Clinical OMICS

JAN-FEB 2018

Healthcare magazine for research scientists, labs, pathologists, hospitals, cancer centers, physicians and biopharma companies providing news articles, expert interviews and videos about molecular diagnostics in precision medicine

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Page 32 of 51 January/February 2018 Clinical OMICs 31 MinION Sketching, on the other hand, allows researchers to conduct cell line authentication in one after- noon. "We hope that the short time and DIY approach will reduce the burden and facilitate authentication," Erlich said. Neville Sanjana, a CRISPR biologist, is excited to make MinION Sketching a regular part of the work done in his lab. "There are very few techniques right now for cell-line authentication," said Sanjana, a member at NYGC and assistant professor at NYU's depart- ment of biology who was not involved in the research. Sanjana said MinION Sketching is a step in the right direction for the field of clinical research. "This technique is one that is fast and more accurate than anything we have now. Cell authenti- cation is really something that every- one should be doing." For the first time, the affordability of the MinION makes eventual wide- spread adoption of cell line authenti- cation possible. The MinION is priced at $1,000, with little additional costs to a laboratory already equipped to work with cancer cell lines. The Sketching code is available for free at github. com, and a link can be found in the online paper. Creating a DNA Sketch But, just how does MinION Sketching work? The entire workflow involved in reidentification of human sam- ples involves collecting the sample, extracting the DNA, creating a library of strands to be sequenced, and sequencing using the MinION, which was created by Oxford Nanopore. The MinION is a nanopore sequencer containing a membrane embedded with nanopore proteins that are just over a billionth of a millimeter wide. A steady ion current runs through the membrane. As single strands of DNA pass through the pores, each nucleo- tide (A, G, T, and C) is identified by the way its unique shape interrupts the ion flow. The MinION generates readouts in real time of random pieces of DNA, while the Sketching software analyzes a selected number of single nucleo- tide polymorphisms, or SNPs, using a Bayesian algorithm. These variants make each person unique. "Every time a DNA read comes out, we are screening in semi–real time for vari- ants that are informative and update the posterior probability. That gives us more strokes of the sketch, and we get better resolution of the match," Zaaijer said. Matches are made by comparisons to a database of known sequences. Researchers looking to use this method can download a SNP database, or, ideally, create their own. In the paper, the researchers describe verifying their method by matching a strain of leukemic cells after three minutes of sequencing by the MinION and comparing it against a reference file in the Cancer Cell Line Encyclopedia database. The sketch required 91 SNPs to reach 99.9% accu- racy. The researchers then contami- nated that line with another and ran the test, again. The method correctly rejected a match if the contamination level climbed above 25%. This rapid procedure, along with the affordability of the MinION sequencer, promises to make cell- line authentication what it should be: standard procedure in every research lab. "No one wants to waste time and reagents working on the wrong cells," Sanjana said. "At the right price, every lab will adopt this." Zaaijer added it also has the potential for a long list of clinical applications. For example, it would take less than an hour before a surgery to ver- ify the correct organ is being transplanted to a patient. Currently, this verification takes a minimum of 24 hours. Likewise, it could be used in diagnostics in which patient samples are tested at various time points, mak- ing them more prone to mix-ups. "The speed of the MinION Sketching makes clinical sample authentication a game changer." Sophie Zaaijer, Ph.D., of the Runway Startup Postdoc Program at the Jacobs Technion-Cor- nell Institute was the lead author of a study that could "democratize DNA fingerprinting." "There are very few techniques right now for cell-line authentication." — Neville Sanjana, New York Genome Center and NYU Department of Biology

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