Indirect response model

6 messages 6 people Latest: May 28, 2007

Indirect response model

From: Nishit Modi Date: May 15, 2007 technical
I am conducting a sequential pharmacokinetic-pharmacodynamic model. The pharmacokinetic fits look good and I was using an indirect response model. The PD model is that the drug inhibits clearance of the analyte (PD response), thus one expects that the response increases with increasing drug (Model II). There is a baseline measured (=Kfor/Kcl) and a dummy dose=1 unit given. It seems despite trying various permutations of the model, eta1 seems to be very small and no covariance step is conducted. The model and data for the first 3 subjects are reproducted below. Any assistance would be appreciated. Note that since conc (COP) are read in, the model only requires a single differential equation. Any insight would be appreciated. Nishit $PROBLEM PD - ADVAN6 $DATA C:\PDDATA.CSV $INPUT ID TIME DV AMT=DOSE COP MDV ; data are subject ID, Time, DV=PD response, Amt (dummy dose of 1 inserted), COP=plasma conc which drive PD model, MDV $SUBROUTINES ADVAN6 TOL=6 $MODEL COMP=(EFFECT, DEFDOSE, DEFOBS) $PK KFOR = THETA(1) KCL = THETA(2)*EXP(ETA(1)) IC50 = THETA(3) IMAX = THETA(4) F1 = KFOR/KCL COEF = IMAX*COP/(IC50+COP) $DES DADT(1) = KFOR-KCL*(1-COEF)*A(1) $ERROR W = F Y = F*EXP(ERR(1)) IPRED = F IRES = DV-IPRED IF (W.LE.0.) W=1 IWRES = IRES/W $THETA (0,0.3) $THETA (0, 0.003) $THETA (0,10) $THETA (0, 0.3, 1) $OMEGA 0.01 $SIGMA 0.5 $ESTIMATION METHOD=1 MAXEVAL=5000 PRINT=20 $COVR $TABLE ID TIME PRED IPRED IRES KFOR KCL IC50 IMAX NOPRINT ONEHEADER FILE=C:\PD.TAB 1001 0 . 1 0 1 1001 0 98.3 . 0 0 1001 168 90.6 . 122.44 0 1001 840 92.8 . 183.69 0 1002 0 . 1 0 1 1002 0 105.1 . 0 0 1002 840 88.5 . 61.253 0 1002 842 106.7 . 106.8 0 1002 844 122.1 . 116.4 0 1002 1848 129.1 . 121.46 0 1002 1850 160.4 . 212.63 0 1002 1852 157.1 . 231.89 0 1101 0 . 1 0 1 1101 0 68.1 . 0 0 1101 840 88.1 . 0.13884 0 1101 842 105.5 . 0.12987 0 1101 844 108.8 . 0.12147 0 1101 1848 113.3 . 227.79 0 1101 1850 62.6 . 379.54 0 1101 1852 138.7 . 412.18 0

