TB APEX

Overview

What Does the TB-APEX Data Platform Contain?

The platform contains Preclinical TB trial datasets currently consisting of Hollow Fiber Systems (In Vitro) and Animal Studies (In Vivo) contributed by the following organizations, to C-Path for use by qualified TB researchers.

1. Evotec

2. Baylor University

3. Johns Hopkins University (JHU)

4. Colorado State University (CSU)

With C-Path’s continued engagement with various TB research initiatives, additional preclinical trial data may be available in the future.

Acknowledgements:

Creation of the TB-APEX data platform was made possible by a grant from the Bill & Melinda Gates Foundation.
Continued hosting and maintenance for the TB-APEX data platform is made possible by a grant from the Innovative Medicines Initiative 2 Joint Undertaking (JU) under grant agreement No 853989. The JU receives support from the European Union’s Horizon 2020 research and innovation programme, and in-kind support from EFPIA, Global Alliance for TB Drug Development, Bill & Melinda Gates Foundation and University of Dundee.

TB-APEX data platform Content and Access:

The TB-APEX data platform will catalog contemporary (TB) preclinical trial data sets and make these data sets available to qualified researchers. Approved researchers can access patient-level data from at least sixty preclinical trials. Additional trial data is expected to be made available in the future.

For more information on TB-APEX or how your organization can contribute data, please contact: codr-eu@c-path.eu

