半面阳光 (2023-06-30 22:13):
#paper DOI:https://doi.org/10.1093/bib/bbab380, Briefings in Bioinformatics, 2022, NiPTUNE: an automated pipeline for noninvasive prenatal testing in an accurate, integrative and flexible framework.这篇文章整合了一个完整的NIPT生物信息流程。文章测试了NIPT生信分析中QC、Fetal fraction估计、fetal gender判断等几个关键步骤的不同分析工具和方法,给出了一套分析效果较好的工具组合。
IF:6.800Q1 Briefings in bioinformatics, 2022-01-17. DOI: 10.1093/bib/bbab380 PMID: 34529041
NiPTUNE: an automated pipeline for noninvasive prenatal testing in an accurate, integrative and flexible framework
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Abstract:
Noninvasive prenatal testing (NIPT) consists of determining fetal aneuploidies by quantifying copy number alteration from the sequencing of cell-free DNA (cfDNA) from maternal blood. Due to the presence of cfDNA of fetal origin in maternal blood, in silico approaches have been developed to accurately predict fetal aneuploidies. Although NIPT is becoming a new standard in prenatal screening of chromosomal abnormalities, there are no integrated pipelines available to allow rapid, accurate and standardized data analysis in any clinical setting. Several tools have been developed, however often optimized only for research purposes or requiring enormous amount of retrospective data, making hard their implementation in a clinical context. Furthermore, no guidelines have been provided on how to accomplish each step of the data analysis to achieve reliable results. Finally, there is no integrated pipeline to perform all steps of NIPT analysis. To address these needs, we tested several tools for performing NIPT data analysis. We provide extensive benchmark of tools performances but also guidelines for running them. We selected the best performing tools that we benchmarked and gathered them in a computational pipeline. NiPTUNE is an open source python package that includes methods for fetal fraction estimation, a novel method for accurate gender prediction, a principal component analysis based strategy for quality control and fetal aneuploidies prediction. NiPTUNE is constituted by seven modules allowing the user to run the entire pipeline or each module independently. Using two cohorts composed by 1439 samples with 31 confirmed aneuploidies, we demonstrated that NiPTUNE is a valuable resource for NIPT analysis.
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