ArticleNature communications2022
Phasing analysis of lung cancer genomes using a long read sequencer.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Novel driver gene MDC1 confers homologous recombination repair deficiency and genomic instability in chemoresistant relapsing ovarian cancer.Journal of translational medicine · 2026Article
- Critical assessment of intratumor and low-biomass microbiome using long-read sequencing.bioRxiv : the preprint server for biology · 2026Article
- Advances in haplotype phasing and genotype imputation.Nature reviews. Genetics · 2026Review
- Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing.Nature biotechnology · 2026Article
- Targeted long-read methylation analysis using hybridization capture suitable for clinical specimens.Cell reports methods · 2025Article
- Mechanism of parent-of-origin effects revealed by multi-omic data in euro-chinese hybrid pigs.Nature communications · 2025Article
- Enhanced identification of novel pathogenic variants in hereditary hearing loss through physical phasing with integrated short and long-read sequencing data.Molecular genetics and genomics : MGG · 2025Article
- Parental Phasing Study Identified Lineage-Specific Variants Associated with Gene Expression and Epigenetic Modifications in European-Chinese Hybrid Pigs.Animals : an open access journal from MDPI · 2025Article
- RNA splicing: Novel star in pulmonary diseases with a treatment perspective.Acta pharmaceutica Sinica. B · 2025Review
- Review
- Unraveling the hidden complexity of cancer through long-read sequencing.Genome research · 2025Review
- Long-read whole-genome sequencing-based concurrent haplotyping and aneuploidy profiling of single cells.Nucleic acids research · 2025Article
- Multi-omics analyses reveal biological and clinical insights in recurrent stage I non-small cell lung cancer.Nature communications · 2025Article
- MalKinID: A classification model for identifying malaria parasite genealogical relationships using identity-by-descent.Genetics · 2025Article
- MalKinID: A Likelihood-Based Model for Identifying Malaria Parasite Genealogical Relationships Using Identity-by-Descent.bioRxiv : the preprint server for biology · 2024Article
- Late-Onset Ataxia-Telangiectasia Presenting With Dystonia and Tremor: The Use of Nanopore Long-Read Sequencing Solving the Variant Phase.Neurology. Genetics · 2024Article
- 3C methods in cancer research: recent advances and future prospects.Experimental & molecular medicine · 2024Review
- The Application of Long-Read Sequencing to Cancer.Cancers · 2024Review
- Scrambling the genome in cancer: causes and consequences of complex chromosome rearrangements.Nature reviews. Genetics · 2024Review
- Whole-genome sequencing reveals the molecular implications of the stepwise progression of lung adenocarcinoma.Nature communications · 2023Article
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chromosomal backgrounds of cancerous mutations still remain elusive. Here, we conduct the phasing analysis of non-small cell lung cancer specimens of 20 Japanese patients. By the combinatory use of short and long read sequencing data, we obtain long phased blocks of 834 kb in N50 length with >99% concordance rate. By analyzing the obtained phasing information, we reveal that several cancer genomes harbor regions in which mutations are unevenly distributed to either of two haplotypes. Large-scale chromosomal rearrangement events, which resemble chromothripsis events but have smaller scales, occur on only one chromosome, and these events account for the observed biased distributions. Interestingly, the events are characteristic of EGFR mutation-positive lung adenocarcinomas. Further integration of long read epigenomic and transcriptomic data reveal that haploid chromosomes are not always at equivalent transcriptomic/epigenomic conditions. Distinct chromosomal backgrounds are responsible for later cancerous aberrations in a haplotype-specific manner.
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