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Genotype Imputation

Definition
AI-generated

Genotype imputation statistically infers untyped or missing genotypes in a study sample by matching phased haplotypes to a dense reference panel (often WGS), typically using HMM-based methods that exploit LD and shared haplotype structure.

Topics
GWAS
Related
1000 Genomes Project BGEN Genotype

Why it matters in GWAS

Arrays cover a subset of variants; imputation expands SNP coverage for association testing, boosts power for common and low-frequency variants, and harmonizes cohorts genotyped on different chips for meta-analysis.

Example usage

"At this locus, Genotype Imputation annotations were used to prioritize plausible biological mechanisms."

1000 Genomes Project BGEN Genotype Genotype Dosage Genotype Imputation Server Genotyping Array GLIMPSE2 Haplotype Haplotype Reference Consortium (HRC) Imputation Quality Metric Imputation Reference Panel Linkage Disequilibrium (LD) Meta-Imputation Haplotype Phasing Trans-Omics for Precision Medicine (TOPMed) Whole-Genome Sequencing (WGS) Genome-Wide Association Study (GWAS)
Related-term network

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Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • Li N, Stephens M. (2003). Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics.
  • Sun Q, Li Y. (2026). Advances in haplotype phasing and genotype imputation. Nat Rev Genet. https://doi.org/10.1038/s41576-025-00895-2
  • GWASTutorial: Imputation.
← Genotype Dosage Genotype Imputation Server →

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