01. JMC_NBS Market Research Quote_corrected.1649245386462.pdf

Oregon Health Authority Focused Market Research for Public Health

Lab Newborn Screening and Laboratory Information Management System (LIMS)

April 6, 2022

Technical and Price Proposal Submitted by: J Michael Consulting, LLC

OHA Focused Market Research for Public Health Lab

12/11/2020 i

Table Contents

1. Executive Summary

2. Methodology and Schedule

2.1 Management / Technical Approach

2.1.1 Phase I – LIMS Evaluation

2.1.2 Phase II – Need Assessment and Market Research

2.1.3 Phase III – PM Support during LIMS Procurement Process

2.1.4 Phase IV – Value Add – PM and SME Support during Implementation

2.2 Schedule

3. Staffing Approach

4. Pricing

4.1 Estimate for Phases I-III, Fixed Price

4.2 Estimate for Optional Phase IV

5. Past Experience

5.1 Public Health Laboratory Projects

5.1.1 Connecticut Public Health Laboratory

5.1.2 South Carolina Public Health Laboratory: OpenELIS LIMS

5.1.3 Philadelphia Orchard LIMS Implementation

5.1.4 CDC FluLIMS

5.1.5 CDC LIMS Lite Support Services

5.1.6 Summary of Experience

6. Summary

7. Glossary of Terms and Acronyms

8. Resumes

8.1 Monica Akre

8.2 Jason Scott

8.3 Michelle Wells

8.4 Melanie Kourbage

9. Pricing Sheet (Appendix A)

10. Reference Check Forms (Appendix B)

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1. Executive Summary J Michael Consulting (JMC) offers a complete public health informatics consulting and support solution to the Oregon Health Authority (OHA). Since our founding in August 2011, JMC has made a mark on public health informatics, working with the Association of Public Health Laboratories (APHL), the Centers for Disease Control and Prevention (CDC), the Food and Drug Administration (FDA), and laboratories and agencies at the Local, State and Federal level, and partnering with many of the leading health information technology firms on a variety of projects and initiatives.

The JMC approach includes leveraging extensive hands-on expertise and experience in four main areas: Laboratory Informatics, Surveillance Informatics, Data Standards and Interoperability, and Project and Program Management; though many of our projects cross domains. The JMC Team uses our deep experience, subject matter expertise, and proven project management approaches to successfully deliver in-depth evaluation of current laboratory informatics solution for the newborn screening and communicable disease areas of public health laboratories (e.g., Connecticut Department of Health).

The JMC Team has also done in-depth gap analysis for newborn screening at the national level working with the Association of Public Health Laboratories (APHL) and the Colorado School of Public Health as part of the NewSteps program.

2. Methodology and Schedule

2.1 Management / Technical Approach

We understand that the Oregon State Public Health Laboratory (OSPHL) is seeking to evaluate its current newborn screening (NBS) and communicable disease (CD) LIMS, conduct market research to assess viable replacement options for both, assemble a solicitation and plan, and contract with a selected LIMS vendor. We have developed a mature methodology to evaluate a LIMS, document the As Is state of workflows and dataflows within the laboratory, and compare the business needs of the laboratory to the current functionalities of the LIMS currently deployed. We have also developed reusable tools and templates to document optimized laboratory workflows (the “To Be” workflows) and define the technical and functional requirements for the LIMS to enable the lab to reach the desired To Be state. Throughout this process, we emphasize transparency and collaboration with our client; we work closely with project sponsors to ensure that they are informed and engaged in throughout the project lifecycle. We will apply this methodology during a three-phase engagement with OSPHL.

During Phase I, JMC will evaluate the current LIMS that OSPHL uses for NBS and CD and conduct interviews with OSPHL staff involved in NBS and CD workflows. In Phase II, JMC will identify potential LIMS solutions based on information collected during Phase I, and we will conduct market research to determine how well each solution may meet OSPHL’s requirements, as well as the

4/6/2022 2 feasibility of implementing the solution. In Phase III, JMC will support OHA during the LIMS procurement process, including preparing a Request for Proposal package and an evaluation of vendor proposal plan.

For all laboratory areas in NBS and CD, the JMC team will work with OSPHL using a proven system of determining and documenting current lab workflows and data flows. This process combines remote work together with intensive onsite sessions.

1. Remote Discovery – JMC will provide OSPHL with a set of tools for data collection, and provide training on the tools. These tools include questionnaires and worksheets to capture current processes, instruments, workload, etc. These tools will be customized to the needs of OSPHL through the initial kick-off and overview discussions. The JMC team will summarize and diagram the information collected in these tools to draft initial workflow and dataflow diagrams for each laboratory section.

2. Onsite Discovery - During the onsite visit, the JMC team will meet with each applicable team to review and refine the draft workflows.

3. Remote Data Synthesis – JMC will continue to synthesize the results of the remote discovery and onsite discovery sessions. The JMC team may reach out to the OSPHL team for ad hoc questions and/or meetings for clarification if needed.