TB-APEX Study List

Study ID	Area	No. of Animals or Cartridges	Title	Drugs	Contributors	Study Type
EV-LY-TBa19003	Tuberculosis Mouse Model	265	EV-LY-TBa19003	Bedaquiline, Isoniazid, Linezolid, Moxifloxacin, Pretomanid, Rifampicin, Pyrazinamide	EVOTEC	In Vivo
EV-TL-PK2019	Tuberculosis Mouse Model	144	EV-TL-PK2019	Bedaquiline, Isoniazid, Linezolid, Moxifloxacin, Pretomanid, Rifampicin, Pyrazinamide	EVOTEC	In Vivo
Gates-03	Tuberculosis Mouse Model	174	Gates-03	Rifampin, Isoniazid, Moxifloxacin, Pyrazinamide, Ethambutol	Colorado State University (CSU)	In Vivo
Gates-11	Tuberculosis Mouse Model	194	Gates-11	Rifampin, Isoniazid, Pyrazinamide, Ethambutol	Colorado State University (CSU)	In Vivo
Gates-12	Tuberculosis Mouse Model	36	Gates-12	Rifampin, Isoniazid, Pyrazinamide, Ethambutol	Colorado State University (CSU)	In Vivo
Gates-17	Tuberculosis Mouse Model	38	Gates-17	Rifampin, Isoniazid, Pyrazinamide, Ethambutol	Colorado State University (CSU)	In Vivo
Gates-B	Tuberculosis Mouse Model	477	Gates-B	Rifampin, Isoniazid, Pyrazinamide, Moxifloxacin	Colorado State University (CSU)	In Vivo
JHU-2013-Expt-3c	Tuberculosis Mouse Model	241	JHU-2013-Expt-3c	Rifampin, Isoniazid, Pyrazinamide, Bedaquiline, Pretomanid, Linezolid, Sutezolid	Johns Hopkins University (JHU)	In Vivo
JHU-2014-Expt-3c	Tuberculosis Mouse Model	160	JHU-2014-Expt-3c	Rifampin, Isoniazid, Pyrazinamide, Bedaquiline, Pretomanid, Linezolid	Johns Hopkins University (JHU)	In Vivo
JHU-2016-Expt-3c	Tuberculosis Mouse Model	72	JHU-2016-Expt-3c	Bedaquiline, Pretomanid, Linezolid	Johns Hopkins University (JHU)	In Vivo
JHU-CFZ-Study1	Tuberculosis Mouse Model	100	JHU-CFZ-Study1	Rifampin, Isoniazid, Pyrazinamide, Ethambutol	Johns Hopkins University (JHU)	In Vivo
JHU-CFZ-Study2	Tuberculosis Mouse Model	54	JHU-CFZ-Study2	Rifampin, Isoniazid, Pyrazinamide, Ethambutol	Johns Hopkins University (JHU)	In Vivo
JHU-CFZ-Study3	Tuberculosis Mouse Model	83	JHU-CFZ-Study3	Rifampin, Isoniazid, Pyrazinamide, Ethambutol	Johns Hopkins University (JHU)	In Vivo
JHU-CFZ-Study4	Tuberculosis Mouse Model	81	JHU-CFZ-Study4	Rifampin, Isoniazid, Pyrazinamide, Ethambutol	Johns Hopkins University (JHU)	In Vivo
JHU-CFZ-Study5	Tuberculosis Mouse Model	63	JHU-CFZ-Study5	Rifampin, Isoniazid, Pyrazinamide, Ethambutol	Johns Hopkins University (JHU)	In Vivo
JHU-MXF-Study1	Tuberculosis Mouse Model	157	JHU-MXF-Study1	Rifampin, Isoniazid, Pyrazinamide, Moxifloxacin	Johns Hopkins University (JHU)	In Vivo
JHU-MXF-Study2	Tuberculosis Mouse Model	254	JHU-MXF-Study2	Rifampin, Isoniazid, Pyrazinamide, Moxifloxacin	Johns Hopkins University (JHU)	In Vivo
JHU-PMD-Study1	Tuberculosis Mouse Model	96	JHU-PMD-Study1	Rifampin, Pyrazinamide, Moxifloxacin, Pretomanid	Johns Hopkins University (JHU)	In Vivo
JHU-PMD-Study2	Tuberculosis Mouse Model	283	JHU-PMD-Study2	Rifampin, Isoniazid, Pyrazinamide, Moxifloxacin, Pretomanid	Johns Hopkins University (JHU)	In Vivo
JHU-PMD-Study3	Tuberculosis Mouse Model	112	JHU-PMD-Study3	Rifampin, Isoniazid, Rifapentine, Pyrazinamide, Moxifloxacin, Pretomanid	Johns Hopkins University (JHU)	In Vivo
JHU-PMD-Study4	Tuberculosis Mouse Model	194	JHU-PMD-Study4	Rifampin, Isoniazid, Bedaquiline, Pyrazinamide, Moxifloxacin, Pretomanid	Johns Hopkins University (JHU)	In Vivo
JHU-PMD-Study5	Tuberculosis Mouse Model	242	JHU-PMD-Study5	Rifampin, Isoniazid, Pyrazinamide, Moxifloxacin, Pretomanid	Johns Hopkins University (JHU)	In Vivo
JHU-PMD-Study6	Tuberculosis Mouse Model	100	JHU-PMD-Study6	Rifampin, Isoniazid, Pyrazinamide, Moxifloxacin, Pretomanid	Johns Hopkins University (JHU)	In Vivo
JHU-PMD-Study7	Tuberculosis Mouse Model	172	JHU-PMD-Study7	Rifampin, Isoniazid, Pyrazinamide, Moxifloxacin, Pretomanid	Johns Hopkins University (JHU)	In Vivo
JHU-PMD-Study8	Tuberculosis Mouse Model	181	JHU-PMD-Study8	Rifampin, Isoniazid, Pyrazinamide, Moxifloxacin, Pretomanid	Johns Hopkins University (JHU)	In Vivo
JHU-PZA-Study1	Tuberculosis Mouse Model	107	JHU-PZA-Study1	Rifampin, Isoniazid, Pyrazinamide, Ethambutol	Johns Hopkins University (JHU)	In Vivo
