Rapid re-identification of human samples using portable DNA sequencing

• Published in: eLife Vol. 6
• Main Authors: Zaaijer, Sophie, Gordon, Assaf, Speyer, Daniel, Piccone, Robert, Groen, Simon Cornelis, Erlich, Yaniv
• Format: Journal Article
• Language: English
• Published: England eLife Sciences Publications Ltd 28.11.2017; eLife Sciences Publications, Ltd
• Subjects: Cancer; Cell Biology; cell line authentication; Cell lines; Computational Biology - methods; Computer science; Contamination; Data processing; Deoxyribonucleic acid; DNA; DNA - chemistry; DNA - genetics; DNA fingerprinting; DNA sequencing; Forensic science; Forensic sciences; forensics; Genetic testing; Genetics and Genomics; Genomes; Genotyping Techniques - methods; Humans; Identification; Laboratories; Laboratory equipment; Latency; nanopore sequencing; Polymorphism, Single Nucleotide; Probability; re-identification; Sequence Analysis, DNA - methods; Single-nucleotide polymorphism; Time Factors; Tools and Resources; United States > US; nanopore sequencing; forensics; cell biology; evolutionary biology; cell line authentication; re-identification; genomics; DNA fingerprinting; human
• ISSN: 2050-084X; 2050-084X
• DOI: 10.7554/eLife.27798

DNA re-identification is used for a broad suite of applications, ranging from cell line authentication to forensics. However, current re-identification schemes suffer from high latency and limited access. Here, we describe a rapid, inexpensive, and portable strategy to robustly re-identify human DNA called 'MinION sketching'. MinION sketching requires as few as 3 min of sequencing and 60-300 random SNPs to re-identify a sample enabling near real-time applications of DNA re-identification. Our method capitalizes on the rapidly growing availability of genomic reference data for cell lines, tissues in biobanks, and individuals. This empowers the application of MinION sketching in research and clinical settings for periodic cell line and tissue authentication. Importantly, our method enables considerably faster and more robust cell line authentication relative to current practices and could help to minimize the amount of irreproducible research caused by mix-ups and contamination in human cell and tissue cultures.