ArticleNucleic acids research2014
Long insert whole genome sequencing for copy number variant and translocation detection.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Genomic Staging of Multifocal Lung Squamous Cell Carcinomas Is Independent of the Comprehensive Morphologic Assessment.Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer · 2024Article
- Single-cell sequencing of genomic DNA resolves sub-clonal heterogeneity in a melanoma cell line.Communications biology · 2020Article
- Article
- Identification of therapeutic targets in chordoma through comprehensive genomic and transcriptomic analyses.Cold Spring Harbor molecular case studies · 2018Article
- Somatic inactivating PTPRJ mutations and dysregulated pathways identified in canine malignant melanoma by integrated comparative genomic analysis.PLoS genetics · 2018Article
- Prospective Feasibility Trial for Genomics-Informed Treatment in Recurrent and Progressive Glioblastoma.Clinical cancer research : an official journal of the American Association for Cancer Research · 2018Article
- Cat-D: a targeted sequencing method for the simultaneous detection of small DNA mutations and large DNA deletions with flexible boundaries.Scientific reports · 2017Article
- Integrated genomic analyses reveal frequentGenome research · 2017Article
- Case report: whole exome sequencing of primary cardiac angiosarcoma highlights potential for targeted therapies.BMC cancer · 2017Article
- Clinical Implementation of Integrated Genomic Profiling in Patients with Advanced Cancers.Scientific reports · 2016Article
- A somatic reference standard for cancer genome sequencing.Scientific reports · 2016Article
- Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals.Nature communications · 2015Article
- Evidence Suggesting That Discontinuous Dosing of ALK Kinase Inhibitors May Prolong Control of ALK+ Tumors.Cancer research · 2015Article
- Non-random DNA fragmentation in next-generation sequencing.Scientific reports · 2014Article
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Authors and funding
11 authors.
Funding
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Abstract
As next-generation sequencing continues to have an expanding presence in the clinic, the identification of the most cost-effective and robust strategy for identifying copy number changes and translocations in tumor genomes is needed. We hypothesized that performing shallow whole genome sequencing (WGS) of 900-1000-bp inserts (long insert WGS, LI-WGS) improves our ability to detect these events, compared with shallow WGS of 300-400-bp inserts. A priori analyses show that LI-WGS requires less sequencing compared with short insert WGS to achieve a target physical coverage, and that LI-WGS requires less sequence coverage to detect a heterozygous event with a power of 0.99. We thus developed an LI-WGS library preparation protocol based off of Illumina's WGS library preparation protocol and illustrate the feasibility of performing LI-WGS. We additionally applied LI-WGS to three separate tumor/normal DNA pairs collected from patients diagnosed with different cancers to demonstrate our application of LI-WGS on actual patient samples for identification of somatic copy number alterations and translocations. With the evolution of sequencing technologies and bioinformatics analyses, we show that modifications to current approaches may improve our ability to interrogate cancer genomes.
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