Hi George, The two variables you mentioned in your message are the ones I've been using; the data set we were provided included a single sequence number that was populated by NAACCR Item 380 or 560, depending on the participating site. (Some sites use Central while others use Hospital Sequence Number.)
I'm not certain what you mean about making each tumor unique. To be clear, each tumor in the dataset is not given its very own sequence number. The numbers can repeat across patients, but they should not repeat within a given patient. Therefore, each tumor can be uniquely identified using Study ID and sequence number. Hope this helps... Brad -----Original Message----- From: Kowalski, George [mailto:[email protected]] Sent: Tuesday, February 02, 2016 2:34 PM To: McDowell, Bradley D Cc: [email protected] Subject: Re: data issues Bradley, W When you say there are “ Duplicate records (indicated with equivalent sequence number”, what field are you basing this off of ? http://www.naaccr.org/Applications/ContentReader/default.aspx?c=9 shows only two sequence numbers , both with not enough room to make each tumor unique . [cid:B0AA3B86-D2F3-40F2-B462-3E055238E77C] and [cid:A6D5DCC0-5C33-46C4-8DD1-08D83F723388] George Kowalski 414.805.7318 (office) / [email protected]<mailto:[email protected]> From: <[email protected]<mailto:[email protected]>> on behalf of "McDowell, Bradley D" <[email protected]<mailto:[email protected]>> Date: Monday, February 1, 2016 at 11:00 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: FW: data issues Dan asked me to forward this message to this group: From: McDowell, Bradley D Sent: Tuesday, January 26, 2016 11:00 AM To: Dan Connolly ([email protected]<mailto:[email protected]>) Cc: Chrischilles, Elizabeth A; Gryzlak, Brian M Subject: data issues Hi Dan, Betsy asked me to provide a list of the issues that have been uncovered so far with respect to the oncology registry data. The hope is that we can establish tickets for each problem. There are some problems that are easy to describe, and some that are not so easy. Some of the easy ones: · Missing MCW patient (https://informatics.gpcnetwork.org/trac/Project/ticket/453) · Duplicate records (indicated with equivalent sequence number for same Study ID), some with updated surgery, class of case variables · Some duplicate records have dx dates that appear to have been copied from last contact date (dx date not the same across duplicates) · UMN switched | and : for NAACCR variables (not “*.Descriptor” variables) For the duplicated records, I have put together a spreadsheet that nicely illustrates the problem, and I’m happy to share that. We’ll have to transfer it via redcap or some other secure means since it contains patient level data. Regarding the not so easy issues: · One problem concerns inconsistencies in coded values. For example, gpc_language has four different values for “English”. In general, UIOWA is not using the same descriptor values as other sites, and that accounts for most of these. It is not the only offender, however. MCW uses a different convention for seer_site_breast (as does UIOWA) and Race descriptors are different for UIOWA and WISC. These inconsistencies have percolated through to the derived GPC variables. I am writing a mapping program to handle this with the registry data we have received so far. I’m certainly willing to share what I have if it would help you. · Another big problem concerns missing values. I have attached a report that provides the percentage of missing values, organized by site and variable. This illustrates, for example, that UIOWA has no data for the Race 5 variable (i.e., 100% of the values equal “NA”; this does NOT reflect cases where a value is assigned for the NAACCR code for ‘missing’). It also illustrates some other things that we have discussed; for example, sites that reported data for central sequence number did not report data for hospital sequence number (and vice versa). o UIOWA and MCRF appear to have the biggest problems with missing data. · We also need to figure out why so many patients in our database do not appear to have tumors diagnosed between 01JAN2013 and 01MAY2014. (General observation: You’ll notice that each of the NAACCR concepts correspond to two variables (e.g., N0670_Surg_Prim_Site and N0670_Surg_Prim_Site_D). Vince and I settled on this arrangement for the datamart. Since then, though, I’ve come to believe that the redundancy makes the database difficult to use. Perhaps we could keep that in mind for future data cuts.) I’m very happy to work on these problems with you. Would you like to schedule a phone call to plan out how to approach these issues? Thanks, Brad ------------------------------------------------------------ Bradley D. McDowell, Ph.D. Director, Population Research Core Holden Comprehensive Cancer Center 5240 MERF | The University of Iowa | Iowa City, IA | 52242 Office: 319-384-1768 _______________________________________________ Gpc-dev mailing list [email protected] http://listserv.kumc.edu/mailman/listinfo/gpc-dev
