ArticleGenome research2015
Read clouds uncover variation in complex regions of the human genome.
Article in Genome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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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.
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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
43 citing papers in PubMed.
- Genetic Landscape of Opsoclonus-Myoclonus-Ataxia Syndrome in Children.Pediatric neurology · 2025Article
- A haplotype-resolved chromatin landscape connects cis-regulatory variants to trait variation in Citrus.BMC genomics · 2025Article
- Genome sequence of a marine threespine stickleback (Gasterosteus aculeatus) from Rabbit Slough in the Cook Inlet.G3 (Bethesda, Md.) · 2025Article
- Hybridization of Atlantic puffins in the Arctic coincides with 20th-century climate change.Science advances · 2023Article
- Co-evolution ofNAR cancer · 2023Article
- Genome graphs detect human polymorphisms in active epigenomic state during influenza infection.Cell genomics · 2023Article
- Caecilian Genomes Reveal the Molecular Basis of Adaptation and Convergent Evolution of Limblessness in Snakes and Caecilians.Molecular biology and evolution · 2023Article
- FarGen: Elucidating the distribution of coding variants in the isolated population of the Faroe Islands.European journal of human genetics : EJHG · 2023Article
- MetaTrass: A high-quality metagenome assembler of the human gut microbiome by cobarcoding sequencing reads.iMeta · 2022Article
- A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta).GigaScience · 2022Article
- Fourth Report on Chicken Genes and Chromosomes 2022.Cytogenetic and genome research · 2022Review
- A pan-cancer landscape of somatic mutations in non-unique regions of the human genome.Nature biotechnology · 2021Article
- Whole genome and exome sequencing reference datasets from a multi-center and cross-platform benchmark study.Scientific data · 2021Article
- Perspectives and Benefits of High-Throughput Long-Read Sequencing in Microbial Ecology.Applied and environmental microbiology · 2021Review
- Accurate haplotype-resolved assembly reveals the origin of structural variants for human trios.Bioinformatics (Oxford, England) · 2021Article
- ARBitR: an overlap-aware genome assembly scaffolder for linked reads.Bioinformatics (Oxford, England) · 2021Article
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- SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme.BMC bioinformatics · 2021Article
- Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale.Genome medicine · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
Although an increasing amount of human genetic variation is being identified and recorded, determining variants within repeated sequences of the human genome remains a challenge. Most population and genome-wide association studies have therefore been unable to consider variation in these regions. Core to the problem is the lack of a sequencing technology that produces reads with sufficient length and accuracy to enable unique mapping. Here, we present a novel methodology of using read clouds, obtained by accurate short-read sequencing of DNA derived from long fragment libraries, to confidently align short reads within repeat regions and enable accurate variant discovery. Our novel algorithm, Random Field Aligner (RFA), captures the relationships among the short reads governed by the long read process via a Markov Random Field. We utilized a modified version of the Illumina TruSeq synthetic long-read protocol, which yielded shallow-sequenced read clouds. We test RFA through extensive simulations and apply it to discover variants on the NA12878 human sample, for which shallow TruSeq read cloud sequencing data are available, and on an invasive breast carcinoma genome that we sequenced using the same method. We demonstrate that RFA facilitates accurate recovery of variation in 155 Mb of the human genome, including 94% of 67 Mb of segmental duplication sequence and 96% of 11 Mb of transcribed sequence, that are currently hidden from short-read technologies.
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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.