Create or Upgrade a Cytogenetics Laboratory


June 2021 - Vol.10 No. 6 - Page #8

Over a five-year period from 2011 to 2015, I was fortunate to have gained the opportunities to both create a cytogenetics laboratory from scratch and move existing cytogenetics lab operations to an off-site, core laboratory facility at two different hospital institutions. Two of the most important lessons I learned throughout these processes involved first, the need to collaborate with stakeholders from different departments (ranging from colleagues in adjoining labs to administration, information services, security, environmental safety, facility management, and janitorial services), and second, the need to thoroughly plan ahead—including planning for the unexpected.

Start with the Big Picture

From a management-level perspective, there are several key areas to keep in mind when initially planning for cytogenetic operations. These include the physical plant, licenses for operation, equipment, staffing, establishing the test menu, and the all-important laboratory setup itself. These logistical considerations are in addition to more business-oriented necessities, such as a due diligence market analysis, a well-developed business plan, and selection of the new laboratory site.

Once an appropriate site for the new lab has been established, the fun begins. Now is the time to envision the ideal operational workspace and then design the layout and workflow accordingly. Before we get to that, start with a site overview plan and delineate the areas that need to be included for your specific cytogenetics operations. In particular, look to answer the following questions via initial design:

  • Is there a need for more than one department at the site?
  • How will specimens be received in the facility and transported to the different departments?
  • Is there need for a lobby or reception area where visitors, mail, and office supplies are received?
  • How will the lab interact with any loading dock and storage areas for cytogenetic laboratory supplies and reagents?
  • Will all internal/external transitions occur at the same location, or can the facility accommodate two or three separate entrances?

The answers to these questions will vary by laboratory, but most operations will need some kind of office or managerial areas and a meeting room area, a break room or locker room for staff to store their belongings, access to restrooms, as well as an eye wash station, emergency shower station, and biohazardous waste storage and disposal areas.

Physical Plant and Infrastructure

Depending on the location of the cytogenetics lab (on site, off site, adjacent, etc), there may be additional concerns such as staff parking and entry/security systems (eg, employee badge access, fire alarm systems, emergency shut down buttons, security cameras, and security personnel in parking areas at shift change, particularly at night). Although such physical plant concerns may not be part of all new lab services builds, as a laboratory director, it is important to gain knowledge of these subjects in the event such an opportunity comes along.

Further to the physical plant elements, internal engineering and architectural considerations must be accounted for, including HVAC (heating, ventilation, and air conditioning) systems and information technology (IT) support systems (eg, data and phone lines for offices and benches as applicable). Then there are the more specific necessities for cytogenetics, such as strict and robust warm and cold temperature control and monitoring systems, vacuum lines, and CO2 and N2 gas lines for incubators, along with attendant, automated manifolds to switch tanks when empty (and to help render the facility ADA compliant). Depending on the intended scope of operations in the lab, decisions will need to be made regarding positive and/or negative pressure rooms, how fume hoods and biological safety cabinets (BSCs) will be vented, and the appropriate number or capacity of power generators in case of emergency.

Ideal State Workflow Mapping

The next steps involve mapping out the individual departments using workflow diagrams. This is when input from front-line technicians is essential. Have them walk through specific actions involved in the gamut of sample processing, including ideal placements of work tools and supplies.

In a typical cytogenetics laboratory, samples are processed in BSCs and moved to incubators to culture from 24 to 96 hours, depending on sample type. The samples are then harvested, fixed, and mounted on microscope slides before staining. At this point the analysis begins and this process is contingent upon the skills of the cytogenetic technologists. Analyzing a cytogenetic sample remains largely a manual process, and while there is some automated equipment involved in the above-mentioned steps, analysis is still a very hands-on process and requires a highly specialized skill set.

Key Work Areas

With ideal-state workflows in mind, the initial physical plant questions come back into play. Most cytogenetics laboratories will require at least three rooms: one for tissue culture, one for fluorescence in situ hybridization (FISH) processes, and one for analysis. Each room likewise has its own special requirements:

  • The tissue culture room normally contains an operations-appropriate number of BSCs, incubators, centrifuges, water baths, refrigerators, and freezers. Therefore, the requisite ventilation, CO2 and N2 gas lines, and vacuum lines all must be accessible within this room.
  • The FISH room normally houses a slide processor, denaturing and hybridization equipment, fluorescent microscopes, and hopefully, an automated slide scanner for taking images of slides for technologists to analyze, as well as any necessary centrifuges, refrigerators, or freezers. Given the use of fluorescence, the room should remain dark most of the time with just enough ambient light to process the sample and fill out paperwork at the microscope or on a computer. Both the tissue culture room and the FISH room will need sinks and dedicated emergency power outlets for the incubators, refrigerators, and freezers.
  • The analysis room is the most basic from a needs standpoint, likely containing information system computers, printers, and additional microscopes.

