Development of coupling controlled polymerizations by adapter-ligation in mate-pair sequencing for detection of various genomic variants in one single assay. (7th June 2019)

• Record Type: Journal Article
• Authors: Dong, Zirui; Zhao, Xia; Li, Qiaoling; Yang, Zhenjun; Xi, Yang; Alexeev, Andrei; Shen, Hanjie; Wang, Ou; Ruan, Jie; Ren, Han; Wei, Hanmin; Qi, Xiaojuan; Li, Jiguang; Zhu, Xiaofan; Zhang, Yanyan; Dai, Peng; Kong, Xiangdong; Kirkconnell, Killeen; Alferov, Oleg; Giles, Shane; Yamtich, Jennifer; Kermani, Bahram G; Dong, Chao; Liu, Pengjuan; Mi, Zilan; Zhang, Wenwei; Xu, Xun; Drmanac, Radoje; Choy, Kwong Wai; Jiang, Yuan
• Is Part Of: DNA research. Volume 26:Number 4(2019)
• Page Start: 313
• Page End: 325
• Publication Date: 2019-06-07
• Subjects: mate-pair sequencing -- controlled polymerization -- adapter-ligation -- integrated platform; Genes -- Periodicals; Genomes -- Periodicals; Genes -- Research -- Periodicals; Genomics -- Periodicals; DNA -- Research -- Periodicals; 572.86072
• DOI: 10.1093/dnares/dsz011
• Languages: English
• ISSNs: 1340-2838

Abstract

Abstract: The diversity of disease presentations warrants one single assay for detection and delineation of various genomic disorders. Herein, we describe a gel-free and biotin-capture-free mate-pair method through coupling Controlled Polymerizations by Adapter-Ligation (CP-AL). We first demonstrated the feasibility and ease-of-use in monitoring DNA nick translation and primer extension by limiting the nucleotide input. By coupling these two controlled polymerizations by a reported non-conventional adapter-ligation reaction 3′ branch ligation, we evidenced that CP-AL significantly increased DNA circularization efficiency (by 4-fold) and was applicable for different sequencing methods but at a faction of current cost. Its advantages were further demonstrated by fully elimination of small-insert-contaminated (by 39.3-fold) with a ∼50% increment of physical coverage, and producing uniform genome/exome coverage and the lowest chimeric rate. It achieved single-nucleotide variants detection with sensitivity and specificity up to 97.3 and 99.7%, respectively, compared with data from small-insert libraries. In addition, this method can provide a comprehensive delineation of structural rearrangements, evidenced by a potential diagnosis in a patient with oligo-atheno-terato-spermia. Moreover, it enables accurate mutation identification by integration of genomic variants from different aberration types. Overall, it provides a potential single-integrated solution for detecting various genomic variants, facilitating a genetic diagnosis in human diseases.