replicateBE

Comparative BA-calculation for the EMA’s Average Bioequivalence with Expanding Limits (ABEL)

Helmut Schütz

2019-06-14

suppressMessages(library(replicateBE))

Disclaimer

Program offered for Use without any Guarantees and Absolutely No Warranty. No Liability is accepted for any Loss and Risk to Public Health Resulting from Use of this R-Code.

Introduction

The library provides data sets (internal .rda and in CSV-format in /extdata/) given by Schütz et al.1 which support users in a black-box performance qualification (PQ) of their software installations.

The methods given in the EMA’s Q&A document for reference-scaling according to the EMA’s Guideline on the Investigation of Bioequivalence are implemented. Potential influence of outliers on the variability of the reference can be assessed by box plots of studentized and standardized residuals as suggested at a joint EGA/EMA workshop.

Methods

function method.A()

A linear model of log-transformed PK responses and effects
    sequence, subject(sequence), period, treatment
where all effects are fixed (i.e., ANOVA). Estimated via function lm() of library stats.

function method.B()

A linear model of log-transformed PK responses and effects
    sequence, subject(sequence), period, treatment
where subject(sequence) is a random effect and all others are fixed.
Two options are provided

  1. Estimated via function lmer() of library lmerTest. Uses Satterthwaite’s degrees of freedom.
    method.B(..., option = 1)
  1. Estimated via function lme() of library nlme. Uses degrees of freedom equivalent to SAS’ DDFM=CONTAIN and Phoenix/WinNonlin’s DF Residual. Implicitly preferred according to the Q&A document.
    method.B(..., option = 2), the default.

function ABE()

Conventional Average Bioequivalence, where the model is identical to Method A. Tighter limits for narrow therapeutic index drugs (EMA 90.00 – 111.11%) or wider limits (75.00 – 133.33% for Cmax according to the guideline of the GCC2) can be specified.

Tested designs

Details about the reference data sets:

help("data", package = "replicateBE")
?replicateBE::data

Four period (full) replicates

Both the test and the reference treatments are administered at least once.

TRTR | RTRT
TRRT | RTTR
TTRR | RRTT
TRTR | RTRT | TRRT | RTTR 3
TRRT | RTTR | TTRR | RRTT 4

Three period (full) replicates

The test treatment is administered at least once to ½ of the subjects and the reference treatment at least once to the respective other ½ of the subjects.

TRT | RTR
TRR | RTT

Two period (full) replicate

The test and reference treatments are administered once to ½ of the subjects (for the estimation of the CI). I.e., the first group of subjects follow a conventional 2×2×2 trial. In the second group the test and reference treatments are administered at least once to ¼ of the subjects, repectively (for the estimation of CVwT and CVwR).

TR | RT | TT | RR 5

Three period (partial) replicates

The test treatment is administered once and the reference treatment at least once.

TRR | RTR | RRT
TRR | RTR 6

Data structure

Columns must have the headers subject, period, sequence, treatment, PK, and/or logPK.7 Any order of columns is acceptable. Uppercase and mixed case headers will be internally converted to lowercase headers.

variable format
subject Integer numbers or any combination of alphanumerics (A-Z, a-z, -, _, #, 0-9)
period Integer numbers
sequence Numbers or any other literal sequences not listed in the tested designs are not accepted (e.g., ABAB).
treatment The Test treatment must be coded T and the Reference R (both uppercase).

Relevant data are used for the estimation of CVwR (and CVwT in full replicate designs) and BE, i.e., the data sets might be different (see the example). It is good practice to state that in the Statistical Analysis Plan (SAP).

Incomplete data

Estimation of CVw

If a subject drops out from the study in a higher period, data of repeated administrations will still be used for the estimation of CVw, although data of the other treatment might be missing. Examples for the estimation of CVwR (missings denoted by .):
RTRTRTR.
TRRTTRR.
RRTTRRT. or RR..
RRTRR..

