Abstract 4820: A comparison of bulk versus single-cell whole-exome sequencing to study cancer genetic heterogeneity
Authors: John B. Williamson, Hongyong Zhang, Paul Lott, Ruta Sahasrabudhe, Stephanie Soares, Susie Airhart, Clifford Tepper, Chong-Xian Pan, Ralph DeVere-White, Luis Carvajal-Carmona
Journal: Cancer Research (2015)

Abstract Cancer is a heterogeneous disease consisting of subclonal cell populations at the genetic level that possess a selective growth advantage over normal tissue. Furthermore, these subclones have differential responses to therapeutic interventions, particularly molecularly targeted approaches to treatment. Traditional cancer genomics techniques obtain sequence data at a single time point from bulk tumor tissue. This method provides a snapshot of somatic mutational profiles at the population level, but is limited in its sensitivity to detect rare and potentially important subclones by sample quality, sequencing depth, and subclonal population frequency. Current methods to map the clonal architecture of tumors use bulk sequencing coupled with bioinformatic approaches using read depths to determine allele frequencies and groups subclones based on these frequencies. However, this approach is unable to separate subclonal populations comprised of variants present at similar allele frequencies, thus hindering the ability to precisely determine the cellular distribution of somatic mutations. Recent technological advances in the field of single cell genomics now allow for the interrogation of genetic aberrations at a single cell resolution in a high throughput fashion, providing the means to more fully map the clonal architecture of a tumor. However, a single cell approach requires large amounts of amplification, prompting concerns regarding polymerase fidelity, allelic imbalances and dropout, and incomplete target coverage. By comparing high depth bulk tumor to single cell exome sequencing results, we can assess the advantages and disadvantages of bulk sequencing vs. single cell methods to study genetic heterogeneity. To this end, we have performed single cell whole-exome sequencing (WES) on the K562 leukemia cell line and a muscle-invasive bladder cancer patient derived xenograft (PDX) using the Fluidigm C1 microfluidic system. We have captured over 300 cells from both cancer lines, and obtained an average of &amp;gt;100ng amplified DNA per cell. We have performed WES of 43 individual K562 cells resulting in a mean coverage of 11X across covered regions and 90% of passed filter bases aligned to the targeted regions. Analysis of WES data from 40 PDX cells is currently underway, and a detailed comparison of the single cell to high-depth bulk WES in K562 and PDX samples will be carried out to characterize amplification biases, fidelity, coverage, and sensitivity of a single cell based approach. Citation Format: John B. Williamson, Hongyong Zhang, Paul Lott, Ruta Sahasrabudhe, Stephanie Soares, Susie Airhart, Clifford Tepper, Chong-Xian Pan, Ralph DeVere-White, Luis Carvajal-Carmona. A comparison of bulk versus single-cell whole-exome sequencing to study cancer genetic heterogeneity. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4820. doi:10.1158/1538-7445.AM2015-4820