2.1.1 Phase I – LIMS Evaluation

During Phase I, JMC will evaluate the current LIMS that OSPHL uses for newborn screening and for communicable disease. JMC will initiate the phase in a virtual kickoff meeting with OHA. During this meeting, JMC will provide an overview of the LIMS evaluation information gathering process to OHA and review a detailed IT Landscape Assessment (ITLA) questionnaire, as well as additional tools to capture information about laboratory processes, resources, and workflows. JMC will support OHA as these tools are completed on a predetermined timeline. JMC will gather and review documentation provided from each laboratory section, including SOPs, workflow charts, examples of reports, and forms. Upon completion of this process JMC will conduct and document interviews with OHA staff from each NBS laboratory section, each communicable disease section, and the Programs that use laboratory-generated NBS data to further refine the submitted materials.

JMC will create workflow diagrams and business process maps to summarize the current workflows from each laboratory section, and important lab-adjacent units such as Quality Assurance and Information Technology. Those As Is diagrams will be shared and revised based on feedback received, resulting in revisions and final review.

JMC will leverage industry knowledge and experience to identify opportunities for process improvements. Using multiple sources of information, including interview notes and recordings, submitted documentation and materials, ITLA information, and workflow analysis, JMC will generate new draft optimal workflows and dataflows, called To Be

JMC will share these To Be workflows with OHA. We will catalogue and analyze gaps between the As Is and the To Be as opportunities for improvement in a worksheet. A Gap Analysis Summary worksheet table will be created to highlight crosscutting issues. The summary worksheet will be shared with OHA and will serve as the basis for the process improvement summary in the LIMS Evaluation Report. We will collect comments and feedback on prioritization to move into Phase II.

The deliverables for Phase I are described in Exhibit 2-1.

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Phase I: LIMS Evaluation Deliverables Deliverable Description

Project Management Plan Describes the plan for completing the work in Phase I. JMC will update this plan at the conclusion of Phase I.

Documented Workflows Defines inputs, outputs, requirements, and resources for all tests and processes within all OSPHL lab sections

LIMS Evaluation Report

Describes the findings of the discovery activities conducted during Phase I. Sections within the evaluation report will include, among others, the LIMS Gap Analysis and a Process Improvement Summary.

Exhibit 2-1 Deliverables – Phase I

2.1.2 Phase II – Need Assessment and Market Research

JMC will assemble a list of LIMS solutions based on information documented in Phase I from interviews with OSPHL staff from the NBS and CD lab areas. JMC has developed an assessment tool that is based on APHL’s Requirements for Public Health Laboratory Information Management Systems (APHL and partners, 2003). This tool will be customized to meet the OHA NBS and CD labs’ and programs’ needs. The Requirements outline the 16 business processes that should be provided by informatics in public health laboratories and provide recommendations for the prioritization of business processes in a LIMS selection/implementation. JMC has used this tool in the past to assist with a LIMS assessment for the Connecticut Health Department Public Health Laboratory.

These Requirements will be used to solicit information from LIMS vendors. JMC will assemble a list of LIMS vendors, then contact each vendor via web-form, email, and phone calls. Each vendor will be provided with a list of requirements as a Request for Information (RFI) to collect responses on how well their software meets these specific requirements. Together with OHA the JMC team will review these responses and generate a comparison report. At the end of this Phase, the LIMS Comparison and Recommendation Report will complement the Process Improvement Summary provided in the LIMS Evaluation Report and provide detailed information to compare specific systems to meet the improvements recommended for OSPHL, including a description of the system capabilities for ETOR/Fast Healthcare Interoperability Resources (FHIR). The goal is to provide options that meet the needs of the NBS and CD lab areas and lay out options available, including implementing a single system for NBS and CD testing, or separate LIMS for each laboratory area. This report will include charts to provide a quick visual comparison across systems to identify similarities and differences; the charts will be grouped by Priority Groups and organized by Business Processes.

The deliverables for Phase II are described in Exhibit 2-2.

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Phase II: Need Assessment and Market Research Deliverables

System Requirements and Software Features

Lists the desired software features and system requirements, including operability and maintainability characteristics, that are needed to perform the To Be business processes effectively and efficiently in all lab sections

LIMS Comparison and Recommendation Report

Summarizes recommendations that stem from the needs assessment and market research; these recommendations will influence the LIMS project plan prior to the RFP process. This report will include a comparison of OSPHL software requirements to publicly available information about current LIMS products on the market, as well as an analysis of the costs and benefits of these replacement options and the associated maintenance options for OSPHL

Exhibit 2-2 Deliverables – Phase II

2.1.3 Phase III – PM Support during LIMS Procurement Process

In Phase III, JMC will support OHA in the LIMS procurement process using the documentation developed in Phases I and II. The Gap Analysis Summary worksheet, the customized requirements tool, the LIMS Comparison Report, and the To Be workflows and dataflows will be used by JMC to create a detailed and complete list of system requirements for the desired future state. We will work with OSPHL leadership to rank system requirements into priority groups including: Must Have, Important Business Function, Would Be Nice, Can Live Without. JMC will prepare and deliver materials for the Request for Proposal (RFP). While the RFP is posted, we will develop scoring tools to evaluate proposals for written submission and for demonstration and establish a final review team and timeline. During this time, we will also work with OSPHL to develop a list of documents to be written to cover all the future state business processes including Standard Operating Procedures (SOPs), training, and competency evaluations.

