title: DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution.
abstract: 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.affiliation: Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada.
authors.forename: Ester
authors.initials: E
authors.lastname: Falconer
authors.forename: Mark
authors.initials: M
authors.lastname: Hills
authors.forename: Ulrike
authors.initials: U
authors.lastname: Naumann
authors.forename: Steven S S
authors.initials: SS
authors.lastname: Poon
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Chavez
authors.forename: Ashley D
authors.initials: AD
authors.lastname: Sanders
authors.forename: Yongjun
authors.initials: Y
authors.lastname: Zhao
authors.forename: Martin
authors.initials: M
authors.lastname: Hirst
authors.forename: Peter M
authors.initials: PM
authors.lastname: Lansdorp
mesh_terms: D000818:Animals; D002478:Cells, Cultured; D023281:Genomics; D051379:Mice; D017422:Sequence Analysis, DNA / Q000379:methods*; D012854:Sister Chromatid Exchange; D013698:Templates, Genetic