Structural Alterations in Cancer Genomes -- Peter Park
April 6, 2015

Peter discussing whole genome sequencing analysis challenges, motivating with
throughput and storage/compute demands for large scale analysis of cancer
tumor/normals. Benefits of WGS in cancer analysis: structural variants, copy
number variations, and non-coding mutations intersected with functional
data. Structural variant calling with short reads is challenging. Examples of
usefulness: TERT promoter broken with structural changes + CNVs. Chromothripsis:
shattering of a chromosome via translocations. Aneuploidy: is a driver of
cancer, or by-product of tumor growth? Associated with missing tumor-suppressor
genes or extra oncogenes: tumor growth result, not driver. How many cancer
related genes are there? ~320 tumor suppressor genes and 250 oncogenes using
consistent patterns of mutation.

Tumor heterogeneity with single cell: lots of it. High depth sequencing of
somatic brain tissue: lots of neuronal subtypes and transposable elements could
contribute to it. 16x single cell samples, found deletions copy number changes
and transposable element identifications.
