Sources Sought HT0050-20-RFI-0084 JPC.pdf

Sources Sought (HT0050-20-RFI-0084): Defense Health Agency (DHA) – Joint Pathology

Center (JPC) Digital Pathology Modernization Effort

The Defense Health Agency (DHA) is issuing this Sources Sought as a means of conducting market research to identify resources and capability to provide integration and support for Joint

Pathology Center (JPC)

Background:

The Joint Pathology Center (JPC) is the premier pathology reference center for the federal government and part of the Defense Health Agency (DHA). As of 2011, the JPC tissue repository contains approximately 55 million glass slides, 31 million paraffin-embedded tissue blocks, and over 500,000 wet tissue samples that have been collected over the last 102 years -making it the largest collection of human pathology specimens in the word. The repository represents a priceless resource for clinicians, pathologists, and health care data analysts to better understand and diagnose rare diseases and cancers.

An example of the repository’s invaluable influence on medicine is the use of tissue specimens in the repository to sequence the 1918 influenza virus, which killed more than 40 million people worldwide. The resulting research ultimately provided guidance for avoiding future influenza outbreaks that could affect military readiness, fighting strength, and global health. Additionally, in 1983 researchers examined repository cases of children who had Reye’s syndrome, which causes damage to the brain and liver. They found that the syndrome was linked to the use of aspirin in patients with chickenpox and upper respiratory infections. After that discovery, the

Food and Drug Administration issued a warning about the use of aspirin in children and infants who had influenza or chickenpox, and the warning has correlated with a decline in the occurrence of Reye’s syndrome

In addition to maintaining the largest tissue repository in the world, the JPC provides subspecialty secondary consultations for facilities across the Department of Defense (DoD) and

Veterans Affairs Administration (VA). The JPC’s consultation practice includes a unique veterinary pathology consultative service. Lastly, the JPC enables pathologist-driven research in support of DoD and other federal government priorities and provides graduate medical education rotations and other support to federal government residencies/fellowships.

Description:

At the present time and in accordance with the National Defense Authorization Act of 2008, the

JPC is pursuing a complete digital pathology modernization effort. This effort has several components, including scanning the majority of our tissue repository. The wealth of information housed in the JPC’s repository holds significant potential for personalized medicine, particularly for machine learning algorithms and molecular findings that help establish the diagnosis, prognosis and personalized therapies for patients. The Defense Digital Service (DDS) and the

JPC are seeking a vendor(s) with the capabilities of digitizing the JPC’s repository in order to preserve this invaluable source of medical data, enhance biomedical research for infectious diseases and cancer, and enable easier data sharing with researchers, diagnosticians, and educators to facilitate collaboration and medical advances.

Please review the following sections and provide a response detailing which section(s) your company is capable of providing.

I. Laboratory Information System (LIS) Features:

The JPC depends on a LIS to support its mission to deliver the best possible patient care. As the

JPC adopts digital pathology processes and best practices within our consultation workflow, we are looking for a comprehensive LIS solution that can support our pathologists and staff throughout the pre-analytical, analytical, and post-analytical phases. The LIS will need to support consultations for both human and veterinary cases. At a high level, the LIS will be used for the following foundational use cases:

“Hub-and-Spoke” Online Consult Requisition

The JPC supports a number of federal customers, including a geographically distributed network of military treatment facilities (MTFs). For secondary consultation requests, MTFs utilize JPC’s paper-based requisition process. However, this paper-based process increases pathology turnaround-times and leads to error-prone manual processes. As a result, the JPC wants to migrate to a web-based solution that supports a hub-and-spoke consultation network powered by whole slide imaging (WSI). To execute this approach, high-capacity WSI scanners will be installed at larger MTFs, which will be integrated with JPC’s cloud infrastructure to store the images generated at the time of scanning.

This newly envisioned consultation workflow will begin when a pathologist at spoke site (e.g.

