Two preprints. Two days apart. Same mission: crack the genotype × transcriptome code at single-cell resolution.
Let's break this down:
Saurty-Seerunghen, Lee et al. (Nam, Martelotto & Grillo teams) – GoT-Multi-Gap for RNA-templated gap filling. Clever enzymatic trick: BstFL polymerase does RT nick translation to gap-fill between flanking probes on RNA, then ligates. Bolts directly onto probe-based scRNA-seq (think 10x Flex-type workflows). Whole transcriptome mutation calls from the SAME cell. Multiplexed — target many mutations at once Leverages existing probe-based platforms → low barrier to adoption
biorxiv.org/content/10.64898…
Blattman, Maslah et al. (MSK/Pe'er, Charlinge & Lareau teams) – GIFT Genotyping In Fixed Transcriptomes. This one is a biobank's dream. >99% genotyping accuracy — that's wild. Scales to HUNDREDS of mutations per cell. and THE best part...it works on FFPE 🤯 — unlocks archival clinical samples. Clonal lineage tracing in heterogeneous tumors.
biorxiv.org/content/10.64898…
So how do they compare? Gap filling → elegant chemistry, seamless integration with fresh-sample probe-based scRNA-seq workflows. Minimal disruption to existing pipelines. GIFT → sheer scale FFPE compatibility. If you have a tumor biobank, this is your ticket to retrospective clonal mapping.
Both obliterate the old limitation of choosing between genotype OR transcriptome. The convergence of these approaches means we're entering an era where every single-cell experiment can also be a clonal evolution experiment. 🚀