Next, JMC will manage the process to evaluate vendor proposals and demonstrations. We will collect, synthesize, and present the scoring results for vendor analysis of LIMS solutions that met the collaboratively defined functional requirements. JMC will work with the OHA project procurement manager to ensure there is no favoritism to a particular vendor. We will use performance metrics to evaluate a vendor’s quality, flexibility, and timeliness. We will monitor and control documentation and record keeping during all interactions and evaluation activities with vendors to ensure transparency and accuracy of delivery as compared to planned implementation. JMC will assist in supporting OHA to create a service level agreement (SLA) that confirms with the laboratory need.

The deliverables for Phase III are described in Exhibit 2-3.

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Phase III: PM Support during LIMS Procurement Process Deliverables

RFP Package

Will include documentation for the RFP that will be posted for vendors, as well as evaluation criteria and a targeted vendor list for OHA internal use. RFP package materials may include technical requirements, scope of services, narrative opportunity description, demonstration requirements and timeline, a system requirements matrix, and other supporting material

Draft LIMS Implementation Project Plan

Lays out the prospective implementation plan, including a summary of key findings in the RFP process, recommendations for phased LIMS implementation approach, Controlled Document List of new procedures related to processes that use that software, and other key findings to allow laboratory leadership to begin planning for and managing implementation

Exhibit 2-3 Deliverables – Phase III

2.1.4 Phase IV – Value Add – PM and SME Support during Implementation

While several factors contribute to the success of this model, laboratory and technical staff availability are key. It is our experience that LIMS vendors bring deep expertise in their own systems. However, they are not as strong when it comes to day-to-day operations and workflow of a public health laboratory. It is critical that the laboratory requirements are documented and communicated clearly to the vendor. It is also very important to build and execute a quality assurance plan to validate that the system is built to specifications. Often there are tasks that require specialized skills and experience that are needed only for a short time during the implementation process. On similar implementation projects, JMC has served as an objective, experienced advocate for the laboratory. Our role is to ensure that the LIMS vendor implements a system that meets or exceeds the laboratory’s requirements. Our team becomes an extension of the lab staff to ensure a successful LIMS implementation. This is the model utilized by the Philadelphia Orchard LIMS project described below in the Past Performance section of this proposal.

In section 4.2, we provide pricing for this optional Phase IV – Project Management (PM) and Subject Matter Expert (SME) support. As OSPHL navigates through Phases I-III to identify and select a LIMS, the full scope of work for the LIMS implementation will become clear. If OSPHL determines that a dedicated resource can guide the LIMS implementation project through to completion more efficiently than OSPHL resources alone, JMC can provide this support. Note as well that JMC has the staff and resources to support the implementation beyond project management, should the need arise;

these resources include LIMS configuration analysts, system integration experts, Rhapsody programmers, and standards and interoperability specialists. We are confident that we can bring the expertise and experience to fill gaps as they are identified to ensure a successful implementation that is on-time and in budget. We have included an additional optional budget, for project management and subject matter expertise support during the LIMS implementation phase. The JMC Team would act as an extension of the OSPHL staff, to ensure a timely, and satisfactory LIMS implementation.

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2.2 Schedule

The project plan below includes allowance for a gap analysis for 2 systems, NBS and CD, and may be adjusted if the final engagement indicates a single system will be selected to support only NBS, and not CD.

The project schedule will include:

Phase I: LIMS Evaluation - Evaluation of laboratory processes and suggestion of improvements, and assessment of the LIMS, instrument interfacing, manual work processes, and electronic tests orders.

Phase II: Needs Assessment and Market Research - For gap analysis, a needs assessment will be generated through interviews and assessment tools. Market research and analysis will be conducted to generate a comparison chart of which vendors may meet the laboratory’s needs.

Phase III: PM Support During LIMS Procurement Process – Identification, evaluation, and selection of the LIMS vendor.

Note: We know that procurement and leadership decisions have many dependencies and risks that could affect the schedule.

Exhibit 2-4 Project Schedule

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3. Staffing Approach JMC offers a unique mix of expertise and experience to support this project. Our team brings years of project management, business analysis, and laboratory subject matter expertise. This combination of experience in requirements analysis, public health, and laboratory sciences and processes is precisely what is required for this project. Resumes are included below.

We are proposing a team approach for Phases I, II, and III. The team will include a laboratory subject matter expert (SME), a business analyst (BA), and project manager (PM). The division of responsibilities will allow our laboratory SME to concentrate on those items that require a deep understanding of laboratory processes and systems. Our PM will ensure that the project is run smoothly and efficiently. Note that the same team would be available to support the optional Phase IV to ensure consistency.

Name Role Responsibilities Monica Akre, PhD Laboratory

Process SME Serve as laboratory process subject matter expert

Jason Scott Sr. Business Analyst

Serve as a technical expert/business analyst with technical expertise in the analysis and development of laboratory workflows and informatics solutions

Michelle Wells, PMP Sr. Project Manager

Provide high-level guidance and project planning, as well as all project coordination; ensure delivery of all milestones

While we are proposing specific individuals for this project, it should be noted that our project staff will have access to the full JMC Team, including SMEs who have worked extensively with the OSPHL and OHA on other projects, or on similar LIMS implementation projects. We have multiple practice areas at JMC including both laboratory informatics and project management practice areas.

