title: Genome-wide detection of single-nucleotide and copy-number variations of a single human cell.
abstract: Kindred cells can have different genomes because of dynamic changes in DNA. Single-cell sequencing is needed to characterize these genomic differences but has been hindered by whole-genome amplification bias, resulting in low genome coverage. Here, we report on a new amplification method-multiple annealing and looping-based amplification cycles (MALBAC)-that offers high uniformity across the genome. Sequencing MALBAC-amplified DNA achieves 93% genome coverage ≥1x for a single human cell at 25x mean sequencing depth. We detected digitized copy-number variations (CNVs) of a single cancer cell. By sequencing three kindred cells, we were able to identify individual single-nucleotide variations (SNVs), with no false positives detected. We directly measured the genome-wide mutation rate of a cancer cell line and found that purine-pyrimidine exchanges occurred unusually frequently among the newly acquired SNVs.
authors.affiliation: Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Chenghang
authors.initials: C
authors.lastname: Zong
authors.forename: Sijia
authors.initials: S
authors.lastname: Lu
authors.forename: Alec R
authors.initials: AR
authors.lastname: Chapman
authors.forename: X Sunney
authors.initials: XS
authors.lastname: Xie
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics; D045744:Cell Line, Tumor; D015179:Colorectal Neoplasms / Q000235:genetics*; D056915:DNA Copy Number Variations; D004273:DNA, Neoplasm / Q000235:genetics*; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D059645:Mutation Rate; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*; D017354:Point Mutation; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods; D059010:Single-Cell Analysis
chemical_list: D004273:DNA, Neoplasm