BioProject

Although DNA extracted from FFPE samples is suitable for massively parallel sequencing, building

sequencing libraries from multiple FFPE samples remains technically challenging and costly. Here,

we present a method, CUTseq, that allows multiplexed genome barcoding, amplification and

reduced representation sequencing of DNA extracted from individual FFPE tissue sections or

multiple sub-regions in them. CUTseq uses restriction enzymes to fragment and barcode the

genome at defined locations, and the T7 phage promoter to amplify the DNA sequence surrounding

the cut sites before a sequencing library is prepared. We compared CUTseq with a standard way for

preparing sequencing libraries compatible with Illumina technology using DNA extracted from

FFPE sections of different tumor types, demonstrating a strong correlation between DNA copy

number profiles obtained with two approaches. Furthermore, by applying CUTseq to DNA

extracted from dozens of small (<10 mm 2 ) regions inside individual FFPE tissue sections of primary

breast cancers and matched metastases, we were able to study intra-tumor heterogeneity in DNA

copy number, at a spatial resolution so far unattained. CUTseq is a versatile and cost-effective

method for multiplexed reduced representation genome sequencing that can be applied to both fixed

and non-fixed samples. Less...