ArticleDevelopmental dynamics : an official publication of the American Association of Anatomists2014
Poly peak parser: Method and software for identification of unknown indels using sanger sequencing of polymerase chain reaction products.
Article in Developmental dynamics : an official publication of the American Association of Anatomists, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 152 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
152 citing papers in PubMed.
- Prevalence of five treatable sexually transmitted infections among women in Lower River region of The Gambia.BMC infectious diseases · 2023Trial
- Global pelagic dispersal traits datasets for early-life stages of marine fishes.Scientific data · 2026Article
- Axonal defasciculation is restricted to specific branching points during regeneration of the lateral line nerve in zebrafish.Development (Cambridge, England) · 2026Article
- The Asymmetric Threat of Maternal Cell Contamination in Prenatal Single-Gene Testing.Diagnostics (Basel, Switzerland) · 2026Article
- Article
- FACS-based dual fluorescence reporter assay demonstrates efficacy of antisense oligonucleotide therapy of novelMolecular therapy. Nucleic acids · 2026Article
- Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning.Nature communications · 2026Article
- Higher Genetic Diversity Across Several Small Patches Compared to a Single Large Patch: A Within-Species Test of SLOSS.Evolutionary applications · 2026Article
- TCF4 at the crest of development: a zebrafish model to explore craniofacial and gastrointestinal defects in Pitt-Hopkins syndrome.Frontiers in cell and developmental biology · 2026Article
- Characterization and Phenotypic Assessment of Zebrafish Disease Models for Splice Modulation Studies.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A Novel Supergene Controls Queen Size and Colony Social Organization in the Ant Myrmica ruginodis.Molecular biology and evolution · 2025Article
- SAGPEK: fast and flexible approach to identify genotypes of Sanger sequencing data.BMC bioinformatics · 2025Article
- Article
- Distinct cellular and reproductive consequences of meiotic chromosome synapsis defects in syce2 and sycp1 mutant zebrafish.PLoS genetics · 2025Article
- C to U RNA editing of MFN1 is regulated by ADARB1 and associates with favourable prognosis in chronic lymphocytic leukemia.Scientific reports · 2025Article
- Axonal defasciculation is restricted to specific branching points during regeneration of the lateral line nerve in zebrafish.bioRxiv : the preprint server for biology · 2025Article
- Genetic variation reveals a homeotic long noncoding RNA that modulates human hematopoietic stem cells.bioRxiv : the preprint server for biology · 2025Article
- Engineering precision zebrafish alleles of human disease.bioRxiv : the preprint server for biology · 2025Article
- NovelAntimicrobial agents and chemotherapy · 2025Article
- PtWAVE: a high-sensitive deconvolution software of sequencing trace for the detection of large indels in genome editing.BMC bioinformatics · 2025Article
92 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
backgroundGenome editing techniques, including ZFN, TALEN, and CRISPR, have created a need to rapidly screen many F1 individuals to identify carriers of indels and determine the sequences of the mutations. Current techniques require multiple clones of the targeted region to be sequenced for each individual, which is inefficient when many individuals must be analyzed. Direct Sanger sequencing of a polymerase chain reaction (PCR) amplified region surrounding the target site is efficient, but Sanger sequencing genomes heterozygous for an indel results in a string of "double peaks" due to the mismatched region.
resultsTo facilitate indel identification, we developed an online tool called Poly Peak Parser (available at http://yost.genetics.utah.edu/software.php) that is able to separate chromatogram data containing ambiguous base calls into wild-type and mutant allele sequences. This tool allows the nature of the indel to be determined from a single sequencing run per individual performed directly on a PCR product spanning the targeted site, without cloning.
conclusionsThe method and algorithm described here facilitate rapid identification and sequence characterization of heterozygous mutant carriers generated by genome editing. Although designed for screening F1 individuals, this tool can also be used to identify heterozygous indels in many contexts.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.