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comorbidity.sas
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comorbidity.sas
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******* To compute combined comorbidity scores based on ICD-9 and ICD-10 codes *******;
*** DX_set must contain patid, Dx_CodeType (alphabetic 09 or 10), DX ***
*** You should customize macrovariables dx_set and score_set before running ***
***************************************************************************************;
*source;
*https://assets.website-files.com/5ddc21a55d412bcfa838a006/5f4520e0df1b213317f0604e_combined_comorbidity_score_ICD9_10_code.txt;
*paper;
*https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3100405/;
*run the prepare_comorb_data.sas first;
%let dx_set = samenh_long_nodup;
%let score_set = combined_comorb_score_set;
proc sql;
create table for_combined_comorbidity_score as
select patid,
MAX(case when Dx_CodeType = "09" and DX = "2911" then 1
when Dx_CodeType = "09" and DX = "2912" then 1
when Dx_CodeType = "09" and DX = "2915" then 1
when Dx_CodeType = "09" and DX = "2918" then 1
when Dx_CodeType = "09" and DX = "2919" then 1
when Dx_CodeType = "09" and DX >= "3039" and DX <= "30393" then 1
when Dx_CodeType = "09" and DX >= "3050" and DX <= "30503" then 1
when Dx_CodeType = "09" and DX = "V113" then 1
when Dx_CodeType = "10" and DX = "E52" then 1
when Dx_CodeType = "10" and DX like "F10%" then 1
when Dx_CodeType = "10" and DX = "G621" then 1
when Dx_CodeType = "10" and DX = "I426" then 1
when Dx_CodeType = "10" and DX like "K292%" then 1
when Dx_CodeType = "10" and DX = "K700" then 1
when Dx_CodeType = "10" and DX like "K703%" then 1
when Dx_CodeType = "10" and DX = "K709" then 1
when Dx_CodeType = "10" and DX like "T51%" then 1
when Dx_CodeType = "10" and DX = "Z658" then 1
when Dx_CodeType = "10" and DX like "Z714%" then 1
else 0
end) as Alcohol_abuse,
MAX(case when Dx_CodeType = "09" and DX >= "140" and substr(DX, 1, 3) <= "171" then 1
when Dx_CodeType = "09" and DX >= "174" and substr(DX, 1, 3) <= "195" then 1
when Dx_CodeType = "09" and DX >= "200" and substr(DX, 1, 3) <= "208" then 1
when Dx_CodeType = "09" and DX = "2730" then 1
when Dx_CodeType = "09" and DX = "2733" then 1
when Dx_CodeType = "09" and DX = "V1046" then 1
when Dx_CodeType = "10" and DX >= "C00" and substr(DX, 1, 3) <= "C26" then 1
when Dx_CodeType = "10" and DX >= "C30" and substr(DX, 1, 3) <= "C34" then 1
when Dx_CodeType = "10" and DX >= "C37" and substr(DX, 1, 3) <= "C41" then 1
when Dx_CodeType = "10" and DX like "C43%" then 1
when Dx_CodeType = "10" and DX >= "C45" and substr(DX, 1, 3) <= "C58" then 1
when Dx_CodeType = "10" and DX >= "C60" and substr(DX, 1, 3) <= "C75" then 1
when Dx_CodeType = "10" and DX like "C76%" then 1
when Dx_CodeType = "10" and DX >= "C81" and substr(DX, 1, 4) <= "C943" then 1
when Dx_CodeType = "10" and DX like "C948%" then 1
when Dx_CodeType = "10" and DX like "C95%" then 1
when Dx_CodeType = "10" and DX >= "C960" and DX <= "C964" then 1
when Dx_CodeType = "10" and DX = "C969" then 1
when Dx_CodeType = "10" and DX = "C96A" then 1
when Dx_CodeType = "10" and DX = "C96Z" then 1
when Dx_CodeType = "10" and DX = "D45" then 1
when Dx_CodeType = "10" and DX = "D89" then 1
when Dx_CodeType = "10" and DX = "Z8546" then 1
else 0
end) as Any_tumor,
MAX(case when Dx_CodeType = "09" and DX = "42610" then 1
when Dx_CodeType = "09" and DX = "42611" then 1
when Dx_CodeType = "09" and DX = "42613" then 1
