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

TLDR

Genomic heterogeneity among related cells arises from dynamic DNA changes, yet single‑cell sequencing has been limited by amplification bias that reduces genome coverage. The study aims to introduce MALBAC, a new amplification method that provides high genome‑wide uniformity. MALBAC uses multiple annealing and looping cycles to achieve uniform amplification across the genome. MALBAC‑amplified DNA yields 93 % genome coverage at 25× depth, enabling detection of CNVs and accurate SNV calling without false positives, and revealing an unusually high purine‑pyrimidine exchange rate in a cancer cell line.

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.