Colleagues,
One of my clients is approaching submission of an NDA to FDA. I did the pop PK analysis; the files that I generated are in three formats - text, PDF, and csv. NONMEM text output is saved in two formats (text and PDF); NONMEM tables are saved in two formats (text and csv); graphics created in R are saved in PDF format. Datasets used for each step of the analysis are archived in two formats, text (an exact copy of the input file plus an exact copy of the FDATA file) and csv (the FDATA file formatted as csv).
Our plan (based on my other recent submissions to FDA, none of which has elicited any complaints from them), was to submit these documents in the formats described above. However, my client received a request from FDA that: "datasets [used in the analysis] should be submitted as SAS transport (*.xpt) files". In addition, the company managing the submission wants to convert all my other csv files to xpt format (although there was no specific request for this).
Can anyone (particularly anyone at FDA) clarify this for me? In that NONMEM will not accept .xpt files, I am surprised that FDA would want datasets in that format. Should my client honor the request or should they explain to the project manager that NONMEM requires text files so we plan to submit these files in text format (either .txt or csv).
Thanks for any insights on this.
Dennis
Dennis Fisher MD
P < (The "P Less Than" Company)
Phone: 1-866-PLessThan (1-866-753-7784)
Fax: 1-415-564-2220
www.PLessThan.com
Format for submission to FDA
All,
I would also be very interested in your responses. Recently, we've attempted to submit a Berkeley Madonna file as part of a submission, and that file type has caused some problems. While it is possible to take the BM code out as a flat .txt and the embedded data set out as a .csv or .xls (or even .xpt, I suppose), I questioned the utility of that. "Reconstituting" the analysis from the components might be possible here, but it's error prone and, frankly, inefficient.
In the end, we were able to simple embed the BM file (extension .mmd) into the eCTD format and send it along. Someone without the BM tool installed on their computer would receive a puzzled response from their web browser when trying to open the file. However, someone with the tool installed is able to correctly open the BM file.
Again, comments from our regulatory colleagues would be very helpful here. How can we package and transport complex analysis (my example was single BM file, Dennis suggests a series of NONMEM runs in a file structure) and share that with regulatory bodies?
Regards,
Mike Dodds
Quoted reply history
-----Original Message-----
From: owner-nmusers
Behalf Of Dennis Fisher
Sent: Monday, June 29, 2009 1:36 PM
To: nmusers
Subject: [NMusers] Format for submission to FDA
Colleagues,
One of my clients is approaching submission of an NDA to FDA. I did
the pop PK analysis; the files that I generated are in three formats -
text, PDF, and csv. NONMEM text output is saved in two formats (text
and PDF); NONMEM tables are saved in two formats (text and csv);
graphics created in R are saved in PDF format. Datasets used for each
step of the analysis are archived in two formats, text (an exact copy
of the input file plus an exact copy of the FDATA file) and csv (the
FDATA file formatted as csv).
Our plan (based on my other recent submissions to FDA, none of which
has elicited any complaints from them), was to submit these documents
in the formats described above. However, my client received a request
from FDA that:
"datasets [used in the analysis] should be submitted as SAS transport
(*.xpt) files".
In addition, the company managing the submission wants to convert all
my other csv files to xpt format (although there was no specific
request for this).
Can anyone (particularly anyone at FDA) clarify this for me? In that
NONMEM will not accept .xpt files, I am surprised that FDA would want
datasets in that format. Should my client honor the request or should
they explain to the project manager that NONMEM requires text files so
we plan to submit these files in text format (either .txt or csv).
Thanks for any insights on this.
Dennis
Dennis Fisher MD
P < (The "P Less Than" Company)
Phone: 1-866-PLessThan (1-866-753-7784)
Fax: 1-415-564-2220
www.PLessThan.com
All,
I would also be very interested in your responses. Recently, we've attempted
to submit a Berkeley Madonna file as part of a submission, and that file type
has caused some problems. While it is possible to take the BM code out as a
flat .txt and the embedded data set out as a .csv or .xls (or even .xpt, I
suppose), I questioned the utility of that. "Reconstituting" the analysis from
the components might be possible here, but it's error prone and, frankly,
inefficient.