Keeping Records During Relocation

Materials

If a new cytogenetics lab requires moving materials and equipment from an existing location to a new one, spreadsheets detailing equipment status for each laboratory can be invaluable. For each piece of equipment, columns can be assigned for several factors:

  • New or existing instrument
  • Current location
  • ID/asset #
  • Manufacturer
  • Model
  • Description
  • Measurements
  • Future location/bench
  • Move date
  • Date/time to disconnect
  • Decontaminate
  • Date/time to reconnect
  • Plumbing/drains
  • Filter needs
  • Power needs (eg, amp, 3-prong plug), including backup
  • Hood or BSC need
  • Temperature monitoring
  • CO2 and N2 needs
  • Vendor contact
  • Field engineer need

In addition to these, include a notes section to list any special concerns during the relocation (eg, handling of sensitive robotic parts).

Personnel

A second spreadsheet for managing any staff and support personnel involved in the move also is advised. This document should detail staff responsibilities related to the move and the new lab setup, staff locations on move days, and contact information. A spreadsheet subsection can further indicate who is responsible for instrument calibration, verification, and validation, as well as information regarding onsite review of the facility by staff member, initial competency assessments, and participation in emergency drills.

Consider a Staged Approach

Clearly, the proper setup of equipment and instrumentation is key to an efficient ramp up to go live. Thus, it may be wise to stage processes related to installation, calibration, and test verification and validation over two weekends (or a similarly interspersed time frame). During the first moving stage, focus on installing BSCs, incubators, refrigerators and freezers, and brightfield and fluorescent microscopes. The remaining equipment, largely comprising IT and support systems, can then be installed during the second stage. In doing it this way, incubators have time to equilibrate and refrigeration equipment can stabilize, while temperatures and other data can be monitored for 5 to 6 days before establishing the remaining systems. A segmented rollout also provides the opportunity to confirm the incubator’s sterility and cell growth capabilities, as well as determine the mitotic index for chromosome analysis.

The second stage’s installation of computers and analysis systems is an ideal time to request any relevant vendor representatives to be onsite to confirm connectivity and ensure all hardware and software is working appropriately.

Conclusion of Part One

Thus far, we have focused on initial cytogenetic laboratory considerations, some of which (eg, security) may not be applicable to your project depending on whether your cytogenetics operations are new, are being updated, and/or involve new physical plant operations. Regardless, the next phase will focus on optimizing operations once the lab is up and running.

In the meantime, here are a few considerations to keep in mind, particularly for laboratories that are moving their existing cytogenetics operations. During the first stage of implementation when installing incubators and refrigeration, begin splitting cell pellets and sending them to the new lab to perform comparison and verification studies for FISH probes based on probe design. Two to three days after that (midweek), begin to split samples also to send to the new lab for comparison and verification studies for chromosome processing and analysis by specimen type. Obviously, enabling these actions will require a technologist(s) working at the new lab facility and performing these studies, so be sure to account for the extra logistics this requires beyond the usual operational scope. The lab director will need to determine the number of samples and extent of the verification, and will likely have a very busy couple days writing up the verification studies so that the lab is ready for clinical testing as soon as possible.

This is the first of a multi-part series discussing new cytogenetics operations in clinical laboratories and how this valuable discipline can benefit health care institutions of all kinds.


Virginia C. Thurston, PhD, DABMG, is the director of the Parke Cytogenetics Laboratory at the Carolinas HealthCare System in Charlotte, North Carolina. The Parke Cytogenetics Laboratory performs chromosome analysis, fluorescence in situ hybridization, and chromosomal microarray testing for over 50 hospitals. After earning her PhD from the University of Alabama at Birmingham, Jennie completed her clinical cytogenetics fellowship at Indiana University School of Medicine (IUSM). Following her fellowship, she joined the faculty and became the assistant director of the IUSM cytogenetics laboratory. While at IUSM, Jennie also was vice chair of education for the department of medical and molecular genetics, wherein she served as course director of medical genetics for the medical school and clinical cytogenetics for the graduate school. After leaving IUSM, Jennie established and directed the BayCare Cytogenetics Laboratory in Tampa, Florida.

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