Multi-modal single-cell and whole-genome sequencing of minute, frozen specimens to propel clinical applications

Single-cell genomics are enabling technologies, but their broad clinical application remains challenging. We report an easily adaptable approach for single-cell transcriptome and T cell receptor (TCR)-sequencing, and matched whole-genome sequencing from tiny, frozen clinical specimens. We achieve similar quality and biological outputs while reducing artifactual signals compared to data from matched fresh tissue samples. Profiling sequentially collected melanoma samples from the KEYNOTE-001 trial, we resolve cellular, genomic, and clonotype dynamics that encapsulate molecular patterns of tumor evolution during anti-PD-1 therapy. To demonstrate applicability to banked biospecimens of rare diseases, we generate a large uveal melanoma liver metastasis single-cell and matched WGS atlas, which revealed niche-specific impairment of clonal T cell expansion. This study provides a foundational framework for propelling single-cell genomics to the clinical arena. ### Competing Interest Statement B.I. is a consultant for Volastra Therapeutics Inc, Merck, AstraZeneca and Johnson&Johnson. G.A-R. has received honoraria from consulting with Arcus Biosciences. A.R. has received honoraria from consulting with Amgen, Bristol-Myers Squibb, Chugai, Genentech, Merck, Novartis, Roche and Sanofi, is or has been a member of the scientific advisory board and holds stock in Arcus, Compugen, CytomX, Highlight, ImaginAb, Isoplexis, Kite-Gilead, Lutris, Merus, PACT, RAPT, Synthekine and Tango Therapeutics. AMT receives research support from Ono Pharmaceuticals. B.S.H. participated in advisory boards for AstraZeneca and Ideaya.