For the question of “is the deletion burden observed similar to those for other cancers? Then again there must be estimates of deletion burden for different types of cancers from TCGA studies”, our response is that we did search of CNAs observed in other cancer based on TCGA studies, although there are limited studies, we addressed this issue in the discussion section (page 8) “…Using the TCGA data, a recent study identified nine regions of deletion that were unique to ER+ post menopause tumors in patients with breast cancer, including deletion in 7p22.3 where our newly identified deletion in cases only located and it contains known tumor suppressor gene”.
2) is the deletion burden observed similar to those for other cancers? Then again there must be estimates of deletion burden for different types of cancers from TCGA studies. Please cite those.