Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes

Nat Commun. 2018 Feb 26;9(1):828. doi: 10.1038/s41467-018-03273-1.


High-throughput sequencing provides the means to determine the allelic decomposition for any gene of interest-the number of copies and the exact sequence content of each copy of a gene. Although many clinically and functionally important genes are highly polymorphic and have undergone structural alterations, no high-throughput sequencing data analysis tool has yet been designed to effectively solve the full allelic decomposition problem. Here we introduce a combinatorial optimization framework that successfully resolves this challenging problem, including for genes with structural alterations. We provide an associated computational tool Aldy that performs allelic decomposition of highly polymorphic, multi-copy genes through using whole or targeted genome sequencing data. For a large diverse sequencing data set, Aldy identifies multiple rare and novel alleles for several important pharmacogenes, significantly improving upon the accuracy and utility of current genotyping assays. As more data sets become available, we expect Aldy to become an essential component of genotyping toolkits.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles*
  • Chromosome Mapping
  • Cytochrome P-450 CYP2D6 / classification
  • Cytochrome P-450 CYP2D6 / genetics*
  • Cytochrome P-450 CYP2D6 / metabolism
  • DNA Copy Number Variations
  • Genome, Human*
  • Genotype*
  • Genotyping Techniques
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Isoenzymes / classification
  • Isoenzymes / genetics
  • Isoenzymes / metabolism
  • Phenotype
  • Polymorphism, Genetic*
  • Sequence Analysis, DNA
  • Software*


  • Isoenzymes
  • Cytochrome P-450 CYP2D6