ArticleThe Journal of molecular diagnostics : JMD2022
Optimizing Insertion and Deletion Detection Using Next-Generation Sequencing in the Clinical Laboratory.
Article in The Journal of molecular diagnostics : JMD, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 21 citations in OpenAlex.
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- Molecular characterization of gliosarcoma reveals prognostic biomarkers and clinical parallels with glioblastoma.Journal of neuro-oncology · 2025Article
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- Personalized oncology in pheochromocytomas and paragangliomas: integrating genetic analysis with machine learning.Medical oncology (Northwood, London, England) · 2024Article
- Measurable (Minimal) Residual Disease in Myelodysplastic Neoplasms (MDS): Current State and Perspectives.Cancers · 2024Review
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- Screening of genes interacting with high myopia and neuropsychiatric disorders.Scientific reports · 2023Article
- Management and Molecular Characterization of Intraventricular Glioblastoma: A Single-Institution Case Series.International journal of molecular sciences · 2023Article
- Pitfalls in 2HG Detection With TE-Optimized MRS at 3T.Journal of neuroimaging : official journal of the American Society of NeuroimagingArticle
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Detection of insertions and deletions (InDels) by short-read next-generation sequencing (NGS) technology can be challenging because of frequent misaligned reads. A systematic analysis of short InDels (1 to 30 bases) and fms-related receptor tyrosine kinase 3 (FLT3) internal tandem duplications (ITDs; 6 to 183 bases) from 46 clinical cases of solid or hematologic malignancy processed with a clinical NGS assay identified misaligned reads in every case, ranging from 3% to 100% of reads with the InDel showing mismapped bases. Mismaps also increased with InDel size. As a consequence, the clinical NGS bioinformatics pipeline undercalled the variant allele frequency by 1% to 84%, incorrectly called simultaneous single-base substitutions along with InDels, or did not report an FLT3 ITD that had been detected by capillary electrophoresis. To improve the ability of the pipeline to better detect and quantify InDels, we utilized a software program called Assembly-Based ReAligner (ABRA2) to more accurately remap reads. ABRA2 was able to correct 41% to 100% of the reads with mismapped bases and led to absolute increases in the variant allele frequency from 1% to 61% along with correction of all of the single-base substitutions except for two cases. ABRA2 could also detect multiple FLT3 ITD clones except for one 183-base ITD. Our analysis has found that ABRA2 performs well on short InDels as well as FLT3 ITDs that are <100 bases.
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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.