MTF) electronically submits a case to the hub (JPC) for a second opinion. The submission of an electronic case will be facilitated via the JPC website or another web-based solution. In addition to the electronic consult request, the spoke site will also transmit any applicable whole slide images. The LIS will need to integrate into this new workflow by digitally accessioning each new case and WSI to ensure the case is visible to the correct pathology subspecialty group at the

JPC. The LIS integration will also need to allow for QC-related activities such as an accessioner rejecting an electronic consult case due to incomplete data. Lastly, the LIS integration will also need to notify the spoke site that their case and WSI have been digitally accessioned and placed in a queue to be further analyzed by a JPC pathologist.

Case and Specimen Accessioning

While the JPC is committed to moving to an online and WSI based consultation approach, we recognize that not every customer will have the ability to digitally transmit consult requests and specimens to the JPC. As a result, the LIS will also need to accommodate an analog version of case and specimen accessioning. Specifically, the LIS must allow JPC staff responsible for receiving and accessioning to:

1. Accession each case and specimen

2. Manually enter patient and specimen data

3. Assign a unique accession number

4. Perform QC work on each case and specimen to determine if the right data and specimens have been received

5. Generate, print, and label each specimen with a 2D barcode for specimen tracking

6. Notify JPC customer that case request and specimen have been successfully received and accessioned

Specimen Tracking & Barcoding

The continued accessioning of physical specimens as well as the JPC’s vast physical tissue repository will necessitate the LIS to track the status and location of all specimens. For incoming specimens, this will include the need to track from accessioning to the signout and archiving of a case. JPC customers will also need to be able to virtually track the status of their case after it has been accessioned. To achieve this, the JPC requires the ability to generate and print barcodes for each individual specimen.

Barcodes will then be added to each cassette and/or glass slide. Barcodes generated by the LIS need to handle data elements such as patient name, patient ID, accession number, special stains, IHC, etc. Through barcoding and the integration of specimen tracking in the LIS, the JPC will ensure specimens can be identified, located, standardized, and audited to achieve high levels of laboratory efficiency and patient safety.

In addition to supporting our robust specimen tracking needs, barcoding will also enable our whole slide imaging efforts. We require barcoding and a LIS integration that will allow our high-throughput WSI scanners (Leica GT-450) to read barcodes on each glass slide and automatically assign the image to the right case within our LIS.

As part of the barcoding and specimen tracking effort, the JPC will require specific hardware, including high-throughput barcode printers, labels, and scanners.

Lab & Stain Ordering

Our pathologists regularly request lab orders (e.g. staining of samples or molecular testing) as part of their day-to-day consultation workflow. As a result, the LIS should have functionality to support a user-friendly and configurable test catalog and ordering mechanism. Key requirements that should be considered are:

1. The system should allow pathologists to order re-cuts, immunostains, special stains, etc directly from the LIS with the ability to add comments/special instructions.

2. The system should allow pathologists to place orders directly from a case while drafting a report

3. The system should allow pathologists to edit or cancel an order

4. The system should allow pathologists to split laboratory orders so one order can comprise of multiple tests requiring multiple specimens and accessions

5. The system should allow for group ordering

6. The system should allow for a test catalog that can be made consistent and complete via regular updates

7. The system should have the ability to relay lab orders to different interfaced systems, for example, another LIS in a separate institution or reference laboratory, without manual intervention

8. Use of LIS barcodes to be used and integrated with other test systems (immunostainer that is barcode dependent). Remove the need for double bar codes.

Additionally, throughout the lab ordering process, the LIS should track and organize the workflow in the laboratory, largely through the use of histology logs and protocols. The LIS logs should contain a list of specimens the laboratory will process for an upcoming period of time

(e.g. work shift). The specimen data on the logs will correspond to the data entered upstream by pathologists requesting tests/stains as they analyze their various consult cases. These logs should include routine histology logs, special stain request logs, and immunohistochemistry logs.

