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<p>Prediction of CRISPR/Cas outcomes remains unsatisfactory in embryos due to distinct DNA repair preferences and the lack of large-scale embryo editing profiles. We introduce inDecay, a flexible system for predicting the proportion of CRISPR-induced indels from the target sequence. Owing to its parameter-efficient and cell-type-aware design, inDecay performs well in both in-sample training and out-of-sample fine-tuning. Starting with cross-cell-line predictions, we observed that inDecay maintains high accuracy in mouse zygote editing and in goat, cattle and porcine embryos. inDecay may accelerate mouse model generation, livestock embryonic editing, and gene therapy applications.</p>

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Accurate prediction of CRISPR editing outcomes in somatic cell lines and zygotes with few-shot learning with inDecay

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年7月27日

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  • Weizhong Zheng,
  • Lu Yu,
  • Chao Wu,
  • Shaoxian Cao,
  • Mengying Zhao,
  • Guoliang Wang,
  • Kam Ho So,
  • Jun Song,
  • Chen Cheng,
  • Joshua W. K. Ho,
  • Xueqin Liu,
  • Meng Wu,
  • Zhonghua Liu,
  • Huili Wang,
  • Pentao Liu,
  • Guocheng Lan,
  • Yuanhua Huang

摘要

Prediction of CRISPR/Cas outcomes remains unsatisfactory in embryos due to distinct DNA repair preferences and the lack of large-scale embryo editing profiles. We introduce inDecay, a flexible system for predicting the proportion of CRISPR-induced indels from the target sequence. Owing to its parameter-efficient and cell-type-aware design, inDecay performs well in both in-sample training and out-of-sample fine-tuning. Starting with cross-cell-line predictions, we observed that inDecay maintains high accuracy in mouse zygote editing and in goat, cattle and porcine embryos. inDecay may accelerate mouse model generation, livestock embryonic editing, and gene therapy applications.