Re: Indirect response model

From: Jurgen Bulitta Date: May 15, 2007 technical
Dear Nishit, If I understand correctly, you are using concentration (COP) of your drug as a time dependent covariate which is then used as forcing function for your PD model. As concentrations change over time, you probably need the CALLFL = 0 option ($PK CALLFL=0) to read in the concentration at every new time. I would write out COP in $TABLE in order to check, if COP changes over time as it should. This should work much better, but it will still give you a piecewise constant concentration profile. This may cause numerical problems. Instead, I would include the differential equations for your PK model. This should give you better numerical stability and more correct concentration predictions. You could start with reading in the individual PK parameters (IPP approach, see reference below) and then go to more complex PKPD analyses. You might try the MATRIX=S statement in $COV, if you like to get the covariance step to work. Hope some of this works. Best regards Juergen Reference: Zhang, L., S. L. Beal, and L. B. Sheiner. 2003. Simultaneous vs. sequential analysis for population PK/PD data I: best-case performance. J Pharmacokinet Pharmacodyn 30:387-404. ----------------------------------------------- Juergen Bulitta, PhD, Post-doctoral Fellow Pharmacometrics, University at Buffalo, NY, USA Phone: +1 716 645 2855 ext. 281, [EMAIL PROTECTED] ----------------------------------------------- -----Ursprüngliche Nachricht----- Von: "Modi, Nishit [ALZUS]" <[EMAIL PROTECTED]> Gesendet: 15.05.07 18:31:57 An: [EMAIL PROTECTED] CC: [email protected] Betreff: [NMusers] Indirect response model I am conducting a sequential pharmacokinetic-pharmacodynamic model. The pharmacokinetic fits look good and I was using an indirect response model. The PD model is that the drug inhibits clearance of the analyte (PD response), thus one expects that the response increases with increasing drug (Model II). There is a baseline measured (=Kfor/Kcl) and a dummy dose=1 unit given. It seems despite trying various permutations of the model, eta1 seems to be very small and no covariance step is conducted. The model and data for the first 3 subjects are reproducted below. Any assistance would be appreciated. Note that since conc (COP) are read in, the model only requires a single differential equation. Any insight would be appreciated. Nishit $PROBLEM PD - ADVAN6 $DATA C:\PDDATA.CSV $INPUT ID TIME DV AMT=DOSE COP MDV ; data are subject ID, Time, DV=PD response, Amt (dummy dose of 1 inserted), COP=plasma conc which drive PD model, MDV $SUBROUTINES ADVAN6 TOL=6 $MODEL COMP=(EFFECT, DEFDOSE, DEFOBS) $PK KFOR = THETA(1) KCL = THETA(2)*EXP(ETA(1)) IC50 = THETA(3) IMAX = THETA(4) F1 = KFOR/KCL COEF = IMAX*COP/(IC50+COP) $DES DADT(1) = KFOR-KCL*(1-COEF)*A(1) $ERROR W = F Y = F*EXP(ERR(1)) IPRED = F IRES = DV-IPRED IF (W.LE.0.) W=1 IWRES = IRES/W $THETA (0,0.3) $THETA (0, 0.003) $THETA (0,10) $THETA (0, 0.3, 1) $OMEGA 0.01 $SIGMA 0.5 $ESTIMATION METHOD=1 MAXEVAL=5000 PRINT=20 $COVR $TABLE ID TIME PRED IPRED IRES KFOR KCL IC50 IMAX NOPRINT ONEHEADER FILE=C:\PD.TAB 1001 0 . 1 0 1 1001 0 98.3 . 0 0 1001 168 90.6 . 122.44 0 1001 840 92.8 . 183.69 0 1002 0 . 1 0 1 1002 0 105.1 . 0 0 1002 840 88.5 . 61.253 0 1002 842 106.7 . 106.8 0 1002 844 122.1 . 116.4 0 1002 1848 129.1 . 121.46 0 1002 1850 160.4 . 212.63 0 1002 1852 157.1 . 231.89 0 1101 0 . 1 0 1 1101 0 68.1 . 0 0 1101 840 88.1 . 0.13884 0 1101 842 105.5 . 0.12987 0 1101 844 108.8 . 0.12147 0 1101 1848 113.3 . 227.79 0 1101 1850 62.6 . 379.54 0 1101 1852 138.7 . 412.18 0

