Genetics and statistical genomics · BEGINNER LESSON
SNP-based heritability
SNP-based heritability is the proportion of differences in a trait across people that can be explained by additive effects of single-nucleotide polymorphisms (SNPs), which are one-letter DNA variants. It is usually written as h2SNP and is estimated from measured genetic variation, not from all possible causes of the trait.
What it is and what is measured
Heritability here means the fraction of variation in a trait, also called phenotypic variance, that can be linked to genetic differences among people. SNP-based heritability focuses only on SNPs, short for single-nucleotide polymorphisms, which are single-DNA-letter changes measured across a sample. The key quantity is the total proportion of trait variation explained by the additive effects of those SNPs, written h2SNP.
[1] Estimation and mapping of the missing heritability of human phenotypes [3] Integrated Genomic Approaches to Elucidate the Genetic Basis of ...
How it is estimated and what it tells us
Researchers estimate SNP-based heritability by using genome-wide data to ask how genetically similar people are and whether more similar genomes tend to have more similar traits. One common approach builds genetic relationship matrices, which summarize shared SNP patterns, and then uses statistical models such as GREML, short for generalized restricted maximum likelihood. This estimate matters because it helps set the statistical power of genome-wide association studies, or GWAS, and gives an upper bound for how well genomic data may predict a trait.
[1] Estimation and mapping of the missing heritability of human phenotypes [3] Integrated Genomic Approaches to Elucidate the Genetic Basis of ...
Why it is usually lower than pedigree heritability
Pedigree-based heritability uses family resemblance and can include effects that are not captured well by common SNPs alone. The gap can come from rare variants, structural variants, shared environment between relatives, or non-additive genetic effects such as interactions between variants or between genes and environment. Because older estimates often used only common SNPs, SNP-based heritability can be systematically lower than narrow-sense heritability from family studies.
[1] Estimation and mapping of the missing heritability of human phenotypes
Limitations and caution
These estimates depend on which variants are measured and which people are studied. One source notes restriction to European ancestry samples in a large study because other ancestry groups were too small, and another notes that sex chromosomes were not included, so their contribution is unclear. Some estimates may also be inflated or uncertain if rare variants are only weakly detected or if replication in an independent cohort is not available.
[1] Estimation and mapping of the missing heritability of human phenotypes [3] Integrated Genomic Approaches to Elucidate the Genetic Basis of ...
SEE THE IDEA
How SNP-based heritability works
Collect genome-wide SNP data from many people.
Ask whether people with more similar SNP patterns also have more similar trait values.
Use a statistical model to estimate the fraction of variance explained by additive SNP effects.
Compare with GWAS-detected variance and family-based estimates to see what may be missing.
Each step builds on the previous one: measured SNPs are compared across people, then modeled to estimate explained trait variation.
SNP-based heritability is an estimate from observed genome data, not a direct count of all genetic causes.
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Sources and further reading
This general lesson was generated from public source material. It explains a concept; it does not interpret a private paper or provide medical advice.