when Dx_CodeType = "09" and DX >= "4262" and DX <= "4264" then 1
when Dx_CodeType = "09" and DX >= "42650" and DX <= "42653" then 1
when Dx_CodeType = "09" and DX >= "4266" and DX <= "4268" then 1
when Dx_CodeType = "09" and DX = "4270" then 1
when Dx_CodeType = "09" and DX = "4272" then 1
when Dx_CodeType = "09" and DX = "42731" then 1
when Dx_CodeType = "09" and DX = "4276" then 1
when Dx_CodeType = "09" and DX = "4279" then 1
when Dx_CodeType = "09" and DX = "7850" then 1
when Dx_CodeType = "09" and DX = "V450" then 1
when Dx_CodeType = "09" and DX = "V533" then 1
when Dx_CodeType = "10" and DX = "I440" then 1
when Dx_CodeType = "10" and DX = "I441" then 1
when Dx_CodeType = "10" and DX >= "I443" and DX <= "I452" then 1
when Dx_CodeType = "10" and DX >= "I454" and substr(DX, 1, 4) <= "I458" then 1
when Dx_CodeType = "10" and DX = "I459" then 1
when Dx_CodeType = "10" and DX >= "I47" and substr(DX, 1, 3) <= "I49" then 1
when Dx_CodeType = "10" and DX = "R000" then 1
when Dx_CodeType = "10" and DX = "R001" then 1
when Dx_CodeType = "10" and DX = "R008" then 1
when Dx_CodeType = "10" and DX like "T821%" then 1
when Dx_CodeType = "10" and DX like "Z450%" then 1
when Dx_CodeType = "10" and DX = "Z950" then 1
when Dx_CodeType = "10" and DX = "Z95810" then 1
when Dx_CodeType = "10" and DX = "Z95818" then 1
when Dx_CodeType = "10" and DX = "Z959" then 1
else 0
end) as Cardiac_arrhythmias,
MAX(case when Dx_CodeType = "09" and DX = "4150" then 1
when Dx_CodeType = "09" and DX = "4168" then 1
when Dx_CodeType = "09" and DX = "4169" then 1
when Dx_CodeType = "09" and DX >= "491" and substr(DX, 1, 3) <= "494" then 1
when Dx_CodeType = "09" and DX like "496%" then 1
when Dx_CodeType = "10" and DX like "I260%" then 1
when Dx_CodeType = "10" and DX >= "I272" and DX <= "I279" then 1
when Dx_CodeType = "10" and DX >= "J40" and substr(DX, 1, 3) <= "J47" then 1
when Dx_CodeType = "10" and DX >= "J60" and substr(DX, 1, 3) <= "J67" then 1
when Dx_CodeType = "10" and DX = "J684" then 1
when Dx_CodeType = "10" and DX = "J701" then 1
when Dx_CodeType = "10" and DX = "J703" then 1
else 0
end) as Chronic_pulmonary_disease,
MAX(case when Dx_CodeType = "09" and DX >= "2860" and DX <= "2869" then 1
when Dx_CodeType = "09" and DX = "2871" then 1
when Dx_CodeType = "09" and DX >= "2873" and DX <= "2875" then 1
when Dx_CodeType = "10" and DX >= "D65" and substr(DX, 1, 3) <= "D68" then 1
when Dx_CodeType = "10" and DX = "D691" then 1
when Dx_CodeType = "10" and DX >= "D693" and DX <= "D696" then 1
else 0
end) as Coagulopathy,
MAX(case when Dx_CodeType = "09" and DX >= "2504" and DX <= "25073" then 1
when Dx_CodeType = "09" and DX >= "25090" and DX <= "25093" then 1
when Dx_CodeType = "10" and DX >= "E102" and DX <= "E108" then 1
when Dx_CodeType = "10" and DX >= "E112" and DX <= "E118" then 1
when Dx_CodeType = "10" and DX >= "E122" and DX <= "E128" then 1
when Dx_CodeType = "10" and DX >= "E132" and substr(DX, 1, 4) <= "E138" then 1
else 0
end) as Complicated_diabetes,
MAX(case when Dx_CodeType = "09" and DX = "40201" then 1
when Dx_CodeType = "09" and DX = "40211" then 1
when Dx_CodeType = "09" and DX = "40291" then 1
when Dx_CodeType = "09" and DX like "425%" then 1
when Dx_CodeType = "09" and DX like "428%" then 1
when Dx_CodeType = "09" and DX = "4293" then 1
when Dx_CodeType = "10" and DX = "A1884" then 1
when Dx_CodeType = "10" and DX = "I099" then 1
when Dx_CodeType = "10" and DX = "I110" then 1
when Dx_CodeType = "10" and DX = "I130" then 1