RE: Indirect response model

From: Sunny Chapel Date: May 15, 2007 technical
Hi Nishit, Isn't F1 a reserved parameter in the PK block? I would try the following code. $PK KFOR = THETA(1) KCL = THETA(2)*EXP(ETA(1)) IC50 = THETA(3) IMAX = THETA(4) BASE = KFOR/KCL COEF = IMAX*COP/(IC50+COP) $DES DADT(1) = BASE*KCL-KCL*(1-COEF)*A(1) Regards, Sunny
Quoted reply history
________________________________ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Modi, Nishit [ALZUS] Sent: Tuesday, May 15, 2007 12:21 PM To: [EMAIL PROTECTED] Cc: [email protected] Subject: [NMusers] Indirect response model I am conducting a sequential pharmacokinetic-pharmacodynamic model. The pharmacokinetic fits look good and I was using an indirect response model. The PD model is that the drug inhibits clearance of the analyte (PD response), thus one expects that the response increases with increasing drug (Model II). There is a baseline measured (=Kfor/Kcl) and a dummy dose=1 unit given. It seems despite trying various permutations of the model, eta1 seems to be very small and no covariance step is conducted. The model and data for the first 3 subjects are reproducted below. Any assistance would be appreciated. Note that since conc (COP) are read in, the model only requires a single differential equation. Any insight would be appreciated. Nishit $PROBLEM PD - ADVAN6 $DATA C:\PDDATA.CSV $INPUT ID TIME DV AMT=DOSE COP MDV ; data are subject ID, Time, DV=PD response, Amt (dummy dose of 1 inserted), COP=plasma conc which drive PD model, MDV $SUBROUTINES ADVAN6 TOL=6 $MODEL COMP=(EFFECT, DEFDOSE, DEFOBS) $PK KFOR = THETA(1) KCL = THETA(2)*EXP(ETA(1)) IC50 = THETA(3) IMAX = THETA(4) F1 = KFOR/KCL COEF = IMAX*COP/(IC50+COP) $DES DADT(1) = KFOR-KCL*(1-COEF)*A(1) $ERROR W = F Y = F*EXP(ERR(1)) IPRED = F IRES = DV-IPRED IF (W.LE.0.) W=1 IWRES = IRES/W $THETA (0,0.3) $THETA (0, 0.003) $THETA (0,10) $THETA (0, 0.3, 1) $OMEGA 0.01 $SIGMA 0.5 $ESTIMATION METHOD=1 MAXEVAL=5000 PRINT=20 $COVR $TABLE ID TIME PRED IPRED IRES KFOR KCL IC50 IMAX NOPRINT ONEHEADER FILE=C:\PD.TAB 1001 0 . 1 0 1 1001 0 98.3 . 0 0 1001 168 90.6 . 122.44 0 1001 840 92.8 . 183.69 0 1002 0 . 1 0 1 1002 0 105.1 . 0 0 1002 840 88.5 . 61.253 0 1002 842 106.7 . 106.8 0 1002 844 122.1 . 116.4 0 1002 1848 129.1 . 121.46 0 1002 1850 160.4 . 212.63 0 1002 1852 157.1 . 231.89 0 1101 0 . 1 0 1 1101 0 68.1 . 0 0 1101 840 88.1 . 0.13884 0 1101 842 105.5 . 0.12987 0 1101 844 108.8 . 0.12147 0 1101 1848 113.3 . 227.79 0 1101 1850 62.6 . 379.54 0 1101 1852 138.7 . 412.18 0 ---------------------------------------------------------------------- LEGAL NOTICE Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail or any action taken (or not taken) in reliance on it is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately.

