--------------- README.virology --------------- ----------------------------------------------------------------- ACTG 175 documentation for the following publication: "THE RELATION OF VIROLOGIC AND IMMUNOLOGIC MARKERS TO CLINICAL OUTCOMES AFTER NUCLEOSIDE THERAPY IN HIV-INFECTED ADULTS WITH 200 TO 500 CD4 CELLS PER CUBIC MILLIMETER." Copyright, 1996, by the Massachusetts Medical Society Published in the New England Journal of Medicine on October 10, 1996 by David Katzenstein, M.D., Scott M. Hammer, M.D., Michael D. Hughes, Ph.D., Holly Gundacker, M.S., J. Brooks Jackson, M.D., Susan Fiscus, Ph.D., Suraiya Rasheed, M.D., Tarik Elbeik, Ph.D., Richard Reichman, M.D., Anthony Japour, M.D., Thomas C. Merigan, M.D., and Martin S. Hirsch, M.D., For the AIDS Clinical Trials Group Study 175 Study Team. ---------------------------------------------------------------------------- ACTG 175 was a randomized, double-blind, placebo-controlled trial to compare monotherapy with zidovudine or didanosine with combination therapy with zidovudine and didanosine or zidovudine and zalcitabine in HIV-1-infected subjects with CD4 cell counts between 200 and 500 per cubic millimeter. The virology subgroup consisted of 391 subjects enrolled at 11 of the study sites Blood was collected in acid citrate dextrose on two occasions, at least 72 hours apart, during the 14 days preceding treatment, to determine plasma HIV RNA concentrations. Plasma HIV RNA concentations were measured at weeks 8, 20, and 56, provided that the subjects continued to receive the assigned treatment. After 8 weeks, the mean decrease from baseline in the concentration of HIV RNA, expressed as the change in the base 10 log of the number of copies per millimeter, was 0.25 +/- 0.06 for patients treated with zidovudine alone, 0l65 +/- 0.07 for didanosine alone, 0.93 +/- 0.10 for zidovudine plus didanosine, and 0l89 +/- 0.06 for zidovudine plus zalcitabine. Both the risk of progression of HIV disease and the efficacy of antiretroviral therapy are strongly associated with the plasma level of HIV RNA and with the viral phenotype. The changes in the plasma concentration of HIV RNA predict the changes in CD4 cell counts and survival after treatment with reverse-transcriptase inhibitors. The datasets on this disk are the final analysis data sets for virology data collected in the virology substudy of ACTG 175. The datasets are restricted to the 391 subjects who had any p24, quantitative microculture or HIV RNA measurements completed prior to starting treatment in ACTG 175. All 391 subjects started treatment. The following is a brief description of each of the data sets, followed by a more complete description of each variable. baseline.ssd01 - This includes baseline demographic data etc. as well as the baseline (pre-treatment) p24, qmc, rna and cd4 values. Ideally there would be two baseline values for each measured on the same two days. However, while all subjects have one or two CD4 values, some have no p24, or no qmc, or no rna values. In addition, many subjects have (for example) the two p24 values on days which differ from the days of the CD4 values. For simplicity, the value labelled 1 (e.g. qmc1 or cd4_1) is the result for a specimen obtained closest to the start of treatment, and 2 (e.g. qmc2 or cd4_2) is the result for the preceding specimen. For the p24, not all subjects had follow-up specimens tested. For those that did, one of the pre-treatment specimens may have been tested again; this is labelled p24_3. status.ssd01 - Treatment codes, important follow-up dates including crossover information. endpoint.ssd01 - 50% CD4 declines, verified AIDS events and deaths cd4_fup, p24_fup, qmc_fup, rna_fup - Follow-up results (any measurements taken mt2_fup after the date of starting treatment). data215.ssd01 This dataset contains baseline 215 mutation data. ---- Baseline.ssd01 - Alphabetic List of Variables and Attributes----- # Variable Type Len Pos Format Label ------------------------------------------------------------------------------------------ 40 AGE Num 8 235 