Summary of single-cell studies in CLL
| Reference . | Sample input . | Methodology . | Insight . |
|---|---|---|---|
| Zhao et al49 | 116 CLL cells from 2 time points | Whole-genome DNA amplification in individual PCR tubes | sCNA identified and subclonal architecture determined |
| Wang et al50 | 1152 CLL cells from 5 patients | Plate-based targeted multiplex PCR assay following whole-genome amplification | sCNA and sSNV identified and subclonal architecture determined |
| Landau et al58 | 393 CD19+ B cells from 2 healthy donors and 111 CLL cells from 1 patient | Multiplexed scRRBS | Uniformly high proportion of discordant reads in CLL cells compared with normal B cells |
| Chaligne et al59 | 383 CD19+ B cells from 4 healthy donors and 324 CLL cells from 3 patients | Multiplexed scRRBS | Epigenetic phylogenetic tree reconstruction |
| Chaligne et al59 | 42 CLL cells | Multiplexed scRRBS and scRNA sequencing | Increasing phylogenetic distance correlates with decreasing transcriptional similarity |
| Zhao et al49 | 362 CLL cells from 5 time points (35-126 cells per time point) | Plate-based Smart-Seq2 scRNA sequencing | Identification of 6 transcriptional clusters and their evolution over time and with treatment |
| Wang et al50 | 289 CLL cells from 4 patients | Fluidigm C1 System Smart-Seq scRNA sequencing | Using pathway and gene set overdispersion analysis identified unique biological processes demonstrating transcriptional heterogeneity |
| Wang et al44 | 845 CLL cells from 6 patients | Plate-based targeted qPCR using Fluidigm BioMark | Single-cell correlation of alternative splicing variants with SF3B1 mutational status |
| Landau et al13 | 310 CLL cells from 4 patients | Fluidigm C1 System Smart-Seq scRNA sequencing | Correlational of single-cell transcriptional heterogeneity with methylation data |
| Burger et al12 | 473 cells from 3 time points | Plate-based targeted qPCR using Fluidigm BioMark | Mutation detection to determine subclonal architecture |
| Burger et al12 | Polydimethylsiloxane microfluidic device and targeted qPCR | High-sensitivity mutation detection, including demonstration of the presence of rare resistant cells before ibrutinib initiation |
| Reference . | Sample input . | Methodology . | Insight . |
|---|---|---|---|
| Zhao et al49 | 116 CLL cells from 2 time points | Whole-genome DNA amplification in individual PCR tubes | sCNA identified and subclonal architecture determined |
| Wang et al50 | 1152 CLL cells from 5 patients | Plate-based targeted multiplex PCR assay following whole-genome amplification | sCNA and sSNV identified and subclonal architecture determined |
| Landau et al58 | 393 CD19+ B cells from 2 healthy donors and 111 CLL cells from 1 patient | Multiplexed scRRBS | Uniformly high proportion of discordant reads in CLL cells compared with normal B cells |
| Chaligne et al59 | 383 CD19+ B cells from 4 healthy donors and 324 CLL cells from 3 patients | Multiplexed scRRBS | Epigenetic phylogenetic tree reconstruction |
| Chaligne et al59 | 42 CLL cells | Multiplexed scRRBS and scRNA sequencing | Increasing phylogenetic distance correlates with decreasing transcriptional similarity |
| Zhao et al49 | 362 CLL cells from 5 time points (35-126 cells per time point) | Plate-based Smart-Seq2 scRNA sequencing | Identification of 6 transcriptional clusters and their evolution over time and with treatment |
| Wang et al50 | 289 CLL cells from 4 patients | Fluidigm C1 System Smart-Seq scRNA sequencing | Using pathway and gene set overdispersion analysis identified unique biological processes demonstrating transcriptional heterogeneity |
| Wang et al44 | 845 CLL cells from 6 patients | Plate-based targeted qPCR using Fluidigm BioMark | Single-cell correlation of alternative splicing variants with SF3B1 mutational status |
| Landau et al13 | 310 CLL cells from 4 patients | Fluidigm C1 System Smart-Seq scRNA sequencing | Correlational of single-cell transcriptional heterogeneity with methylation data |
| Burger et al12 | 473 cells from 3 time points | Plate-based targeted qPCR using Fluidigm BioMark | Mutation detection to determine subclonal architecture |
| Burger et al12 | Polydimethylsiloxane microfluidic device and targeted qPCR | High-sensitivity mutation detection, including demonstration of the presence of rare resistant cells before ibrutinib initiation |
PCR, polymerase chain reaction; qPCR, quantitative PCR; sCNA, somatic copy number alteration; scRNA, single-cell RNA; scRRBS, single-cell reduced representation bisulfite sequencing; sSNV, somatic single nucleotide variant.