Scalable genotyping in fixed transcriptomes resolves clonal heterogeneity via single-cell sequencing [GIFT-seq]

However, technical limitations of widely-used platforms have been challenging to link cellular states from transcriptome-wide analyses to somatic mutations at scale. Here, we introduce Genotyping in Fixed Transcriptomes by sequencing (GIFT-seq), a novel assay for detection of hundreds of targeted genetic variants concomitant with whole transcriptome quantification.

By pairing a short, rationally- designed gapfilling reaction between adjacent single-stranded DNA (ssDNA) probes, GIFT enables the scalable profiling of >100 mutations per cell with >99% genotyping accuracy, including from FFPE (Formalin-Fixed Paraffin-Embedded) tissue. We demonstrate the unique scalability of GIFT by profiling >700,000 cells from 35 donors with myeloproliferative neoplasms, revealing mutation-dependent stem and progenitor responses to systemic inflammation incurred by the characteristic JAK2V617 mutation.