In the end, we were able to simple embed the BM file (extension .mmd) into the
eCTD format and send it along. Someone without the BM tool installed on their
computer would receive a puzzled response from their web browser when trying to
open the file. However, someone with the tool installed is able to correctly
open the BM file.
Again, comments from our regulatory colleagues would be very helpful here. How
can we package and transport complex analysis (my example was single BM file,
Dennis suggests a series of NONMEM runs in a file structure) and share that
with regulatory bodies?
Regards,
Mike Dodds
Quoted reply history
-----Original Message-----
From: [email protected] [mailto:[email protected]] On
Behalf Of Dennis Fisher
Sent: Monday, June 29, 2009 1:36 PM
To: [email protected]
Subject: [NMusers] Format for submission to FDA
Colleagues,
One of my clients is approaching submission of an NDA to FDA. I did
the pop PK analysis; the files that I generated are in three formats -
text, PDF, and csv. NONMEM text output is saved in two formats (text
and PDF); NONMEM tables are saved in two formats (text and csv);
graphics created in R are saved in PDF format. Datasets used for each
step of the analysis are archived in two formats, text (an exact copy
of the input file plus an exact copy of the FDATA file) and csv (the
FDATA file formatted as csv).
Our plan (based on my other recent submissions to FDA, none of which
has elicited any complaints from them), was to submit these documents
in the formats described above. However, my client received a request
from FDA that:
"datasets [used in the analysis] should be submitted as SAS transport
(*.xpt) files".
In addition, the company managing the submission wants to convert all
my other csv files to xpt format (although there was no specific
request for this).
Can anyone (particularly anyone at FDA) clarify this for me? In that
NONMEM will not accept .xpt files, I am surprised that FDA would want
datasets in that format. Should my client honor the request or should
they explain to the project manager that NONMEM requires text files so
we plan to submit these files in text format (either .txt or csv).
Thanks for any insights on this.
Dennis
Dennis Fisher MD
P < (The "P Less Than" Company)
Phone: 1-866-PLessThan (1-866-753-7784)
Fax: 1-415-564-2220
www.PLessThan.com
Hi Dennis et. al.
The electronic gateway at FDA has adopted the SAS XPT as a standard.
http://www.fda.gov/downloads/Drugs/DevelopmentApprovalProcess/FormsSubmissionRequirements/ElectronicSubmissions/UCM163561.pdf
According to my understanding, they have discontinued the old ASCII format
or are in the process of doing so. You can find more useful links at
http://www.sas.com/govedu/fda/index.html with FAQs.
If the software is highly specialized, you may explore alternative ways of
data submission (CD-ROM etc.) by consulting with the regulatory liaisons
(requires a combination of paper and electronic submission). However, for
several reasons I would recommend taking slightly extra effort to convert
files to SAS XPT format. It helps to maintain the process and ensure the
central availability of information. Please note that POPPK/PD/modeling
datasets constitute only a minor fraction of data received by FDA.
Hope it helps.
Pravin
On Mon, Jun 29, 2009 at 6:20 PM, MIDO (Michael Dodds) <doddsm
> All,
>
> I would also be very interested in your responses. Recently, we've
> attempted to submit a Berkeley Madonna file as part of a submission, and
> that file type has caused some problems. While it is possible to take the
> BM code out as a flat .txt and the embedded data set out as a .csv or .xls
> (or even .xpt, I suppose), I questioned the utility of that.
> "Reconstituting" the analysis from the components might be possible here,
> but it's error prone and, frankly, inefficient.
