Decoding Sanger Sequencing Chromatograms from CRISPR-Induced Mutations

  • Xianrong Xie
  • Xingliang Ma
  • Yao-Guang LiuEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1917)


In many diploid organisms, the majority mutations induced by clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genome editing are non- chimeric, including biallelic, homozygous, and heterozygous mutations. Direct Sanger sequencing of the PCR amplicons containing non-homozygous mutations superimposes sequencing chromatograms, displaying overlapping peaks beginning from the mutation sites. In this chapter we describe the degenerate sequence decoding (DSD) strategy and its automatic web-based tool, DSDecodeM, for decoding the Sanger sequencing chromatograms from different types of targeted mutations. DSDecodeM, as a convenient and versatile tool, can considerably facilitate the genotyping work of CRISPR-induced mutants.

Key words

CRISPR Genome editing Sanger sequencing Superimposed chromatogram Decoding DSD DSDecodeM 



This work is supported by grants from Guangdong Province Public Interest Research and Capacity Building Special Fund (2015B020201002) and the Ministry of Agriculture of the People’s Republic of China (2016ZX08010-001, 2016ZX08009-002) and the Postdoctoral Science Foundation of China (2016 M602480).


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.College of Life SciencesSouth China Agricultural UniversityGuangzhouChina

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