Appendix_4__QA_Guidelines.pdf

Guidelines for conducting NTP Pathology Quality Assessment (APS, PDR, & QA)

Index

A. Overview of NTP Pathology Peer Review Processes

1. Audit of Pathology Specimens (APS)

2. Pre-QA Pathology Data Review (PDR)

3. Pathology Quality Assessment (QA)

4. Pathology Working Group (PWG)

5. Pathology Peer Review (PPR)

B. Study types undergoing NTP pathology peer review

1. Chronic studies

2. Subchronic studies

3. RACB and MOG studies

4. Immunotoxicity studies

5. Neurodevelopmental studies

C. Detailed description of specific tasks

1. Development of SOPs

2. Pre-QA Pathology Data Review

3. Audit of pathology materials

4. Anatomic Pathology Data Quality Assessment

5. Special requirements

6. Deliverables and reporting requirements

A. Overview of NTP Pathology Peer-Review Processes

Since a program of the magnitude and diversification of the NTP requires cooperation and collaboration of numerous testing laboratories throughout the nation, there is a need for assessment of uniformity, consistency, and accuracy of pathology data, diagnostic criteria, and procedures. The recognition of a need for independent verification of the pathology findings resulted in the first pathology peer review contract being awarded by the National Cancer Institute (NCI) in 1978 for their long-term carcinogenicity studies. The current NTP contracts for pathology have been in place since 1984.

The NTP Pathology peer-review process is viewed as an international gold standard by agencies such as EPA, FDA, NIOSH, and IARC. It is a rigorous and integral part of providing high quality pathology data for NTP Technical, Toxicity, and Genetically Modified Model Report series. Its goal is to verify and establish consistency in pathology results by using standardized criteria and review by experts. It is composed of 4 types of activities, namely:

Audit of Pathology Specimens (APS) Pre-QA Pathology Data Review (PDR) Pathology Quality Assessment (QA) Pathology Working Group (PWG) Pathology Peer Review (PPR)

The main purpose of the pathology peer-review process is to achieve consensus on pathology diagnoses of all neoplasms, unusual lesions, and all potentially treatment-related neoplastic and non-neoplastic lesions. This is accomplished by resolving diagnostic discrepancies that arise during the pathology review of NTP studies. Through contract support, the initial gross and microscopic pathology evaluation for each study is conducted by a preferably ACVP board-certified pathologist at the study laboratory (called study pathologist or SP). The pathology findings, reports, data, blocks, slides, wet tissues, and any other materials generated at the study laboratory are submitted to the NTP Archives.

1. Audit of Pathology Specimens (APS)

The laboratory report and pathology data are then subjected to a multi-level pathology review and an audit of pathology specimens (APS). The APS is an NTP audit of all the materials (data, tables, glass slides, blocks, etc.) and documents (lab reports, etc.) as well as a check on whether the lab adhered to NTP specifications. The APS for immunotoxicity, RACB, MOG, and neurodevelopmental studies is identical.

2. Pre-QA Pathology Data Review (PDR)

In parallel to the APS, pathology data are reviewed from the NTP and NCTR studies for positive and negative trends relative to treatment/exposure, and for unusual trends, inappropriate terminology, or possible duplication of terminology. Also, there is a review of the pathology narrative for both species and results of subchronic studies to see if it accurately reflects the pathology diagnoses and indicates what might have been expected in the 2-year study. The PDR identifies any potential target organs, unusual findings, and potential discrepancies. This is a key timeframe whereby possible investigative studies are proposed to address biological or toxicologic mechanisms or modes of action. The PDR for immunotoxicity, RACB, MOG, and neurodevelopmental studies is identical.

3. Pathology Quality Assessment (QA)

The Quality Assessment (QA) includes evaluation of pathology records, evaluation of the pathology diagnoses and comparison with the histological material. Since pathology results are usually the crucial endpoint for decision making there is a need for independent verification of the pathology and clinical pathology findings. The purpose of the QA is to provide that independent verification, and to achieve consistency of data within and between studies.

Pathology materials for all studies are first received by NTP archives and, after inventory, are forwarded to the QA contractor for the PDR, APS, QA, and PWG.

For all studies, the QA contract pathologist shall perform a technical review for slide quality, tissues present and the quality of the pathology evaluation. During the evaluation, the QA pathologist (QAP) shall identify lesions likely to be reported as treatment-related in the technical reports, or any unusual background sporadic lesions, and take representative photomicrographs for inclusion in the QA pathology report and for the NTP digital database.