JHU-REMox-Study1	Tuberculosis Mouse Model	136	JHU-REMox-Study1	Rifampin, Isoniazid, Pyrazinamide, Moxifloxacin, Ethambutol	Johns Hopkins University (JHU)	In Vivo
JHU-RPT-Study1	Tuberculosis Mouse Model	220	JHU-RPT-Study1	Rifampin, Isoniazid, Pyrazinamide, Moxifloxacin, Rifapentine	Johns Hopkins University (JHU)	In Vivo
JHU-RPT-Study2	Tuberculosis Mouse Model	156	JHU-RPT-Study2	Rifampin, Isoniazid, Pyrazinamide, Moxifloxacin, Rifapentine	Johns Hopkins University (JHU)	In Vivo
HFS-50	Tuberculosis Hollow Fiber	12	PAMZ_log_phase_CPTR	PA-824, Moxifloxacin, Pyrazinamide, Isoniazid, Rifampicin	BAYLOR	In Vitro
HFS-53	Tuberculosis Hollow Fiber	12	PaMZ_semidormant	PA-824, Moxifloxacin, Pyrazinamide, Isoniazid, Rifampicin	BAYLOR	In Vitro
HFS-63	Tuberculosis Hollow Fiber	12	PaMZ_Intracellular	PA-824, Moxifloxacin, Pyrazinamide, Isoniazid, Rifampicin	BAYLOR	In Vitro
HFS-64	Tuberculosis Hollow Fiber	24	HF64_CPTR_Sutezolid Revised.2	Sutezolid	BAYLOR	In Vitro
HFS-82	Tuberculosis Hollow Fiber	24	HF82_CPTR_Sutezolid Final Data Set	Sutezolid	BAYLOR	In Vitro
HFS-83	Tuberculosis Hollow Fiber	24	HF83_CPTR_Sutezolid @ ph5.8	Sutezolid	BAYLOR	In Vitro
HFS-84	Tuberculosis Hollow Fiber	30	HFS84_CPTR_Delamanid_data_set_LPG	Delamanid	BAYLOR	In Vitro
HFS-86	Tuberculosis Hollow Fiber	6	HF86_CPTR_BDQ pK Data Set	Bedaquiline	BAYLOR	In Vitro
HFS-87	Tuberculosis Hollow Fiber	18	CPTR HFS 87_Oxazolidinine_LPG	Linezolid, Sutezolid, Tedizolid	BAYLOR	In Vitro
HFS-94	Tuberculosis Hollow Fiber	24	HF94_CPTR_Delaminid at 5.8_Data Set	Delamanid	BAYLOR	In Vitro
HFS-96	Tuberculosis Hollow Fiber	24	HFS-96_OPC_LogPhase	OPC	BAYLOR	In Vitro
HFS-97	Tuberculosis Hollow Fiber	12	CPTR HF97_Oxazolidinine_head-to-head_SDB	Linezolid, Sutezolid, Tedizolid	BAYLOR	In Vitro
HFS-99	Tuberculosis Hollow Fiber	20	HFS99 Delamanid_data_set_intracellular	Delaminid	BAYLOR	In Vitro
HFS-100	Tuberculosis Hollow Fiber	12	CPTR_HF100_IC_oxzolidinone_head-to-head	Linezolid, Sutezolid, Tedizolid	BAYLOR	In Vitro
HFS-101	Tuberculosis Hollow Fiber	24	HFS-101_OPC_H37Ra_IntraCellular_	OPC	BAYLOR	In Vitro
HFS-102	Tuberculosis Hollow Fiber	24	HFS-102_OPC_H37Rv_SemiDormant_Phase	OPC	BAYLOR	In Vitro
HFS-105	Tuberculosis Hollow Fiber	24	HSF-105 sutezolid plus metabolite	Sutezolid, metabolite	BAYLOR	In Vitro
HFS-107	Tuberculosis Hollow Fiber	26	HF107_CPTR_OPC_Del_H37Ra LogPhase	OPC-167832 &/or Delaminid or Isoniazid, Rifampicin, Pyrazinamide	BAYLOR	In Vitro
HFS-108	Tuberculosis Hollow Fiber	26	HF108_OPC_Del_Combo_H37Rv_Sterilizing	OPC-167832 &/or Delaminid or Isoniazid, Rifampicin, Pyrazinamide	BAYLOR	In Vitro
HFS-109	Tuberculosis Hollow Fiber	26	HF109_OPC_Del_Combo_H37Ra_IntraCellular	OPC-167832 &/or Delaminid or Isoniazid, Rifampicin, Pyrazinamide	BAYLOR	In Vitro
HFS-115	Tuberculosis Hollow Fiber	24	HF115_CPTR_Bedaquiline_H37Rv_SRB	Bedaquiline	BAYLOR	In Vitro
HFS-116	Tuberculosis Hollow Fiber	22	HF116_CPTR_Comb_H37Rv_SRB_Final_Report	Bedaquiline, Delaminid, Moxifloxacin, OPC, Pretomanid, Sutezolid, Pyrazinamide, INH, RMP	BAYLOR	In Vitro
HFS-117	Tuberculosis Hollow Fiber	22	HF117_CPTR_Comb_H37Ra_LogPhase_Final Rpt	Bedaquiline, Delaminid, Moxifloxacin, OPC, Pretomanid, Sutezolid, Pyrazinamide, INH, RMP	BAYLOR	In Vitro
HRZE-R1	Tuberculosis Hollow Fiber	10	HRZE R1	Isoniazid, Rifampicin, Pyrazinamide, Ethambutol	EVOTEC	In Vitro
HRZE-R2	Tuberculosis Hollow Fiber	10	HRZE R2	Isoniazid, Rifampicin, Pyrazinamide, Ethambutol	EVOTEC	In Vitro
HRZE-R3	Tuberculosis Hollow Fiber	10	HRZE R3	Isoniazid, Rifampicin, Pyrazinamide, Ethambutol	EVOTEC	In Vitro
PaMZ-R1	Tuberculosis Hollow Fiber	10	PaMZ R1	Pretomanid, Moxifloxacin, Pyrazinamide	EVOTEC	In Vitro
PaMZ-R2	Tuberculosis Hollow Fiber	10	PaMZ R2	Pretomanid, Moxifloxacin, Pyrazinamide	EVOTEC	In Vitro
PaMZ-R3	Tuberculosis Hollow Fiber	10	PaMZ R3	Pretomanid, Moxifloxacin, Pyrazinamide	EVOTEC	In Vitro
REMox-R1	Tuberculosis Hollow Fiber	10	REMox R1	Rifampicin, Ethambutol, Moxifloxacin, Pyrazinamide	EVOTEC	In Vitro
REMox-R2	Tuberculosis Hollow Fiber	10	REMox R2	Rifampicin, Ethambutol, Moxifloxacin, Pyrazinamide	EVOTEC	In Vitro
REMox-R3	Tuberculosis Hollow Fiber	10	REMox R3	Rifampicin, Ethambutol, Moxifloxacin, Pyrazinamide	EVOTEC	In Vitro