>
> In the end, we were able to simple embed the BM file (extension .mmd) into
> the eCTD format and send it along. Someone without the BM tool installed on
> their computer would receive a puzzled response from their web browser when
> trying to open the file. However, someone with the tool installed is able
> to correctly open the BM file.
>
> Again, comments from our regulatory colleagues would be very helpful here.
> How can we package and transport complex analysis (my example was single BM
> file, Dennis suggests a series of NONMEM runs in a file structure) and share
> that with regulatory bodies?
>
> Regards,
> Mike Dodds
>
>
Quoted reply history
> -----Original Message-----
> From: owner-nmusers
> On Behalf Of Dennis Fisher
> Sent: Monday, June 29, 2009 1:36 PM
> To: nmusers
> Subject: [NMusers] Format for submission to FDA
>
> Colleagues,
>
> One of my clients is approaching submission of an NDA to FDA. I did
> the pop PK analysis; the files that I generated are in three formats -
> text, PDF, and csv. NONMEM text output is saved in two formats (text
> and PDF); NONMEM tables are saved in two formats (text and csv);
> graphics created in R are saved in PDF format. Datasets used for each
> step of the analysis are archived in two formats, text (an exact copy
> of the input file plus an exact copy of the FDATA file) and csv (the
> FDATA file formatted as csv).
>
> Our plan (based on my other recent submissions to FDA, none of which
> has elicited any complaints from them), was to submit these documents
> in the formats described above. However, my client received a request
> from FDA that:
> "datasets [used in the analysis] should be submitted as SAS
> transport
> (*.xpt) files".
> In addition, the company managing the submission wants to convert all
> my other csv files to xpt format (although there was no specific
> request for this).
>
> Can anyone (particularly anyone at FDA) clarify this for me? In that
> NONMEM will not accept .xpt files, I am surprised that FDA would want
> datasets in that format. Should my client honor the request or should
> they explain to the project manager that NONMEM requires text files so
> we plan to submit these files in text format (either .txt or csv).
>
> Thanks for any insights on this.
>
> Dennis
>
>
> Dennis Fisher MD
> P < (The "P Less Than" Company)
> Phone: 1-866-PLessThan (1-866-753-7784)
> Fax: 1-415-564-2220
> www.PLessThan.com http://www.plessthan.com/
>
>
>
>
Hi Dennis et. al.
The electronic gateway at FDA has adopted the SAS XPT as a standard.
http://www.fda.gov/downloads/Drugs/DevelopmentApprovalProcess/FormsSubmissionRequirements/ElectronicSubmissions/UCM163561.pdf
According to my understanding, they have discontinued the old ASCII format
or are in the process of doing so. You can find more useful links at
http://www.sas.com/govedu/fda/index.html with FAQs.
If the software is highly specialized, you may explore alternative ways of
data submission (CD-ROM etc.) by consulting with the regulatory liaisons
(requires a combination of paper and electronic submission). However, for
several reasons I would recommend taking slightly extra effort to convert
files to SAS XPT format. It helps to maintain the process and ensure the
central availability of information. Please note that POPPK/PD/modeling
datasets constitute only a minor fraction of data received by FDA.
Hope it helps.
Pravin
Quoted reply history
On Mon, Jun 29, 2009 at 6:20 PM, MIDO (Michael Dodds) <[email protected]>wrote:
> All,
>
> I would also be very interested in your responses. Recently, we've
> attempted to submit a Berkeley Madonna file as part of a submission, and
> that file type has caused some problems. While it is possible to take the
> BM code out as a flat .txt and the embedded data set out as a .csv or .xls
> (or even .xpt, I suppose), I questioned the utility of that.
> "Reconstituting" the analysis from the components might be possible here,
> but it's error prone and, frankly, inefficient.
>
> In the end, we were able to simple embed the BM file (extension .mmd) into
> the eCTD format and send it along. Someone without the BM tool installed on
> their computer would receive a puzzled response from their web browser when
> trying to open the file. However, someone with the tool installed is able
> to correctly open the BM file.