The JPC histology lab should be able to configure the format of the logs and the data to be displayed if they do not wish to utilize the LIS’ default configurations. Data elements in the histology logs may include the accession number, histology protocol(s) ordered, other stains ordered, and comments about the specimen or the request.

Lastly, the LIS has to support the tracking of individual slides during this step in the consultation workflow through the use of barcoding. Pathologists should be able to utilize the LIS to track their lab orders and receive notifications as an order makes its way through the laboratory log.

Additionally, histotechnologists need the ability to generate new barcodes and accession new slides into the LIS as they create new glass slides from tissue blocks.

Pathologist Analysis and Final Report Generation and Distribution

The LIS should provide a dashboard for each pathology subspeciality group and individual pathologist to understand and view their “bench” of cases for the day. For each consult case, the

LIS should provide pathologists with complete information about the case (patient data, initial pathology report, etc). Additionally, pathologists should be able to view what specimens have been accessioned to the case to ensure they have the correct glass slides. For cases that have associated whole slides images, please see the requirements around WSI viewing and image analysis detailed further in this document.

Pathologists should be able to use the LIS to enter a pathologic diagnosis and, if applicable, descriptive comments and microscopic description into relevant data fields in the LIS. To facilitate the entry of diagnosis text, the LIS must include capabilities such as speech-to-text conversion and the creation of predefined templates, checklists, and other similar formats.

Default codes for diagnosis (International Classification of Diseases) linked to a specimen type definition should auto-populate into final reports.

Final pathology reports should be stored within the LIS database as discrete data elements. The goal of this is to utilize final pathology reports in AI/ML generation. To achieve this, the final reports should be amenable to database queries and analysis.

Once a report is finalized, the LIS needs to support the distribution of the reports; both electronic and/or hard copy. A pathologist should be able to finalize a report (“sign out a case”) by entering an electronic signature, which locks the case in the LIS database. For hard copy report distribution, the LIS should send these reports based on rules and definitions (e.g. recipient fax number). Lastly, the LIS should support the ability to trigger a transmission of the final report to the patient’s EHR/EMR.

Additional capabiltyfor this LIS functionality include:

1. The system should allow standard word processing functionality such as bolding, underling, tabs, copy and paste, etc

2. The system should perform spell checks based on English, medical, and anatomic pathology terminology

3. The system should allow pathologists to capture, store, and integrate gross and microscopic images into their final reports

4. The system will allow for discrete reporting for pathology (synoptic reports)

Report Amendments and Addenda

The LIS should accommodate amended reports and report addenda. Once an electronic signature is affixed to a report in the LIS, the report can be changed by creating an amendment. If a report is changed or corrected, the LIS should automatically mark the amended case as such in the database and automatically label any new reports generated from the case as amended reports.

The LIS should categorize and display the reasons for the amendment.

An addendum report should be created in the LIS in cases when new information, such as special stain results, is added to a previously finalized report. Addenda do not involve changing any information in the original report. Pathologists should be able to finalize amended and addended reports with a new electronic signature in the LIS

The LIS should have the ability to also update the patient’s EMR/EHR with the amended report or addenda.

Lab Administration and Quality Assurance

In addition to supporting the day-to-day needs of the JPC, the LIS should offer functionality that supports management and leadership activities in the laboratory. The LIS needs to offer JPC leadership the option of using management reports that are predefined in the LIS, modifying predefined reporting, or creating custom reports using LIS data. Examples of these reports include turnaround time (TAT), cases not signed out (pending case backlog), volume of specimens/blocks/slides, utilization (special stains), volume of cases with each pathology subspeciality group, billing reports, and error logs.

Billing

The LIS needs to capture and maintain patient, submitter, and other client demographic and billing information for costing, invoicing, collecting, reporting, and other critical billing activities. Additionally, the LIS’ billing module should support CPT codes.