The practice areas provide support with common templates, processes, and tools. Additionally, the practice areas meet on a regular basis to share knowledge and draw upon one another’s experience.

JMC has worked with Oregon in the past, and has a basic familiarity OSPHL’s organizational structure and business processes. We are aware that the State of Oregon issued a vaccination mandate in 2021, and we are prepared to complete a Vaccination Compliance Form for all staff who will work with OSPHL on this engagement.

Monica Akre| JMC|makre@jmichael-consulting.com

Dr. Monica Akre has over ten years of experience in clinical and research laboratories using multiple documentation, informatics, and quality management systems solutions. Monica is dedicated to improving usability of laboratory tools and improving day-to-day work experience. Her approachable demeanor and open curiosity allow her to quickly identify dynamics contributing to work and data flows. Her experience as a laboratory technologist and supervisor allows for analyses with depth and detail.

Monica will serve as the laboratory subject matter expert to ensure the OSPHL requirements and workflows are captured and documented accurately. She will also serve as lead author on all JMC deliverables. Monica will be supported by a JMC project manager who will provide coordination, scheduling, tracking, and general support, and a business analyst who will facilitate the meetings and document requirements. This team approach will allow Monica to concentrate on those areas that require laboratory subject matter expertise.

Jason Scott| JMC| jscott@michael-consulting.com

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Jason Scott is a laboratory informatics subject matter expert who has spent the last 16 years supporting Laboratory Response Network (LRN) operations, with the last 11.5 years working directly with LRN labs to integrate their data systems with the LRN system. Jason has managed the integration of 41 laboratory data systems with CDC’s central LRN data system. Jason has also worked extensively public health laboratories as a technical assistance resource through the APHL Electronic Laboratory Reporting Technical Assistance (ELRTA) Program, including with OSPHL.

Jason will serve as the business analyst on this project. Jason has extensive experience documenting requirements for technical projects through his work with CDC, including on the Immunization Data Lake, the CDC LIMS Lite Project, and the LRN. He has expertise in laboratory workflows and public health informatics.

Michelle Wells| JMC| mwells@jmichael-consulting.com

Michelle Wells is a senior project manager with over 20 years’ experience in Healthcare Project Management including Public Health, Hospitals, and Skilled Nursing Facilities. Her project management experience includes project planning, budgeting, hiring, stakeholder development and reporting, team management, crisis mitigation and full Software Development Life Cycle (SDLC.)

Michelle’s Project Management Office (PMO) experience includes managing multiple concurrent projects and reporting to diverse clinical stakeholder groups. Working with the Tacoma-Pierce County Health Department, she helped the department successfully implement a COVID vaccine clinical deployment for Washington’s second largest county. She has managed multiple implementation projects, including in laboratory settings.

Michelle will serve as the project manager supporting Monica and Jason on this project

Melanie Kourbage, MA, PMP| JMC| mkourbage@jmichael-consulting.com

Melanie will serve as the JMC Account Manager in a non-billable capacity. She will ensure that JMC delivers on all contractual deliverables. She will serve as an escalation point for any issues that cannot be resolved at the team level. Additionally, Melanie will be available to provide support, coaching, guidance and quality assurance on JMC deliverables.

Melanie is also the account manager and project manager on a project with the OSPHL to implement Electronic Test Orders and Results (ETOR).

4. Pricing In section 4.1, we include an estimate for a Phases I-III, broken out by project deliverable. This estimate assumes a fixed price contract, based on deliverables. In section 4.2, we provide an estimate for an optional Phase IV to support OSPHL during the LIMS implementation. Based on responses to questions asked during the RFQ process, we have included a full assessment of both the NBS and CD LIMS in our estimates. If OHA determines that the assessment will focus on NBS, then we anticipate that the overall estimate for work will decrease by about 30%.

JMC understands that OHA is seeking a fixed price contract, but, given our experience on similar implementation projects, we recommend that OHA consider a time and materials model, with a predetermined not-to-exceed amount. We believe this approach will be to Oregon’s benefit in that overall costs are capped, and the budget will be predictable. However, if the work does not require the total hours estimated, OHA may gain some cost savings (especially if there is an option to re-allocate funds). Moreover, we have found that time and materials contracts require less administrative overhead and allow us to offer better rates to our clients. JMC can provide labor rates upon request.

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4.1 Estimate for Phases I-III, Fixed Price

See below for a detailed breakdown of pricing for each phase. Exhibit 4.1 assumes a fixed price contract, payable upon the completion of each phase.

In addition to the deliverables mentioned, we strongly recommend a travel budget of $4,000. As discussed in section 2.1 above, onsite meetings during the early phases of the project can greatly accelerate the evaluation and ensure that JMC has full access to information and people during requirements gathering.

The total estimate for all three phases, plus a $4,000 travel budget, for a fixed price contract is $134,000. Again, this estimate assumes that JMC will complete a full assessment of both NBS and CD laboratory workflows. If OSPHL determines that it will focus on NBS workflows, then the overall estimate for these deliverables will decrease by about 30%. Furthermore, if an onsite meeting is not required or desired, we will discount the travel budget amount from the estimate.

