Documentation / Trio and Family Variant Analysis
Trio and Family Variant Analysis
Family context can add evidence that is unavailable from a proband-only analysis. Folklore uses parental genotypes to identify technically supported de novo candidates, determine whether two variants in a recessive gene are in trans, and measure segregation within the limits of the available pedigree.
The current production workflow supports a complete trio only: proband, mother, and father. Duo, sibling-only, extended-pedigree, and multiple-proband workflows are not part of the present production pipeline.
One Call Set, Two Evidence Layers
The proband classification and the parental genotype evidence are derived from the same normalized joint VCF. The family module records inheritance evidence beside the upstream ACMG classification; it does not silently overwrite or replace that classification.
Required Inputs
Either one compatible joint multi-sample VCF or separate proband, maternal, and paternal gVCFs.
Sample identifiers, sex, family role, and affected status for each member.
An inheritance hypothesis and phenotype specificity when available.
A compatible reference genome and contig naming scheme.
Production Workflow
Validate the Complete Trio
The production workflow requires one proband, one mother, and one father with compatible gVCF inputs and recorded pedigree metadata.
Prepare the Joint Call Set
Separate member gVCFs are joint-genotyped into one normalized multi-sample VCF. A compatible laboratory-provided joint VCF can be validated and used directly.
Classify the Proband
A proband-only VCF is extracted from the joint call set and processed through the standard Variant Analysis workflow. ACMG classification belongs to the proband.
Build the Trio Evidence Store
The joint genotypes are combined with the classified proband data. PLINK relationship quality control checks the declared parent-child relationships, parental relatedness, and possible duplicate samples.
Compute Inheritance Evidence
The family module evaluates de novo candidates, compound heterozygous phase, segregation scores, and categorical inheritance patterns without replacing the proband ACMG classification.
De Novo Candidates
A candidate de novo variant must be present in the proband and supported by reference genotypes in both parents. Folklore records high- or low-confidence technical states, together with excluded and not-applicable control states. Confidence describes support for de novo origin, not pathogenicity.
The clinical-grade reporting layer applies additional quality, population-frequency, consequence, and splice-signal filters to identify a focused review subset. This reporting layer does not independently change PS2 criterion semantics.
Compound Heterozygous Candidates
Within each gene, the workflow evaluates pairs of heterozygous coding or splice-relevant variants. A pair receives strongest technical support when parental genotypes demonstrate that one variant was inherited from each parent, establishing an in-trans configuration.
An in-trans result establishes candidate phase. It does not by itself establish that both alleles are clinically significant; each variant still requires its own evidence review.
Segregation Limits
A complete trio contributes at most two informative parent-to-proband transmissions. Its maximum raw LOD is approximately 0.602 before phenotype specificity is applied. Depending on the inheritance hypothesis, informative transmissions, and phenotype specificity, a trio result can remain Indeterminate or reach the lower Supporting band.
Moderate, Strong, and Very Strong segregation bands require additional informative relatives in an extended pedigree. Extended-pedigree analysis is outside the current production scope.
Outputs for Clinical Review
A normalized joint multi-sample VCF for the complete trio.
A classified proband dataset produced through the standard ACMG workflow.
Pairwise relationship quality-control results from PLINK Identity-by-Descent analysis.
Per-variant de novo confidence and supporting technical evidence.
Candidate compound heterozygous pairs with parental-origin phase information.
Segregation scores and evidence bands, including explicit trio-only limits.
A separate clinical-grade reporting subset for focused review.
Clinical Boundary
Family Analysis is clinical decision support. It records technically derived inheritance evidence and makes the evidence traceable for review. A qualified genetics professional decides how that evidence affects the final case interpretation.
In This Section
De Novo Variant Analysis
Trio genotype requirements, confidence states, reporting filters, PS2 and PM6 boundaries, and mosaicism limits.
Compound Heterozygous Variants
Candidate pairing, parental-origin phasing, trans and cis states, multiple partners, clinical-grade filtering, and PM3 boundaries.
Segregation Analysis
Per-variant LOD scoring, phenotype multipliers, evidence bands, trio limits, and PP1 or BS4 review boundaries.
Trio Quality Control
PLINK IBD analysis, PI_HAT thresholds, sample-swap and duplicate alerts, related parents, skipped checks, and interpretation limits.
Inheritance Patterns
Categorical pattern summaries, sex-gated X-linked states, unclear results, and ACMG boundaries.
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