Authentication, characterization and contamination detection of cell lines, xenografts and organoids by barcode deep NGS sequencing

Misidentification and contamination of biobank samples have plagued biomedical research. Short-tandem repeat and single-nucleotide polymorphism (SNP) assays are widely used to authenticate biosamples and detect contamination, but with insufficient sensitivity at 5-10% and 3-5%, respectively. Here we describe a deep NGS-based method with significantly higher sensitivity. It can be used to authenticate human and mouse cell lines, xenografts and organoids. It can also reliably identify and quantify contamination of human cell line samples, contaminated with only small amount of other cell samples; detect and quantify species-specific components in human-mouse mixed samples; detect mycoplasma contamination; infer population structure and gender of human samples.