Deliverables Payment Phase I: LIMS Evaluation $ 65,000.00

During Phase I, JMC will evaluate the current LIMS that OSPHL uses for newborn screening and communicable disease testing. Deliverables from this phase will include:

Project Management Plan Documented Workflows LIMS Evaluation Report

Phase II: Need Assessment and Market Research $ 26,000.00 During Phase II, JMC will conduct a needs assessment of OSPHL laboratory sections to determine the software features and system requirements that a LIMS must possess to meet OSPHL’s needs. We will conduct market research to compare these requirements to the features LIMS products currently on the market. Deliverables from this phase will include:

System requirements and software features LIMS Comparison Report Recommendation Plan

Phase III: PM Support during LIMS Procurement Process $ 39,000.00 During Phase III, JMC will provide support to OHA throughout the RFP process. Deliverables from this phase will include:

RFP Package Draft LIMS Implementation Project Plan Summary Findings Report

Travel Budget $ 4,000.00 JMC strongly recommends a multi-day site visit to meet with OSPHL laboratory technicians in person and to conduct intense requirements gathering sessions with OSPHL staff

$ 134,000.00 Exhibit 4-1 Estimate – Fixed Price

4.2 Estimate for Optional Phase IV

As discussed in section 2.1.4 above, it is critical that the laboratory’s specific workflows and business needs are communicated to the LIMS vendor and incorporated into the implementation plan. It is

4/6/2022 10 helpful during this process to have resources dedicated to this project to ensure that the LIMS vendor implements a system that meets or exceeds the laboratory’s requirements.

Our not-to-exceed estimate for this optional Phase IV – Project Management (PM) and Subject Matter Expert (SME) support is $150,000, including travel budget for two site visits. JMC will provide labor rates for our staff upon request. If OSPHL determines that a dedicated resource can guide the LIMS implementation project through to completion more efficiently than OSPHL resources alone, the same JMC team can provide this support. Importantly, the same team would be available for Phase IV, so they will be intimately familiar with OSPHL processes and workflows. Note as well that JMC has the staff and resources to support the implementation beyond project management, should the need arise;

these resources include LIMS configuration analysts, system integration experts, Rhapsody programmers, and standards and interoperability specialists.

5. Past Experience The JMC Team has successfully completed informatics system evaluations and implementation support for multiple clients. As specified in Section 6 “Offeror Qualifications” of the Request for Quote (RFQ), JMC has extensive experience in public health laboratory business practices and workflows, and in newborn screening workflows more specifically. As part of Appendix B, we are providing three references of clients for whom we have performed similar services within the past five years. In this section, we summarize some of this previous work experience.

5.1 Public Health Laboratory Projects

5.1.1 Connecticut Public Health Laboratory

Contract Number: DPHM1-0000071326 Customer/Agency Name: Connecticut State Public Health Laboratory

Contract Title: Information Management System Evaluation and Implementation Dollar Value: $310,248. Contract Type: Time and Materials Period of Performance: 2/5/2021 – Present Place of Performance: Remote Number & Types of Personnel

Project Manager (1) Lab SME (1)

Terminologist (1) Technical Architect (1)

Customer Contacts

Dr. Jafar Razeq Laboratory Director Connecticut Department of Public Health Lab 860-920-6503 Jafar.Razeq@ct.gov

Jeff Curran Laboratory IT Manager Connecticut Department of Public Health Lab 860-920-6507 Jeffrey.Curran@ct.gov

Description:

The Connecticut State Public Health Laboratory (CTPHL) conducts communicable disease testing, newborn screening, and environmental testing. CTPHL contracted with JMC to design an ETOR solution for all clinical testing and newborn screening.

The project scope includes a first phase, which consists of evaluation of the existing LIMS, identification of gaps between current and desired state, and recommendations based on a landscape analysis of current LIMS on the market. In the second phase of the project, JMC is coordinating with the laboratory and vendor(s) during implementation of the software systems and training and competency documentation of laboratory, support, and administrative staff. The CTPHL successfully selected three LIMS in March 2022 and is now entering Phase Two.

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Specifically in Phase Two, JMC is providing project management for implementation of the solutions documented in Phase One. Implementation will include coordinating with the LIMS vendors and CTPHL for installation, configuration and/or development of software, interfacing of laboratory equipment, training, etc.

Relevance:

CTPHL provides over 2 million test results on approximately 250,000 specimens and samples it receives each year. Analytical data is used to monitor for agents harmful to the public health, identify the causes of outbreaks of disease, and assure that control measures (e.g., vaccines, antibiotics, environmental remediation, etc.) are effective.

Problems Encountered/Corrective Actions:

LIMS vendor selection was delayed a few months due to concerns over new procurement policies and legislation, project funding, and rise of COVID-19 cases. JMC worked side-by-side with CTPHL and Procurement to facilitate internal discussions and provide tools for scoring and analysis.

Significant Accomplishments:

In the Spring of 2021, JMC evaluated the current LIMS that the CTPHL uses for newborn screening, infectious disease, and environmental testing for related business operations. It is important to note that JMC performed this work remotely during a global pandemic, which required collaborative and productive meetings to stay aligned and on-track. JMC completed a needs assessment to meet CTPHL’s established goal and conducted market research to determine the feasibility of this goal.

