"Detecting Unique Genomic Variations and Rare Phenotypic Switching in Single Cells"

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Date/Time:Monday, 18 Feb 2013 from 3:10 pm to 4:00 pm
Location:Hoover 1213
Phone:515-294-5441
Channel:Colloquium
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Chenghang (Chuck) Zong (Harvard University)

Abstract
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, and were also able to directly measure the genome-wide mutation rate of a cancer cell line. As the first application of MALBAC, we mapped the recombination events of single sperm. In one of the clinical applications, MALBAC allows us to successfully characterize genome variations of low abundant circulating tumor cells isolated from clinical samples.

In addition to detecting unique genomic variations in single cells, I will present a study of rare phenotypic switching (as rare as 10-9 per cell generation) in a classical system: the lysogeny state of bacteriophage λ. By quantifying transcription bursts using single molecule FISH, we were able to reconstruct the gene regulation in silico and quantitatively analyze the robustness of this regulation of the lysogeny state. To test our quantitative modeling, we predicted the probability of rare phenotypic switching events, which agrees well with the experimentally measured probability.

Bio
Dr. Zong currently works in Prof. Sunney Xie's lab at Harvard University with the interest in technology development and application of single cell analysis in biological studies and clinical applications. Before that, Dr. Zong studied cellular decision-making process of bacteriophage in Prof. Ido Golding's lab at University of Illinois. As a graduate student, Dr. Zong studied theoretical biophysics in Dr. Peter Wolynes' lab at UC San Diego.