title: Performance comparison between rapid sequencing platforms for ultra-low coverage sequencing strategy.
abstract: Ultra-low coverage sequencing (ULCS) is one of the most promising strategies for sequencing based clinical application. These clinical applications, especially prenatal diagnosis, have a strict requirement of turn-around-time; therefore, the application of ULCS is restricted by current high throughput sequencing platforms. Recently, the emergence of rapid sequencing platforms, such as MiSeq and Ion Proton, brings ULCS strategy into a new era. The comparison of their performance could shed lights on their potential application in large-scale clinic trials. In this study, we performed ULCS (<0.1X coverage) on both MiSeq and Ion Proton platforms for 18 spontaneous abortion fetuses carrying aneuploidy and compared their performance on different levels. Overall basic data and GC bias showed no significant difference between these two platforms. We also found the sex and aneuploidy detection indicated 100% sensitivity and 100% specificity on both platforms. Our study generated essential data from these two rapid sequencing platforms, which provides useful reference for later research and potentially accelerates the clinical applications of ULCS.
authors.affiliation: State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China; BGI-Shenzhen, Shenzhen, China; Shenzhen Municipal Key Laboratory of Birth Defects Screening and Engineering, BGI-Shenzhen, Shenzhen, China; Guangdong Provincial Key Laboratory of Human Diseases Genome, BGI-Shenzhen, Guangdong, China; BGI-Nanjing, Nanjing, China; The Key Technology R&D Program of Jiangsu Province, Nanjing, China.
authors.forename: Shengpei
authors.initials: S
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China; BGI-Shenzhen, Shenzhen, China.
authors.forename: Sheng
authors.initials: S
authors.lastname: Li
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Weiwei
authors.initials: W
authors.lastname: Xie
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Xuchao
authors.initials: X
authors.lastname: Li
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Chunlei
authors.initials: C
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China; BGI-Shenzhen, Shenzhen, China.
authors.forename: Haojun
authors.initials: H
authors.lastname: Jiang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Zheng
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Xiaoyu
authors.initials: X
authors.lastname: Pan
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Hancheng
authors.initials: H
authors.lastname: Zheng
authors.affiliation: Research Group, Complete Genomics, Mountain View, California, United States of America.
authors.forename: Jia Sophie
authors.initials: JS
authors.lastname: Liu
authors.affiliation: Department of Stomatology, The Second People's Hospital of Shenzhen, Shenzhen, China.
authors.forename: Yongqiang
authors.initials: Y
authors.lastname: Deng
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Fang
authors.initials: F
authors.lastname: Chen
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Jiang
mesh_terms: D000782:Aneuploidy; D001482:Base Composition / Q000235:genetics; D005260:Female; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods* / Q000592:standards*; D006801:Humans; D008297:Male; D012730:Sex Chromosomes / Q000235:genetics