Next, JMC provided project management on behalf of the CTPHL Management Team and collaborated with their IT Project Manager and Procurement for the LIMS RFP process. During the performance of the services, JMC had to thoroughly document and understand the CTPHL’s current operations, connectivity, data exchange, electronic transfer of records status and understand the CTPHL’s overall goals. Additionally, JMC was able to provide the necessary support to ensure a successful procurement process was conducted by partnering with internal and external stakeholders.

Ultimately, CTPHL selected 3 different LIMS with the support of JMC.

5.1.2 South Carolina Public Health Laboratory: OpenELIS LIMS

Contract Number: OE - JMC Contract - South Carolina-2017- 03-27

Customer/Agency Name: OpenELIS Foundation

Contract Title: OpenELIS Implementation Dollar Value: $1,487,000 Contract Type: Time & Materials Period of Performance: 01/07/2018 – Present Place of Performance: Columbia, SC Number & Types of Personnel

Project Manager (1) LIMS Configuration Analyst (3)

Terminologist (1) Technical Architect (2)

Customer Contacts

Gary Jones Executive Director OpenELIS Foundation

(651) 271-9094 Gary.jones@openelis.org

Chadwick Knight Enterprise Project Management Director SC DHEC Project Management Office

(814) 490-8743 Chadwick159@hotmail.com

Description:

The South Carolina Department of Health and Environmental Control (SC DHEC) engaged the Open Enterprise Laboratory Information Management System (OpenELIS) Foundation to support the implementation of the open-source OpenELIS laboratory information system as a cloud-hosted

4/6/2022 12 solution on the APHL Informatics Messaging Services (AIMS) platform. OpenELIS in turn has contracted with JMC to provide consulting services to South Carolina, including project management, business analyses, workflow and test configuration, quality assurance, and training.

During the discovery phase of OpenELIS implementation in the South Carolina Laboratory, the JMC Team sought to understand and document the current lab processes. The team began the discovery with a site visit to view and document the high-level organization and stakeholders of the lab. As each lab group was identified, the JMC Team met with representatives from each group and gathered granular requirements for the accessioning, workflow configuration, and reporting of each test. The JMC Team identified gaps between the existing code and the lab work process and collaborated with the lab to either submit a change request to the development team or update the lab work process to accommodate the difference.

The JMC Team provides all the implementation support for the laboratory, including project management, workflow configuration, development support, testing, and training. The team has also applied standard vocabulary and implemented Health Level Seven (HL7) electronic laboratory reporting (ELR) and electronic test orders and results (ETOR) with external laboratory partners. Additional tasks performed by the JMC Team on this project include instrument integration via Rhapsody and a custom billing application. The JMC Team also serves as a liaison between the laboratory and the software developers participating as representatives of the lab on the OpenELIS foundation change control committee.

Relevance:

OpenELIS significantly enhances the overall capacity and capabilities of the SC DHEC Public Health Laboratory to perform its public health mission. OpenELIS will augment SC DHEC’s capabilities to accession and track samples, store and process results, and share data with providers, hospitals, epidemiologists, and CDC.

Problems Encountered/Corrective Actions:

The South Carolina implementation represents the first time that OpenELIS has been deployed in the cloud. This cloud-hosted solution has presented unique technical challenges in terms of system configurations, continuity of operations, and security protocols. The multi-faceted goals of the implementation, which includes the validation and interface of new instruments, system integrations, and the establishment of new data exchanges, has required the collaboration of diverse stakeholders.

In response to these challenges, JMC has facilitated discussions to define and verify the roles and responsibilities of each stakeholder on the project.

Significant Accomplishments:

"JMC has been working with us to implement our new Laboratory Informational Management software system over the last year. Having worked in the field of project management for over 15 years, I can truly state that they are one of the best consultants that I have had the pleasure to work with.

Their project management expertise and background knowledge in public health, laboratory science, and operations is second to none. In addition, they're extremely detail oriented, motivated, inventive, and generally enjoyable to work with. They're like a well-oiled machine.

I’d highly recommend them to anyone searching for creative project management and laboratory solutions.”

Chadwick Knight, PhD, PMP, CSM, Director of Strategic Project Management, South Carolina Department of Health

& Environmental Control

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The SC DHEC Public Health Laboratory went live with OpenELIS for COVID testing in March 2020. The Virology and Rabies section and the Tuberculosis (TB) section went into production in Fall 2020. We anticipate that the remaining laboratory sections will go live in the next six months.

5.1.3 Philadelphia Orchard LIMS Implementation

Contract Number: 56401-150-049-17 Customer/Agency Name: APHL/Philadelphia PHL Contract Title: Philadelphia Orchard LIMS Dollar Value: $277,000 Contract Type: Time and Materials Period of Performance: 1/26/2018 – Present Place of Performance: Remote and On-site Number & Types of Personnel

LIMS SME/Configuration Analyst (1), Integration Analyst (1)

Customer Contacts

Patina Zarcone Director, Strategic Initiatives and Research Association of Public Health Laboratories Patina.Zarcone@aphl.org

Bernadette Matthis, MSBA MT (ASCP) Laboratory Director Philadelphia Department of Public Health | Bureau of Laboratories 609-284-0355 Bernadette.Matthis@phila.gov

Description:

The Philadelphia Public Health Laboratory (PHL) implemented a new LIMS – Orchard and Copia, to replace the existing system (Novius). JMC, under a contract through the Association of Public Health Laboratories (APHL), provided consultant support to help the Philadelphia PHL staff implement the system.

