G&T-seq: Separation and parallel sequencing of the genomes and transcriptomes of single cells

Iain Macaulay1, Wilfried Haerty2, Parveen Kumar3, Yang Li2, Tim Hu2, Mabel Teng1, Niels van der Aa3, Paul Coupland1, Chris Ponting1,2, Thierry Voet1,3
1Sanger Institute, United Kingdom; 
2MRC Functional Genomics Unit, Oxford; 
3KU Leuven

Advances in genome and transcriptome sequencing from single cells now offer a unique perspective from which to investigate cellular heterogeneity in development and disease. Here we present a novel method, G&T-seq, which permits simultaneous sequencing of the genome and the transcriptome from the same single cell.
G&T-seq provides whole genome amplified genomic DNA and full-length transcript sequence and with automation, 96 samples can be processed in parallel.
Using cancer cell lines and other models, we are exploring the relationship between DNA copy number and gene expression. From single cells from the breast cancer cell line HCC38 and matched normal control cells, several thousand transcripts were detected per cell, while low coverage genome sequencing demonstrated that copy number variants observed in bulk sequencing were preserved in the genomic analysis of single cells. Integrated analysis of the genome and transcriptome of single cells also allows validation of genomic single nucleotide variants in transcripts, as well as the detection fusion transcripts and their associated genomic rearrangements.

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