when Dx_CodeType = "10" and DX = "I132" then 1
when Dx_CodeType = "10" and DX = "I255" then 1
when Dx_CodeType = "10" and DX like "I42%" then 1
when Dx_CodeType = "10" and DX like "I43%" then 1
when Dx_CodeType = "10" and DX like "I50%" then 1
when Dx_CodeType = "10" and DX = "I517" then 1
when Dx_CodeType = "10" and DX = "P290" then 1
else 0
end) as Congestive_heart_failure,
MAX(case when Dx_CodeType = "09" and DX >= "2801" and DX <= "2819" then 1
when Dx_CodeType = "09" and DX = "2859" then 1
when Dx_CodeType = "10" and DX >= "D501" and DX <= "D509" then 1
when Dx_CodeType = "10" and DX >= "D51" and substr(DX, 1, 3) <= "D53" then 1
when Dx_CodeType = "10" and DX = "D649" then 1
else 0
end) as Deficiency_anemia,
MAX(case when Dx_CodeType = "09" and DX like "290%" then 1
when Dx_CodeType = "09" and DX = "3310" then 1
when Dx_CodeType = "09" and DX = "3311" then 1
when Dx_CodeType = "09" and DX = "3312" then 1
when Dx_CodeType = "10" and DX >= "F01" and substr(DX, 1, 3) <= "F03" then 1
when Dx_CodeType = "10" and DX = "F05" then 1
when Dx_CodeType = "10" and DX like "G30%" then 1
when Dx_CodeType = "10" and DX = "G3101" then 1
when Dx_CodeType = "10" and DX = "G3109" then 1
when Dx_CodeType = "10" and DX = "G311" then 1
else 0
end) as Dementia,
MAX(case when Dx_CodeType = "09" and DX like "276%" then 1
when Dx_CodeType = "10" and DX = "E222" then 1
when Dx_CodeType = "10" and DX like "E86%" then 1
when Dx_CodeType = "10" and DX like "E87%" then 1
else 0
end) as Fluid_and_electrolyte_disorders,
MAX(case when Dx_CodeType = "09" and DX >= "042" and substr(DX, 1, 3) <= "044" then 1
when Dx_CodeType = "10" and DX like "B20%" then 1
else 0
end) as HIV_AIDS,
MAX(case when Dx_CodeType = "09" and DX like "342%" then 1
when Dx_CodeType = "09" and DX like "344%" then 1
when Dx_CodeType = "10" and DX = "G041" then 1
when Dx_CodeType = "10" and DX = "G114" then 1
when Dx_CodeType = "10" and DX = "G801" then 1
when Dx_CodeType = "10" and DX = "G802" then 1
when Dx_CodeType = "10" and DX like "G81%" then 1
when Dx_CodeType = "10" and DX like "G82%" then 1
when Dx_CodeType = "10" and DX like "G83%" then 1
else 0
end) as Hemiplegia,
MAX(case when Dx_CodeType = "09" and DX = "4011" then 1
when Dx_CodeType = "09" and DX = "4019" then 1
when Dx_CodeType = "09" and DX = "40210" then 1
when Dx_CodeType = "09" and DX = "40290" then 1
when Dx_CodeType = "09" and DX = "40410" then 1
when Dx_CodeType = "09" and DX = "40490" then 1
when Dx_CodeType = "09" and DX = "40511" then 1
when Dx_CodeType = "09" and DX = "40519" then 1
when Dx_CodeType = "09" and DX = "40591" then 1
when Dx_CodeType = "09" and DX = "40599" then 1
when Dx_CodeType = "10" and DX like "I10%" then 1
when Dx_CodeType = "10" and DX >= "I11" and substr(DX, 1, 3) <= "I13" then 1
when Dx_CodeType = "10" and DX like "I15%" then 1
when Dx_CodeType = "10" and DX = "N262" then 1
else 0
end) as Hypertension,
MAX(case when Dx_CodeType = "09" and DX = "07032" then 1
when Dx_CodeType = "09" and DX = "07033" then 1
when Dx_CodeType = "09" and DX = "07054" then 1
when Dx_CodeType = "09" and DX = "4560" then 1
when Dx_CodeType = "09" and DX = "4561" then 1
when Dx_CodeType = "09" and DX = "45620" then 1
when Dx_CodeType = "09" and DX = "45621" then 1
when Dx_CodeType = "09" and DX = "5710" then 1
when Dx_CodeType = "09" and DX = "5712" then 1
when Dx_CodeType = "09" and DX = "5713" then 1
when Dx_CodeType = "09" and DX >= "57140" and DX <= "57149" then 1
when Dx_CodeType = "09" and DX = "5715" then 1
