Systematic evaluation of multiple NGS platforms for structural variants detection

Meng，Xuan1; Wang，Miao2; Luo，Mingjie2; Sun，Lei2; Yan，Qin2; Liu，Yongfeng2

2023-12-01

10.1016/j.jbc.2023.105436

Journal of Biological Chemistry   影响因子和分区

0021-9258

1083-351X

Structural variations (SV) are critical genome changes affecting human diseases. Although many hybridization-based methods exist, evaluating SVs through next-generation sequencing (NGS) data is still necessary for broader research exploration. Here, we comprehensively compared the performance of 16 SV callers and multiple NGS platforms using NA12878 whole genome sequencing (WGS) datasets. The results indicated that several SV callers performed well relatively, such as Manta, GRIDSS, LUMPY, TARDIS, FermiKit, and Wham. Meanwhile, all NGS platforms have a similar performance using a single software. Additionally, we found that the source of undetected SVs was mostly from long reads datasets, therefore, the more appropriate strategy for accurate SV detection will be an integration of long and shorter reads in the future. At present, in the period of NGS as a mainstream method in bioinformatics, our study would provide helpful and comprehensive guidelines for specific categories of SV research.

GenoLab M NA12878 next-generation sequencing structural variations (SV) WGS

EI

英语

NI论文

第一

20235115232023

BIOLOGY & BIOCHEMISTRY

2-s2.0-85179620141

Scopus

1.School of Medicine,Southern University of Science and Technology,Shenzhen,China
2.Research Cooperation Department,GeneMind Biosciences Company Limited,Shenzhen,China

Meng，Xuan,Wang，Miao,Luo，Mingjie,et al. Systematic evaluation of multiple NGS platforms for structural variants detection[J]. Journal of Biological Chemistry,2023,299(12).

Meng，Xuan,Wang，Miao,Luo，Mingjie,Sun，Lei,Yan，Qin,&Liu，Yongfeng.(2023).Systematic evaluation of multiple NGS platforms for structural variants detection.Journal of Biological Chemistry,299(12).

Meng，Xuan,et al."Systematic evaluation of multiple NGS platforms for structural variants detection".Journal of Biological Chemistry 299.12(2023).