patient age at randomization 48 AVECD4 Num 8 271 mean of two baseline cd4 counts 49 B50CD4 Num 8 279 50% of baseline cd4 counts: endpoint tri 26 CD4DT1 Num 8 134 DATE7. CD4 specimen date (1) 28 CD4DT2 Num 8 150 DATE7. CD4 specimen date (2) 25 CD4_1 Num 8 126 CD4 (1) (cells/ml) 27 CD4_2 Num 8 142 CD4 (2) (cells/ml) 14 CENS1 Char 5 58 QMC censoring (1) 19 CENS2 Char 5 88 QMC censoring (2) 17 FRFRZ1 Char 1 79 QMC fresh (F) or frozen (Z) (1) 22 FRFRZ2 Char 1 109 QMC fresh (F) or frozen (Z) (2) 45 HEMOPHI Char 1 261 hemophiliac 46 HOMOSEX Char 1 262 homosexual activity 44 IVDRUG Char 1 260 history of intravenous drug use 51 KARNOF Num 8 295 karnofsky score 36 MT2 Char 3 208 MT2 result (SI/NSI/IND) 39 MT2ADT Num 8 227 DATE7. MT2 assay date 4 MT2DATA Char 1 3 Does patient have baseline mt2 data? 38 MT2DT Num 8 219 DATE7. MT2 specimen date 37 MT2LAB Num 8 211 MT2 lab at baseline 55 OTHPRIOR Char 1 320 Non-ZDV arv therapy prior to 175: Y/N 7 P24ADT1 Num 5 17 DATE7. P24 assay date of batch 1 (1) 10 P24ADT2 Num 5 35 DATE7. P24 assay date of batch 1 (2) 13 P24ADT3 Num 5 53 DATE7. P24 assay date of batch 2 1 P24DATA Char 1 0 Does patient have baseline p24 data? 5 P24DT1 Num 5 4 DATE7. P24 date of batch 1 (1) 8 P24DT2 Num 5 22 DATE7. P24 date of batch 1 (2) 11 P24DT3 Num 5 40 DATE7. P24 date of batch 2 6 P24_1 Num 8 9 P24 batch 1 (1) (pg/ml) 9 P24_2 Num 8 27 P24 batch 1 (2) (pg/ml) 12 P24_3 Num 8 45 P24 batch 2 (pg/ml) 59 PIDNUM Num 8 338 patient id number 53 PREANTI Num 8 311 days of pre-175 antiretroviral therapy 18 QMC1 Num 8 80 QMC (1) (IUPM) 23 QMC2 Num 8 110 QMC (2) (IUPM) 16 QMCADT1 Num 8 71 DATE7. QMC set-up date (1) 21 QMCADT2 Num 8 101 DATE7. QMC set-up date (2) 2 QMCDATA Char 1 1 Does patient have baseline qmc data? 15 QMCDT1 Num 8 63 DATE7. QMC specimen date (1) 20 QMCDT2 Num 8 93 DATE7. QMC specimen date (2) 24 QMCLAB Num 8 118 QMC lab at baseline 41 RACETH Num 8 243 patient race/ethnicity 31 RNA1 Num 8 171 RNA (1) (copies/ml) 34 RNA2 Num 8 192 RNA (2) (copies/ml) 30 RNAADT1 Num 8 163 DATE7. RNA assay date (1) 33 RNAADT2 Num 8 184 DATE7. RNA assay date (2) 3 RNADATA Char 1 2 Does patient have baseline rna data? 29 RNADT1 Num 5 158 DATE7. RNA specimen date (1) 32 RNADT2 Num 5 179 DATE7. RNA specimen date (2) 35 RNALAB Num 8 200 RNA lab for all pre-trt & follow-up 47 SCRCD4 Num 8 263 screening cd4 count 43 SEX Char 1 259 patient gender 42 SITE Num 8 251 randomization institution 57 STR2 Num 8 322 antiretroviral history: naive/experience 52 STRAT Num 8 303 antiretroviral therapy history stratific 58 SYMPTOM Num 8 330 symptomatic/asymptomatic status 50 WTKG Num 8 287 weight kg 54 ZDV30 Char 1 319 ZDV in the 30 days prior to 175: Y/N 56 ZDVPRIOR Char 1 321 ZDV prior to 175: Y/N The following is a listing of the locations of the variables in the ascii data file baseline.dat: @1 pidnum @7 age @10 avecd4 @14 b50cd4 @18 cd4dt1 @26 cd4dt2 @34 cd4_1 @38 cd4_2 @42 cens1 @48 cens2 @54 frfrz1 @56 frfrz2 @58 hemophi @60 homosex @62 ivdrug @64 karnof @68 mt2 @72 mt2adt date7. @80 mt2data @82 mt2dt date7. @90 mt2lab @93 othprior @95 p24adt1 date7. @103 p24adt2 date7. @111 p24adt3 date7. @119 p24data @121 p24dt1 date7. @129 p24dt2 date7. @137 p24dt3 date7. @145 p24_1 @153 p24_2 @161 p24_3 @169 preanti @174 qmc1 @183 qmc2 @192 qmcadt1 date7. @200 qmcadt2 date7. @208 qmcdata @210 qmcdt1 date7. @218 qmcdt2 date7. @226 qmclab @229 raceth @231 rna1 @239 rna2 @247 rnaadt1 date7. @255 rnaadt2 date7. @263 rnadata @265 rnadt1 date7. @273 rnadt2 date7. @281 rnalab @283 scrcd4 @287 sex @289 site @291 str2 @293 strat @295 symptom @297 wtkg @306 zdv30 @308 zdvprior ----- Data215.ssd01 Alphabetic List of Variables and Attributes----- # Variable Type Len Pos Format Label --------------------------------------------------------------------------------------- 2 ASSAYDT Num 8 3 DATE7. date of 215 assay 1 LAB Num 3 0 lab for 215 assay 5 PIDNUM Num 8 20 4 RES215 Char 1 19 215 result (W=wild, M=mutant, X=mixed) 3 SPECDT Num 8 11 DATE7. date of specimen for 215 The variables in data215.dat are in the following locations: @1 pidnum @7 lab @10 assaydt