The QA pathologist shall consult with the NTP pathologist and arrange the PWG. Thus, the QA pathologist must work closely with the NTP pathologist. However, for some studies, the Head of NTP Pathology may assign another contract pathologist, called a Pathology Working Group Coordinator (PWGC), to review the discrepancies between the QA and study pathologists, as well as potential treatment-related findings and other tissues as deemed necessary, and arrange the pathology working group (PWG). The decision to assign a PWGC (separate from the QA pathologist) will be made on a case-by-case basis. If a separate PWGC is assigned, that pathologist must not be employed by the same contractor as the QA pathologist.

4. NTP Pathology Working Group (PWG)

The QA pathologist (or PWGC) shall work with the PWG Administrator to coordinate the activities of the PWG panel of pathologists who convene to review and discuss selected histopathological lesions and the relevant pathology/toxicology data from each study. Prior to the PWG meeting, the PWG Coordinator, in consultation with the NTP Study Pathologist, shall select the histopathological lesions for review and determine the issues that are to be discussed and resolved. PWG meetings shall ordinarily be conducted at the NIEHS; however, the Contractor may be required to conduct PWG sessions at NTP contract laboratories or at other Government facilities such as National

Center for Toxicological Research (NCTR) in Arkansas.

The PWG comprises an invited panel of 7-12 veterinary toxicologic pathologists, preferably ACVP board certified, who convene to review and discuss selected histopathological lesions and the relevant pathology/toxicology data from each study.

The study pathologist (SP) may also (when possible) be asked to attend the PWG in person or by tele- or videoconference and participate/vote in reaching final consensus.

The PWG reviews and resolves all discrepancies, reviews possible treatment-related lesions, and achieves consensus regarding the terminology, diagnoses, and their interpretation. This represents the culmination of the NTP pathology peer-review process. The findings of the PWG are considered the “final pathology results.” These results form the basis for the analysis of the findings, development of study conclusions by NTP staff, and preparation of the draft report in the appropriate NTP report series. A PWG will be held for all chronic studies and selected special and subchronic studies.

Immediately upon completion of the PWG, the PWGC shall, along with the NTP pathologist, determine whether the photography needs for the study have been fulfilled, and if not the PWGC shall complete the process.

5. Pathology Peer Review (PPR)

For most subchronic and other short-term or special studies, resolution of discrepancies and any other pathology issues will be resolved by the SP, QAP, PWGC and NTP pathologist and may require input from 1-2 experts for a small PWG-like review (called a Pathology Peer Review or PPR). As with the PWGs, these smaller reviews (PPRs) shall be arranged by the PWGC unless otherwise directed by the NTP.

B. Study types undergoing NTP pathology peer review

NTP toxicity and carcinogenicity studies yield large amounts of data, including data from pathology evaluations of necropsied animals in all phases of the testing protocols. Studies are conducted according to Good Laboratory Practices (GLP). Study types include:

1. Chronic studies are usually 2-year exposures, with or without perinatal exposure, and in some cases having interim time points, typically at 3, 9 and/or 15 months. Chronic studies generally are comprised of at least 800 animals (usually 3 dose groups plus one control group, 50 animals per group, both sexes, and include both rats and mice). Each study produces an average of 20 slides containing about 40 tissues per animal, for a total of approximately 30,000 tissues with a range upwards to 17,000 slides.

2. Subchronic studies are usually 90-day exposures There are 5 dose groups of 10 per group with controls, both sexes, and both rats and mice. Each study produces an average of 11 slides per animal, or a total of approximately 2,600 slides.

(i) Typically, 2-3 chronic studies and two 90-day subchronic studies are performed by the National Center for Toxicologic Research (NCTR) near Little Rock, Arkansas. They are similar in magnitude and quantity to the NTP chronic and subchronic studies.

3. The NTP has recently expanded its evaluation of various organ systems with a more focused review of the tissues. These organ systems include the male and female reproductive tracts. The NTP now carries out developmental and reproductive toxicology studies (DART) including reproductive assessment by continuous breeding (RACB) studies, and newly designed modified one-generation (MOG) studies. The RACB and MOG studies have thousands of slides including about 5,000 H&E slides in addition to vaginal cytology for estrus staging, stage awareness for spermatogenesis, and evaluation of mammary gland whole mounts. MOG studies may have up to 5 cohort studies.

4. The immune system has an expanded review for special immunotoxicity studies that includes a detailed, enhanced review of the lymphoid system including the following tissues: spleen, thymus, lymph nodes, bone marrow, and mucosa-associated lymphoid tissue.

