NOV 12, 2020 10:00 AM PST

Representative sampling to address tumor heterogeneity

Speaker
  • Research Leader, Roche Sequencing Solutions
    Biography

      Nelson Alexander received his Ph.D. in Cancer Biology from the University of Arizona, followed by a post-doctoral fellowship at Vanderbilt University. Looking to have a more direct impact on patient care, he joined Roche Tissue Diagnostics (RTD) in 2007 where he has held multiple roles in R&D, as well as Research & Early Development. During his time at RTD Nelson became very interested in the interface between tumor heterogeneity and sampling bias. Nelson currently lead a research team within Roche Sequencing Solutions that is pioneering a new sampling process that enables the evaluation and quantification of tumor diversity at the genomic, transcriptomic, and cellular levels from entire solid tumors.


    Abstract

    Ensuring that clinical tests are not affected by tumor heterogeneity requires a sampling methodology that captures the genomic, proteomic, and cellular diversity of entire solid tumors. However, today the vast majority of surgically removed solid tumor tissue is considered surgical waste and incinerated, or bio-banked as formalin fixed blocks. In fact, in a clinical survey we show that standard molecular tests use only 0.0005% of the initial tumor volume. Other fields outside of medicine such as the mining industry and political polling have solved the challenge of heterogeneity through the statistically powered process of representative sampling. We have applied the principle of representative sampling to solid tumors by homogenizing residual fixed tumor tissue not taken for pathology into a well-mixed solution across multiple tumor types including breast, NSCLC, and colon adenocarcinoma. Representative sampling followed by NGS (Rep-Seq) allows for clear discernment of clonal vs. sub-clonal variants and detects more total variants compared to single biopsies. The homogenized representative sample can be further processed to enable flow cytometry and a comprehensive quantification of infiltrating immune cells, activated fibroblasts, and the percentage of cancer cells within the tumor. Representative sampling of tumors through homogenization of fixed, unused tumor tissue enables researchers and clinicians to generate data sets that are not biased by spatial heterogeneity, and to assess the genomic and cellular diversity of solid tumors.


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