CHILD: A new tool for detecting low-abundance insertions and deletions in standard sequence traces

National Institute for Biotechnology in the Negev, Beer Sheva 84105, Israel.
Nucleic Acids Research (Impact Factor: 9.11). 04/2011; 39(7):e47. DOI: 10.1093/nar/gkq1354
Source: PubMed


Several methods have been proposed for detecting insertion/deletions (indels) from chromatograms generated by Sanger sequencing. However, most such methods are unsuitable when the mutated and normal variants occur at unequal ratios, such as is expected to be the case in cancer, with organellar DNA or with alternatively spliced RNAs. In addition, the current methods do not provide robust estimates of the statistical confidence of their results, and the sensitivity of this approach has not been rigorously evaluated. Here, we present CHILD, a tool specifically designed for indel detection in mixtures where one variant is rare. CHILD makes use of standard sequence alignment statistics to evaluate the significance of the results. The sensitivity of CHILD was tested by sequencing controlled mixtures of deleted and undeleted plasmids at various ratios. Our results indicate that CHILD can identify deleted molecules present as just 5% of the mixture. Notably, the results were plasmid/primer-specific; for some primers and/or plasmids, the deleted molecule was only detected when it comprised 10% or more of the mixture. The false positive rate was estimated to be lower than 0.4%. CHILD was implemented as a user-oriented web site, providing a sensitive and experimentally validated method for the detection of rare indel-carrying molecules in common Sanger sequence reads.


Available from: Eitan Rubin
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    • "Sanger sequencing can become expensive when many clones need to be screened. Moreover standard Sanger sequencing data can be difficult to interpret because indel mutations cause chromatogram phase shifts, so that it can be difficult to distinguish homozygous and heterozygous mutants [16]. We showed that dual gRNAs do not reduce (and may marginally enhance) targeting efficiency and simplify genotyping by causing more extensive deletions that are easily detected by PCR genotyping. "
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    • "In the Indelligent algorithm, dynamic programming is used to convert the IUPAC code into two nucleotides (i.e., M is converted into A/C, W into A/T, Y into C/T, K into G/T, and S into G/C) [9] [10]. For ambiguous bases that cannot be decomposed with Indelligent, major and minor sequences are assigned according to the intensities of the corresponding fluorescence signals (Figure 1 "
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    Biodiversity, 10/2011; , ISBN: 978-953-307-715-4
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