Re: Indirect response model

From: David H Salinger Date: May 16, 2007 technical
Dear Nishit, Jurgen is correct, you are using concentration (COP) as a forcing function. But, in ID 1101, for example, the COP has a value of 0 from TIME=0 to 840 and then values around 0.12 until TIME 1848. Unless this is what you had in mind, I would suggest two steps: 1. Include more time points for COP. These need not coincide with TIMEs were you have DV values. 2. Create a linear interpolation of COP to be used in the $DES block. One way to do this linear interpolation is to add two columns to your data file: PTME (previous time) and PCOP (previous concentration). Then, compute SLOPE = (COP-PCOP)/(TIME-PTME) and use a linear interpolation of conc: PCOP +SLOPE*(T-PTME) in place of COP in computing your COEF parameter (must be in $DES block). I hope this helps, David Salinger RFPK, Univ. of Washington
Quoted reply history
On Tue, 15 May 2007, Jurgen Bulitta wrote: > Dear Nishit, > > If I understand correctly, you are using concentration (COP) of > your drug as a time dependent covariate which is then used as > forcing function for your PD model. > > As concentrations change over time, you probably need the > CALLFL = 0 option ($PK CALLFL=0) to read in the concentration > at every new time. I would write out COP in $TABLE in order to > check, if COP changes over time as it should. > > This should work much better, but it will still give you a piecewise > constant concentration profile. This may cause numerical problems. > Instead, I would include the differential equations for your PK > model. This should give you better numerical stability and more > correct concentration predictions. You could start with reading in > the individual PK parameters (IPP approach, see reference below) > and then go to more complex PKPD analyses. > > You might try the MATRIX=S statement in $COV, if you like to get > the covariance step to work. > > Hope some of this works. > > Best regards > Juergen > > Reference: > Zhang, L., S. L. Beal, and L. B. Sheiner. 2003. Simultaneous vs. > sequential analysis for population PK/PD data I: best-case performance. > J Pharmacokinet Pharmacodyn 30:387-404. > > ----------------------------------------------- > Juergen Bulitta, PhD, Post-doctoral Fellow > Pharmacometrics, University at Buffalo, NY, USA > Phone: +1 716 645 2855 ext. 281, [EMAIL PROTECTED] > ----------------------------------------------- > > -----Ursprüngliche Nachricht----- > Von: "Modi, Nishit [ALZUS]" <[EMAIL PROTECTED]> > Gesendet: 15.05.07 18:31:57 > An: [EMAIL PROTECTED] > CC: [email protected] > Betreff: [NMusers] Indirect response model > > I am conducting a sequential pharmacokinetic-pharmacodynamic model. The > pharmacokinetic fits look good and I was using an indirect response model. The > PD model is that the drug inhibits clearance of the analyte (PD response), thus > one expects that the response increases with increasing drug (Model II). There > is a baseline measured (=Kfor/Kcl) and a dummy dose=1 unit given. It seems > despite trying various permutations of the model, eta1 seems to be very small > and no covariance step is conducted. The model and data for the first 3 > subjects are reproducted below. Any assistance would be appreciated. Note > that since conc (COP) are read in, the model only requires a single > differential equation. Any insight would be appreciated. > > Nishit > > $PROBLEM PD - ADVAN6 > > $DATA C:\PDDATA.CSV > > $INPUT ID TIME DV AMT=DOSE COP MDV > > ; data are subject ID, Time, DV=PD response, Amt (dummy dose of 1 inserted), > COP=plasma conc which drive PD model, MDV > > $SUBROUTINES ADVAN6 TOL=6 > > $MODEL > > COMP=(EFFECT, DEFDOSE, DEFOBS) > > $PK > > KFOR = THETA(1) > > KCL = THETA(2)*EXP(ETA(1)) > > IC50 = THETA(3) > > IMAX = THETA(4) > > F1 = KFOR/KCL > > COEF = IMAX*COP/(IC50+COP) > > $DES > > DADT(1) = KFOR-KCL*(1-COEF)*A(1) > > $ERROR > > W = F > > Y = F*EXP(ERR(1)) > > IPRED = F > > IRES = DV-IPRED > > IF (W.LE.0.) W=1 > > IWRES = IRES/W > > $THETA (0,0.3) > > $THETA (0, 0.003) > > $THETA (0,10) > > $THETA (0, 0.3, 1) > > $OMEGA 0.01 > > $SIGMA 0.5 > > $ESTIMATION METHOD=1 MAXEVAL=5000 PRINT=20 > > $COVR > > $TABLE ID TIME PRED IPRED IRES KFOR KCL IC50 IMAX > > NOPRINT ONEHEADER > > FILE=C:\PD.TAB > > 1001 0 . 1 0 1 > > 1001 0 98.3 . 0 0 > > 1001 168 90.6 . 122.44 0 > > 1001 840 92.8 . 183.69 0 > > 1002 0 . 1 0 1 > > 1002 0 105.1 . 0 0 > > 1002 840 88.5 . 61.253 0 > > 1002 842 106.7 . 106.8 0 > > 1002 844 122.1 . 116.4 0 > > 1002 1848 129.1 . 121.46 0 > > 1002 1850 160.4 . 212.63 0 > > 1002 1852 157.1 . 231.89 0 > > 1101 0 . 1 0 1 > > 1101 0 68.1 . 0 0 > > 1101 840 88.1 . 0.13884 0 > > 1101 842 105.5 . 0.12987 0 > > 1101 844 108.8 . 0.12147 0 > > 1101 1848 113.3 . 227.79 0 > > 1101 1850 62.6 . 379.54 0 > > 1101 1852 138.7 . 412.18 0

