (GEDCOM, PED, Phenopackets v2, CanRisk, HL7 FHIR FamilyMemberHistory).
• Illustrative outputs of published family-history risk-model algorithms.
• AI-assisted draft summaries that describe the pedigree structure and the inheritance patterns visible in the recorded family. Draft summaries are presented for the user to review and use for teaching, research notes, or family-history documentation; they are not intended to replace, augment, or support professional clinical judgement, and they do not generate diagnostic, screening, or referral recommendations.

Evagene does not generate clinical decision support, prescriptive screening recommendations, prescriptive testing recommendations, or any output framed as a recommendation issued by the platform. Where published guidelines describe thresholds (for example, NICE CG164 / NG101 referral criteria), Evagene illustrates how the family-history pattern relates to those published thresholds; it does not issue referral instructions of its own.

For the canonical positioning statement, see the terms of service.

How Evagene compares with other clinical pedigree tools

Evagene sits in a market with several established platforms. The comparison index covers the full set; a brief positioning summary follows.

• Progeny — established enterprise pedigree platform, widely deployed in hospital genetics services. Strong on EHR-integrated workflows; markets itself as clinical software. Where Progeny ticks rows that depend on clinical-workflow integration, Evagene does not, by design.
• PhenoTips — phenotyping-first platform anchored on the Human Phenotype Ontology. Strong fit for diagnostic genetics and rare-disease research where deep phenotyping drives the case.
• TrakGene — cloud-based clinical-genetics platform with HL7 FHIR support; strong on managing the testing workflow.
• FamGenix — patient-facing family-history intake with automatic pedigree generation; positioned for scaled intake before a clinical encounter.
• CanRisk — not a competitor in the pedigree-drawing sense but a complementary platform: BOADICEA is computed there, and Evagene's CanRisk export is the bridge.

Evagene's distinguishing combination is gesture-based pedigree drawing, in-tool implementations of multiple published risk-model algorithms framed as illustrative, a 1,900-entry help catalogue, GEDCOM/PED/Phenopackets/CanRisk interoperability, and a research- and education-grade positioning that is consistent across every page of the site.

Choosing a pedigree tool: questions to ask

• Does the tool enforce NSGC 2022 notation by default?
• Does it handle three-generation capture, consanguinity loops, twins, and pregnancy outcomes natively?
• Does it annotate affected individuals against a structured catalogue (ICD-10, OMIM, HPO, HGNC), not free text?
• Does it export GEDCOM, PED, Phenopackets v2, CanRisk, and PDF/PNG/SVG?
• Does it run published family-history risk-model algorithms directly on the pedigree, and is the boundary between in-tool computation and canonical clinical-grade computation explicit?
• Does it have a sensible answer to data residency and consent for multi-person family-history records?
• Is the tool's regulatory positioning clear and consistent across its marketing, documentation, and outputs?

Frequently asked questions

Related reading

• Pedigree drawing software
• Pedigree drawing tool
• Clinical pedigree drawing (overview)
• Clinical pedigree drawing guidelines (NSGC 1995/2008/2022)
• Pedigree chart
• NSGC pedigree notation
• How to draw a pedigree chart
• Hereditary cancer risk assessment
• Mendelian inheritance calculator