How to set-up molecular diagnostics lab or biotechnology lab |

India’s bio-economy is growing at a rapid pace and medical biotechnology or molecular diagbostics has come into main stream, especially since Covid-19. Molecular diagnostics is now commonly performed along with conventional histopathological and serology methods. While requirements may vary somewhat depending on the spectrum of the tests that will be performed, there are several basic needs to be fulfilled for standardization. Adequate space, appropriate equipment, qualified personnel and stringent SOPs especially with a view to preventing contamination are required to set-up molecular diagnostics lab of good standards. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10510618/

The Indian Molecular Diagnostics equipment market can be primarily segmented based on application and technology. Based on application, the market is segmented into infectious disease, blood screening, genetic testing and oncology testing, out of which oncology testing segment is the dominant segment in the short-to-medium term, followed by the infectious disease segment. In terms of technology the market is divided into PCR, In-situ Hybridization, Chips and Microarrays and Others. During Covid-19 years the application in infectious disease segment and RT-PCR or the Polymerase Chain Reaction (PCR) based methods became highly popular.

Equipment for a basic biotechnology lab

If you are setting up or expanding an existing lab to include RT-PCR assays, at a minimum, your lab will need these small laboratory equipment items to prepare and perform tests for various infectious diseases like COVID-19 PCR tests. A basic biotechnology lab setup typically needs the following equipment:

1. RT-PCR (Polymerase Chain Reaction) machine or Thermocycler and Gel Electrophoresis
2. Deep Freezer (-80 degrees)
3. Freezer (-20 degrees)
4. BioSafety Cabinet
5. Laminar Airflow
6. Refrigerated Centrifuge
7. Vortex Mixer
8. Binocular Microscope
9. Incubator
10. Autoclave/ sterilizer
11. Micro-centrifuge
12. Refrigerator

However, to establish a successful medical biotechnology lab, adequate space with proper layout, appropriate equipment and qualified personnel are a must. This is because PCR testing is vulnerable to cross contamination, especially from external DNA sources like hair and body fluids from technicians’ itself.

Contamination can lead to erroneous results and irreparable damage to lab’s reputation. Also, the clean-up/sterilization process and efforts to identify the source of contamination can lead to lab downtime and delays, which have negative financial and performance impacts. Good laboratory design, rigorous training staff and stringent deployment of SOP (Standard Operating Procedures) is the most effective way to ensure contamination is rare. Hence, special considerations, such as providing adequate space, appropriate equipment, and qualified personnel, must be made.

This blog will address only the information related to required medical equipment for a RT-PCR or biotechnology lab and only provide pointers for other information related to lab design etc.

PCR based testing process

The complete test is done in four steps as follows:

1. Pre-PCR procedures
   1. Sample preparation – microdissection and/or DNA/RNA extraction
   1. PCR / Reagent preparation  
2. Post-PCR procedures
   1. Polymerase Chain reaction (PCR) 
   1. Post-PCR analysis

Ideally, a molecular testing laboratory should have three or four separate rooms for each step of the process. At the very least two rooms are recommended — clean room for sample and reagent preparation, dirty room for PCR amplification and analysis always ensuring unidirectional flow from clean to dirty and never back.

Molecular lab equipment and devices

Every area or room in a molecular testing laboratory should be equipped adequately and appropriately to the work done. To avoid any contamination, dedicated equipment should be provided and sharing equipment must be avoided. Standard appliances and equipment to set-up molecular diagnostics lab include the following:

Reagent preparation process

Objective – This reagent preparation room must be the cleanest areas in a molecular testing laboratory. This area is dedicated to the preparation and aliquoting of reagent stock and preparing reaction mixes. If there is any biomaterial such as DNA/RNA, this may contaminate the reagents and this will only get amplified in the next step. Hence, positive air-pressure must be maintained in the room so that no external material comes even through the air. If a separate room is not possible, then the reagent preparation is recommended to be done in laminar hood.

Equipment used in reagent preparation

• Equipment required in PCR reagent preparation room includes pipettes/ micropipettes and tips, vortex mixers, spin-down centrifuges, a refrigerator,-20⁰ freezer (~100L capacity) and laminar hoods.

Sample receipt & preparation

Objective – Sample preparation process includes nucleic acid extraction and addition to PCR reaction mixes. Preferably both these processes should be done in two different rooms. If there is insufficient space for two rooms, the two steps can be done in the same room but in different areas or compartments. Proper sample preparation area is crucial to set-up molecular diagnostics lab.

A vortex mixer is used to remove the cell material from the sample received. This process can take around 30 minutes. Nucleic acid extraction and addition to reaction mix should be ideally done in biosafety cabinets to protect the technician, the sample and the environment from potentially getting infected. Stringent waste management system should be in place or else all good work in the lab can go to waste due to contamination from improperly discarded/ handled waste.

• Equipment required for the sample preparation includes high-speed centrifuges, vortex mixers, pipettes, autoclaves, refrigerated and non-refrigerated centrifuges or separation of components based on density, refrigerators, -20°C and -80 °C deep freezer for storage of tissue culture and frozen samples, bio-safety cabinets and laminar flow hoods.

Other equipment in sample preparation

Other equipment and appliances that could be additionally used in sample preparation if samples are varied and volumes are high are listed below:

Amplification and post-amplification analysis

Objective – The main objective of the PCR process is to amplify the DNA quantity from available sample, which is insufficient to conduct a test. The post-PCR process may involve DNA detection, quantification and sequencing depending on investigation required.  These two comprise the contaminated (dirty) rooms. Therefore, no equipment or material used in these rooms can be transferred to or used in other rooms. A laminar flow hood is recommended for any steps requiring the opening of tubes containing amplicons. To control contamination further, it is also critical that laboratory technicians performing post-PCR analysis do not return to pre-PCR work areas on the same day.

Equipment used in PCR process

• Equipment required in PCR process includes the RT-PCR machine or Thermocycler, pipettes, spin-down centrifuges and laminar hoods.

Equipment used in Post-PCR analysis process

• If Thermocycler has been used for PCR, equipment required in Post-PCR analysis process includes the Gel Electrophoresis machine, Spectrophotometer and/ or DNA sequencer, as required. RT-PCR machine however handles both amplification and analysis in real-time at the end of each cycle.

Conclusion – To set-up molecular diagnostics lab

Equipment and appliances may slightly differ between molecular pathology laboratories based on their testing profile. To set-up molecular diagnostics lab, most other equipment and consumables used in the routine pathology setting must also be available in a molecular pathology laboratory, as well, like Lab coat, ethanol, gloves, test tubes, safety glasses, waste bins etc.

Just providing adequate space is not good enough. To set-up molecular diagnostics lab, proper lab design including; mechanical barriers to prevent contamination, spatial separation of pre- and post-amplification work areas, adequate equipment and devices in each area, unidirectional workflow, proper ventilation and air pressure in each area is necessary to prevent contamination.

Check out the following link for an excellent lab layout and other information related to set-up molecular diagnostics lab.