Important Information about the TB-APEX Platform

What data does the TB-APEX data platform contain?

The platform contains Preclinical TB trial datasets currently consisting of Hollow Fiber Systems (In Vitro) and Animal Studies (In Vivo) contributed by the following organizations, to C-Path for use by qualified TB researchers.

1. Evotec
2. Baylor University
3. Johns Hopkins University (JHU)
4. Colorado State University (CSU)

With C-Path’s continued engagement with various TB research initiatives, additional preclinical trial data may be available in the future.

How do I suggest improvements to the TB-PACTS data platform?

We appreciate suggestions on improvements to the TB-PACTS data platform. Please send your comments and suggestions to Richard Liwski (u003ca href=u0022mailto:rliwski@c-path.orgu0022 target=u0022_blanku0022 rel=u0022noopeneru0022u003erliwski@c-path.orgu003c/au003e).

What data are contained in the TB-PACTS data platform?

The TB-PACTS data platform contains TB clinical study data, which includes demographic information, concomitant medications information, dose/concentration information, outcomes data, and relevant covariates of interest. Additional information specific to data content will be available to registered users of the TB-PACTS data platform.

How are the data standardized?

The data are mapped to the Clinical Data Interchange Standards Consortium (CDISC) Standard Data Tabulation Model (SDTM), and TB-specific Therapeutic Area User Guide (v2) to maximize utility of aggregated data for statistical analysis. All data are fully anonymized.

Important Information about the TB-APEX Data Platform Content and Access:

The database contains, but is not limited to data on:

Treatments
Drug resistance
Demographics
Biospecimen Events
Body Weight
Disposition
Pharmacokinetics Concentration
Pharmacokinetics Parameters
Microbiology Specimen
Microbiology Susceptibility
Biospecimen Events
Trial Level Data

Please note that in light differences in experimental protocols and approaches per data contributor, the data listed above may vary per study. All data have been remapped to a common data standard such that data can be analyzed across all studies.

