Chenghang Zong

Department of Chemistry and Chemical Biology

Harvard University

Whole Genome Amplification and Sequencing of Single Human Cells

Single cell sequencing is needed to characterize the genomic differences between individual cells. However, this approach has been hindered by whole-genome amplification bias, resulting in low genome coverage. In this talk, I will present 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 call individual single nucleotide variations (SNVs) with no false positives observed. We directly measured the genome-wide mutation rate of a cancer cell line. As another application of MALBAC, we sequenced 99 sperm from an Asian male to phase the personal genome and map at high-resolution recombination events, which are non-uniformly distributed across the genome. As one of the first clinical applications, we captured and sequenced rare circulating tumor cells (CTCs). We observed common CNV patterns among CTCs and metastasized cells.

Host: Ken Dill, Laufer Center