when Dx_CodeType = "09" and DX = "5716" then 1
when Dx_CodeType = "09" and DX = "5718" then 1
when Dx_CodeType = "09" and DX = "5719" then 1
when Dx_CodeType = "09" and DX = "5723" then 1
when Dx_CodeType = "09" and DX = "5728" then 1
when Dx_CodeType = "09" and DX = "V427" then 1
when Dx_CodeType = "10" and DX like "B18%" then 1
when Dx_CodeType = "10" and DX like "I85%" then 1
when Dx_CodeType = "10" and DX = "I864" then 1
when Dx_CodeType = "10" and DX like "K70%" then 1
when Dx_CodeType = "10" and DX = "K711" then 1
when Dx_CodeType = "10" and DX >= "K713" and DX <= "K715" then 1
when Dx_CodeType = "10" and DX = "K717" then 1
when Dx_CodeType = "10" and DX like "K721%" then 1
when Dx_CodeType = "10" and DX like "K729%" then 1
when Dx_CodeType = "10" and DX >= "K73" and substr(DX, 1, 3) <= "K74" then 1
when Dx_CodeType = "10" and DX = "K754" then 1
when Dx_CodeType = "10" and DX = "K7581" then 1
when Dx_CodeType = "10" and DX = "K760" then 1
when Dx_CodeType = "10" and DX >= "K762" and DX <= "K769" then 1
when Dx_CodeType = "10" and DX = "Z4823" then 1
when Dx_CodeType = "10" and DX = "Z944" then 1
else 0
end) as Liver_disease,
MAX(case when Dx_CodeType = "09" and DX >= "196" and substr(DX, 1, 3) <= "199" then 1
when Dx_CodeType = "10" and DX = "C459" then 1
when Dx_CodeType = "10" and DX >= "C77" and substr(DX, 1, 3) <= "C80" then 1
else 0
end) as Metastatic_cancer,
MAX(case when Dx_CodeType = "09" and DX like "440%" then 1
when Dx_CodeType = "09" and DX = "4412" then 1
when Dx_CodeType = "09" and DX = "4414" then 1
when Dx_CodeType = "09" and DX = "4417" then 1
when Dx_CodeType = "09" and DX = "4419" then 1
when Dx_CodeType = "09" and DX >= "4431" and DX <= "4439" then 1
when Dx_CodeType = "09" and DX = "4471" then 1
when Dx_CodeType = "09" and DX = "5571" then 1
when Dx_CodeType = "09" and DX = "5579" then 1
when Dx_CodeType = "09" and DX = "V434" then 1
when Dx_CodeType = "10" and DX = "E0851" then 1
when Dx_CodeType = "10" and DX = "E0852" then 1
when Dx_CodeType = "10" and DX = "E0951" then 1
when Dx_CodeType = "10" and DX = "E0952" then 1
when Dx_CodeType = "10" and DX = "E1051" then 1
when Dx_CodeType = "10" and DX = "E1052" then 1
when Dx_CodeType = "10" and DX = "E1151" then 1
when Dx_CodeType = "10" and DX = "E1351" then 1
when Dx_CodeType = "10" and DX = "E1352" then 1
when Dx_CodeType = "10" and DX = "I7779" then 1
when Dx_CodeType = "10" and DX = "I670" then 1
when Dx_CodeType = "10" and DX like "I70%" then 1
when Dx_CodeType = "10" and DX like "I71%" then 1
when Dx_CodeType = "10" and DX = "I731" then 1
when Dx_CodeType = "10" and DX like "I738%" then 1
when Dx_CodeType = "10" and DX = "I739" then 1
when Dx_CodeType = "10" and DX = "I771" then 1
when Dx_CodeType = "10" and DX >= "I7771" and DX <= "I7774" then 1
when Dx_CodeType = "10" and DX like "I79%" then 1
when Dx_CodeType = "10" and DX = "K551" then 1
when Dx_CodeType = "10" and DX = "K558" then 1
when Dx_CodeType = "10" and DX = "K559" then 1
when Dx_CodeType = "10" and DX like "Z9582%" then 1
when Dx_CodeType = "10" and DX = "Z959" then 1
else 0
end) as Peripheral_vascular_disease,
MAX(case when Dx_CodeType = "09" and DX >= "295" and DX <= "29899" then 1
when Dx_CodeType = "09" and DX = "2991" then 1
when Dx_CodeType = "09" and DX = "29911" then 1
when Dx_CodeType = "10" and DX like "F20%" then 1
when Dx_CodeType = "10" and DX >= "F22" and substr(DX, 1, 3) <= "F25" then 1
when Dx_CodeType = "10" and DX like "F28%" then 1
