Epic AP Beaker Implementation 2026

While the most significant workflow changes will occur within the Department of Pathology and Laboratory Medicine, many clinical and operational teams will experience changes to ordering, specimen collection, labeling, tracking, documentation, and result review.

Key changes include:

• Integrated Epic workflows for pathology ordering, specimen tracking, and result reporting
• Barcode-driven specimen identification and chain-of-custody tracking throughout the entire pathology workflow to improve patient safety and specimen traceability
• Enhanced visibility into specimen status and pathology results within the Epic electronic health record
• Standardized workflows
• Improved communication between clinical teams and the pathology laboratory through integrated work queues, notifications, and documentation
• Electronic ordering and tracking 
• Structured pathology reporting designed to improve report consistency, quality, and data accessibility

Although most users will continue to access pathology reports through Epic as they do today, some workflows, including pathology ordering, specimen labeling, collection procedures, and documentation may change depending on each department's role. Training and educational resources will be provided before go-live to ensure all impacted users are prepared for a successful transition.

Anatomic Pathology (AP) workflows will transition into Epic Beaker AP, including:

• Surgical pathology case management
• Cytology workflows
• Grossing documentation
• Molecular diagnostics
• Molecular genetics
• Electron microscopy
• Histopathology
• Slide tracking and block management
• Pathologist sign-out and final reporting

Legacy AP LIS systems will be retired with limited access to read-only model.

Direct clinical stakeholders will be impacted, including:

• Providers (attending physicians, advanced practice providers, residents, and fellows) 
• Nursing (inpatient, ambulatory, procedural, and perioperative nursing) 
• Clinical care teams (medical assistants, clinical support staff, and care coordinators) 
• Operating room (OR) and procedural services (Surgery, Endoscopy, Interventional Radiology, Women's Health, and other procedural areas) 
• Emergency Department (ED) 
• Patient Access, Registration, and Scheduling 
• Health Information Management (HIM) 
• Revenue Cycle, Revenue Integrity, Coding, and Billing 
• Information Technology, Epic Applications, and Technical Support 
• Quality, Patient Safety, Risk Management, and Regulatory Compliance 
• Hospital and clinical leadership 
• Pathologists 
• Pathologists' assistants (PAs) 
• Anatomic Pathology laboratory staff (accessioning, gross room, histology, cytology, and administrative staff) 
• Laboratory Informatics and Epic Beaker analysts 
• Specimen transport and courier services 
• Community health centers
• Outpatient locations
• Third party clients

Epic AP Beaker is scheduled to go live October 31 through November 2, 2026. During this period, departments may experience temporary workflow changes, planned downtime activities, increased support presence, and slightly longer turnaround times as staff adapt to the new system. Patient safety and continuity of care remain the highest priorities throughout the transition.

Possibly. Some pathology orders and specimen collection workflows will be updated to align with Epic AP Beaker. Depending on your role, you may notice changes to order entry, specimen collection documentation, or barcode labeling. Education, job aids, and tip sheets will be available before go-live. The Pathology Operations team has already rounded to impacted clinical areas across the health system to map current workflow and discuss changes. 

Yes. Epic AP Beaker relies on barcode-driven specimen identification and electronic tracking throughout the pathology workflow. Clinical staff should continue following established specimen collection policies while using updated Epic labels and workflows introduced during implementation. Proper labeling at the time of collection remains critical to patient safety. There will not be a printed requisition unless the workflow exists outside of the BMCHS version of Epic (Community Connect sites are within the BMCHS version of Epic). 

Existing specimen transport processes will largely remain the same. However, specimen tracking will be enhanced through barcode scanning and electronic chain-of-custody documentation whenever applicable. Departments should continue following established transport policies while using updated labeling and tracking procedures.

Operating room staff will continue collecting and submitting surgical specimens, but they may notice updates to pathology order entry, specimen labeling, barcode scanning, frozen section requests, and documentation within Epic. Education will focus on maintaining accurate specimen identification and ensuring complete communication with the pathology laboratory.

Frozen section requests will continue to follow established clinical workflows while being documented and tracked within Epic AP Beaker. Operating room staff and Pathology personnel will use standardized communication and specimen tracking processes to support timely intraoperative consultation.

Procedural areas will continue to submit biopsy and tissue specimens as they do today, but pathology orders, labeling, specimen tracking, and documentation may be updated within Epic AP Beaker. Staff should follow new workflows introduced during training to ensure specimens are accurately identified and tracked.

Clinics will continue ordering pathology testing through Epic. However, some ordering screens, specimen labeling, and documentation workflows may change. Providers and clinical staff should complete required training before go-live to become familiar with the updated process.

