ArticleNucleic acids research2015
Utilizing mapping targets of sequences underrepresented in the reference assembly to reduce false positive alignments.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
28 citing papers in PubMed, 1 synthesis or guideline pooled it, 36 citations in OpenAlex.
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- Beyond blacklists: a critical assessment of exclusion set generation strategies and alternative approaches.Bioinformatics (Oxford, England) · 2026Article
- Beyond Blacklists: A Critical Assessment of Exclusion Set Generation Strategies and Alternative Approaches.bioRxiv : the preprint server for biology · 2025Article
- excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies.Bioinformatics (Oxford, England) · 2023Article
- GFI1-Dependent Repression ofCancers · 2022Article
- Variation and Evolution of Human Centromeres: A Field Guide and Perspective.Annual review of genetics · 2021Review
- µ-Crystallin: A thyroid hormone binding protein.Endocrine regulations · 2021Review
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- Precise Identification of Recurrent Somatic Mutations in Oral Cancer Through Whole-Exome Sequencing Using Multiple Mutation Calling Pipelines.Frontiers in oncology · 2021Article
- Systematic microsatellite repeat expansion cloning and validation.Human genetics · 2020Article
- Centromere studies in the era of 'telomere-to-telomere' genomics.Experimental cell research · 2020Review
- Mechanisms generating cancer genome complexity from a single cell division error.Science (New York, N.Y.) · 2020Article
- Computational Analysis Concerning the Impact of DNA Accessibility on CRISPR-Cas9 Cleavage Efficiency.Molecular therapy : the journal of the American Society of Gene Therapy · 2020Article
- Human contamination in bacterial genomes has created thousands of spurious proteins.Genome research · 2019Article
- Review
- Construction of JRG (Japanese reference genome) with single-molecule real-time sequencing.Human genome variation · 2019Article
- Heterochromatin-Encoded Satellite RNAs Induce Breast Cancer.Molecular cell · 2018Article
- High-depth whole genome sequencing of an Ashkenazi Jewish reference panel: enhancing sensitivity, accuracy, and imputation.Human genetics · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The human reference assembly remains incomplete due to the underrepresentation of repeat-rich sequences that are found within centromeric regions and acrocentric short arms. Although these sequences are marginally represented in the assembly, they are often fully represented in whole-genome short-read datasets and contribute to inappropriate alignments and high read-depth signals that localize to a small number of assembled homologous regions. As a consequence, these regions often provide artifactual peak calls that confound hypothesis testing and large-scale genomic studies. To address this problem, we have constructed mapping targets that represent roughly 8% of the human genome generally omitted from the human reference assembly. By integrating these data into standard mapping and peak-calling pipelines we demonstrate a 10-fold reduction in signals in regions common to the blacklisted region and identify a comprehensive set of regions that exhibit mapping sensitivity with the presence of the repeat-rich targets.
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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.