CAAD (Carotid Artery Atherosclerosis Disease)

Estimates of CAAD cases across eMERGE sites based on the eMERGE Record Counter are:

For details see document "Estimate of network-wide CAAD cases" in the Files section of this page.

Group Health recommends the following rule for selecting documents for CAAD NLP processing. This rule requires querying the full text of each possible procedure report to identify those that contain minimally necessary textual content. Note that this assume procedure reports can be distinguished from other types of clinical documents such as progress notes.

Rule: Process all procedure reports that contain text satisfying at least one of the following conditions:

1.Report contains text strings "carotid" and ("doppler" or "us" or "u/s" or "ultrasound").

2.Report contains text strings ("head" or "neck") and ("us" or "u/s" or "ultrasound" or "ct" or "tomography").

3.Report contains text strings ("catheter" or "ct" or "mr") and "angiography".

If you cannot distinguish procedure reports from other clinical notes (such as progress reports) you can still apply this rule to all documents. This will result in processing more documents than necessarily, but is unlikely to yield misleading NLP results. This is because documents other than relevant procedure reports are highly unlikely to contain sufficient information to satisfy the NLP system's rules for identifying carotid stenosis findings.

A zip archive has been posted that includes SAS code illustrating how to identify CAAD cases and controls by post-processing the CAAD NLP system's results data.  The archive (listed above as "SAS code illustrating how to identify cases and controls from the CAAD NLP system's output") includes the SAS code as well as all data files that would be required and created if you processed the CAAD test documents shipped with the CAAD NLP system.  CAAD cases identified by NLP are defined as patients with at least one stenosis measurement greater than or equal to 50%.  CAAD controls identified by NLP are are defined as patients whose maximum measured stenosis is less than or equal to 15%.  Keep in mind that cases and controls can also be defined by structured data alone (defined elsewhere).
-David Carrell

We have changed the minimum health system contact criterion (criterion 6.1 in the pseudo code document).  The new criterion is more relazed than the previous definition, yet still assures that there is sufficient contact with the patients to reduce the likelihood that CAAD disease is present in a patient but undocumented in the EMR (a threat to the NPV in our control selection algorithm).

SAS code for implementing the new definition is available upon request (email David Carrell).

Hi All,

We have posted the final version of the CAAD phenotype pseudo code (document dated 12/29/2014).  It includes several changes to criteria for defining both cases and controls.  Please let us know if you have any questions.

We included in the pseudo code document a table of counts of cases, controls, and excluded patients for GH/UW subjects broken out by age group.  We hope this table is useful for helping you assess whether the counts of cases and controls you generate are reasonably comparable to ours.  Of course, differences in setting (e.g., managed care versus university hospital) may also account for substantial differences in yield for cases and controls, as may other factors.

Also updated today is the User Guide which explains how to install and use the CAAD NLP system, and a SAS code file that illustrates how data generated by the NLP system may be post-processed (using SAS) to generate the necessary person-level results for measured carotid stenosis.

-David Carrell

The updated version of the CAAD NLP system User Guide (2/11/2015) includes a new section explaining which of the two versions of the NLP system you should choose to process your reports.

David

Today we post an updated version of the portable CAAD NLP system that addresses modifications designed to improve performance at Mayo Clinic.  We continue to offer two versions of the NLP system--one which checks each report for a relevant exam type description (e.g., "CAROTID ULTRASOUND") before processing the report, and one that assumes all incoming reports are relevant carotid studies and processes each report regardless of its content. 

The system posted today is the one that checks for exam type before processing each report.

The system posted today appears in the list of downloadable files as "Version 0.5.4 of CAAD Portable NLP System (checks exam type)."  The file that will be downloaded from this link is named "PortableNLP_Check_Exam_Type_v0.5.4.zip."

We belive these modification will improve performance at Mayo without degrading performance elsewhere.  (We have therefore hidded the previous version of this NLP system but it is still stored on PheKB and we can make it available if anyone wants it.)

