Single-cell genotyping

Overview

Single-cell genotyping via clonal expansion followed by whole-exome or targeted sequencing enables mutation calling at single-cell resolution in normal tissues. Cells are individually expanded into colonies, then sequenced to determine their somatic mutation profiles PMID:39091884.

Used by

  • PMID:39091884 — 137 keratinocytes, 131 melanocytes, and 23 fibroblasts from 22 skin biopsies across 15 donors (ages 35–95) were profiled by single-cell clonal expansion followed by whole-exome sequencing (~95X coverage); revealed that keratinocytes have lower mutation burdens than melanocytes (median 1.14 vs. 3.91 mut/Mb), pathogenic mutations break UV repair capacity in keratinocytes, and AK-to-cSCC evolution is traceable in phylogenetic trees PMID:39091884.
  • PMID:38895302 — single-cell clonal expansion followed by WES and RNA-seq (G&T-seq protocol) on 182 melanocytes from normal skin biopsies of tanning bed users and controls; demonstrated significantly higher mutation burdens in tanning bed users (p = 0.0128), enrichment of COSMIC signature 11 (p = 0.0405) PMID:38895302.
  • PMID:39975212 — single-cell genotyping via clonal expansion of 297 melanocytes from 58 skin biopsies of 31 donors; colonies of ~230 cells subjected to joint DNA/RNA amplification using G&T-Seq + Smart-Seq2; variant calling against hg19 (BWA-MEM v2.0.5, GATK v4.1.2.0) identified bimodal UV-burden subpopulations (HighMut enriched for SBS7, LowMut enriched for SBS1/SBS5) within the same biopsy PMID:39975212.
  • Applied to 210 breast cancer PDX nuclei (SA494 and SA501) to genotype 40–45 somatic SNV + germline amplicons per nucleus; Bayesian phylogenetic inference confirmed that a <5% originating tumor clone expanded to dominance in the SA494 xenograft PMID:25470049

Notes

  • The clonal expansion approach provides high coverage per cell but is limited to cells that can be cultured (keratinocytes, melanocytes, fibroblasts) PMID:39091884.
  • Corpus-grown slug; not present in canonical ontology.

Sources

This page was processed by entity-page-writer on 2026-05-01. - PMID:25470049

This page was processed by wiki-cli on 2026-05-14.