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<p>Long-read single-cell RNA sequencing enables simultaneous and unbiased detection of transcriptomic variants and gene expression, but its application is limited by low read coverage, restricting genotype-phenotype analyses at single-cell resolution. We systematically evaluate short-read whole-transcriptome amplification (SR-WTA), long-read whole-transcriptome amplification (LR-WTA), and long-read targeted sequencing (LR-Twist). Based on these comparisons, we develop a hybrid strategy combining SR-WTA and LR-Twist within a Snakemake pipeline to leverage the strengths of both approaches. SR-WTA provides broad transcriptome coverage, while LR-Twist enriches a 50-gene panel for deeper variant detection. This approach improves the power to link mutational profiles with transcriptional programs at single-cell resolution.</p>

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Hybrid untargeted short-read and targeted long-read RNA sequencing facilitates genotype-phenotype associations at single-cell resolution

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年6月1日

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  • Jiayi Wang,
  • Maria Constanza Maldifassi,
  • Anna Bratus-Neuenschwander,
  • Qin Zhang,
  • Felix Beuschlein,
  • David Penton,
  • Mark D. Robinson

摘要

Long-read single-cell RNA sequencing enables simultaneous and unbiased detection of transcriptomic variants and gene expression, but its application is limited by low read coverage, restricting genotype-phenotype analyses at single-cell resolution. We systematically evaluate short-read whole-transcriptome amplification (SR-WTA), long-read whole-transcriptome amplification (LR-WTA), and long-read targeted sequencing (LR-Twist). Based on these comparisons, we develop a hybrid strategy combining SR-WTA and LR-Twist within a Snakemake pipeline to leverage the strengths of both approaches. SR-WTA provides broad transcriptome coverage, while LR-Twist enriches a 50-gene panel for deeper variant detection. This approach improves the power to link mutational profiles with transcriptional programs at single-cell resolution.