Exercise PK15 - Toxicokinetics

2020-11-12

Background

  • Structure - Non Compartmental Analysis

  • Route of administration - Oral

  • Dosage Regimen - 10, 56 and 320 μmol/kg/day

  • Number of Subjects - 30

  • Study Period - 12 month safety study in male and female dogs

Learning Outcome

Application of Non Compartmental data analysis

Objectives

  • To analyze the kinetics by means of means of Non-compartmental Analysis (NCA)

  • To analyze the exposure to test comounds by means of Cmax and AUC.

Libraries

call the "necessary" libraries to get start

using Pumas
using PumasTutorials
using Plots
using CSV
using StatsPlots

Import the Dataset

Import the dataset and perform data-wrangling to make the datset ready for read_nca

  • Time = hrs

  • Conc = μmol/kg

  • Dose_grp = μmol/kg

  • Period = weeks

data = DataFrame(CSV.File(joinpath(dirname(pathof(PumasTutorials)), "..", "data", "PKPDDataAnalysisBook", "pk15data.csv")))

##delete the first row which contains untits
delete!(data, [1])

##sort by Subject ID, Period and Time
sort!(data, [:Subject_ID,:Period,:Time])

##remove rows containing other Periods and Dose_grp
filter!(x -> x.Period in ["11","26", "52"], data)
filter!(x -> x.Dose_grp in ["10","56","320"], data)

## Convert the colums to necesaary types for input
data[:Conc] = parse.(Float64,data[:Conc])
data[:Time] = parse.(Float64,data[:Time])
data[:Period] = parse.(Int64,data[:Period])
data[:Dose_grp] = parse.(Int64,data[:Dose_grp])

##sort by Subject ID, Period and Time
sort!(data, [:Subject_ID,:Period,:Time])

## Add new column for Route of administration - extravascular
data[!,:route] .= "ev"

Plots

Period - Week 11, Males
male_11 = filter(x -> x.Period == 11, data)
filter!(x -> x.Gender == "male", male_11)
male_11_gr1 = filter(x -> x.Dose_grp == 10, male_11)
male_11_gr2 = filter(x -> x.Dose_grp == 56, male_11)
male_11_gr3 = filter(x -> x.Dose_grp == 320, male_11)


@df male_11_gr1 plot(:Time, :Conc, yaxis=:log,
                      title = "Period (Week) = 11, male", xlabel = "Time (hr)", ylabel = "Concentration (uM)",
                      xticks = [0,5,10,15,20,25], xlims = (0,25), yticks = [0.01,0.1,1,10,100], ylims = (0.01,100),
                      group=:Subject_ID, colour=[:red], label=false)
@df male_11_gr2 plot!(:Time, :Conc, yaxis=:log, group=:Subject_ID, colour=[:blue], label=false)
@df male_11_gr3 plot!(:Time, :Conc, yaxis=:log, group=:Subject_ID, colour=[:grey], label=false)
Period - Week 26, Males
male_26 = filter(x -> x.Period == 26, data)
filter!(x -> x.Gender == "male", male_26)
male_26_gr1 = filter(x -> x.Dose_grp == 10, male_26)
male_26_gr2 = filter(x -> x.Dose_grp == 56, male_26)
male_26_gr3 = filter(x -> x.Dose_grp == 320, male_26)


@df male_26_gr1 plot(:Time, :Conc, yaxis=:log,
                      title = "Period (Week) = 26, male", xlabel = "Time (hr)", ylabel = "Concentration (uM)",
                      xticks = [0,5,10,15,20,25], xlims = (0,25), yticks = [0.01,0.1,1,10,100], ylims = (0.01,100),
                      group=:Subject_ID, colour=[:red], label=false)
@df male_26_gr2 plot!(:Time, :Conc, yaxis=:log, group=:Subject_ID, colour=[:blue], label=false)
@df male_26_gr3 plot!(:Time, :Conc, yaxis=:log, group=:Subject_ID, colour=[:grey], label=false)
Period - Week 52, Males
male_52 = filter(x -> x.Period == 52, data)
filter!(x -> x.Gender == "male", male_52)
male_52_gr1 = filter(x -> x.Dose_grp == 10, male_52)
male_52_gr2 = filter(x -> x.Dose_grp == 56, male_52)
male_52_gr3 = filter(x -> x.Dose_grp == 320, male_52)


