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.

生物样本库（biobank）样本的误鉴定与污染问题长期困扰生物医学研究。短串联重复序列（short-tandem repeat）与单核苷酸多态性（single-nucleotide polymorphism, SNP）检测技术被广泛用于生物样本的身份验证与污染检测，但二者的灵敏度分别仅为5%~10%与3%~5%，检测灵敏度不足。本文介绍一种基于深度下一代测序（next-generation sequencing, NGS）的方法，其灵敏度显著优于现有技术。该方法可用于验证人源与鼠源细胞系、异种移植瘤（xenografts）及类器官（organoids）的身份；还可精准识别并定量仅含极少量异源细胞污染的人源细胞系样本污染情况，检测并定量人鼠混合样本中的物种特异性组分，检测支原体（mycoplasma）污染，以及推断人类样本的群体结构与性别。