The TB-APEX Data Platform is available to qualified researchers who have submitted a sound TB research proposal, have agreed to the “TB-APEX Terms and Conditions for Data Use”, and have been approved through the TB-APEX access review process.

Important information about data standardization:

The data is mapped to the Clinical Data Interchange Standards Consortium (CDISC) Standard for Exchange of Nonclinical Data (SEND), Standard Data Tabulation Model (SDTM), Animal Rule Guide (SENDIG-AR v1.0) and Pharmacogenomics/Genetics Guide (PGxIG v1). Knowledge of SDTM and SEND is required for effective use of the data. Information and training on SDTM and SEND are available on the CDISC website (http://www.cdisc.org/Education).

Selected domains contained in the TB-APEX Data Platform
CDISC Domain	Variables of Interest
DM	Age, Gender, Species, Strain, Trial Arm
MS	Drug Resistance Information
MB	Culture Results (CFU)
BW	Body Weight of Animal
EX	Drug Name, Drug Dose, Route & Drug Strength
AG	Procedure Agent Name & Dose
PC	Concentration measurements for administered compounds and their metabolites

FAQs/Training

General Questions

Is there a fee for using the TB-APEX data platform?

There is no fee to use the TB-APEX data platform.

How do I suggest improvements to the TB-APEX data platform?

We appreciate suggestions on improvements to the TB-APEX data platform. Please send your comments and suggestions to: codr-eu@c-path.eu.

What data are contained in the TB-APEX data platform?

The TB-APEX data platform contains TB preclinical study data, which includes demographic information, dose/concentration information, drug resistance information, biospecimen events, subject body weight, subject disposition, PK results and parameter, microbiological specimen results and study level information.

Additional information specific to data content will be available to registered users of the TB-APEX data platform.

How are the data standardized?

The data is mapped to the Clinical Data Interchange Standards Consortium (CDISC) Standard for Exchange of Nonclinical Data (SEND), Standard Data Tabulation Model (SDTM), Animal Rule Guide (SENDIG-AR v1.0) and Pharmacogenomics/Genetics Guide (PGxIG v1) to maximize utility of aggregated data for statistical analysis.

Registration for Access Questions:

How do I register for access to the TB-APEX data platform?

A: Visit the Data Archive Platform page on this website to register for access. You must first review and agree to the Terms and Conditions for Use of the TB-APEX data platform. Once completed, researchers will be directed to the online application form.

How long will it take to process my access request?

The TB-APEX Steering Committee will review all user access applications in a timely manner, and this may take up to 4 weeks to process.

Data Contribution Questions:

How and when can I contribute my data to the TB-APEX data platform?

Individuals, organizations, institutions, and countries (health ministries, national TB programs, etc.) are encouraged to contribute preclinical study data. In addition to the study dataset, submitting organizations will be requested to provide information regarding study methodology and demographic data for their submissions. For additional information please contact: codr-eu@c-path.eu.

Will I retain ownership of the data that I am contributing to the TB-APEX data platform?

Yes, data ownership is always retained by the data contributor.

What measures are in place to ensure data platform security?

TB-APEX data platform policies for data transfer, validation, processing and access include the following features to ensure that the data are safe and secure:

Secure file transfer
OS hardening and security updates
Host-based intrusion detection/prevention system
Anti-malware protection
Automated log monitoring and alert system
Data access controls for incoming server, investigational database, analysis datasets
Data backup and disaster recovery
Data provenance – changes to data will be traceable and auditable throughout its lifecycle
Multi-factor authentication
Multi-tier network structure
File integrity monitor

How should data be formatted for contribution to the TB-APEX data platform?

Multiple data formats can be accommodated including text, csv, xls or SAS transport files. Supporting information can be PDF, text, Microsoft Word or other document formats. Critical Path Institute will provide guidance as needed to data contributors.

TB-Platform for the Aggregation of Preclinical Experiments Data (TB-APEX)