@df male_52_gr1 plot(:Time, :Conc, yaxis=:log,
                      title = "Period (Week) = 52, male", xlabel = "Time (hr)", ylabel = "Concentration (uM)",
                      xticks = [0,5,10,15,20,25], xlims = (0,25), yticks = [0.01,0.1,1,10,100], ylims = (0.01,100),
                      group=:Subject_ID, colour=[:red], label=false)
@df male_52_gr2 plot!(:Time, :Conc, yaxis=:log, group=:Subject_ID, colour=[:blue], label=false)
@df male_52_gr3 plot!(:Time, :Conc, yaxis=:log, group=:Subject_ID, colour=[:grey], label=false)
Period - Week 11, Females
female_11 = filter(x -> x.Period == 11, data)
filter!(x -> x.Gender == "female", female_11)
female_11_gr1 = filter(x -> x.Dose_grp == 10, female_11)
female_11_gr2 = filter(x -> x.Dose_grp == 56, female_11)
female_11_gr3 = filter(x -> x.Dose_grp == 320, female_11)


@df female_11_gr1 plot(:Time, :Conc, yaxis=:log,
                      title = "Period (Week) = 11, female", xlabel = "Time (hr)", ylabel = "Concentration (uM)",
                      xticks = [0,5,10,15,20,25], xlims = (0,25), yticks = [0.01,0.1,1,10,100], ylims = (0.01,100),
                      group=:Subject_ID, colour=[:red], label=false)
@df female_11_gr2 plot!(:Time, :Conc, yaxis=:log, group=:Subject_ID, colour=[:blue], label=false)
@df female_11_gr3 plot!(:Time, :Conc, yaxis=:log, group=:Subject_ID, colour=[:grey], label=false)
Period - Week 26, Females
female_26 = filter(x -> x.Period == 26, data)
filter!(x -> x.Gender == "female", female_26)
female_26_gr1 = filter(x -> x.Dose_grp == 10, female_26)
female_26_gr2 = filter(x -> x.Dose_grp == 56, female_26)
female_26_gr3 = filter(x -> x.Dose_grp == 320, female_26)


@df female_26_gr1 plot(:Time, :Conc, yaxis=:log,
                      title = "Period (Week) = 26, female", xlabel = "Time (hr)", ylabel = "Concentration (uM)",
                      xticks = [0,5,10,15,20,25], xlims = (0,25), yticks = [0.01,0.1,1,10,100], ylims = (0.01,100),
                      group=:Subject_ID, colour=[:red], label=false)
@df female_26_gr2 plot!(:Time, :Conc, yaxis=:log, group=:Subject_ID, colour=[:blue], label=false)
@df female_26_gr3 plot!(:Time, :Conc, yaxis=:log, group=:Subject_ID, colour=[:grey], label=false)
Period - Week 52, Females
female_52 = filter(x -> x.Period == 52, data)
filter!(x -> x.Gender == "female", female_52)
female_52_gr1 = filter(x -> x.Dose_grp == 10, female_52)
female_52_gr2 = filter(x -> x.Dose_grp == 56, female_52)
female_52_gr3 = filter(x -> x.Dose_grp == 320, female_52)


@df female_52_gr1 plot(:Time, :Conc, yaxis=:log,
                      title = "Period (Week) = 52, female", xlabel = "Time (hr)", ylabel = "Concentration (uM)",
                      xticks = [0,5,10,15,20,25], xlims = (0,25), yticks = [0.01,0.1,1,10,100], ylims = (0.01,100),
                      group=:Subject_ID, colour=[:red], label=false)
@df female_52_gr2 plot!(:Time, :Conc, yaxis=:log, group=:Subject_ID, colour=[:blue], label=false)
@df female_52_gr3 plot!(:Time, :Conc, yaxis=:log, group=:Subject_ID, colour=[:grey], label=false)