Digital Pathology System Integration

The integration of digital pathology tools into the JPC ecosystem, and specifically into the LIS, is a critical step to ensure a seamless workflow and improved efficiency. The LIS should fully integrate with every WSI scanner and digital pathology software that supports digital image management, whole slide viewing, sharing and collaboration, and computational pathology/image analysis. In other words, the LIS needs to be vendor agnostic in terms of hardware and software integrations.

Data Migration

If the JPC adopts a new LIS solution, it will require data migration services to migrate data from its current homegrown LIS to the new solution. The JPC would like to understand what internal and third-party tools and services LIS vendors have used to migrate historical legacy data into the new LIS. The JPC would also like to know what would be required of the JPC to support the migration, the typical timeline for a migration from a homegrown LIS, and key conditions that affect the timeline and overall success of the migration.

Specifically, any migration effort and LIS will need to support JPC’s unique accession number methodology:

1. JPC’s current numbering system uses a seven-digit patient/accession number followed by a sequence number which identifies how many submissions we received on that patient.

For example, 1111111-00, 11111111-01 whereby 00 is the first instance, and 01 is the second and so on

Additional LIS Requirements

The LIS should also meet the following general Capabilities:

1. Security:

i. The system must follow DoD cyber guidelines for the Risk Management

Framework (RMF) in order to successfully integrate into the JPC ecosystem and network. More information on RMF can be found here:

https://csrc.nist.gov/Projects/Risk-Management/rmf-overview

ii. They have to work with the federal government to meet the cyber requirements to allow us to integrate and have the authority to connect it to the network

iii. Restrict access to specific areas of the application based on user role

iv. Allow password protection at different levels (system admin, histotechnologist, pathologist, etc)

v. Support CAC authentication capabilities to meet DoD security protocols for access

vi. Maintain an automated system log of user sign-on activity

vii. The system makes authority checks to ensure only authorized individuals can use the system to perform an operation

viii. The system allows authorized users to generate detailed user access records

ix. The system allows for select users to review audit logs

2. Configuration

i. The system can be configured to meet the workflow of a laboratory without additional (or minimal) programming https://csrc.nist.gov/Projects/Risk-Management/rmf-overview

ii. The system architecture is modular/extensible and can easily and efficiently be modified to facilitate the addition of new functionality as business needs change

iii. The system uses open data standards

iv. The system has an application programming interface (API) that uses standard protocols and formats

v. The system admin can create custom screens, applications, and reports

vi. The system allows users to independently update fields and data dictionary entities without requiring reconfiguration of the system, even after routine upgrades and maintenance

3. Search

i. The system provides natural language search capabilities

ii. The system provides full database and field search capabilities, including the use of multiple search criteria

iii. The system allows users to build, save, and edit queries for future use

iv. The system allows users to filter and sort search results

4. Registration

i. The system allows for an unlimited number of patient registrations into the LIS

ii. The system allows the JPC to track multiple patient encounters

iii. The system allows users to perform duplicate checks to prevent assignment of duplicate medical records at registration

5. Regulations & Standards

i. The system meets or exceeds regulatory agencies requirements for HIPAA, CAP, ISO 15189, and FDA.

II. Whole Slide Image Viewer & Image Management Features

One of the goals of JPC’s modernization effort is to integrate whole slide imaging into our day-to-day consult workflow. In order to do this, we need to integrate a robust image viewing capability with our lab information system. Some key requirements include:

a. Image Viewing

1. The system allows users to pan and zoom so images can be moved and reoriented

2. The system allows users to rotate images to any desired orientation

3. The system allows the user to adjust image brightness and contrast

4. The system allows the user to capture specific regions or fields of view and export locally to the user’s machine

5. The system allows users to collaborate with colleagues in real time

6. The system allows users to create annotations and measurements

7. The system allows users to view multiple whole slide images at once

b. System Integration

1. The system should support seamless integration and connection with any LIS, EHR, and EMR

2. The system can ingest JPC barcodes

3. The system can be configured so that images and data are automatically routed from the scanner to their final destination point in the image management system

