Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell

• Published in: Science (American Association for the Advancement of Science) Vol. 338; no. 6114; pp. 1622 - 1626
• Main Authors: Zong, Chenghang, Lu, Sijia, Chapman, Alec R., Xie, X. Sunney
• Format: Journal Article
• Language: English
• Published: Washington, DC American Association for the Advancement of Science 21.12.2012; The American Association for the Advancement of Science
• Subjects: Adenocarcinoma - genetics; Amplification; Annealing; Biological and medical sciences; Cell Line, Tumor; Cell lines; Cells; Cellular biology; Colorectal Neoplasms - genetics; Diverse techniques; DNA; DNA Copy Number Variations; DNA, Neoplasm - genetics; False positive errors; Fundamental and applied biological sciences. Psychology; Gene sequencing; Genetic mutation; Genome, Human; Genomes; Genomics; Heterogeneity; High-Throughput Nucleotide Sequencing; Human; Humans; Molecular and cellular biology; Mutation Rate; Mutations; Nucleic Acid Amplification Techniques - methods; Point Mutation; Polymerase chain reaction; Polymorphism, Single Nucleotide; Scientific method; Sequence Analysis, DNA - methods; Sequencing; Single-Cell Analysis; Uniformity; Human; Copy number variation; Isolated cell; Nucleotide; Diagnosis; Method; Detection
• ISSN: 0036-8075; 1095-9203
• DOI: 10.1126/science.1229164

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.