>
> Again, comments from our regulatory colleagues would be very helpful here.
> How can we package and transport complex analysis (my example was single BM
> file, Dennis suggests a series of NONMEM runs in a file structure) and share
> that with regulatory bodies?
>
> Regards,
> Mike Dodds
>
>
> -----Original Message-----
> From: [email protected] [mailto:[email protected]]
> On Behalf Of Dennis Fisher
> Sent: Monday, June 29, 2009 1:36 PM
> To: [email protected]
> Subject: [NMusers] Format for submission to FDA
>
> Colleagues,
>
> One of my clients is approaching submission of an NDA to FDA. I did
> the pop PK analysis; the files that I generated are in three formats -
> text, PDF, and csv. NONMEM text output is saved in two formats (text
> and PDF); NONMEM tables are saved in two formats (text and csv);
> graphics created in R are saved in PDF format. Datasets used for each
> step of the analysis are archived in two formats, text (an exact copy
> of the input file plus an exact copy of the FDATA file) and csv (the
> FDATA file formatted as csv).
>
> Our plan (based on my other recent submissions to FDA, none of which
> has elicited any complaints from them), was to submit these documents
> in the formats described above. However, my client received a request
> from FDA that:
> "datasets [used in the analysis] should be submitted as SAS
> transport
> (*.xpt) files".
> In addition, the company managing the submission wants to convert all
> my other csv files to xpt format (although there was no specific
> request for this).
>
> Can anyone (particularly anyone at FDA) clarify this for me? In that
> NONMEM will not accept .xpt files, I am surprised that FDA would want
> datasets in that format. Should my client honor the request or should
> they explain to the project manager that NONMEM requires text files so
> we plan to submit these files in text format (either .txt or csv).
>
> Thanks for any insights on this.
>
> Dennis
>
>
> Dennis Fisher MD
> P < (The "P Less Than" Company)
> Phone: 1-866-PLessThan (1-866-753-7784)
> Fax: 1-415-564-2220
> www.PLessThan.com http://www.plessthan.com/
>
>
>
>
I've had this request many times from the FDA (NONMEM datasets as SAS
transport files) and have complied each time. Although NONMEM does not
read XPT files, they are easy to convert to TXT files. The nice thing
about XPT files is that the labels can accomany the columns. Keep in mind
though that even though the current versions of SAS can have long label
names (20 characters I think) and long label descriptors (up to 80
characters), the FDA wants the old, archaic variable names and labels.
Variable names of no more than 8 characters and labels of less than 40
characters (this last I one I am unsure of the exact number).
Peter L. Bonate, PhD, FCP, FAAPS
Director, Clinical Pharmacology, Modeling, and Simulation
GlaxoSmithKline
5 Moore Drive, 17.2259
Research Triangle Park, NC 27709
email: peter.l.bonate
phone: 919-483-7534
fax: 919-483-8948
?There is nothing wrong with change, if it is in the right direction? -
Winston Churchill
"MIDO (Michael Dodds)" <doddsm
Sent by: owner-nmusers
29-Jun-2009 18:20
To
"nmusers
cc
Subject
RE: [NMusers] Format for submission to FDA
All,
I would also be very interested in your responses. Recently, we've
attempted to submit a Berkeley Madonna file as part of a submission, and
that file type has caused some problems. While it is possible to take the
BM code out as a flat .txt and the embedded data set out as a .csv or .xls
(or even .xpt, I suppose), I questioned the utility of that.
"Reconstituting" the analysis from the components might be possible here,
but it's error prone and, frankly, inefficient.
In the end, we were able to simple embed the BM file (extension .mmd) into
the eCTD format and send it along. Someone without the BM tool installed
on their computer would receive a puzzled response from their web browser
when trying to open the file. However, someone with the tool installed is
able to correctly open the BM file.