C. Specific Tasks

1. Develop Standard Operating Procedures (SOPs).

The Contractor shall:

Develop a complete set of SOPs for all defined procedures and tasks specific to the conduct of the QA.

2. Pre-QA Pathology Data Review (PDR).

(i) Review pathology data for deviations from historical control data, duplications and inappropriate use of topographies, and tissues with low tissue accountability.

During this review, the pathologists shall identify all positive, negative or unusual trends in the occurrence of potentially treatment-related changes. The data submitted shall be compared with the narrative prepared by the study pathologist to determine if the pathologist addressed all relevant issues.

(ii) Convene a PDR meeting with NTP staff to review the pathology findings of the study. Following this meeting, a PDR report will be drafted by the contract PDR pathologist. The report shall contain recommendations for tissue/lesion review and beneficial special studies. The PDR report shall also include a review of in-life reports, necropsy and histology records and individual animal pathology records for completeness, accuracy and internal consistency of the information present in these pathology records, as well as include representative excerpts from the study laboratory’s pathology narrative as a summary of the original findings.

(iii) Submit a final PDR report after approval by the NTP pathologist. The submission should include an electronic version (i.e., a pdf) and color-print hard copy that is submitted to the NTP Data Coordination Unit (DCU) and the NTP pathologist, with an email notice to the COR. The PDR pathologist will finalize the tissue review list and select animals to be reviewed in the audit of pathology materials.

The first draft and final report of the PDR should be completed not more than 30 and 50 calendar days, respectively, after receipt of all pathology records from the study laboratory.

3. Audit of Pathology Materials.

(i) Examine the residual formalin fixed wet tissues, paraffin blocks and microscope slides from randomly selected animals as well as from animals identified from the PDR as determined by NTP personnel; it will usually involve approximately 8% of the animals. All residual wet tissues in jars and/or bags, slides and blocks for the random sample of 10% animals in each dose group and those from any animals with discrepancies identified in the PDR report. The percentage of tissues reviewed may be increased at the discresion of the NTP.

(ii) Examine the residual formalin-fixed tissues to evaluate the accuracy of animal identification, the adequacy of the necropsy and gross trimming of the tissues, and the possible presence of gross lesions, which were not described at necropsy or trimmed for microscopic examination.

(iii) Examine the microscope slides to determine that they are labeled according to the

NTP Statement of Specifications and to determine if required tissues are present and have been consistently sampled. The slides shall be examined for tissue accountability and for histotechnical quality.

(iv) Examine paraffin blocks to assess whether they are properly labeled and that all blocks have been sectioned with corresponding microscope slides available for examination.

(v) Submit a final APS report within 30 calendar days of completion of the PDR.

4. Anatomic Pathology Data Quality Assessment

(i) Have a means for automating the receipt of pathology data in electronic form and transferring the pathology data to QA tables and QA reports for use in the pathology QA process. The NTP-preferred data management system that allows pathology data to be stored as print files or discs and will be made available to the contractor. These files are used to format and print the QA tables, which will include tumor diagnoses, tissues with potential treatment related lesions, other diagnoses or animals as required by the QA process, and for the PDR.

(ii) For subchronic toxicity studies: (QA pathologist) review all histological slides from a percentage (usually 60 percent) of the high dose and control animals plus all tissues with potential treatment related (positive and negative) lesions from higher dosed animals down to a clear no-effect-level. This task should be completed within 90 working days of completion of the PDR.

(iii) Format and print the QA tables, which will include tumor diagnoses, tissues with potential treatment related lesions, other diagnoses or animals as required by the QA process, and for the PDR.

(iv) Perform microscopic examination of designated tissues/lesions to evaluate the consistency and accuracy of the histopathological diagnoses and to ensure that all treatment-related effects are reviewed and identified. The QA pathologist will prepare an interpretative pathology narrative of the results of this review for submission to the NTP. This task will also include an assessment of the proper identification of the microscope slides, evaluation of the quality of the hematoxylin and eosin stained tissue sections, and an overall evaluation of adherence to the pathology protocol.

(v) Include an assessment of the proper identification of the microscope slides, evaluation of the quality of the hematoxylin and eosin stained tissue sections, and an overall evaluation of adherence to the NTP pathology protocol (NTP Specifications 2011 – weblink).

(vi) Evaluate the histotechnique quality and accuracy of the original tissue counts.

