Performance comparisons of methylation and structural variants from low-input whole-genome methylation sequencing

Zhifu Sun; Saurabh Behati; Panwen Wang; Aditya Bhagwate; Samantha Mcdonough; Vivian Wang; William Taylor; Julie Cunningham; John Kisiel

doi:10.2217/epi-2022-0453

Performance comparisons of methylation and structural variants from low-input whole-genome methylation sequencing

Zhifu Sun, Saurabh Behati, Panwen Wang, Aditya Bhagwate, Samantha Mcdonough, Vivian Wang, William Taylor, Julie Cunningham, John Kisiel

Research output: Contribution to journal › Article › peer-review

Abstract

Aim: Whole-genome methylation sequencing carries both DNA methylation and structural variant information (single nucleotide variant [SNV]; copy number variant [CNV]); however, limited data is available on the reliability of obtaining this information simultaneously from low-input DNA using various library preparation and sequencing protocols. Methods: A HapMap NA12878 sample was sequenced with three protocols (EM-sequencing, QIA-sequencing and Swift-sequencing) and their performance was compared on CpG methylation measurement and SNV and CNV detection. Results: At low DNA input (10-25 ng), EM-sequencing was superior in almost all metrics except CNV detection where all protocols were similar. EM-sequencing captured the highest number of CpGs and true SNVs. Conclusion: EM-sequencing is suitable to detect methylation, SNVs and CNVs from single sequencing with low-input DNA.

Original language	English (US)
Pages (from-to)	11-19
Number of pages	9
Journal	Epigenomics
Volume	15
Issue number	1
DOIs	https://doi.org/10.2217/epi-2022-0453
State	Published - Jan 1 2023

Keywords

CpG methylation
EM-seq
QIAseq
SWIFT-seq
copy number variation
single nucleotide variation
whole-genome methylation sequencing

ASJC Scopus subject areas

Genetics
Cancer Research

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10.2217/epi-2022-0453

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title = "Performance comparisons of methylation and structural variants from low-input whole-genome methylation sequencing",

abstract = "Aim: Whole-genome methylation sequencing carries both DNA methylation and structural variant information (single nucleotide variant [SNV]; copy number variant [CNV]); however, limited data is available on the reliability of obtaining this information simultaneously from low-input DNA using various library preparation and sequencing protocols. Methods: A HapMap NA12878 sample was sequenced with three protocols (EM-sequencing, QIA-sequencing and Swift-sequencing) and their performance was compared on CpG methylation measurement and SNV and CNV detection. Results: At low DNA input (10-25 ng), EM-sequencing was superior in almost all metrics except CNV detection where all protocols were similar. EM-sequencing captured the highest number of CpGs and true SNVs. Conclusion: EM-sequencing is suitable to detect methylation, SNVs and CNVs from single sequencing with low-input DNA.",

keywords = "CpG methylation, EM-seq, QIAseq, SWIFT-seq, copy number variation, single nucleotide variation, whole-genome methylation sequencing",

author = "Zhifu Sun and Saurabh Behati and Panwen Wang and Aditya Bhagwate and Samantha Mcdonough and Vivian Wang and William Taylor and Julie Cunningham and John Kisiel",

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doi = "10.2217/epi-2022-0453",

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T1 - Performance comparisons of methylation and structural variants from low-input whole-genome methylation sequencing

AU - Sun, Zhifu

AU - Behati, Saurabh

AU - Wang, Panwen

AU - Bhagwate, Aditya

AU - Mcdonough, Samantha

AU - Wang, Vivian

AU - Taylor, William

AU - Cunningham, Julie

AU - Kisiel, John

PY - 2023/1/1

Y1 - 2023/1/1

N2 - Aim: Whole-genome methylation sequencing carries both DNA methylation and structural variant information (single nucleotide variant [SNV]; copy number variant [CNV]); however, limited data is available on the reliability of obtaining this information simultaneously from low-input DNA using various library preparation and sequencing protocols. Methods: A HapMap NA12878 sample was sequenced with three protocols (EM-sequencing, QIA-sequencing and Swift-sequencing) and their performance was compared on CpG methylation measurement and SNV and CNV detection. Results: At low DNA input (10-25 ng), EM-sequencing was superior in almost all metrics except CNV detection where all protocols were similar. EM-sequencing captured the highest number of CpGs and true SNVs. Conclusion: EM-sequencing is suitable to detect methylation, SNVs and CNVs from single sequencing with low-input DNA.

AB - Aim: Whole-genome methylation sequencing carries both DNA methylation and structural variant information (single nucleotide variant [SNV]; copy number variant [CNV]); however, limited data is available on the reliability of obtaining this information simultaneously from low-input DNA using various library preparation and sequencing protocols. Methods: A HapMap NA12878 sample was sequenced with three protocols (EM-sequencing, QIA-sequencing and Swift-sequencing) and their performance was compared on CpG methylation measurement and SNV and CNV detection. Results: At low DNA input (10-25 ng), EM-sequencing was superior in almost all metrics except CNV detection where all protocols were similar. EM-sequencing captured the highest number of CpGs and true SNVs. Conclusion: EM-sequencing is suitable to detect methylation, SNVs and CNVs from single sequencing with low-input DNA.

KW - CpG methylation

KW - EM-seq

KW - QIAseq

KW - SWIFT-seq

KW - copy number variation

KW - single nucleotide variation

KW - whole-genome methylation sequencing

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Performance comparisons of methylation and structural variants from low-input whole-genome methylation sequencing

Abstract

Keywords

ASJC Scopus subject areas

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