when Dx_CodeType = "10" and DX like "F29%" then 1
when Dx_CodeType = "10" and DX >= "F30" and substr(DX, 1, 3) <= "F33" then 1
when Dx_CodeType = "10" and DX = "F348" then 1
when Dx_CodeType = "10" and DX = "F349" then 1
when Dx_CodeType = "10" and DX like "F39%" then 1
when Dx_CodeType = "10" and DX = "F4489" then 1
when Dx_CodeType = "10" and DX = "F843" then 1
else 0
end) as Psychosis,
MAX(case when Dx_CodeType = "09" and DX like "416%" then 1
when Dx_CodeType = "09" and DX = "4179" then 1
when Dx_CodeType = "10" and DX like "I26%" then 1
when Dx_CodeType = "10" and DX like "I27%" then 1
when Dx_CodeType = "10" and DX = "I280" then 1
when Dx_CodeType = "10" and DX = "I288" then 1
when Dx_CodeType = "10" and DX = "I289" then 1
else 0
end) as Pulmonary_circulation_disorders,
MAX(case when Dx_CodeType = "09" and DX = "40311" then 1
when Dx_CodeType = "09" and DX = "40391" then 1
when Dx_CodeType = "09" and DX = "40412" then 1
when Dx_CodeType = "09" and DX = "40492" then 1
when Dx_CodeType = "09" and DX like "585%" then 1
when Dx_CodeType = "09" and DX like "586%" then 1
when Dx_CodeType = "09" and DX = "V420" then 1
when Dx_CodeType = "09" and DX = "V451" then 1
when Dx_CodeType = "09" and DX = "V560" then 1
when Dx_CodeType = "09" and DX = "V568" then 1
when Dx_CodeType = "10" and DX = "I120" then 1
when Dx_CodeType = "10" and DX like "I13%" then 1
when Dx_CodeType = "10" and DX >= "N032" and DX <= "N037" then 1
when Dx_CodeType = "10" and DX >= "N052" and DX <= "N057" then 1
when Dx_CodeType = "10" and DX like "N18%" then 1
when Dx_CodeType = "10" and DX like "N19%" then 1
when Dx_CodeType = "10" and DX = "N250" then 1
when Dx_CodeType = "10" and DX = "Z3932" then 1
when Dx_CodeType = "10" and DX = "Z4822" then 1
when Dx_CodeType = "10" and DX like "Z490%" then 1
when Dx_CodeType = "10" and DX = "Z4931" then 1
when Dx_CodeType = "10" and DX = "Z9115" then 1
when Dx_CodeType = "10" and DX = "Z940" then 1
when Dx_CodeType = "10" and DX = "Z992" then 1
else 0
end) as Renal_failure,
MAX(case when Dx_CodeType = "09" and DX >= "260" and substr(DX, 1, 3) <= "263" then 1
when Dx_CodeType = "10" and DX >= "E40" and substr(DX, 1, 3) <= "E46" then 1
when Dx_CodeType = "10" and DX = "E640" then 1
when Dx_CodeType = "10" and DX = "R634" then 1
when Dx_CodeType = "10" and DX = "R64" then 1
else 0
end) as Weight_loss
from &dx_set
group by patid
order by patid;
quit;
data &score_set;
set for_combined_comorbidity_score;
combinedscore = (5 * Metastatic_cancer);
combinedscore + (Congestive_heart_failure * 2);
combinedscore + (Dementia * 2);
combinedscore + (Renal_failure * 2);
combinedscore + (Weight_loss * 2);
combinedscore + (Hemiplegia);
combinedscore + (Alcohol_abuse);
combinedscore + (Any_tumor);
combinedscore + (Cardiac_arrhythmias);
combinedscore + (Chronic_pulmonary_disease);
combinedscore + (Coagulopathy);
combinedscore + (Complicated_diabetes);
combinedscore + (Deficiency_anemia);
combinedscore + (Fluid_and_electrolyte_disorders);
combinedscore + (Liver_disease);
combinedscore + (Peripheral_vascular_disease);
combinedscore + (Psychosis);
combinedscore + (Pulmonary_circulation_disorders);
combinedscore + (HIV_AIDS * -1);
combinedscore + (Hypertension * -1);
keep patid combinedscore;
run;
proc freq data= combined_comorb_score_set;
tables combinedscore;
run;
proc export data=combined_comorb_score_set
outfile='\\prfs.cri.uchicago.edu\sanghavi-lab\Zoey\gardner\data\merge_output\pu\medpar_mds_final\secondary_only_comorbidity_new.csv'
dbms=csv
replace;
run;