Again, comments from our regulatory colleagues would be very helpful here.
How can we package and transport complex analysis (my example was single
BM file, Dennis suggests a series of NONMEM runs in a file structure) and
share that with regulatory bodies?
Regards,
Mike Dodds
Quoted reply history
-----Original Message-----
From: owner-nmusers
On Behalf Of Dennis Fisher
Sent: Monday, June 29, 2009 1:36 PM
To: nmusers
Subject: [NMusers] Format for submission to FDA
Colleagues,
One of my clients is approaching submission of an NDA to FDA. I did
the pop PK analysis; the files that I generated are in three formats -
text, PDF, and csv. NONMEM text output is saved in two formats (text
and PDF); NONMEM tables are saved in two formats (text and csv);
graphics created in R are saved in PDF format. Datasets used for each
step of the analysis are archived in two formats, text (an exact copy
of the input file plus an exact copy of the FDATA file) and csv (the
FDATA file formatted as csv).
Our plan (based on my other recent submissions to FDA, none of which
has elicited any complaints from them), was to submit these documents
in the formats described above. However, my client received a request
from FDA that:
"datasets [used in the analysis] should be submitted as
SAS transport
(*.xpt) files".
In addition, the company managing the submission wants to convert all
my other csv files to xpt format (although there was no specific
request for this).
Can anyone (particularly anyone at FDA) clarify this for me? In that
NONMEM will not accept .xpt files, I am surprised that FDA would want
datasets in that format. Should my client honor the request or should
they explain to the project manager that NONMEM requires text files so
we plan to submit these files in text format (either .txt or csv).
Thanks for any insights on this.
Dennis
Dennis Fisher MD
P < (The "P Less Than" Company)
Phone: 1-866-PLessThan (1-866-753-7784)
Fax: 1-415-564-2220
www.PLessThan.com
I've had this request many times from the FDA (NONMEM datasets as SAS
transport files) and have complied each time. Although NONMEM does not
read XPT files, they are easy to convert to TXT files. The nice thing
about XPT files is that the labels can accomany the columns. Keep in mind
though that even though the current versions of SAS can have long label
names (20 characters I think) and long label descriptors (up to 80
characters), the FDA wants the old, archaic variable names and labels.
Variable names of no more than 8 characters and labels of less than 40
characters (this last I one I am unsure of the exact number).
Peter L. Bonate, PhD, FCP, FAAPS
Director, Clinical Pharmacology, Modeling, and Simulation
GlaxoSmithKline
5 Moore Drive, 17.2259
Research Triangle Park, NC 27709
email: [email protected]
phone: 919-483-7534
fax: 919-483-8948
?There is nothing wrong with change, if it is in the right direction? -
Winston Churchill
"MIDO (Michael Dodds)" <[email protected]>
Sent by: [email protected]
29-Jun-2009 18:20
To
"[email protected]" <[email protected]>
cc
Subject
RE: [NMusers] Format for submission to FDA
All,
I would also be very interested in your responses. Recently, we've
attempted to submit a Berkeley Madonna file as part of a submission, and
that file type has caused some problems. While it is possible to take the
BM code out as a flat .txt and the embedded data set out as a .csv or .xls
(or even .xpt, I suppose), I questioned the utility of that.
"Reconstituting" the analysis from the components might be possible here,
but it's error prone and, frankly, inefficient.
In the end, we were able to simple embed the BM file (extension .mmd) into
the eCTD format and send it along. Someone without the BM tool installed
on their computer would receive a puzzled response from their web browser
when trying to open the file. However, someone with the tool installed is
able to correctly open the BM file.
Again, comments from our regulatory colleagues would be very helpful here.
How can we package and transport complex analysis (my example was single
BM file, Dennis suggests a series of NONMEM runs in a file structure) and
share that with regulatory bodies?