date7. @18 specdt date7. @26 res215; ---- mt2_fup.ssd01 Alphabetic List of Variables and Attributes----- # Variable Type Len Pos Format Label ------------------------------------------------------------------------ 3 ASSAYDT Num 8 11 DATE7. MT2 assay date 4 LAB Num 8 19 MT2 lab 1 MT2 Char 3 0 MT2 result (SI/NSI/IND) 5 PIDNUM Num 8 27 2 SPECDATE Num 8 3 DATE7. MT2 specimen date The variables for mt2_fup.dat are arranged as follows: @1 pidnum @7 mt2 @11 specdate date7. @19 assaydt date7. @27 lab; ---- qmc_fup.ssd01 Alphabetic List of Variables and Attributes----- # Variable Type Len Pos Format Label ---------------------------------------------------------------------------- 4 ASSAYDT Num 8 17 DATE7. QMC set-up date 1 CENS Char 5 0 QMC censoring 5 FRFRZ Char 1 25 QMC fresh (F) or frozen (Z) 2 LAB Num 4 5 QMC lab 7 PIDNUM Num 8 34 6 QMC Num 8 26 QMC titer (IUPM) 3 SPECDATE Num 8 9 DATE7. QMC specimen date The variables for qmc_fup.dat are arranged as follows: @1 pidnum @7 cens @13 lab @15 specdate date7. @23 assaydt date7. @31 frfrz @33 qmc; ---- status.ssd01 - Alphabetic List of Variables and Attributes----- # Variable Type Len Pos Format Label --------------------------------------------------------------------------------------- 2 CRSDT Num 8 8 DATE7. date of cross-over randomization 13 CRSTRT Char 1 255 cross-over treatment assignment 15 CRSTYPE Num 8 264 type of endpoint used to crossover 11 DEATHDT Num 8 246 DATE7. date of death 14 LSTCD4DT Num 8 256 date of last cd4 count before 2/28/95 8 OFFSDT Num 8 180 DATE7. off study date 9 OFFSRSN Num 8 188 off study reason 4 OFFTRDT Num 8 24 DATE7. off treatment date 5 OFFTRSN Num 8 32 off treatment reason 10 OSDESC Char 50 196 off study reason description 6 OTDESC1 Char 70 40 off treatment reason description 1 7 OTDESC2 Char 70 110 off treatment reason description 2 16 PIDNUM Num 8 272 3 RANDDT Num 8 16 DATE7. randomization date 1 STRTDT Num 8 0 DATE7. date of start treatment 12 TRT Char 1 254 initial treatment assignment The variables for status.dat are arranged as follows: @1 pidnum @7 strtdt date7. @15 crsdt date7. @23 randdt date7. @31 offtrdt date7. @39 offtrsn @42 otdesc1 @114 otdesc2 @185 offsdt date7. @193 offsrsn @196 osdesc @247 deathdt date7. @255 trt @258 crstrt @260 lstcd4dt date7. @269 crstype; ---- CD4_fup.ssd01 - Alphabetic List of Variables and Attributes----- # Variable Type Len Pos Format Label --------------------------------------------------------------------- 1 CD4 Num 8 0 cd4 cell count (mm3) 3 PIDNUM Num 8 16 2 SPECDATE Num 8 8 DATE7. date of cd4 specimen CD4_fup.dat has variables arranged as follows: @1 pidnum @7 specdate date7. @15 cd4; ----- Endpoint.ssd01 - Alphabetic List of Variables and Attributes----- # Variable Type Len Pos Format Label -------------------------------------------------------------------------------------- 5 AIDSCAT Char 29 58 category for AIDS endpoint type 2 DTHCAT Char 15 5 category for HIV related death status 1 EVENT Char 5 0 type of study endpoint/event 3 EVTDESC Char 30 20 description of endpoint 4 EVTDT Num 8 50 DATE7. date of study endpoint/event 6 PIDNUM Num 8 87 Endpoint.dat has variables arranged as follows: @1 pidnum @7 event @13 dthcat @39 evtdesc @70 evtdt date7. @78 aidscat; ---- P24_fup.ssd01 - Alphabetic List of Variables and Attributes----- # Variable Type Len Pos Format Label ------------------------------------------------------------------ 3 ASSAYDT Num 5 13 DATE7. P24 assay date 2 P24 Num 8 5 P24 (pg/ml) 4 PIDNUM Num 8 18 1 SPECDATE Num 5 0 DATE7. P24 specimen date The variables in P24_fup.dat are arranged as follows: @1 pidnum @7 specdate date7. @15 p24 @22 assaydt date7.; ----- RNA_fup.ssd01 - Alphabetic List of Variables and Attributes----- # Variable Type Len Pos Format Label ------------------------------------------------------------------ 2 ASSAYDT Num 8 5 DATE7. RNA assay date 4 PIDNUM Num 8 21 3 RNA Num 8 13 RNA (copies/ml) 1 SPECDATE Num 5 0 DATE7. RNA specimen date The variables in RNA_fup.dat are in the following locations: @1 pidnum @7 specdate date7. @15 assaydt date7. @23 rna;