ArticleBioinformatics (Oxford, England)2018
Identifying structural variants using linked-read sequencing data.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed.
- Resolving the Haplotype Complexity of Colorectal Cancer Genomes with Droplet Barcode Sequencing.Life (Basel, Switzerland) · 2026Article
- The additional diagnostic yield of long-read sequencing in undiagnosed rare diseases.Genome research · 2025Review
- The known structural variations in hearing loss and their diagnostic approaches: a comprehensive review.Molecular biology reports · 2025Review
- Blackbird: structural variant detection using synthetic and low-coverage long-reads.Bioinformatics advances · 2025Article
- Harpy: a pipeline for processing haplotagging linked-read data.Bioinformatics advances · 2025Article
- The Bioinformatic Applications of Hi-C and Linked Reads.Genomics, proteomics & bioinformatics · 2024Review
- Somatic mutation phasing and haplotype extension using linked-reads in multiple myeloma.bioRxiv : the preprint server for biology · 2024Article
- Improved assembly of the Pungitius pungitius reference genome.G3 (Bethesda, Md.) · 2024Article
- Transposable Element Insertions Are Associated with Batesian Mimicry in the Pantropical Butterfly Hypolimnas misippus.Molecular biology and evolution · 2024Article
- BLR: a flexible pipeline for haplotype analysis of multiple linked-read technologies.Nucleic acids research · 2023Article
- Most large structural variants in cancer genomes can be detected without long reads.Nature genetics · 2023Article
- Co-evolution ofNAR cancer · 2023Article
- Review
- Linked-read based analysis of the medulloblastoma genome.Frontiers in oncology · 2023Article
- Detection and genomic analysis of BRAF fusions in Juvenile Pilocytic Astrocytoma through the combination and integration of multi-omic data.BMC cancer · 2022Article
- Efficient detection and assembly of non-reference DNA sequences with synthetic long reads.Nucleic acids research · 2022Article
- Structural variants in the barley gene pool: precision and sensitivity to detect them using short-read sequencing and their association with gene expression and phenotypic variation.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Multi-Omic Investigations of a 17-19 Translocation LinksInternational journal of molecular sciences · 2022Article
- inGAP-family: Accurate Detection of Meiotic Recombination Loci and Causal Mutations by Filtering Out Artificial Variants due to Genome Complexities.Genomics, proteomics & bioinformatics · 2022Article
- Progress in Methods for Copy Number Variation Profiling.International journal of molecular sciences · 2022Review
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
motivationStructural variation, including large deletions, duplications, inversions, translocations and other rearrangements, is common in human and cancer genomes. A number of methods have been developed to identify structural variants from Illumina short-read sequencing data. However, reliable identification of structural variants remains challenging because many variants have breakpoints in repetitive regions of the genome and thus are difficult to identify with short reads. The recently developed linked-read sequencing technology from 10X Genomics combines a novel barcoding strategy with Illumina sequencing. This technology labels all reads that originate from a small number (∼5 to 10) DNA molecules ∼50 Kbp in length with the same molecular barcode. These barcoded reads contain long-range sequence information that is advantageous for identification of structural variants.
resultsWe present Novel Adjacency Identification with Barcoded Reads (NAIBR), an algorithm to identify structural variants in linked-read sequencing data. NAIBR predicts novel adjacencies in an individual genome resulting from structural variants using a probabilistic model that combines multiple signals in barcoded reads. We show that NAIBR outperforms several existing methods for structural variant identification-including two recent methods that also analyze linked-reads-on simulated sequencing data and 10X whole-genome sequencing data from the NA12878 human genome and the HCC1954 breast cancer cell line. Several of the novel somatic structural variants identified in HCC1954 overlap known cancer genes. AVAILABILITY AND IMPLEMENTATION: Software is available at compbio.cs.brown.edu/software. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.