title: Scalable whole-genome single-cell library preparation without preamplification.
abstract: Single-cell genomics is critical for understanding cellular heterogeneity in cancer, but existing library preparation methods are expensive, require sample preamplification and introduce coverage bias. Here we describe direct library preparation (DLP), a robust, scalable, and high-fidelity method that uses nanoliter-volume transposition reactions for single-cell whole-genome library preparation without preamplification. We examined 782 cells from cell lines and triple-negative breast xenograft tumors. Low-depth sequencing, compared with existing methods, revealed greater coverage uniformity and more reliable detection of copy-number alterations. Using phylogenetic analysis, we found minor xenograft subpopulations that were undetectable by bulk sequencing, as well as dynamic clonal expansion and diversification between passages. Merging single-cell genomes in silico, we generated 'bulk-equivalent' genomes with high depth and uniform coverage. Thus, low-depth sequencing of DLP libraries may provide an attractive replacement for conventional bulk sequencing methods, permitting analysis of copy number at the cell level and of other genomic variants at the population level.
authors.affiliation: Genome Science and Technology Graduate Program, University of British Columbia, Vancouver, British Columbia, Canada.|Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: Hans
authors.initials: H
authors.lastname: Zahn
authors.affiliation: Genome Science and Technology Graduate Program, University of British Columbia, Vancouver, British Columbia, Canada.|Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada.
authors.forename: Adi
authors.initials: A
authors.lastname: Steif
authors.affiliation: Genome Science and Technology Graduate Program, University of British Columbia, Vancouver, British Columbia, Canada.|Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada.
authors.forename: Emma
authors.initials: E
authors.lastname: Laks
authors.affiliation: Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada.|Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: Peter
authors.initials: P
authors.lastname: Eirew
authors.affiliation: Genome Science and Technology Graduate Program, University of British Columbia, Vancouver, British Columbia, Canada.|Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: Michael
authors.initials: M
authors.lastname: VanInsberghe
authors.affiliation: Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada.|Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.|Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada.
authors.forename: Sohrab P
authors.identifier: 0000-0001-6402-523X
authors.initials: SP
authors.lastname: Shah
authors.affiliation: Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada.|Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.|Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada.
authors.forename: Samuel
authors.identifier: 0000-0002-0487-9599
authors.initials: S
authors.lastname: Aparicio
authors.affiliation: Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.|Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: Carl L
authors.initials: CL
authors.lastname: Hansen
mesh_terms: D000818:Animals; D001943:Breast Neoplasms / Q000235:genetics / Q000473:pathology; D045744:Cell Line, Tumor; D005260:Female; D015723:Gene Library; D023281:Genomics / Q000379:methods*; D006801:Humans; D056656:Lab-On-A-Chip Devices; D016513:Mice, SCID; D010802:Phylogeny; D059010:Single-Cell Analysis / Q000295:instrumentation / Q000379:methods*; D023041:Xenograft Model Antitumor Assays