Assessment of BE

If a subject drops out from the study in a higher period, data with at least one administration of the Test and Reference will be used in the assessment of BE. Examples (missings denoted by .):

TRTRTRT. or → TR..
RTRTRTR. or → RT..
TRRTTRR. or → TR..
RTTRRTT. or → RT..
TTRRTTR.
TRTTR.
RTRRT.
TRRTR.
RTRRT.
RTTRT.

Example of different data sets

Study started with 16 subjects. In sequence RTRT one dropout in the 2nd period and one in the 4th period. In sequence TRTR one dropout in the 3rd period and one in the 4th.

1 RTR.  5 RTRT  9 TRTR 13 RTRT
2 RTRT  6 TR.. 10 TRTR 14 TRT.
3 RTRT  7 RTRT 11 RTRT 15 TRTR
4 TRTR  8 R... 12 TRTR 16 TRTR

We obtain these data sets:

purpose included subjects excluded
Estimation of CVwR 13 who received 2 treatments R 6, 8, 14
Estimation of CVwT 12 who received 2 treatments T 1, 6, 8
Assessment of BE 15 who received ≥1 treatment T and R 8

Notes on the methods

Estimation of intra-subject variability

The EMA proposed a linear model of log-transformed PK responses of the reference treatment
    sequence, subject(sequence), period
where all effects are fixed. Estimated via function lm() of library stats:

For informational purposes in full replicate designs (required by the WHO for reference-scaling of AUC) the same model is run with data = data[data$treatment = "T", ].

Special conditions for the sample size in three period full replicate designs:

The question raised asks if it is possible to use a design where subjects are randomised to receive treatments in the order of TRT or RTR.

[…] if a 3-period replicate design, where treatments are given in the order TRT or RTR, is to be used to justify widening of a confidence interval for Cmax then it is considered that at least 12 patients would need to provide data from the RTR arm. This implies a study with at least 24 patients in total would be required if equal number of subjects are allocated to the 2 treatment sequences.

Q&A document (June 2015 and later revisions)

If less than twelve subjects remain in sequence RTR of a TRT | RTR design (and in analogy in sequence TRR of a TRR | RTT design), the user is notified about the uncertain estimate of CVwR. However, in a sufficiently powered study such a case is extremely unlikely.

Model structure

The EMA’s models assumes equal [sic] intra-subject variances of Test and Reference (like in 2×2×2 trials) – even if proven false in one of the full replicate designs (were both CVwT and CVwR can be estimated). Hence, amongst bio­statis­ticians it is called the ‘crippled model’ because the replicative nature of the study is ignored.

The nested structure subject(sequence) of the methods leads to an over-specificed model.8 The simple model
    sequence, subject, period, treatment
gives identical estimates of the residual variance and the treatment effect and hence, its confidence interval.

The same holds true for the EMA’s model to estimate CVwR. The simple model
    subject, period
gives an identical estimate of the residual variance.

Reference-scaling is acceptable for Cmax (immediate release products9) and Cmax, Cmax,ss, Cτ,ss, partialAUC (modified release products10) if high variability of the reference product (CVwR >30%) was demonstrated.

The intention to widen the limits has to be stated in the protocol and – contrary to the FDA’s RSABE – a clinical justification provided.

Those HVDP for which a wider difference in Cmax is considered clinically irrelevant based on a sound clinical justification can be assessed with a widened acceptance range. The request for widened inter­val must be prospectively specified in the protocol.

BE Guideline (January 2010)

BE limits, PE restriction, rounding issues

The limits can be expanded based on CVwR.

In reference-scaling a so-called mixed (a.k.a. aggregate) criterion is applied. In order to pass BE,

In order to avoid discontinuities due to double rounding, expanded limits are calculated in full numeric precision and only the confidence interval is rounded according to the GL.

