Open AccessImproving the efficiency of single-cell genome sequencing based on overlapping pooling strategy and CNV analysis
Author(s) -
Jing Tu,
Zengyan Yang,
Na Lü,
Lu Zhang
Publication year - 2022
Publication title -
royal society open science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.84
H-Index - 51
ISSN - 2054-5703
DOI - 10.1098/rsos.211330
Subject(s) - single cell sequencing , pooling , genome , computational biology , copy number variation , dna sequencing , biology , computer science , deep sequencing , genetics , gene , exome sequencing , phenotype , artificial intelligence
Single-cell genome sequencing has become a useful tool in medicine and biology studies. However, an independent library is required for each cell in single-cell genome sequencing, so that the cost grows with the number of cells. In this study, we report a study which efficiently analyses single-cell copy number variation (CNV) using overlapping pooling strategy and branch and bound (B&B ) algorithm. Single cells were overlapped pooled before sequencing, and later were assorted into specific types by estimating their CNV patterns byB&B algorithm. Instead of constructing libraries for each cell, a library is required only for each pool. As the number of pools is smaller than the cells, fewer libraries are required, which means lower cost. Through computer simulations, we overlapped pooled 80 cells into 40 or 27 pools and classified them into cell types based on CNV pattern. The results showed that 84% cells in 40 pools and 76.5% cells in 27 pools were correctly classified on average, while only half or one-third of the sequencing libraries were required. Combining with traditional approaches, our method is expected to significantly improve the efficiency of single-cell genome sequencing.