A temporary decrease in productivity is expected during the first several weeks following implementation as users become familiar with new workflows. Turnaround times will be closely monitored, and additional support resources will be available to minimize any impact on patient care.

Yes. Pathology reports may have a more standardized format with improved organization, enhanced synoptic reporting, and structured data. While the appearance may change, providers will continue to access pathology reports through the Epic patient chart.

Yes. Pathology reports will continue to be available within Epic, and providers will continue to receive results and notifications according to established organizational workflows and notification preferences.

Outside specimens and consultation requests will continue to follow existing submission policies. Documentation and tracking within Epic AP Beaker may differ from current workflows, and updated procedures will be communicated to departments before go-live.

Immediately contact the Pathology Department. Do not relabel or alter a specimen without following established organizational policy. Pathology staff will work with the submitting department to determine the appropriate corrective action while maintaining patient safety and regulatory compliance.

During planned or unplanned downtime, approved downtime procedures will be followed using paper requisitions, manual documentation, and established specimen tracking processes. Once systems are restored, all pathology cases will be reconciled within Epic AP Beaker to ensure complete and accurate documentation.

After a downtime, all cases must be:

• Back-entered into Beaker AP
• Reconciled with physical specimens
• Audited for completeness (chain-of-custody compliance)

Support will be available through multiple resources, including:

• Your department's Epic duper user(s)
• Pathology Department
• Laboratory Informatics
• Epic AP Beaker Command Center
• Department leadership

Issues should be reported as soon as possible to allow prompt investigation and resolution.

Training requirements vary based on each employee's role. Depending on job responsibilities, education may include eLearning modules, instructor-led classes, workflow demonstrations, videos, tip sheets, and hands-on practice. Completion of the training required is expected before users begin working in the new system.

This Epic AP Beaker project website serves as the central communication for project updates. Users will be able to access training materials through Workday, superuser classroom training and online practice for designated groups. 

Yes, Beaker indirectly enforces medical necessity rules through:

• CPT-linked test definitions
• Diagnosis-to-test logic rules
• Reflex testing workflows
• Billing validation at case finalization

Rejected charges or missing indications are resolved by the Pathology billing team or the Revenue Cycle / HIM team.

During go-live, AP will be supported by:

• Super users
• Epic Beaker analysts
• Histology and pathology informatics leads
• Department operational leadership

After go-live, AP team should expect:

• Temporary slowdown in grossing and sign-out
• Increased dependency on super-users
• Iterative build fixes (typically two to six weeks)
• Ongoing template and workflow refinement

Most departments can expect an initial stabilization period of approximately 30 days following go-live, with users typically achieving optimal proficiency and workflow efficiency within 90 days.

Cases are generated in Beaker when:

• A surgical specimen order is placed in Epic
  A paper downtime requisition is converted into an electronic case

Each case receives:

• A unique accession number
• Associated containers (specimens → blocks → slides)

Manual numbering systems are eliminated. Accessioning is now:

• Fully electronic
• Barcode-driven at every step
• Structured by specimen hierarchy (Case → Specimen → Block → Slide)

Gross descriptions are entered directly into the AP case and grossing is performed directly in Beaker using:

• Structured gross templates
• Digital dictation or smart phrases
• Real-time specimen tracking tied to barcode scans

Histology staff now use Beaker-driven:

• Slide tracking: All slides are tracked as discrete Beaker objects
• Block management queues
• Cut/recut and stain requests

Special stains and IHC are ordered electronically from within:

• The AP case
• The specific block or slide context

Orders are automatically routed to histology work queues.

Manual tracking logs are no longer primary documentation. Beaker supports “missing specimen workflows," including:

• Missing slide flags
• Location reconciliation queues
• Chain-of-custody audit logs

Pathologists use the Beaker AP workbench to:

• Review gross and microscopic data
• View slides 
• Enter diagnosis using structured templates
• Finalize and electronically sign reports

After sign-out, reports can only be edited via:

• Addendum workflow
• Formal amendment process
• Audit-tracked revision system

Cytology cases now include:

• Specimen tracking (fluid, FNA, Pap)
• Slide-level organization
• Screening → review → sign-out workflow stages

All interpretation is entered into structured AP cytology templates.

Pap workflows are integrated into Beaker AP or interfaced screening systems, with final results flowing into Epic.

Add-on requests are placed within the case and tied to:

• Existing block
• Existing specimen ID

Beaker verifies availability before accepting the order.

Recuts are:

• Placed as electronic orders
• Routed to histology queue
• Tracked as new slide objects linked to original block