Discrete limits resulting from rounding

Discrete limits resulting from rounding

Degrees of freedom, comparison of methods

The SAS code provided by the EMA in the Q&A document does not specify how the degrees of freedom should be calculated in ‘Method B’. Hence, the default in PROC MIXED, namely DDFM=CONTAIN is applied, i.e., method.B(..., option = 2). For incomplete data (missing periods) Satterthwaite’s approximation of the degrees of freedom, i.e., method.B(..., option = 1) might be a better choice – if stated as such in the SAP.

The EMA seemingly prefers ‘Method A’:

A simple linear mixed model, which assumes identical within-subject variability (Method B), may be acceptable as long as results obtained with the two methods do not lead to different regu­la­tory decisions. However, in borderline cases […] additional analysis using Method A might be required.

Q&A document (January 2011 and later revisions)

The half-width of the confidence interval in log-scale allows a comparison of methods (B v.s. A) where a higher value might point towards a more conservative decision.11 In the provided example data sets – with one exception – the con­clusion of BE (based on the mixed criterion) agrees between ‘Method A’ and ‘Method B’.
However, for the highly incomplete data set 14 ‘Method B’ was liberal (passing by ANOVA but failing by the mixed effects model):

# Compare Method B acc. to the GL with Method A for all reference data sets.
ds <- substr(grep("rds", unname(unlist(data(package = "replicateBE"))),
                  value = TRUE), start = 1, stop = 5)
for (i in seq_along(ds)) {
  A <- method.A(print=FALSE, details = TRUE, data = eval(parse(text = ds[i])))$BE
  B <- method.B(print=FALSE, details = TRUE, data = eval(parse(text = ds[i])))$BE
  r <- paste0("A ", A, ", B ", B, " \u2013 ")
  cat(paste0(ds[i], ":"), r)
  if (A == B) {
    cat("Methods agree.\n")
  } else {
    if (A == "fail" & B == "pass") {
      cat("Method A is conservative.\n")
    } else {
      cat("Method B is conservative.\n")
    }
  }
}
#> rds01: A pass, B pass – Methods agree.
#> rds02: A pass, B pass – Methods agree.
#> rds03: A pass, B pass – Methods agree.
#> rds04: A fail, B fail – Methods agree.
#> rds05: A pass, B pass – Methods agree.
#> rds06: A pass, B pass – Methods agree.
#> rds07: A pass, B pass – Methods agree.
#> rds08: A pass, B pass – Methods agree.
#> rds09: A pass, B pass – Methods agree.
#> rds10: A pass, B pass – Methods agree.
#> rds11: A pass, B pass – Methods agree.
#> rds12: A fail, B fail – Methods agree.
#> rds13: A fail, B fail – Methods agree.
#> rds14: A pass, B fail – Method B is conservative.
#> rds15: A fail, B fail – Methods agree.
#> rds16: A fail, B fail – Methods agree.
#> rds17: A fail, B fail – Methods agree.
#> rds18: A fail, B fail – Methods agree.
#> rds19: A fail, B fail – Methods agree.
#> rds20: A fail, B fail – Methods agree.
#> rds21: A fail, B fail – Methods agree.
#> rds22: A pass, B pass – Methods agree.
#> rds23: A pass, B pass – Methods agree.
#> rds24: A pass, B pass – Methods agree.
#> rds25: A pass, B pass – Methods agree.
#> rds26: A fail, B fail – Methods agree.
#> rds27: A pass, B pass – Methods agree.
#> rds28: A pass, B pass – Methods agree.

Exploring data set 14:

Both variants of ‘Method B’ are more conservative than ‘Method A’. Before rounding the confidence interval, option = 2 with 192 degrees of freedom would be more conservative (lower CL 69.21029) than option = 1 with 197.44 degrees of freedom (lower CL 69.21286). However, given the incompleteness of this data set (four missings in period 2, twelve in period 3, and 19 in period 4), Satterthwaite’s degrees of freedom probably are the better choice.