4. The system can be configured so it can access a middleware solution to retrieve images and data from the LIS

5. The system should ingest images from any WSI scanner

c. General Requirements

1. The system should not require any software installation on a user’s machine

2. The system should have a user-friendly interface

3. The system should support different use functional cases such as tumor board/subspeciality conference support, subspeciality secondary consultations, remote collaboration

4. The system should utilize “out-of-the-box” validated algorithms for image analysis to optimize the secondary consult workflow or provide for an integration with 3rd party

AI/ML tools

5. The system automatically organizes images and metadata into cases which are assigned to pathologists

6. The system should include all necessary tools for pathologists to review, annotate, collaborate on cases.

7. The system allows for an ergonomic case-viewer that integrates digital slides, quantitative data, patient details, and other critical details.

8. The system should provide security considerations such as role based authorization, audit trails, and customizable restricted levels of access

III. Whole Slide Scanning Needs

The JPC seeks to utilize commercially available whole slide scanning capabilities and services in order to accelerate the digitization of our tissue repository. Slides must be scanned for brightfield at least 40x objective lens magnification. We are looking to initially scan roughly 10,000 glass slides per week. Whole slide images will need to be transferred to JPC’s cloud storage and utilize

JPC’s barcoding system. WSI output must be in .tiff format or another non-proprietary format.

JPC is also interested in vendors who can perform QA on slides prior to scanning (checking for fingerprints, label overhangs, etc). Lastly, the vendor must be able to scan standard glass slides as well as whole mount glass slides (e.g. up to 8” X 6” slides, such as brain or complete prostate gland sections).

IV. Digital Pathology Research and Educational Capabilities

The JPC requires a digital pathology system outside of their day-to-day consultation workflow that serves as a central hub for managing single or multi-site research studies by integrating image analysis applications, lab information system, and WSI scanners to streamline image-based workflows. The digital pathology system’s capabilities must include:

a. User Access

1. System supports CAC authentication at login

2. The system can scale and supports an unlimited number of users

b. Image Upload and Allocation

1. The system can be configured so that images and data are automatically routed from the scanner

2. The system can also be configured so that images and data are routed from the LIS via a middleware solution

3. The system can ingest JPC barcodes

4. Users can manually upload whole slide images from their workstations

c. Metadata Management & De-identification

1. The system allows users to easily import metadata from LIS to be associated with images

2. The system allows users to de-identify images/cases as necessary prior to sharing with outside institutions

3. The system allows users to export data for analysis

4. The system allows users to create metadata models for research projects and datasets using preset metadata templates

5. The system allows users to define a data model for a certain type of research projects or studies that can be used repeatedly

d. Search

1. The system allows users to search for specific metadata fields and organize them based on criteria such as name, date created, size, etc

2. The system allows users to search within a specific project or study to find cases, images, or metadata fields

e. Image Organization

1. The system allows for a hierarchical data model with user defined organization

2. The system allows for a drag and drop folder structure

3. The system allows for the copying/cloning of slides, folders, and repositories.

f. Permissions

1. The system allows for dataset based permissions where individual users are granted the appropriate level of data access based on JPC admin preferences

2. The system also allows for public access and image hosting so that certain digital archives can be made available to the public but users have view only access permissions

g. Image Viewer

1. The system allows users to pan and zoom so images can be moved and reoriented

2. The system allows users to rotate images to any desired orientation

3. The system allows the user to adjust image brightness and contrast

4. The system allows the user to capture specific regions or fields of view and export locally to the user’s machine

5. The system allows users to collaborate with colleagues in real time

6. The system allows users to create annotations and measurements

h. Integration

1. The system must integrate difference image formats - particularly brightfield

2. The system must integrate with different scanning vendors - particularly Leica

3. The system must integrate with all image formats - particularly .tiff

4. The system must integrate with the JPC LIS

5. The system must integrate with JPC’s cloud environment

V. Computational Pathology Capabilities

In digitizing its repository and shifting to digital pathology workflows, JPC hopes to leverage artificial intelligence (AI) tools in its own practice, as well as contribute to the development of new AI using digitized data from its repository.