As always, please reach out with any questions or issues you encounter with the CAAD NLP system or pseudo code.

For the remainder of April 2015 please make sure you include David Carrell (carrell.d@ghc.org) in your communications as David Cronkite will be out of the country during this time.

Cheers,

David

Hi All,

Today we upload to PheKB an updated version of the CAAD NLP system.  It appears in the list of downloadable files as "Version 0.5.5 of CAAD Portable NLP System (checks exam type)."  It differs from the previous version in that it now checks for and disqualifies results that are reported for VERTEBRAL ARTERIES or results from CORONARY ANGIOGRAPHY procedures.

As always, please reach out with any questions or issues you encounter with the CAAD NLP system or pseudo code.

For the remainder of April 2015 please make sure you include David Carrell (carrell.d@ghc.org) in your communications as David Cronkite will be out of the country during this time.

Thanks,

David

A question has come up about the minimum contact criteria (section 6.1 of the pseudo code).  We are not changing this specification.  Rather, we are attempting to make the description more clear.

Regarding the criteria establishing minimum contact with the health care system (sec. 6.1), these three criteria are applied within the entire 5-year (or ~1,826-day) period preceding a patient’s last known contact date; these criteria are NOT applied within individual calendar years.  This 5-year period ends on the date of the patient’s most recent contact with the health system, and extends back in time to the date 5 years before that (making a ~1,826 day period).  Within this period test for each of the three conditions:

1) patient has any 2 encounters >= 365 days apart in the relevant ~1,826-day period (e.g., 3/19/2012 and 1/22/2014 – the dates doe not have to be in the same calendar year), OR

2) patient has encounters in any 3 separate calendar quarters in the relevant ~20-quarter period (for example, Q1 2013, Q3 2013 and Q4 2013 qualifies, but so does Q4 2010, Q3 2012, and Q1 2014 – the quarters do not have to be in the same calendar year), OR

3) patient has encounters in any 4 separate calendar months in the relevant ~60-month period (for example, Jan 2012, Feb 2012 and  Nov 2014 – again, the months do not have to be in the same calendar year).

If any one of the above conditions is met the patient meets the minimum contact criterion.

In the following SAS code illustrates this logic.  Here, “adate” is the name of the encounter date variable and “mrn” is a unique patient identifier.

  **  Implement the continuous enrollment requirement (6.1 in pseudo code).
  **
  **    1) Identify the most recent encounter date for each pt.
  **    2) Using the most recent encounter date, get all encounter dates for
  **       the preceding 1,826 days (5 yrs).
  **    3) Calculate the number of days between min and max dates in #2 (and
  **       if >= 365 then set flag_6_1_1 = 1 and 0 otherwise).
  **    4) Add a column to the data from #2 with the encounter date
  **       formatted as SAS format YYQD. (e.g., 2012-1).
  **    5) Add another column to the data from #2 with the encounter date
  **       formatted as SAS format MONYY7. (e.g., DEC2012).
  **    6) Count distinct values of YYQD. (and if >= 3 then set flag_6_1_2 =
  **       1 and 0 otherwise).
  **    7) Count distinct values of MONYY7. (and if >= 4 then set flag_6_1_3 =
  **       1 and 0 otherwise).
  ** ;

%let lookback=1826;

proc sql ;

create table local.caad_01_latest_enc
as
select       b.mrn
            , max(a.adate)            as adate_max            format date9.
            , max(a.adate)-&lookback  as adate_max_minus_5yrs format date9.
  from         em2data.em1_em2_nwigm_all_demog b
               left outer join __vdw.utilization a
                 on a.mrn = b.mrn
  group by     b.mrn
  order by     b.mrn
  ;