During this engagement the JMC Team worked closely with the current Philadelphia LIMS Admin and Project Manager, as well as Orchard support staff. Specific activities included configuration support, testing and validation of system and interfaces, requirements definition and documentation, training, and quality assurance. The JMC Team comprehensively documented existing workflows through interviews with LIMS and program staff; this documentation was used to rebuild these workflows in the new system as faithfully as possible. The JMC Team provided on-site support during the Orchard Go-Live, and post-implementation support to ensure a smooth transition between systems. We also developed extensive training and configuration documentation to aid in training of Public Health Laboratory (PHL) staff long-term after the conclusion of the project.

Philadelphia required their new LIMS to communicate with the existing health system electronic medical record system, point of care devices, and surveillance systems located within the city network. Each system had unique requirements that were met by developing a validation plan between the LIMS and the current system. In addition to routine testing and troubleshooting, significant collaboration efforts were needed to validate and investigate integration issues related to reflexed orders, profile orders, and microbiology results. Philadelphia realized several business process improvements through integration between systems, including improved cancellation functions, order entry and results evaluation rules, and surveillance system integrations.

Problems Encountered/Corrective Actions:

JMC has worked with APHL and the Philadelphia PHL to mitigate the effect of delays in the implementation of the Orchard system. We have supported our partners to adapt the project scope and schedule as necessary. JMC also retained current staff through several work stoppages related to contract issues and brought on additional resources as needed. In other respects, our work has been on time and within budget.

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Significant Accomplishments:

The workflows that were utilized in the previous LIMS have been successfully implemented in the new Orchard system. Extensive training and configuration documentation will allow the PHL to operate and maintain the system after the conclusion of the contract.

Public Health Impact:

An updated LIMS will allow the Philadelphia PHL to more effectively utilize their laboratory instruments and staff. This enhanced functionality will aid them in providing laboratory testing services and protecting the health of Philadelphia citizens.

5.1.4 CDC FluLIMS

Contract Number: GS35F276GA / 75D30119F06468 Customer/Agency Name: The Centers for Disease Control and Prevention (CDC)

Contract Title: FluLIMS Support Services Dollar Value: $4,613,714 (Total – 3 years) Contract Type: Time & Materials Period of Performance: 9/30/2019 - 9/29/2022 Place of Performance: CDC – Atlanta, GA

(contractor site) Number & Types of Personnel

Laboratory SME (1) Project Manager (1) Project Coordinator (1) Business Analyst (2)

Development Lead (1) Developer (3) Security SME (1) Database Administrator (1)

Customer Contacts

Elizabeth Neuhaus, PhD Health Scientist The Centers for Disease Control and Prevention

(CDC)

(404) 639-3368 ebn8@cdc.gov

Maria Shamburger Contract Specialist The Centers for Disease Control and Prevention

(CDC)

(770) 488-2057 heg9@cdc.gov

Description:

The FluLIMS project was started in 2010 after response to the 2009 H1N1 pandemic revealed the inadequacy and fragility of the division’s information system. Since that time, the number of system users has increased to more than 80 users representing 11 laboratory teams; therefore, the need for user support has dramatically increased. Additionally, the level of effort needed to enable complex workflows for multiple teams has also increased and a new major system requirement has emerged (reagent tracking). This increased need for user support and workflow management, coupled with the need for automated support of increasingly more complex and growing laboratory data streams, are the key business needs that drive the division’s requirement for FluLIMS services.

Problems Encountered/Corrective Actions:

The ID at CDC has been dependent on the use of a legacy database (FluLabDB) to complete many of their workflows, including sample tracking and surveillance data aggregation. Due to the complexity of many of the tasks completed using the FluLabDB, the laboratory users were resistant towards fully adopting FluLIMS. Our team worked with ID data managers to deploy a mechanism to move information from FluLIMS directly to the FluLabDB databases so that system can continue to be used while the FluLIMS system functionality is built, tested, and deployed. This allows the users to parallel test FluLIMS with FluLabDB. This approach has proven invaluable in gaining user acceptance from a group that has been resistant to adopt previous LIMS functionality.

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During the incumbent’s contract, the ID undertook the Sequence First Initiative where all samples are sequenced at the beginning of the laboratory workflow. This initiative changed many aspects for the FluLIMS workflows, yet the team readily adapted, changed priorities, and implemented the needed changes. In addition to the changes needed within the FluLIMS application, the team also recognized the need for CDC contract labs to provide data in a format consistent with the FluLIMS changes. This led to the development and deployment of the Contract Lab Accessioning Website (CLAW) application. The deep understanding of the strategic goals and mission of the World Health Organization (WHO) Influenza program has allowed National Center for Immunization and Respiratory Diseases at CDC (NCIRD) to enhance the FluLIMS to adapt to the frequently changing environment of vaccine production.

