ArticleScientific reports2018
IMSindel: An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 14 papers.
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14 citing papers in PubMed, 28 citations in OpenAlex.
- Targeted long-read sequencing enables higher diagnostic yield of ADPKD by accurate PKD1 genetic analysis.NPJ genomic medicine · 2025Article
- Identification of a large intra-exonic deletion inTherapeutic advances in medical oncology · 2023Article
- Optimizing Insertion and Deletion Detection Using Next-Generation Sequencing in the Clinical Laboratory.The Journal of molecular diagnostics : JMD · 2022Article
- Plant pathogenic bacterium can rapidly evolve tolerance to an antimicrobial plant allelochemical.Evolutionary applications · 2022Article
- Whole exome analysis of patients in Japan with hearing loss reveals high heterogeneity among responsible and novel candidate genes.Orphanet journal of rare diseases · 2022Article
- svBreak: A New Approach for the Detection of Structural Variant Breakpoints Based on Convolutional Neural Network.BioMed research international · 2022Article
- Characterization of intermediate-sized insertions using whole-genome sequencing data and analysis of their functional impact on gene expression.Human genetics · 2021Article
- Detection of homozygous and hemizygous complete or partial exon deletions by whole-exome sequencing.NAR genomics and bioinformatics · 2021Article
- Article
- Identification of the novel COL5A1 c.3369_3431dup, p.(Glu1124_Gly1144dup) variant in a patient with incomplete classical Ehlers-Danlos syndrome: The importance of phenotype-guided genetic testing.Molecular genetics & genomic medicine · 2020Article
- Common homozygosity for predicted loss-of-function variants reveals both redundant and advantageous effects of dispensable human genes.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Identification of intermediate-sized deletions and inference of their impact on gene expression in a human population.Genome medicine · 2019Article
- Constructing High-Density Genetic Maps and Developing Sexing Markers in Northern Snakehead (Channa argus).Marine biotechnology (New York, N.Y.) · 2019Article
- Exploration of intermediate-sized INDELs by next-generation multigene panel testing in Han Chinese patients with breast cancer.Human genome variation · 2019Article
Corrections and comments
- Erratum issued
Authors and funding
18 authors at 12 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Insertions and deletions (indels) have been implicated in dozens of human diseases through the radical alteration of gene function by short frameshift indels as well as long indels. However, the accurate detection of these indels from next-generation sequencing data is still challenging. This is particularly true for intermediate-size indels (≥50 bp), due to the short DNA sequencing reads. Here, we developed a new method that predicts intermediate-size indels using BWA soft-clipped fragments (unmatched fragments in partially mapped reads) and unmapped reads. We report the performance comparison of our method, GATK, PINDEL and ScanIndel, using whole exome sequencing data from the same samples. False positive and false negative counts were determined through Sanger sequencing of all predicted indels across these four methods. The harmonic mean of the recall and precision, F-measure, was used to measure the performance of each method. Our method achieved the highest F-measure of 0.84 in one sample, compared to 0.56 for GATK, 0.52 for PINDEL and 0.46 for ScanIndel. Similar results were obtained in additional samples, demonstrating that our method was superior to the other methods for detecting intermediate-size indels. We believe that this methodology will contribute to the discovery of intermediate-size indels associated with human disease.
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