利用人类全基因组亚硫酸氢盐测序数据检测CNVs的研究

doi:10.16288/j.yczz.22-385

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Hereditas(Beijing) ›› 2023, Vol. 45 ›› Issue (4): 324-340.doi: 10.16288/j.yczz.22-385

• Research Article • Previous Articles Next Articles

Study on detection of CNVs using human whole genome bisulfite sequencing data

Dantong Xu(), Yifei Wang, Jiali Cai, Wentao Gong, Xiangchun Pan, Yuhan Tian, Qingpeng Shen, Jiaqi Li, Xiaolong Yuan()

College of Animal Science, South China Agricultural University/Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding/National Engineering Research Center for Breeding Swine Industry, Guangzhou 510642, China

Received:2023-01-18 Revised:2023-03-02 Online:2023-04-20 Published:2023-03-06
Contact: Yuan Xiaolong E-mail:xdt2020@163.com;yxl@scau.edu.cn
Supported by:
Earmarked Fund for China Agriculture Research System(CARS-35);Earmarked Fund for Guangdong Provincial Science and Technology Project(210713156902656)

Abstract

Abstract:

It has been reported that the aberrant DNA methylation may result in copy number variations (CNVs), and the CNVs may alter the levels of DNA methylation. Whole genome bisulfite sequencing (WGBS) is able to generate the sequencing data of DNAs, and shows the potential ability to detect CNVs. However, the evaluations and performances on the detections of CNVs using WGBS data is still unclear. In this study, five software with different strategies for CNV detections, e.g., BreakDancer, cn.mops, CNVnator, DELLY and Pindel, were selected to explore and benchmark the performances of CNV detections with WGBS data. Based on the real (2.62 billion reads) and simulated (12.35 billion reads) WGBS data of humans, we calculated the number, precision, recall, relative ability, memory usage, and running time of CNV detections by 150 times, and tried to figure out the optimal strategy for CNV detections with WGBS data. Based on the real WGBS data, Pindel detected the most deletions and duplications, CNVnator detected the deletions with the highest precision, cn.mops detected the duplications with the highest precision, Pindel detected the deletions with the highest recall, and cn.mops detected the duplications with the highest recall. Based on the simulated WGBS data, BreakDancer detected the most deletions, and cn.mops detected the most duplications. The CNVnator showed the highest precision and recall for both deletions and duplications. In real and simulated WGBS data, the ability of CNVnator to detect CNVs was likely to overtake that in the whole genome sequencing data. Additionally, DELLY and BreakDancer displayed the lowest peak of memory usage and the lest CPU runtime, while CNVnator expressed the highest peak of memory usage and the most CPU runtime. Taken together, CNVnator and cn.mops showed the excellent performances of CNV detections with WGBS data. These results suggested that it was feasible to detect CNVs using WGBS data, and provided the useful information to further investigate both CNVs and DNA methylation using WGBS data alone.

Key words: whole genome bisulfite sequencing, copy number variation, software evaluation

Dantong Xu, Yifei Wang, Jiali Cai, Wentao Gong, Xiangchun Pan, Yuhan Tian, Qingpeng Shen, Jiaqi Li, Xiaolong Yuan. Study on detection of CNVs using human whole genome bisulfite sequencing data[J]. Hereditas(Beijing), 2023, 45(4): 324-340.

Figures/Tables 11

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BAM文件编号	数据类型	测序数据来源(来自NCBI)	样本个体名称
1	WGS	SRR622457	NA12878
2	WGS	ERR3239334	NA12878
3	WGS	ERR194147	NA12878
4	WGBS	SRR10532133、SRR20318446、SRR20318448、SRR20318450	NA12878
5	WGBS	SRR10532131、SRR10532135、SRR6006942、SRR6006945	NA12878
6	WGBS	SRR10532128、SRR6006943、SRR6006944、SRR6006947	NA12878

软件	数据类型	CNVs类型	检出数量均值	标准差	最小值	最大值
BreakDancer	WGBS	DEL	23,049.67	19,583.18	723.00	37,318.00
	WGBS	DUP	0	0	0	0
	WGS	DEL	4,335.67	5,361.69	992.00	10,520.00
	WGS	DUP	0	0	0	0
cn.mops	WGBS	DEL	424.67	19.86	409.00	447.00
	WGBS	DUP	392.00	12.77	378.00	403.00
	WGS	DEL	201.67	37.07	160.00	231.00
	WGS	DUP	157.00	18.33	137.00	173.00
CNVnator	WGBS	DEL	3,066.00	1,506.88	1,954.00	4,781.00
	WGBS	DUP	985.33	291.57	815.00	1,322.00
	WGS	DEL	2,066.33	1,124.41	1,324.00	3,360.00
	WGS	DUP	2,998.67	1,861.44	963.00	4,614.00
DELLY	WGBS	DEL	42,788.00	32,305.60	19,843.00	79,732.00
	WGBS	DUP	1,215.33	353.48	873.00	1,579.00
	WGS	DEL	3,021.67	1,719.65	1,036.00	4,022.00
	WGS	DUP	461.00	384.04	182.00	899.00
Pindel	WGBS	DEL	458,175.33	234,456.02	291,944.00	726,345.00
	WGBS	DUP	21,022.67	13,394.01	12,997.00	36,485.00
	WGS	DEL	577,734.00	201,609.58	414,822.00	803,208.00
	WGS	DUP	8,879.33	4,080.03	4,790.00	12,950.00

Study on detection of CNVs using human whole genome bisulfite sequencing data

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