Detection of rare mutations, copy number alterations, and methylation in the same template DNA molecules.

Wang, Y; Douville, C; Cohen, JD; Mattox, A; Curtis, S; Silliman, N; Popoli, M; Ptak, J; Dobbyn, L; Nehme, N; Dudley, JC; Summers, M; Zhang, M; Ho-Pham, LT; Tran, BNH; Tran, TS; Nguyen, TV; Bettegowda, C; Papadopoulos, N; Kinzler, KW; Vogelstein, B

Detection of rare mutations, copy number alterations, and methylation in the same template DNA molecules.

Wang, Y Douville, C Cohen, JD Mattox, A Curtis, S Silliman, N Popoli, M Ptak, J Dobbyn, L Nehme, N Dudley, JC Summers, M Zhang, M Ho-Pham, LT Tran, BNH Tran, TS Nguyen, TV Bettegowda, C Papadopoulos, N Kinzler, KW Vogelstein, B

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Publisher:: NATL ACAD SCIENCES
Publication Type:: Journal Article
Citation:: Proc Natl Acad Sci U S A, 2023, 120, (15), pp. e2220704120
Issue Date:: 2023-04-11

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Field	Value	Language
dc.contributor.author	Wang, Y
dc.contributor.author	Douville, C
dc.contributor.author	Cohen, JD
dc.contributor.author	Mattox, A
dc.contributor.author	Curtis, S
dc.contributor.author	Silliman, N
dc.contributor.author	Popoli, M
dc.contributor.author	Ptak, J
dc.contributor.author	Dobbyn, L
dc.contributor.author	Nehme, N
dc.contributor.author	Dudley, JC
dc.contributor.author	Summers, M
dc.contributor.author	Zhang, M
dc.contributor.author	Ho-Pham, LT
dc.contributor.author	Tran, BNH
dc.contributor.author	Tran, TS
dc.contributor.author	Nguyen, TV
dc.contributor.author	Bettegowda, C
dc.contributor.author	Papadopoulos, N
dc.contributor.author	Kinzler, KW
dc.contributor.author	Vogelstein, B
dc.date.accessioned	2024-02-27T06:43:33Z
dc.date.available	2024-02-27T06:43:33Z
dc.date.issued	2023-04-11
dc.identifier.citation	Proc Natl Acad Sci U S A, 2023, 120, (15), pp. e2220704120
dc.identifier.issn	0027-8424
dc.identifier.issn	1091-6490
dc.identifier.uri	http://hdl.handle.net/10453/175904
dc.description.abstract	The analysis of cell-free DNA (cfDNA) from plasma offers great promise for the earlier detection of cancer. At present, changes in DNA sequence, methylation, or copy number are the most sensitive ways to detect the presence of cancer. To further increase the sensitivity of such assays with limited amounts of sample, it would be useful to be able to evaluate the same template molecules for all these changes. Here, we report an approach, called MethylSaferSeqS, that achieves this goal, and can be applied to any standard library preparation method suitable for massively parallel sequencing. The innovative step was to copy both strands of each DNA-barcoded molecule with a primer that allows the subsequent separation of the original strands (retaining their 5-methylcytosine residues) from the copied strands (in which the 5-methylcytosine residues are replaced with unmodified cytosine residues). The epigenetic and genetic alterations present in the DNA molecules can then be obtained from the original and copied strands, respectively. We applied this approach to plasma from 265 individuals, including 198 with cancers of the pancreas, ovary, lung, and colon, and found the expected patterns of mutations, copy number alterations, and methylation. Furthermore, we could determine which original template DNA molecules were methylated and/or mutated. MethylSaferSeqS should be useful for addressing a variety of questions relating genetics and epigenetics.
dc.format	Print-Electronic
dc.language	eng
dc.publisher	NATL ACAD SCIENCES
dc.relation.ispartof	Proc Natl Acad Sci U S A
dc.relation.isbasedon	10.1073/pnas.2220704120
dc.rights	info:eu-repo/semantics/openAccess
dc.subject.mesh	Female
dc.subject.mesh	Humans
dc.subject.mesh	Methylation
dc.subject.mesh	DNA Copy Number Variations
dc.subject.mesh	5-Methylcytosine
dc.subject.mesh	DNA
dc.subject.mesh	Mutation
dc.subject.mesh	Neoplasms
dc.subject.mesh	DNA Methylation
dc.subject.mesh	Humans
dc.subject.mesh	Neoplasms
dc.subject.mesh	5-Methylcytosine
dc.subject.mesh	DNA
dc.subject.mesh	DNA Methylation
dc.subject.mesh	Methylation
dc.subject.mesh	Mutation
dc.subject.mesh	Female
dc.subject.mesh	DNA Copy Number Variations
dc.subject.mesh	Female
dc.subject.mesh	Humans
dc.subject.mesh	Methylation
dc.subject.mesh	DNA Copy Number Variations
dc.subject.mesh	5-Methylcytosine
dc.subject.mesh	DNA
dc.subject.mesh	Mutation
dc.subject.mesh	Neoplasms
dc.subject.mesh	DNA Methylation
dc.title	Detection of rare mutations, copy number alterations, and methylation in the same template DNA molecules.
dc.type	Journal Article
utslib.citation.volume	120
utslib.location.activity	United States
pubs.organisational-group	University of Technology Sydney
pubs.organisational-group	University of Technology Sydney/Faculty of Engineering and Information Technology
pubs.organisational-group	University of Technology Sydney/Strength - CHT - Health Technologies
pubs.organisational-group	University of Technology Sydney/Faculty of Engineering and Information Technology/School of Biomedical Engineering
pubs.organisational-group	University of Technology Sydney/Centre for Health Technologies (CHT)
utslib.copyright.status	open_access	*
dc.date.updated	2024-02-27T06:43:30Z
pubs.issue	15
pubs.publication-status	Published
pubs.volume	120
utslib.citation.issue	15

Abstract:

The analysis of cell-free DNA (cfDNA) from plasma offers great promise for the earlier detection of cancer. At present, changes in DNA sequence, methylation, or copy number are the most sensitive ways to detect the presence of cancer. To further increase the sensitivity of such assays with limited amounts of sample, it would be useful to be able to evaluate the same template molecules for all these changes. Here, we report an approach, called MethylSaferSeqS, that achieves this goal, and can be applied to any standard library preparation method suitable for massively parallel sequencing. The innovative step was to copy both strands of each DNA-barcoded molecule with a primer that allows the subsequent separation of the original strands (retaining their 5-methylcytosine residues) from the copied strands (in which the 5-methylcytosine residues are replaced with unmodified cytosine residues). The epigenetic and genetic alterations present in the DNA molecules can then be obtained from the original and copied strands, respectively. We applied this approach to plasma from 265 individuals, including 198 with cancers of the pancreas, ovary, lung, and colon, and found the expected patterns of mutations, copy number alterations, and methylation. Furthermore, we could determine which original template DNA molecules were methylated and/or mutated. MethylSaferSeqS should be useful for addressing a variety of questions relating genetics and epigenetics.

Please use this identifier to cite or link to this item:

http://hdl.handle.net/10453/175904