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Finding rare variants and gene–environment interactions (GXE) is critical in dissecting complex diseases. We consider the problem of detecting GXE where G is a rare haplotype and E is a nongenetic factor. Such methods typically assume G‐E independence, which may not hold in many applications. A pertinent example is lung cancer—there is evidence that variants on Chromosome 15q25.1 interact with smoking...
Two important contributors to missing heritability are believed to be rare variants and gene‐environment interaction (GXE). Thus, detecting GXE where G is a rare haplotype variant (rHTV) is a pressing problem. Haplotype analysis is usually the natural second step to follow up on a genomic region that is implicated to be associated through single nucleotide variants (SNV) analysis. Further, rHTV can...
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