RE: Indirect response model

From: Jakob Ribbing Date: May 17, 2007 technical
Dear all, I agree, implementing the actual PK model (i.e. IPP) or using linear interpolation to describe the individual PK profiles as suggested by Juergen and David is necessary in this example. However, for understanding when input concentrations can be used directly as a reasonable approximation I have the following question: If the input concentrations were to be used, as originally presented by Nishit, wouldn't nonmem use the input concentrations according to last observation carried BACKWARD, rather than forward? In that case, for ID 1101 (the third individual in the dataset): 0 < TIME <= 840 -> COP=0.13884 840 < TIME <= 842 -> COP=0.12987 842 < TIME <= 844 -> COP=0.12147 844 < TIME <= 1848 -> COP=227.79 ... I haven't checked myself that nonmem uses LOCB rather than LOCF, but have been told so by Mats Karlsson which usually makes checking superfluous:>) I think this could be important in other situations as well: The LOCB-rule could induce false covariate relations if the drug affects a potential covariate. For example, disease level/score/stage may falsely appear to affect the drug clearance if investigated within nonmem. To properly quantify such a covariate relation a simultaneous fit of the PK-PD model may be necessary, treating the covariate (biomarker) as an integrated part of the model. Getting back to this thread: Nishit, if using nonmem version 6, the dummy dose into compartment 1 is not needed for initializing the baseline. Dummy-dosing records can be removed from the datafile and this line in the model file: F1 = KFOR/KCL can be replace by A_0(1) = KFOR/KCL Lastly, either fit log-transformed DV:s using an additive error model OR add "INTERACTION" on the $ESTIMATION, to account for the interaction between ETA1 and EPS1 in the current error model. I would prefer the first alternative for several reasons. Kind regards, Jakob $INPUT ID TIME DV AMT=DOSE COP MDV ID 1101 in the dataset: 1101 0 . 1 0 1 1101 0 68.1 . 0 0 1101 840 88.1 . 0.13884 0 1101 842 105.5 . 0.12987 0 1101 844 108.8 . 0.12147 0 1101 1848 113.3 . 227.79 0 1101 1850 62.6 . 379.54 0 1101 1852 138.7 . 412.18 0
Quoted reply history
-----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David H Salinger Sent: den 16 maj 2007 18:14 To: Jurgen Bulitta Cc: Modi, Nishit [ALZUS]; [EMAIL PROTECTED]; [email protected] Subject: Re: [NMusers] Indirect response model Dear Nishit, Jurgen is correct, you are using concentration (COP) as a forcing function. But, in ID 1101, for example, the COP has a value of 0 from TIME=0 to 840 and then values around 0.12 until TIME 1848. Unless this is what you had in mind, I would suggest two steps: 1. Include more time points for COP. These need not coincide with TIMEs were you have DV values. 2. Create a linear interpolation of COP to be used in the $DES block. One way to do this linear interpolation is to add two columns to your data file: PTME (previous time) and PCOP (previous concentration). Then, compute SLOPE = (COP-PCOP)/(TIME-PTME) and use a linear interpolation of conc: PCOP +SLOPE*(T-PTME) in place of COP in computing your COEF parameter (must be in $DES block). I hope this helps, David Salinger RFPK, Univ. of Washington