Outlier analysis

It is an open issue how outliers should be handled.

The applicant should justify that the calculated intra-subject variability is a reliable estimate and that it is not the result of outliers.

BE Guideline

Box plots were ‘suggested’ by the author as a joke [sic] at the EGA/EMA workshop, being aware of their non­para­metric nature and the EMA’s reluctance towards robust methods. Unfortunately, this joke was included in the Q&A document.

[…] a study could be acceptable if the bioequivalence requirements are met both including the outlier subject (using the scaled average bioequivalence approach and the within-subject CV with this sub­ject) and after exclusion of the outlier (using the within-subject CV without this subject).

An outlier test is not an expectation of the medicines agencies but outliers could be shown by a box plot. This would allow the medicines agencies to compare the data between them.

Q&A

With the additional argument ola = TRUE in method.A() and method.B() an outlier analysis is performed, where the default fence = 212 is used.

Results slightly differ depending on software’s algorithms to calculate the median and quartiles. Example with the methods implemented in R:

Example for the reference data set 01:

Outlier analysis
 (externally) studentized residuals
 Limits (2×IQR whiskers): -1.717435, 1.877877
 Outliers:
 subject sequence  stud.res
      45     RTRT -6.656940
      52     RTRT  3.453122

 standarized (internally studentized) residuals
 Limits (2×IQR whiskers): -1.69433, 1.845333
 Outliers:
 subject sequence stand.res
      45     RTRT -5.246293
      52     RTRT  3.214663

If based on studentized residuals outliers are detected, additionally to the scaled limits based on the complete reference data, tighter limits are calculated based on CVwR after exclusion of outliers and BE assessed with the new limits. Standardized residuals are shown for informational purposes only and are not used for exclusion of outliers.

Output for the reference data set 01 (re-ordered for clarity):

CVwR               :  46.96% (reference-scaling applicable)
swR                :   0.44645
Expanded limits    :  71.23% ... 140.40% [100exp(±0.760·swR)]
Assessment based on original CVwR 46.96%
────────────────────────────────────────
Confidence interval: 107.11% ... 124.89%  pass
Point estimate     : 115.66%              pass
Mixed (CI & PE)    :                      pass
 ╟────────┼─────────────────────┼───────■────────◊─────────■───────────────╢

Outlier fence      :  2×IQR of studentized residuals.
Recalculation due to presence of 2 outliers (subj. 45|52)
─────────────────────────────────────────────────────────
CVwR (outl. excl.) :  32.16% (reference-scaling applicable)
swR (recalculated) :   0.31374
Expanded limits    :  78.79% ... 126.93% [100exp(±0.760·swR)]
Assessment based on recalculated CVwR 32.16%
────────────────────────────────────────────
Confidence interval: pass
Point estimate     : pass
Mixed (CI & PE)    : pass
         ╟┼─────────────────────┼───────■────────◊─────────■─╢

Note that the PE and its CI are not affected since the entire data are used and therefore, these values not reported in the second analysis (only the conclusion of the assessement).
The line plot is given for informational puposes (its resolution is only ~0.5%). The filled squares  ■  are the lower and upper 90% confidence limits, the rhombus  ◊  the point estimate, the vertical lines  │  at 100% and the PE restriction (80.00 – 125.00%), and the double vertical lines  ║  the expanded limits. The PE and CI take pre­se­dence over other symbols. In this case the upper limit of the PE restriction is not visible.
Since both analyses arrive at the same conclusion, the study should be acceptable according to the Q&A document.

Applicability, outlook

The EMA’s approach of reference-scaling for highly variable drugs / drug products is currently recommended in other jurisdictions as well (e.g., the WHO; ASEAN States, Australia, Brazil, Egypt, the Russian Federation, the Eurasian Economic Union, the East African Community, New Zealand).

