Cargando…
Performance of copy number variants detection based on whole-genome sequencing by DNBSEQ platforms
BACKGROUND: DNBSEQ™ platforms are new massively parallel sequencing (MPS) platforms that use DNA nanoball technology. Use of data generated from DNBSEQ™ platforms to detect single nucleotide variants (SNVs) and small insertions and deletions (indels) has proven to be quite effective, while the feasi...
Autores principales: | , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2020
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7659224/ https://www.ncbi.nlm.nih.gov/pubmed/33176676 http://dx.doi.org/10.1186/s12859-020-03859-x |
_version_ | 1783608809656156160 |
---|---|
author | Rao, Junhua Peng, Lihua Liang, Xinming Jiang, Hui Geng, Chunyu Zhao, Xia Liu, Xin Fan, Guangyi Chen, Fang Mu, Feng |
author_facet | Rao, Junhua Peng, Lihua Liang, Xinming Jiang, Hui Geng, Chunyu Zhao, Xia Liu, Xin Fan, Guangyi Chen, Fang Mu, Feng |
author_sort | Rao, Junhua |
collection | PubMed |
description | BACKGROUND: DNBSEQ™ platforms are new massively parallel sequencing (MPS) platforms that use DNA nanoball technology. Use of data generated from DNBSEQ™ platforms to detect single nucleotide variants (SNVs) and small insertions and deletions (indels) has proven to be quite effective, while the feasibility of copy number variants (CNVs) detection is unclear. RESULTS: Here, we first benchmarked different CNV detection tools based on Illumina whole-genome sequencing (WGS) data of NA12878 and then assessed these tools in CNV detection based on DNBSEQ™ sequencing data from the same sample. When the same tool was used, the CNVs detected based on DNBSEQ™ and Illumina data were similar in quantity, length and distribution, while great differences existed within results from different tools and even based on data from a single platform. We further estimated the CNV detection power based on available CNV benchmarks of NA12878 and found similar precision and sensitivity between the DNBSEQ™ and Illumina platforms. We also found higher precision of CNVs shorter than 1 kbp based on DNBSEQ™ platforms than those based on Illumina platforms by using Pindel, DELLY and LUMPY. We carefully compared these two available benchmarks and found a large proportion of specific CNVs between them. Thus, we constructed a more complete CNV benchmark of NA12878 containing 3512 CNV regions. CONCLUSIONS: We assessed and benchmarked CNV detections based on WGS with DNBSEQ™ platforms and provide guidelines for future studies. |
format | Online Article Text |
id | pubmed-7659224 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-76592242020-11-13 Performance of copy number variants detection based on whole-genome sequencing by DNBSEQ platforms Rao, Junhua Peng, Lihua Liang, Xinming Jiang, Hui Geng, Chunyu Zhao, Xia Liu, Xin Fan, Guangyi Chen, Fang Mu, Feng BMC Bioinformatics Research Article BACKGROUND: DNBSEQ™ platforms are new massively parallel sequencing (MPS) platforms that use DNA nanoball technology. Use of data generated from DNBSEQ™ platforms to detect single nucleotide variants (SNVs) and small insertions and deletions (indels) has proven to be quite effective, while the feasibility of copy number variants (CNVs) detection is unclear. RESULTS: Here, we first benchmarked different CNV detection tools based on Illumina whole-genome sequencing (WGS) data of NA12878 and then assessed these tools in CNV detection based on DNBSEQ™ sequencing data from the same sample. When the same tool was used, the CNVs detected based on DNBSEQ™ and Illumina data were similar in quantity, length and distribution, while great differences existed within results from different tools and even based on data from a single platform. We further estimated the CNV detection power based on available CNV benchmarks of NA12878 and found similar precision and sensitivity between the DNBSEQ™ and Illumina platforms. We also found higher precision of CNVs shorter than 1 kbp based on DNBSEQ™ platforms than those based on Illumina platforms by using Pindel, DELLY and LUMPY. We carefully compared these two available benchmarks and found a large proportion of specific CNVs between them. Thus, we constructed a more complete CNV benchmark of NA12878 containing 3512 CNV regions. CONCLUSIONS: We assessed and benchmarked CNV detections based on WGS with DNBSEQ™ platforms and provide guidelines for future studies. BioMed Central 2020-11-11 /pmc/articles/PMC7659224/ /pubmed/33176676 http://dx.doi.org/10.1186/s12859-020-03859-x Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Article Rao, Junhua Peng, Lihua Liang, Xinming Jiang, Hui Geng, Chunyu Zhao, Xia Liu, Xin Fan, Guangyi Chen, Fang Mu, Feng Performance of copy number variants detection based on whole-genome sequencing by DNBSEQ platforms |
title | Performance of copy number variants detection based on whole-genome sequencing by DNBSEQ platforms |
title_full | Performance of copy number variants detection based on whole-genome sequencing by DNBSEQ platforms |
title_fullStr | Performance of copy number variants detection based on whole-genome sequencing by DNBSEQ platforms |
title_full_unstemmed | Performance of copy number variants detection based on whole-genome sequencing by DNBSEQ platforms |
title_short | Performance of copy number variants detection based on whole-genome sequencing by DNBSEQ platforms |
title_sort | performance of copy number variants detection based on whole-genome sequencing by dnbseq platforms |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7659224/ https://www.ncbi.nlm.nih.gov/pubmed/33176676 http://dx.doi.org/10.1186/s12859-020-03859-x |
work_keys_str_mv | AT raojunhua performanceofcopynumbervariantsdetectionbasedonwholegenomesequencingbydnbseqplatforms AT penglihua performanceofcopynumbervariantsdetectionbasedonwholegenomesequencingbydnbseqplatforms AT liangxinming performanceofcopynumbervariantsdetectionbasedonwholegenomesequencingbydnbseqplatforms AT jianghui performanceofcopynumbervariantsdetectionbasedonwholegenomesequencingbydnbseqplatforms AT gengchunyu performanceofcopynumbervariantsdetectionbasedonwholegenomesequencingbydnbseqplatforms AT zhaoxia performanceofcopynumbervariantsdetectionbasedonwholegenomesequencingbydnbseqplatforms AT liuxin performanceofcopynumbervariantsdetectionbasedonwholegenomesequencingbydnbseqplatforms AT fanguangyi performanceofcopynumbervariantsdetectionbasedonwholegenomesequencingbydnbseqplatforms AT chenfang performanceofcopynumbervariantsdetectionbasedonwholegenomesequencingbydnbseqplatforms AT mufeng performanceofcopynumbervariantsdetectionbasedonwholegenomesequencingbydnbseqplatforms |