Document Detail


DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution.
MedLine Citation:
PMID:  23042453     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
DNA rearrangements such as sister chromatid exchanges (SCEs) are sensitive indicators of genomic stress and instability, but they are typically masked by single-cell sequencing techniques. We developed Strand-seq to independently sequence parental DNA template strands from single cells, making it possible to map SCEs at orders-of-magnitude greater resolution than was previously possible. On average, murine embryonic stem (mES) cells exhibit eight SCEs, which are detected at a resolution of up to 23 bp. Strikingly, Strand-seq of 62 single mES cells predicts that the mm 9 mouse reference genome assembly contains at least 17 incorrectly oriented segments totaling nearly 1% of the genome. These misoriented contigs and fragments have persisted through several iterations of the mouse reference genome and have been difficult to detect using conventional sequencing techniques. The ability to map SCE events at high resolution and fine-tune reference genomes by Strand-seq dramatically expands the scope of single-cell sequencing.
Authors:
Ester Falconer; Mark Hills; Ulrike Naumann; Steven S S Poon; Elizabeth A Chavez; Ashley D Sanders; Yongjun Zhao; Martin Hirst; Peter M Lansdorp
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't     Date:  2012-10-07
Journal Detail:
Title:  Nature methods     Volume:  9     ISSN:  1548-7105     ISO Abbreviation:  Nat. Methods     Publication Date:  2012 Nov 
Date Detail:
Created Date:  2012-11-07     Completed Date:  2013-01-14     Revised Date:  2013-07-11    
Medline Journal Info:
Nlm Unique ID:  101215604     Medline TA:  Nat Methods     Country:  United States    
Other Details:
Languages:  eng     Pagination:  1107-12     Citation Subset:  IM    
Affiliation:
Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada.
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MeSH Terms
Descriptor/Qualifier:
Animals
Cells, Cultured
Genomics
Mice
Sequence Analysis, DNA / methods*
Sister Chromatid Exchange*
Templates, Genetic*
Grant Support
ID/Acronym/Agency:
105265//Canadian Institutes of Health Research; 294740//European Research Council; R01 GM094146/GM/NIGMS NIH HHS; R01GM094146/GM/NIGMS NIH HHS; RMF-92093//Canadian Institutes of Health Research
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