ReviewFrontiers in bioengineering and biotechnology2015
The challenge of small-scale repeats for indel discovery.
Review in Frontiers in bioengineering and biotechnology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers, 1 of them a synthesis that pooled it.
What it found
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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
37 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Disparities in ABO blood type determination across diverse ancestries: a systematic review and validation in the All of Us Research Program.Journal of the American Medical Informatics Association : JAMIA · 2024Pooled it
- Lancet2: Improved and accelerated somatic variant calling with joint multi-sample local assembly graphs.NAR genomics and bioinformatics · 2026Article
- fRagmentomics: an R package for integrating cell-free DNA fragment features with mutational status to support liquid biopsy interpretation.Bioinformatics (Oxford, England) · 2026Article
- Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit.Genome research · 2026Article
- Evaluating the Genetic Overlap Between Congenital Heart Disease and Neuroblastoma Risk.Pediatric blood & cancer · 2026Article
- Impacts of ribosomal RNA sequence variation on gene expression and phenotype.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Towards accurate indel calling for oncopanel sequencing through an international pipeline competition at precisionFDA.Scientific reports · 2024Article
- The alleles bc-uThe plant genome · 2024Article
- Repetitive DNA sequence detection and its role in the human genome.Communications biology · 2023Review
- Optimizing Insertion and Deletion Detection Using Next-Generation Sequencing in the Clinical Laboratory.The Journal of molecular diagnostics : JMD · 2022Article
- Evaluation of Genetic Kidney Diseases in Living Donor Kidney Transplantation: Towards Precision Genomic Medicine in Donor Risk Assessment.Current transplantation reports · 2022Article
- PNA microprobe for label-free detection of expanded trinucleotide repeats.RSC advances · 2022Article
- Data-driven design of targeted gene panels for estimating immunotherapy biomarkers.Communications biology · 2022Article
- Reversible gene silencing through frameshift indels and frameshift scars provide adaptive plasticity for Mycobacterium tuberculosis.Nature communications · 2021Article
- Reliability of genomic variants across different next-generation sequencing platforms and bioinformatic processing pipelines.BMC genomics · 2021Observational
- An Evolutionary Perspective on the Impact of Genomic Copy Number Variation on Human Health.Journal of molecular evolution · 2020Review
- Novel probes for label-free detection of neurodegenerative GGGGCC repeats associated with amyotrophic lateral sclerosis.Analytical and bioanalytical chemistry · 2019Article
- Article
- Complete nucleotide sequence characterization of DRB5 alleles reveals a homogeneous allele group that is distinct from other DRB genes.Human immunology · 2019Article
- Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome.PLoS computational biology · 2019Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Repetitive sequences are abundant in the human genome. Different classes of repetitive DNA sequences, including simple repeats, tandem repeats, segmental duplications, interspersed repeats, and other elements, collectively span more than 50% of the genome. Because repeat sequences occur in the genome at different scales they can cause various types of sequence analysis errors, including in alignment, de novo assembly, and annotation, among others. This mini-review highlights the challenges introduced by small-scale repeat sequences, especially near-identical tandem or closely located repeats and short tandem repeats, for discovering DNA insertion and deletion (indel) mutations from next-generation sequencing data. We also discuss the de Bruijn graph sequence assembly paradigm that is emerging as the most popular and promising approach for detecting indels. The human exome is taken as an example and highlights how these repetitive elements can obscure or introduce errors while detecting these types of mutations.
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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.