Mutational sequencing for accurate count and long-range assembly

Kumar, Vijay, Rosenbaum, Julie, Wang, Zihua, Forcier, Talitha, Ronemus, Michael, Wigler, Michael, Levy, Dan (June 2017) Mutational sequencing for accurate count and long-range assembly. bioRxiv.

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Abstract

ABSTRACT We introduce a new protocol, mutational sequencing or muSeq, which randomly deaminates unmethylated cytosines at a fixed and tunable rate. The muSeq protocol marks each initial template molecule with a unique mutation signature that is present in every copy of the template, and in every fragmented copy of a copy. In the sequenced read data, this signature is observed as a unique pattern of C-to-T or G-to-A nucleotide conversions. Clustering reads with the same conversion pattern enables accurate count and long-range assembly of initial template molecules from short-read sequence data. We explore count and low-error sequencing by profiling a 135,000 fragment PstI representation, demonstrating that muSeq improves copy number inference and significantly reduces sporadic sequencer error. We explore long-range assembly in the context of cDNA, generating contiguous transcript clusters greater than 3,000 bp in length. The muSeq assemblies reveal transcriptional diversity not observable from short-read data alone.

Item Type:	Paper
Subjects:	bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > cDNA bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > mutations Investigative techniques and equipment > assays > whole genome sequencing
CSHL Authors:	Rosenbaum, Julie Wang, Zihua Forcier, Talitha Ronemus, Michael Wigler, Michael H. Levy, Dan
Communities:	CSHL labs > Hammell M. lab CSHL labs > Levy lab CSHL labs > Wigler lab School of Biological Sciences > Publications
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	13 June 2017
Date Deposited:	10 Jan 2023 20:06
Last Modified:	29 Feb 2024 20:32
URI:	https://repository.cshl.edu/id/eprint/40785

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