The mystery of missing heritability: Genetic interactions create phantom heritability.

Proc Natl Acad Sci U S A
Authors
Keywords
Abstract

Human genetics has been haunted by the mystery of "missing heritability" of common traits. Although studies have discovered >1,200 variants associated with common diseases and traits, these variants typically appear to explain only a minority of the heritability. The proportion of heritability explained by a set of variants is the ratio of (i) the heritability due to these variants (numerator), estimated directly from their observed effects, to (ii) the total heritability (denominator), inferred indirectly from population data. The prevailing view has been that the explanation for missing heritability lies in the numerator--that is, in as-yet undiscovered variants. While many variants surely remain to be found, we show here that a substantial portion of missing heritability could arise from overestimation of the denominator, creating "phantom heritability." Specifically, (i) estimates of total heritability implicitly assume the trait involves no genetic interactions (epistasis) among loci; (ii) this assumption is not justified, because models with interactions are also consistent with observable data; and (iii) under such models, the total heritability may be much smaller and thus the proportion of heritability explained much larger. For example, 80% of the currently missing heritability for Crohn's disease could be due to genetic interactions, if the disease involves interaction among three pathways. In short, missing heritability need not directly correspond to missing variants, because current estimates of total heritability may be significantly inflated by genetic interactions. Finally, we describe a method for estimating heritability from isolated populations that is not inflated by genetic interactions.

Year of Publication
2012
Journal
Proc Natl Acad Sci U S A
Volume
109
Issue
4
Pages
1193-8
Date Published
2012 Jan 24
ISSN
1091-6490
URL
DOI
10.1073/pnas.1119675109
PubMed ID
22223662
PubMed Central ID
PMC3268279
Links
Grant list
U54 HG003067 / HG / NHGRI NIH HHS / United States
HG003067 / HG / NHGRI NIH HHS / United States