ArticleGenome medicine2017
Linked read sequencing resolves complex genomic rearrangements in gastric cancer metastases.
Article in Genome medicine, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers, 1 of them a synthesis that pooled it.
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Who cites it
39 citing papers in PubMed, 1 synthesis or guideline pooled it, 67 citations in OpenAlex.
- Mitochondrial DNA (mtDNA) as fluid biomarker in neurodegenerative disorders: A systematic review.European journal of neurology · 2025Pooled it
- Clinical response to FGFR inhibitors in patients with FGFR2-amplified advanced gastric cancer: two case reports.Frontiers in oncology · 2026Article
- Somatic mutation phasing and haplotype extension using linked-reads in multiple myeloma.bioRxiv : the preprint server for biology · 2024Article
- Neotelomeres and telomere-spanning chromosomal arm fusions in cancer genomes revealed by long-read sequencing.Cell genomics · 2024Article
- Circulating Tumor DNA Enables Sensitive Detection of Actionable Gene Fusions and Rearrangements Across Cancer Types.Clinical cancer research : an official journal of the American Association for Cancer Research · 2024Article
- LRTK: a platform agnostic toolkit for linked-read analysis of both human genome and metagenome.GigaScience · 2024Article
- Neotelomeres and Telomere-Spanning Chromosomal Arm Fusions in Cancer Genomes Revealed by Long-Read Sequencing.bioRxiv : the preprint server for biology · 2023Article
- Nanopore long-read next-generation sequencing for detection of mitochondrial DNA large-scale deletions.Frontiers in genetics · 2023Article
- Linked-read based analysis of the medulloblastoma genome.Frontiers in oncology · 2023Article
- From Samples to Germline and Somatic Sequence Variation: A Focus on Next-Generation Sequencing in Melanoma Research.Life (Basel, Switzerland) · 2022Review
- Efficient detection and assembly of non-reference DNA sequences with synthetic long reads.Nucleic acids research · 2022Article
- Linked-read whole-genome sequencing resolves common and private structural variants in multiple myeloma.Blood advances · 2022Article
- A multi-platform reference for somatic structural variation detection.Cell genomics · 2022Article
- Mako: A Graph-based Pattern Growth Approach to Detect Complex Structural Variants.Genomics, proteomics & bioinformatics · 2022Article
- Integrative single-cell analysis of allele-specific copy number alterations and chromatin accessibility in cancer.Nature biotechnology · 2021Article
- Comparison of Structural and Short Variants Detected by Linked-Read and Whole-Exome Sequencing in Multiple Myeloma.Cancers · 2021Article
- Application of long-read sequencing to the detection of structural variants in human cancer genomes.Computational and structural biotechnology journal · 2021Review
- Integrative analysis of structural variations using short-reads and linked-reads yields highly specific and sensitive predictions.PLoS computational biology · 2020Article
- An integrated Asian human SNV and indel benchmark established using multiple sequencing methods.Scientific reports · 2020Article
- Genome sequencing in cytogenetics: Comparison of short-read and linked-read approaches for germline structural variant detection and characterization.Molecular genetics & genomic medicine · 2020Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundGenome rearrangements are critical oncogenic driver events in many malignancies. However, the identification and resolution of the structure of cancer genomic rearrangements remain challenging even with whole genome sequencing.
methodsTo identify oncogenic genomic rearrangements and resolve their structure, we analyzed linked read sequencing. This approach relies on a microfluidic droplet technology to produce libraries derived from single, high molecular weight DNA molecules, 50 kb in size or greater. After sequencing, the barcoded sequence reads provide long range genomic information, identify individual high molecular weight DNA molecules, determine the haplotype context of genetic variants that occur across contiguous megabase-length segments of the genome and delineate the structure of complex rearrangements. We applied linked read sequencing of whole genomes to the analysis of a set of synchronous metastatic diffuse gastric cancers that occurred in the same individual.
resultsWhen comparing metastatic sites, our analysis implicated a complex somatic rearrangement that was present in the metastatic tumor. The oncogenic event associated with the identified complex rearrangement resulted in an amplification of the known cancer driver gene FGFR2. With further investigation using these linked read data, the FGFR2 copy number alteration was determined to be a deletion-inversion motif that underwent tandem duplication, with unique breakpoints in each metastasis. Using a three-dimensional organoid tissue model, we functionally validated the metastatic potential of an FGFR2 amplification in gastric cancer.
conclusionsOur study demonstrates that linked read sequencing is useful in characterizing oncogenic rearrangements in cancer metastasis.
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