  create table local.caad_01_encs_past_5yrs
  as
  select       put(a.adate, YYQD.)   as adate_yr_qtr
             , put(a.adate, MONYY7.) as adate_yr_mon
             , a.adate               as adate_date   format date9.
             , a.*
  from         __vdw.utilization a
               inner join local.caad_01_latest_enc b
                 on b.mrn = a.mrn
  where        a.adate between b.adate_max and b.adate_max_minus_5yrs
  order by     a.mrn
             , a.adate
  ;

  create table caad_01_encs_summary
  as
  select       a.mrn
             , max(a.adate) as adate_max
             , min(a.adate) as adate_min
             , count(distinct a.adate_yr_qtr)            as adate_yr_qtr_N
             , count(distinct a.adate_yr_mon)            as adate_yr_mon_N
  from         local.caad_01_encs_past_5yrs a
  group by     a.mrn
  order by     a.mrn
  ;
 
  create table local.caad_01_encs_summary
  as
  select       mrn
             , case when adate_max - adate_min >= 365
                         or
                         adate_yr_qtr_N >= 3
                         or
                         adate_yr_mon_N >= 4
                    then 1
                    else 0
                    end as Flag_Meets_Min_Contact
                   
             , adate_max - adate_min as max_days_bn_encs
             , adate_yr_qtr_N
             , adate_yr_mon_N
            
             , case when adate_max - adate_min >= 365 then 1
                    else 0
                    end as flag_6_1_1
             , case when adate_yr_qtr_N >= 3 then 1
                    else 0
                    end as flag_6_1_2
             , case when adate_yr_mon_N >= 4 then 1
                    else 0
                    end as flag_6_1_3
  from         caad_01_encs_summary
  order by     mrn
  ;
 
  quit ;
run ;

proc freq data=local.caad_01_encs_summary ;
table Flag_Meets_Min_Contact ;

proc freq noprint data=local.caad_01_encs_summary ;
    table flag_6_1_1    *
          flag_6_1_2    *
          flag_6_1_3
    /missing out=mylist ;
proc print data=mylist(drop=percent);
    sum count;
run ;

proc contents data=local.caad_01_encs_summary varnum ;
run ;

Hope this helps,

-David

Hi All,

I just posted a minor edit to the pseudo code, clarifying that the ICD-9 diagnoses codes for CAAD include 433.1, 433.10, and 433.11.  In the 12/29/2014 pseudo code document the ICD codes are mentioned in two places, but in one of the places only code 433.1 (with an implicit * following the last digit) was listed.  Now all three qualifying codes (433.1, 433.10, and 433.11) are listed in both places.  The pseudo code document date remains the dete it was when the final pseudo code was posted (12/29/2014) and a note has been addd to the title page acknowledging the edit.

-David Carrell (carrell.d@ghc.org)

eM-3 compliant data dictionaries now posted for this phenotype.  Reach out with any questions.

Hi Marshfield Friends,

Analyzing the CAAD phenotype data the GH/UWgeneticists noticed the field CAAD_INDEX_DATE in the SUBJECT file is missing for all 505 subjects from the Marshfield eMERGE cohort (table below).  From your email below (6/25/2015) I am guessing that you do not have IRB approval to provide such dates as MM/DD/YYYY.  Can you please provide CAAD_INDEX_DATE as the year (YYYY) only?  It is an important measure for the analysis.

Table 1. Marshfield CAAD phenotype subjects  Missing CAAD_INDEX_DATE
Controls 
Control type 1: 35
Control type 2: 426
Cases 
Case type 1: 36
Case type 2: 8
Total 505

From the pseudo code document,  here is the definition of CAAD_INDEX_DATE, modified for the situation at Marshfield:

For case definition #1, case definition #2, and control definition #1 index date is the date year of the earliest qualifying stenosis measurement.  For control definition #2 index date is the date year of the data pull (or date year of death or loss to follow up if the patient is deceased or lost  to follow up at time of the data pull).

Please let me know if it would be helpful to discuss this, or if you would like me to send you the file name of the file you sent.

Cheers,

David