Significant Accomplishments:

Adoption of FluLIMS product by laboratory users for the accessioning and testing of viral isolation samples. In combination, these modules provide the foundation for Sample Management Policy compliance, including workflows to uniquely identify all material derived form a sample.

Implementation of a storage location management module, compliant with CDC specimen management policy, for all influenza samples and reagents housed at CDC. The JMC Team analyzed the policy, evaluated the current workflow, designed, developed, and implemented a system that brings ID into compliance with this important policy.

Continuous improvement of upload processes to accommodate accessioning studies comprised of thousands of samples. These improvements improved the user experience by reducing the upload time and allowing the transparent queuing of samples so that the upload did not require user interaction.

Establishment of a routine, iterative approach to LIMS development, providing high quality features to users quickly and frequently.

Submission of tickets for core bug fixes and enhancements to Abbott Informatics. We received multiple patches, which were successfully tested and deployed to the production environment.

Public Health Impact:

The influenza virus causes significant morbidity and mortality across the globe every year. As a World Health Organization Collaborating Center, the CDC Influenza Division (ID) conducts surveillance on circulating strains to recommend the components of the yearly influenza vaccine. In addition to seasonal influenza, which is generally caused by antigenic drift within the viral genome, the CDC also monitors for an antigenic shift in the virus, which may spark another global influenza pandemic like those seen in 1918, 1957, 1968 and most recently in 2009.

The JMC team has supported the ID in their continuous improvement efforts in the areas of sample handling, test workflows, reagent tracking, quality management, and information management. The JMC team supported the ID in their “sequencing first” initiative which shifted the initial characterization of viruses from traditional antigen detection methods to next generation sequencing, saving critical time in the virus characterization process. The science of detection and characterization of influenza viruses is constantly evolving, and the JMC team has used their scientific knowledge, experience and track record to support the ID by maintaining and developing flexible, scalable approaches for data management.

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STARLIMS Implementation at the Centers for Disease Control and Prevention (FluLIMS).

FluLIMS is a laboratory information management system that improves the efficiency for sharing, storing and analyzing laboratory and epidemiology related data throughout the Influenza Division.

The JMC Team configured and implemented FluLIMS from the Scientific Data Management System (STARLIMS) v11.7 laboratory information management system (LIMS). The JMC Team iteratively onboarded each lab group in the division to support pre-analytical, analytical and post-analytical phases of the specimen lifecycle. FluLIMS currently manages influenza data as well as the integration of that data with a variety of external partners. By understanding the unique requirements of national influenza surveillance, the JMC Team worked within the STARLIMS code base to meet the needs of the division.

5.1.5 CDC LIMS Lite Support Services

Contract Number: GS35F276GA / 75D30119F06639 Customer/Agency Name: The Centers for Disease Control and Prevention (CDC)

Contract Title: LIMS Lite Support Services Dollar Value: $4,610,234 (Total – 3 Years) Contract Type: Time & Materials Period of Performance: 9/30/2019 - 9/29/2022 Place of Performance: CDC – Atlanta, GA

(contractor site) Number & Types of Personnel

Laboratory SME (2) NGS SME (1), Project Manager (1) Project Coordinator (1) Trainer (1) Development Lead (1)

Technical Architect (1) Developers (3) Security SME (1) Business Analyst (1)

Customer Contacts

Elizabeth Neuhaus, PhD Health Scientist The Centers for Disease Control and Prevention

(CDC)

(404) 639-3368 ebn8@cdc.gov

Gordon “Chuck” Barritt Contracting Officer The Centers for Disease Control and Prevention

(CDC)

(770) 488-2724 ins4@cdc.gov

Description:

Advanced Molecular Detection (AMD) is used by CDC programs to improve vaccines, diagnostic methods, and drug interventions. Recently, massively parallel sequencing, a.k.a. Next Generation Sequencing (NGS) has become affordable and available. Support Services for AMD which employ NGS are needed to extend locally developed tools across departments and centers. Portable sequencers are already being field tested, and will further expand NGS access, providing a massive infectious disease surveillance network, if able to be leveraged successfully. The LIMS Lite project will establish a framework to support AMD for public health, by successfully utilizing information technology enhancements that serve divisional, national and global needs.

LIMS Lite Development at the Centers for Disease Control and Prevention. LIMS Lite, is a set of discrete, well-integrated software modules that is configured to collate, analyze, and report against infectious disease isolate characterization and next-generation sequence data elements. The LIMS Lite platform combines data accessioning, processing, quality assurance, and reporting of Next Generation Sequencing (NGS) results. LIMS Lite seamlessly integrates sample accessioning tools and laboratory information management systems (ex. Baobab), laboratory workflow management, instrument controllers, the bioinformatics pipeline, and quality management review.

The JMC Team developed and deployed this software to users at CDC for management of their NGS needs.

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Problems Encountered/Corrective Actions:

JMC has leveraged subject matter expertise in NGS technology and public health informatics to create a vision of the LIMS Lite framework. This vision was selected by CDC for funding. We have supported our partners to build the project scope and success definition as necessary. Our work has been on time and within budget.

Significant…