NCA Analysis

Perform the NCA Analysis

timeu = u"hr"
concu = u"μmol/kg"
amtu  = u"μmol/kg"

nca_analysis = read_nca(data,
                        id    = :Subject_ID,
                        time  = :Time,
                        conc  = :Conc,
                        route = :route,
                        amt   = :Dose,
                        group = [:Period,:Gender],
                        timeu = timeu,
                        concu = concu,
                        amtu  = amtu)

report_nca  = NCAReport(nca_analysis, sigdig=3)

90 rows × 41 columns (omitted printing of 33 columns)

idPeriodGenderdoseamttlagtmaxcmaxtlast
Int64StringStringQuantit…Quantit…Quantit…Quantit…Quantit…
1711female10 μmol kg⁻¹0.0 hr7.5 hr2.0 μmol kg⁻¹24.0 hr
2911female10 μmol kg⁻¹0.0 hr7.5 hr1.4 μmol kg⁻¹24.0 hr
31111female56 μmol kg⁻¹0.0 hr7.5 hr5.0 μmol kg⁻¹24.0 hr
41311female56 μmol kg⁻¹0.0 hr0.5 hr4.9 μmol kg⁻¹24.0 hr
51511female56 μmol kg⁻¹0.0 hr7.5 hr7.1 μmol kg⁻¹24.0 hr
61711female320 μmol kg⁻¹0.0 hr1.0 hr25.0 μmol kg⁻¹24.0 hr
71911female320 μmol kg⁻¹0.0 hr8.0 hr38.0 μmol kg⁻¹24.0 hr
82711female10 μmol kg⁻¹0.0 hr0.5 hr1.2 μmol kg⁻¹24.0 hr
92911female10 μmol kg⁻¹0.0 hr7.5 hr0.56 μmol kg⁻¹24.0 hr
103111female56 μmol kg⁻¹0.0 hr7.5 hr5.9 μmol kg⁻¹24.0 hr
113311female56 μmol kg⁻¹0.0 hr7.5 hr3.5 μmol kg⁻¹24.0 hr
123511female56 μmol kg⁻¹0.0 hr0.5 hr3.5 μmol kg⁻¹24.0 hr
133711female320 μmol kg⁻¹0.0 hr7.5 hr29.0 μmol kg⁻¹24.0 hr
143911female320 μmol kg⁻¹0.0 hr8.0 hr17.0 μmol kg⁻¹24.0 hr
15611male10 μmol kg⁻¹0.0 hr7.5 hr1.3 μmol kg⁻¹24.0 hr
16811male10 μmol kg⁻¹0.0 hr0.5 hr1.0 μmol kg⁻¹24.0 hr
171011male10 μmol kg⁻¹0.0 hr8.0 hr1.1 μmol kg⁻¹24.0 hr
181211male56 μmol kg⁻¹0.0 hr7.5 hr5.5 μmol kg⁻¹24.0 hr
191411male56 μmol kg⁻¹0.0 hr7.5 hr2.6 μmol kg⁻¹24.0 hr
201611male320 μmol kg⁻¹0.0 hr7.5 hr38.0 μmol kg⁻¹24.0 hr
211811male320 μmol kg⁻¹0.0 hr7.5 hr28.0 μmol kg⁻¹24.0 hr
222011male320 μmol kg⁻¹0.0 hr8.0 hr24.0 μmol kg⁻¹24.0 hr
232611male10 μmol kg⁻¹0.0 hr7.5 hr3.0 μmol kg⁻¹24.0 hr
242811male10 μmol kg⁻¹0.0 hr0.5 hr0.15 μmol kg⁻¹24.0 hr
⋮⋮⋮⋮⋮⋮⋮⋮⋮

Published from pk15.jmd using Weave.jl v0.10.6 on 2020-11-12.