The scheme for validation of clinical metagenomics sequencing assay
10.3760/cma.j.cn114452-20220721-00426
- VernacularTitle:病原宏基因组高通量测序性能确认方案
- Author:
Dong ZHANG
1
;
Jingjia ZHANG
;
Juan DU
;
Xuesong SHANG
;
Yu CHEN
;
Jie WU
;
Jie YI
;
Zhuo YANG
;
Yingchun XU
;
Qiwen YANG
Author Information
1. 中国医学科学院北京协和医院检验科 疑难重症及罕见病国家重点实验室，北京 100730
- Keywords:
Noxae;
Next-generation sequencing;
Metagenomics;
Laboratory validation;
Clinical application
- From:
Chinese Journal of Laboratory Medicine
2022;45(9):899-905
- CountryChina
- Language:Chinese
-
Abstract:
Clinical metagenomic next-generation sequencing (mNGS) entails unbiased shotgun sequencing of all microbial and host nucleic acids present in a clinical sample. By analyzing the microbiota diversity, taxonomic, and phylogenetic relationships of clinical specimens, metagenomics related analysis provides an opportunity to investigate substantial biological significance of different microbes. According to the published paper, most studies on mNGS mainly focused on the clinical impact evaluation. However, the studies focused on the analytical performance validation of mNGS before clinical application were rare. Here, a scheme, included intended use, method establishment, assay validation and standard operating protocol, for the laboratory validation of clinical metagenomics sequencing assay was provided by summarizing experiences of clinical laboratory department of Peking Union Medical College Hospital protocol and relevant research. In this scheme, we discussed important topics of mNGS laboratory validation as below: specimen type and pathogen list, bioinformatics pipeline setup, dry lab standard preparation and performance validation, mNGS workflow setup, background nucleotide acid evaluation, wet lab standard preparation and performance validation.
