JOIN US9 genome sequencing labs in Karnataka, claims Sudhakar
Health and Medical Education Minister K Sudhakar on Thursday said that nine genome sequencing labs, including five set up by the state government, are sequencing 1,875 samples in one batch. However, according to the experts only two labs are functioning.
“Karnataka is the first state in the country to set up five genome sequencing labs. Two labs are in Bengaluru, and one each in Mysuru, Belagavi, and Kalaburagi. The preparations are on to set up a lab each in Hubballi and Ballari. The turnaround time is currently two to three days, we’re trying to bring it down to 24 hours to 36 hours,” said Sudhakar.
However, the minister did not say how many of these labs have been made operational. Experts requesting anonymity said as of now, only two are functional: NIMHANS and NCBS labs in Bengaluru.
Researchers also said bringing down the turnaround time to 24 hours to 36 hours, seems to be an overambitious target given the technicalities and resource-intensive processes involved.
One expert said, “The Indian Institute of Science has the capacity to do genome sequencing. But it is not a part of the INSACOG network. Currently, samples are being sent only to NIMHANS and NCBS.”
Explaining the complete time taken for genome sequencing procedure, he said, “The library preparation takes 90 minutes to two days. The DNA library bridge amplification cycles take three hours, depending on the panel, the DNA library sequencing takes six hours to 40 hours, and finally, the alignment and data analysis takes one to two days.”
Midnight protocol
There is a 24-hour midnight protocol that Oxford Nanopore has come up with. “Only if you have a fully integrated system, you can do a midnight protocol. The main problem that INSACOG faces is with sample collection because they have no tie-ups with any sample collection partners. Sample collected from government labs need many quality checks which is a big struggle.
ICMR also does not give the data to INSACOG. Has the government trained the manpower they have got and procured the bioinformatics,” he questioned.
“This will easily take a couple of months. We are not aware of any training that has taken place except in BMCRI. During the Delta wave, six new labs were announced. When the Omicron wave started the government was talking about having nine labs. There is no deadline. This will go on till the next wave,” he added.