In terms of leveraging AI tools in its pathology consultant services, JPC is interested in:

a. Content-based image retrieval models that allow pathologists to retrieve similar images in the JPC repository to the query image.

b. Image generation and enhancement models to improve the quality of WSIs in the JPC repository by removing obstructing elements in images, normalizing images, and improving data completion.

c. Natural language processing algorithms that can extract valuable information from unstructured text files in case records.

JPC also hopes its repository is used by pathologists and researchers inside and outside of the organization to develop new AI tools, such as:

a. Supervised machine learning models, including deep learning models, that enable computer-assisted diagnosis, especially of rare diseases.

b. Big data mining techniques to scan digitized specimen data from the JPC repository and other clinical data to identify unseen patterns and relationships.

In terms of the development of new AI with the JPC repository, JPC anticipates several challenges:

a. To start, most WSIs will not be digitally annotated to indicate areas of interest. WSIs may have “weak labels” in the form of an overall diagnosis for an entire WSI.

b. WSIs may require significant pre-processing to be used in machine learning. For example, each WSI on average is 2-3 gigabytes and may require being split into

“patches” to be used in pre-trained deep learning models. Moreover, many specimens in the JPC repository date back dozens of years and may be degraded. Color variation and other visual artifacts may pose problems in machine learning.

Instruction for Submission of Response:

Response should not exceed 20 pages in length.

Responses should demonstrate the respondent's experience and capability to potentially fulfill the requirement identified above within the time frame required. Responses should identify the company name, company size (small or large), and contracting vehicles (e.g. GSA, NASA

SEWP, etc.) that you are affiliated with. If significant subcontracting or teaming is anticipated in order to deliver technical capability, respondents should address the administrative and management structure of such arrangements. In addition, if a small business, indicate what portion of the work is within your capabilities.

All responses must include the following information:

1) Most updated business information that include company name, address, email address, website address, telephone number, and business size and type of ownership for the company, Cage Code; and

2) Tailored capability statement that addresses the particulars found below, with appropriate documentation (part of the 20-page count) supporting claims of technical, organizational and staff capability:

a. Please review the following sections and provide a response detailing which section(s) your company is capable of providing:

I. Laboratory Information System

II. Whole Slide Image Viewer & Management

III. Whole Slide Scanning

IV. Digital Pathology Research and Education

V. Computational Pathology

b. If your capability in any subset of JPC’s requirements, describe your experience integrating with other solutions. Specifically, describe your capability in use of open data standards, standard API protocols and formats, and software development kits

(SDKs).

c. What experience and capability does the company have in configuring by end users? If configuration cannot be done by the end user, what is the process and timeline for configuring?

d. What experience and capability does the company have on use of cloud services?

Which cloud storage services do you have experience integrating with?

e. What experience and capability does the company have on incorporating user research and iteration into the development?

f. Based on your experiences, please provide your estimate/ rough order of magnitude of the cost of work described in the draft. Please provide a basis for your estimate.

This section is optional and does not count towards page limit. If response, include the page number and paragraph of the draft statement of work/requirement description with each comment/question.

Submit a response to this Sources Sought by CLOSING 17 August 2020 at 16:00 PM CT

(local time in San Antonio, Texas). All responses and any questions under this Sources Sought must be emailed to peichang.wang.civ@mail.mil and Marco.a.cypert.civ@mail.mil.

The Subject line of the email must read “(Type Here Business Name) – Response to Sources

Sought (HT0050-20-RFI-0084): Defense Health Agency (DHA) – Joint Pathology Center (JPC)

Digital Pathology Modernization Effort mailto:peichang.wang.civ@mail.mil mailto:Marco.a.cypert.civ@mail.mil

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