Long-read individual-molecule sequencing reveals CRISPR-induced genetic heterogeneity in human ESCs
Abstract Quantifying the genetic heterogeneity of a cell population is essential to understanding of biological systems. We develop a universal method to label individual DNA molecules for single-base-resolution haplotype-resolved quantitative characterization of diverse types of rare variants, with...
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doaj-8ac7efe6f33542c18c341407186c7d782020-11-25T03:30:18ZengBMCGenome Biology1474-760X2020-08-0121111410.1186/s13059-020-02143-8Long-read individual-molecule sequencing reveals CRISPR-induced genetic heterogeneity in human ESCsChongwei Bi0Lin Wang1Baolei Yuan2Xuan Zhou3Yu Li4Sheng Wang5Yuhong Pang6Xin Gao7Yanyi Huang8Mo Li9Laboratory of Stem Cell and Regeneration, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST)Laboratory of Stem Cell and Regeneration, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST)Laboratory of Stem Cell and Regeneration, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST)Laboratory of Stem Cell and Regeneration, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST)Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST)Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST)Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, College of Chemistry, College of Engineering, Peking-Tsinghua Center for Life Sciences, Peking UniversityComputational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST)Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, College of Chemistry, College of Engineering, Peking-Tsinghua Center for Life Sciences, Peking UniversityLaboratory of Stem Cell and Regeneration, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST)Abstract Quantifying the genetic heterogeneity of a cell population is essential to understanding of biological systems. We develop a universal method to label individual DNA molecules for single-base-resolution haplotype-resolved quantitative characterization of diverse types of rare variants, with frequency as low as 4 × 10−5, using both short- or long-read sequencing platforms. It provides the first quantitative evidence of persistent nonrandom large structural variants and an increase in single-nucleotide variants at the on-target locus following repair of double-strand breaks induced by CRISPR-Cas9 in human embryonic stem cells.http://link.springer.com/article/10.1186/s13059-020-02143-8Human embryonic stem cellCRISPR-Cas9Genome editingNanopore sequencingLong-read sequencingNext-generation sequencing |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Chongwei Bi Lin Wang Baolei Yuan Xuan Zhou Yu Li Sheng Wang Yuhong Pang Xin Gao Yanyi Huang Mo Li |
spellingShingle |
Chongwei Bi Lin Wang Baolei Yuan Xuan Zhou Yu Li Sheng Wang Yuhong Pang Xin Gao Yanyi Huang Mo Li Long-read individual-molecule sequencing reveals CRISPR-induced genetic heterogeneity in human ESCs Genome Biology Human embryonic stem cell CRISPR-Cas9 Genome editing Nanopore sequencing Long-read sequencing Next-generation sequencing |
author_facet |
Chongwei Bi Lin Wang Baolei Yuan Xuan Zhou Yu Li Sheng Wang Yuhong Pang Xin Gao Yanyi Huang Mo Li |
author_sort |
Chongwei Bi |
title |
Long-read individual-molecule sequencing reveals CRISPR-induced genetic heterogeneity in human ESCs |
title_short |
Long-read individual-molecule sequencing reveals CRISPR-induced genetic heterogeneity in human ESCs |
title_full |
Long-read individual-molecule sequencing reveals CRISPR-induced genetic heterogeneity in human ESCs |
title_fullStr |
Long-read individual-molecule sequencing reveals CRISPR-induced genetic heterogeneity in human ESCs |
title_full_unstemmed |
Long-read individual-molecule sequencing reveals CRISPR-induced genetic heterogeneity in human ESCs |
title_sort |
long-read individual-molecule sequencing reveals crispr-induced genetic heterogeneity in human escs |
publisher |
BMC |
series |
Genome Biology |
issn |
1474-760X |
publishDate |
2020-08-01 |
description |
Abstract Quantifying the genetic heterogeneity of a cell population is essential to understanding of biological systems. We develop a universal method to label individual DNA molecules for single-base-resolution haplotype-resolved quantitative characterization of diverse types of rare variants, with frequency as low as 4 × 10−5, using both short- or long-read sequencing platforms. It provides the first quantitative evidence of persistent nonrandom large structural variants and an increase in single-nucleotide variants at the on-target locus following repair of double-strand breaks induced by CRISPR-Cas9 in human embryonic stem cells. |
topic |
Human embryonic stem cell CRISPR-Cas9 Genome editing Nanopore sequencing Long-read sequencing Next-generation sequencing |
url |
http://link.springer.com/article/10.1186/s13059-020-02143-8 |
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