The WHO accepts reference-scaling for AUC (four period full replicate studies are mandatory in order to assess the vari­ability associated with each product). It is not evident how this assessment should be done. In Population Bioequivalence (PBE) and Individual Bioequivalence (IBE) the swT/swR ratio was assessed and similar variability was concluded for a ratio within 0.667 – 1.500. However, the power of comparing variabilities in a study designed to demonstrate ABE is low. This was one of the reasons why PBE and IBE were not implemented in regu­la­tory practice. An alternative approach is given in the FDA’s guidance on warfarin where variabilities are considered compar­able if the upper confidence limit of σwT/σwR is ≤2.5.

Cross-validation

Results of reference data sets agree with ones obtained in SAS (9.3, 9.4) and Phoenix/WinNonlin (6.4 – 8.1).

Contributors

Session Information

Inspect this information for reproducibility. Of particular importance are the versions of R and the packages used to create this workflow. It is considered good practice to record this information with every analysis.

options(width = 80)
devtools::session_info()
#> - Session info ---------------------------------------------------------------
#>  setting  value                       
#>  version  R version 3.6.0 (2019-04-26)
#>  os       Windows 7 x64 SP 1          
#>  system   x86_64, mingw32             
#>  ui       RTerm                       
#>  language EN                          
#>  collate  C                           
#>  ctype    German_Germany.1252         
#>  tz       Europe/Vienna               
#>  date     2019-06-14                  
#> 
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  1. Schütz H, Tomashevskiy M, Labes D, Shitova A, González-de la Parra M, Fuglsang A. Reference Data­sets for Studies in a Replicate Design intended for Average Bioequivalence with Expanding Limits. Manu­script in pre­paration 2019.

  2. Gulf Cooperation Council: Bahrain, Kuwait, Oman, Qatar, Saudi Arabia, and the United Arab Emirates.

  3. Confounded effects (design not recommended).

  4. Confounded effects (design not recommended).

  5. Balaam’s design (not recommended due to its poor power characteristics).

  6. Extra-reference design; biased in the presence of period effects (design not recommended).

  7. Napierian logarithm (base e). The decadic logarithm (base 10) is not supported).

  8. Contradics the law of simplicity. Such a nesting is superfluous since in BE trials subjects are uniquely coded. If, say, subject 1 is allocated to sequence TRTR there is not yet ‘another’ subject 1 allocated to sequence RTRT. This explains the many lines in SAS PROC GML given with . and in Phoenix/WinNonlin as not estimable.

  9. Guideline on the Investigation of Bioequivalence

  10. Guideline on the pharmacokinetic and clinical evaluation of modified release dosage forms

  11. Of course, only if the point estimates are identical.

  12. The fences are given by the lowest datum still within m×IQR of the lower quartile, and the highest datum still within m×IQR of the upper quartile, where IQR is the interquartile range (difference between the 3rd and 1st quartiles). Data outside fences are considered outliers. Decreasing the multiplier m to e.g., 1.5 might result in many outliers whereas increasing the multiplier in only a few.
    Different methods exist to calculate quartiles (nine are available in R, where the default is type = 7). R’s default is used by S, MATLAB, and Excel. Phoenix/WinNonlin, Minitab, and SPSS use type = 6, ScyPy uses type = 4, whereas the default in SAS and Stata is type = 2 (though others are available as well).

  13. Externally studentized: \(\widehat{\sigma}_{(i)}^2={1 \over n-m-1}\sum_{\begin{smallmatrix}j = 1\\j \ne i\end{smallmatrix}}^n \widehat{\varepsilon\,}_j^{\,2}\)

  14. Internally studentized: \(\widehat{\sigma}^2={1 \over n-m}\sum_{j=1}^n \widehat{\varepsilon\,}_j^{\,2}\)

  15. Both are available in SAS and R, whereas only the latter in e.g., Phoenix/WinNonlin. In general the former are slightly more restrictive. Which one will be used has to be stated in the SAP.