Thanks for the input, Dan. The code is being ported to R (the original was written in MS-Access VBA). As soon as porting is done, I will post the two tables (and their contents) and the relatively short code.
The problem is that in the case of "sometimes", the organs involved are covered by peritoneum/pleura/pericardium (a category of tissue called a "serous membrane", which secretes a small amount of lubricating fluid allowing the organs to move about without friction. The serous membrane also acts as a defense mechanism - albeit a modest one - against infection following the puncture of a hollow organ). Mesothelioma (in the histology range 9050-55) is a tumor of the serous membranes almost invariably caused by asbestos exposure (the actor Steve McQueen, of "Bullitt" fame, died of this cancer). It can certainly occur in the places where it is flagged. (It would spread to the SURFACE of the heart, colon, lung or intestine, but not develop INSIDE it.) However, mesothelioma, while one of the less common tumors, is so well known (thanks to asbestos litigation) that when one codes it, it may be reasonable to assume that the histology result is not in error. If the anatomic location is compatible with the tumor morphology/behavior, it should be flagged as valid. In other words, I would interpret the "and sometimes" as valid. ------- From: Dan Connolly [mailto:[email protected]]<mailto:[mailto:[email protected]]> Sent: Thursday, February 19, 2015 4:37 PM To: Nadkarni, Prakash; [email protected]<mailto:[email protected]> Subject: RE: Possible bugs in SEER_Recode.sql The table-driven approach sounds interesting. I trust you'll share the code in due course. As to the exclusions, they're just transcribed by machine* from the seer table<http://seer.cancer.gov/siterecode/icdo3_d01272003/>. The entries you note are marked ", and sometimes..." so it's a question of whether you want false positives or false negatives, I guess. Did you check the other ", and sometimes..." entries? * seer_recode.py is not published... sigh... but it's on elephant. See MultiSiteDev<https://informatics.gpcnetwork.org/trac/Project/wiki/MultiSiteDev>. -- Dan Prakash ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________
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