Clonal genotype and population structure inference from single-cell tumor sequencing

Nat Methods. 2016 Jul;13(7):573-6. doi: 10.1038/nmeth.3867. Epub 2016 May 16.

Abstract

Single-cell DNA sequencing has great potential to reveal the clonal genotypes and population structure of human cancers. However, single-cell data suffer from missing values and biased allelic counts as well as false genotype measurements owing to the sequencing of multiple cells. We describe the Single Cell Genotyper (https://bitbucket.org/aroth85/scg), an open-source software based on a statistical model coupled with a mean-field variational inference method, which can be used to address these problems and robustly infer clonal genotypes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Clone Cells
  • Cystadenocarcinoma, Serous / genetics*
  • Female
  • Genome, Human
  • Genotype
  • High-Throughput Nucleotide Sequencing / methods
  • Humans
  • Leukemia / genetics*
  • Mammary Glands, Human / metabolism*
  • Models, Statistical
  • Ovarian Neoplasms / genetics*
  • Polymorphism, Single Nucleotide / genetics
  • Single-Cell Analysis / methods*
  • Software*