Activities include review of all slides for the presence of protocol-required tissues; and tabulating and correlating the data with the original laboratory report;

and evaluating a representative number of slides for histotechnique quality using ASCP criteria.

(vii) Evaluate a representative number of clinical pathology cytology slides to confirm they are of high quality.

(viii) Review and validate diagnoses for all tumors and all potential treatment related lesions. A review of lesions with unusual trends is also required. Interim sacrifice animals will also be evaluated (same review as performed for the core study animals).

(ix) Prepare a detailed report on the pathology QA. This shall include an introduction detailing the study, type of lesions found, nature and significance of the lesions and a general evaluation of the quality of the slides and original pathology review.

The body of the report will include 1) listing of discrepancies between animal records and computer output 2) details of histotechnique review 3) listing of target tissues and discrepancies between original and QA pathologist 4) lists and summary tables of original and QA tissue counts and 5) other data as necessary.

(x) Immediately after the QA review the NTP and QA pathologist meet to discuss the findings and may resolve minor issues and discrepancies in diagnoses or terminology (It typically takes one full week to complete their task). The NTP pathologist and the QA pathologist decide on what lesions in specific animals need to be brought to the PWG. Once decided, the PWG tables are generated and submitted to staff to have specific tissues with lesions pulled and ready. It is expected to take one week for the QA pathologist to write the QA narrative and 3- 4 weeks to set up the PWG.

5. Special requirements

(i) Transportation of the study package – This procurement includes the review of the technical and diagnostic aspects of the pathology material from NTP studies.

Histological slides, paraffin blocks, wet tissues, QA reports and PWG slide sets will need to be delivered and picked up from the NTP Archive on a daily basis and from NIEHS at least that frequently and delivered to the contract lab. Since original histological slides and paraffin blocks are irreplaceable, specimens from studies often costing several million dollars and requiring years for completion, insuring that these materials are not lost or damaged is of prime concern. Offerer must comply with minimum safety requirements for handling animal tissues in fixatives (neutral buffered formalin) and a Health and Safety plan must be submitted. Materials may not be mailed to a third party without prior NTP approval from the COR.

(ii) Histologic slides, paraffin blocks, fixed animal tissues, cytological specimens and clinical pathology results from the studies will be made available to the contractor at the completion of the initial pathological evaluation for the quality assessment procedure. This material will be inventoried by the NTP Archives prior to submission to the contractor and also on receipt from the contractor to assure that Government material is not lost. Pathology data tables will also be made available to the Contractor for use in the Quality Assurance Program. The Government will provide appropriate computer software compatible with the NIEHS computers and printers so that the Pathology data from the NTP studies can be sent electronically and printed at the QA laboratory for QA review. The pathology data will be in the NTP toxicology data management system electronically.

(iii) The toxicology data management system was developed at NIEHS/NTP to allow staff scientists to monitor the conduct of in-life studies, to manage NTP toxicology and carcinogenesis data collected during the in-life and pathology portions of these studies and to provide standardized reports which are incorporated into the NTP Technical Reports. The toxicology data management system processes data by defining a standardized research protocol; managing a centralized database for archived files; employing rigorous data integrity procedures at the time of data capture; and providing access to tools for data retrieval, report generation, ad-hoc query and statistical analysis.

6. Deliverables and Reporting Requirements

(i) Standard operating procedures (SOP) – An SOP for all defined procedures and tasks specific to this task shall be submitted within 60 days after start of the first study.

(ii) Pre-QA PDR Reports - The PDR report will be submitted, via DCU, to the Head of NTP Pathology, the COR, and the NTP pathologist. The NTP pathologist assigned to the chemical/agent will work with the QA pathologist to finalize the tissue review list and select animals to be reviewed in the audit of pathology materials. The first draft and final draft of the PDR should be completed not less than 30 and 50 calendar days respectively after receipt of all pathology records from the study laboratory.

(iii) Audit of pathology materials report – This report shall be completed within 30 calendar days of completion of the PDR report.

(iv) Pathology QA Reports

(v) The contractor shall submit, via DCU, two (2) complete bound copies and five (5) copies of the summary reports for each per study reviewed of a pathology quality assessment (QA) report to the Head of NTP Pathology, the COR, and the NTP Pathologist. This will include an introduction summarizing the findings and stating a conclusion regarding slide quality, quality of original pathology evaluation, significance of compound related lesions and suggestions for further review if deemed necessary. These will be submitted within two weeks after completion of the Pathology QA Report.

David E. Malarkey, DVM, PhD, DACVP Head, NTP Pathology Group January 18, 2011