RE: Indirect response model

From: Alison Boeckmann Date: May 28, 2007 technical
This is another recent thread that I would like to comment on. On the issue of LOCB vs LOCF: The question is discussed at great length in NONMEM Users Guide VI, PREDPP, in chapter III, section B.2 Time- Varying Concomitant Variables. The idea is that, prior to advancing the state vector from time t1 to time t2, the PK routine is called (i.e., $PK is evaluated) with the next record (time t2), so that the values computed by PK for the record with TIME=t2 are used during the advance from t1 to t2. This is easily justified. If the values on the record with t1 were used, the values (other than TIME) recorded on the last record in the data set would never be seen by PK, and could not enter into the model. Linear interpolation such as you are discussing could not be carried out properly. As it is, the first data record is always seen by PK (because there is always a call to PK with the first data record of the individual record), and subsequent data records are seen prior to the advance to that record. The linear interpolation suggested by Jakob could also be carried out in $PK without any change to the data set. I think that I recall some of Lewis' fellows doing similar interpolations in the past. The following code is a suggestion. I have not tested it!! $PK KFOR = THETA(1) KCL = THETA(2)*EXP(ETA(1)) IC50 = THETA(3) IMAX = THETA(4) F1 = KFOR/KCL IF (TIME.EQ.0) THEN PCOP=0 PTME=0 SLOPE=0 OCOP=0 ELSE SLOPE=(COP-PCOP)/(TIME-PTME) OCOP=PCOP ENDIF PCOP=COP PTME=TIME $DES ICOP=OCOP+SLOPE*(T-PTME) COEF = IMAX*ICOP/(IC50+ICOP) DADT(1) = KFOR-KCL*(1-COEF)*A(1) On Thu, 17 May 2007 11:52:54 +0200, "Jakob Ribbing" <[EMAIL PROTECTED]> said: > Dear all, > > I agree, implementing the actual PK model (i.e. IPP) or using linear > interpolation to describe the individual PK profiles as suggested by > Juergen > and David is necessary in this example. > > However, for understanding when input concentrations can be used directly > as > a reasonable approximation I have the following question: If the input > concentrations were to be used, as originally presented by Nishit, > wouldn't > nonmem use the input concentrations according to last observation carried > BACKWARD, rather than forward? In that case, for ID 1101 (the third > individual in the dataset): > 0 < TIME <= 840 -> COP=0.13884 > 840 < TIME <= 842 -> COP=0.12987 > 842 < TIME <= 844 -> COP=0.12147 > 844 < TIME <= 1848 -> COP=227.79 > ... > I haven't checked myself that nonmem uses LOCB rather than LOCF, but have > been told so by Mats Karlsson which usually makes checking superfluous:>) > I > think this could be important in other situations as well: The LOCB-rule > could induce false covariate relations if the drug affects a potential > covariate. For example, disease level/score/stage may falsely appear to > affect the drug clearance if investigated within nonmem. To properly > quantify such a covariate relation a simultaneous fit of the PK-PD model > may > be necessary, treating the covariate (biomarker) as an integrated part of > the model. Getting back to this thread: > > Nishit, if using nonmem version 6, the dummy dose into compartment 1 is > not > needed for initializing the baseline. Dummy-dosing records can be removed > from the datafile and this line in the model file: > F1 = KFOR/KCL > can be replace by > A_0(1) = KFOR/KCL > > Lastly, either fit log-transformed DV:s using an additive error model OR > add > "INTERACTION" on the $ESTIMATION, to account for the interaction between > ETA1 and EPS1 in the current error model. I would prefer the first > alternative for several reasons. > > Kind regards, > > Jakob > > $INPUT ID TIME DV AMT=DOSE COP MDV > ID 1101 in the dataset: > > 1101 0 . 1 0 1 > 1101 0 68.1 . 0 0 > 1101 840 88.1 . 0.13884 0 > 1101 842 105.5 . 0.12987 0 > 1101 844 108.8 . 0.12147 0 > 1101 1848 113.3 . 227.79 0 > 1101 1850 62.6 . 379.54 0 > 1101 1852 138.7 . 412.18 0 >
Quoted reply history
> -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > On > Behalf Of David H Salinger > Sent: den 16 maj 2007 18:14 > To: Jurgen Bulitta > Cc: Modi, Nishit [ALZUS]; [EMAIL PROTECTED]; [email protected] > Subject: Re: [NMusers] Indirect response model > > Dear Nishit, > > Jurgen is correct, you are using concentration (COP) as a forcing > function. > But, in ID 1101, for example, the COP has a value of 0 from TIME=0 to 840 > and then values around 0.12 until TIME 1848. Unless this is what you > had > in mind, I would suggest two steps: 1. Include more time points for > COP. > These need not coincide with TIMEs were you have DV values. 2. Create a > linear interpolation of COP to be used in the $DES block. > > One way to do this linear interpolation is to add two columns to your > data > file: PTME (previous time) and PCOP (previous concentration). Then, > compute > SLOPE = (COP-PCOP)/(TIME-PTME) > and use a linear interpolation of conc: > PCOP +SLOPE*(T-PTME) > in place of COP in computing your COEF parameter (must be in $DES block). > > I hope this helps, > > David Salinger > RFPK, Univ. of Washington > > -- Alison Boeckmann [EMAIL PROTECTED]