Regards,
Mike Dodds
Quoted reply history
-----Original Message-----
From: [email protected] [mailto:[email protected]]
On Behalf Of Dennis Fisher
Sent: Monday, June 29, 2009 1:36 PM
To: [email protected]
Subject: [NMusers] Format for submission to FDA
Colleagues,
One of my clients is approaching submission of an NDA to FDA. I did
the pop PK analysis; the files that I generated are in three formats -
text, PDF, and csv. NONMEM text output is saved in two formats (text
and PDF); NONMEM tables are saved in two formats (text and csv);
graphics created in R are saved in PDF format. Datasets used for each
step of the analysis are archived in two formats, text (an exact copy
of the input file plus an exact copy of the FDATA file) and csv (the
FDATA file formatted as csv).
Our plan (based on my other recent submissions to FDA, none of which
has elicited any complaints from them), was to submit these documents
in the formats described above. However, my client received a request
from FDA that:
"datasets [used in the analysis] should be submitted as
SAS transport
(*.xpt) files".
In addition, the company managing the submission wants to convert all
my other csv files to xpt format (although there was no specific
request for this).
Can anyone (particularly anyone at FDA) clarify this for me? In that
NONMEM will not accept .xpt files, I am surprised that FDA would want
datasets in that format. Should my client honor the request or should
they explain to the project manager that NONMEM requires text files so
we plan to submit these files in text format (either .txt or csv).
Thanks for any insights on this.
Dennis
Dennis Fisher MD
P < (The "P Less Than" Company)
Phone: 1-866-PLessThan (1-866-753-7784)
Fax: 1-415-564-2220
www.PLessThan.com
Dear Dennis,
Please see the FDA guidance (Providing Regulatory Submissions in Electronic
Format) in the web link below at page 7; the ASCII files (e.g. NONMEM) should
have the txt extension.
http://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Guidances/ucm072349.pdf
Jean
--------------------------------------------
Jean R. Lavigne M.Sc.
Associate Director, Clinical Pharmacology
MDS Pharma Services
4705 Dobrin
St-Laurent, Québec, Canada
H4R 2P7
Phone: (514) 333-0042 ext. 54234
e-mail: [email protected]
--------------------------------------------
MISE EN GARDE CONCERNANT LA CONFIDENTIALITÉ
Ce courriel et tout autre fichier transmis avec lui peut contenir des
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Quoted reply history
-----Original Message-----
From: [email protected] [mailto:[email protected]] On
Behalf Of Dennis Fisher
Sent: Monday, June 29, 2009 16:36
To: [email protected]
Subject: [NMusers] Format for submission to FDA
Colleagues,
One of my clients is approaching submission of an NDA to FDA. I did
the pop PK analysis; the files that I generated are in three formats -
text, PDF, and csv. NONMEM text output is saved in two formats (text
and PDF); NONMEM tables are saved in two formats (text and csv);
graphics created in R are saved in PDF format. Datasets used for each
step of the analysis are archived in two formats, text (an exact copy
of the input file plus an exact copy of the FDATA file) and csv (the
FDATA file formatted as csv).
Our plan (based on my other recent submissions to FDA, none of which
has elicited any complaints from them), was to submit these documents
in the formats described above. However, my client received a request
from FDA that:
"datasets [used in the analysis] should be submitted as SAS transport
(*.xpt) files".
In addition, the company managing the submission wants to convert all
my other csv files to xpt format (although there was no specific
request for this).
Can anyone (particularly anyone at FDA) clarify this for me? In that
NONMEM will not accept .xpt files, I am surprised that FDA would want
datasets in that format. Should my client honor the request or should
they explain to the project manager that NONMEM requires text files so
we plan to submit these files in text format (either .txt or csv).
Thanks for any insights on this.
Dennis
Dennis Fisher MD
P < (The "P Less Than" Company)
Phone: 1-866-PLessThan (1-866-753-7784)
Fax: 1-415-564-2220
www.PLessThan.com
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