Mendelian error¶
A pedigree-genotype incompatibility where a child's called genotype is impossible from recorded parents under a stated Mendelian transmission model, used as a bounded quality-control flag.
Core Idea¶
Mendelian checking compares child and parental genotype calls against possible transmissions at the same locus. An impossible combination indicates that some element of genotype, sample, pedigree, variant representation, ploidy, or biological model needs review.
It does not identify the cause by itself. Technical artifacts are common, while validated de novo variants, mosaicism, copy-number changes, and complex regions require specialized interpretation. Relationship inferences carry sensitivity and privacy obligations.
Scope of Application¶
- Genotyping QC. Detects calling and sample problems.
- Pedigree validation. Finds relationship inconsistencies at aggregate scale.
- De novo studies. Nominates variants for rigorous confirmation.
- Variant pipelines. Tests representation, ploidy, and complex regions.
- Population research. Uses aggregate rates under ethical governance.
Clarity¶
Record genome build, locus and alleles, variant representation, family IDs, stated relationships, sex and ploidy model, genotype likelihoods, depth, allele balance, contamination, sample identity, replicate confirmation, and alternative explanations. Protect sensitive pedigree information. Inclusion test: Flag a Mendelian error only after harmonizing locus, alleles, ploidy, family relationship, and call quality and showing no offspring genotype is possible under the declared inheritance model. Exclusion test: Exclude rare but compatible transmission, phenotype disagreement, population-frequency anomalies, loci with misapplied ploidy, and using the flag alone to infer nonparentage. Nearest boundary: A de novo variant is biologically new in the child; it first appears as an incompatibility but requires validation and exclusion of technical and pedigree explanations. Exit condition: The identity resolves or changes when corrected calls, relationships, locus models, or validated alternative biology restore an explanation. Common misclassifications: It is not a rare inherited allele. It is not proof of nonparentage. It is not phenotype mismatch. It is not valid without locus-specific inheritance assumptions. Nearest named distinctions: De Novo Mutation: One possible validated biological explanation for an apparent incompatibility. Nonpaternity: A sensitive relationship hypothesis requiring genome-wide corroboration and governance. Genotyping Error: A common technical cause, not the definition of the flag. Hardy–Weinberg Disequilibrium: A population-level frequency departure rather than family transmission impossibility.
Manages Complexity¶
The flag compresses a family transmission constraint into an auditable incompatibility. It is valuable precisely because it postpones causal attribution until technical and biological possibilities are investigated.
Abstract Reasoning¶
- Harmonize samples, loci, alleles, and genome representation.
- Select the correct chromosome and ploidy inheritance model.
- Enumerate compatible offspring genotypes.
- Flag calls outside that set with uncertainty retained.
- Review read, sample, pedigree, and complex-locus evidence.
- Classify a cause only after independent confirmation.
Knowledge Transfer¶
The transferable cargo is constraint-based consistency checking across related records. It transfers to other pedigrees and inheritance systems when ploidy and rules are redefined; human pedigree conclusions do not travel automatically.
Neighborhood in Abstraction Space¶
Mendelian error sits in a crowded region of the domain-specific corpus (38th percentile for distinctiveness): several abstractions share nearly its structure, so a description that fits it tends to fit its neighbors too.
Family — Cellular & Evolutionary Biological Processes (16 abstractions)
Nearest neighbors
- Genetic Process — 0.91
- Law of segregation — 0.90
- Ring Species — 0.88
- Evolutionary Process — 0.88
- Evolutionary Taxonomy — 0.87
Computed from structural-signature embeddings · 2026-10-08