American Statistical Association
Somatically-acquired allelic imbalance (AI, i.e. chromosomal duplications, deletions or copy-neutral loss-of-heterozygosity) is an established factor in cancer initiation and has recently been implicated as a marker for cancer risk. While DNA microarrays and next-generation sequencing are effective for whole-genome profiling of AI, in typical settings their sensitivities become extremely limited when the aberrant cell fraction (or tumor purity) is below 10-20%. Yet, this range may be critical for early detection, diagnostics, or studies of pre-disease tissue, since for such applications the samples of interest will be comprised of heterogeneous mixtures of cells with a substantial component of DNA from normal (i.e. representing the germline) rather than aberrant (e.g. the tumor) sources. Here we demonstrate the characterization of AI in the following challenging settings using our haplotype-based statistical technique: tumors with high stromal content, premalignant lesions, normal "field" tissues proximal to a primary tumor, and blood. We conclude with a summary of complementary analyses of The Cancer Genome Atlas: correcting copy number calls for problematic samples and cataloging AI in "normal adjacent to tumor" samples.
|Date:||Wednesday, May 1, 2019|
|Time:||4:00 - 5:00 P.M.|
Memorial Sloan Kettering Cancer Center
Department of Epidemiology and Biostatistics
485 Lexington Avenue
(Between 46th & 47th Streets)
2nd Floor, Conference Room B
New York, New York
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