ArticleNucleic acids research2015
BreaKmer: detection of structural variation in targeted massively parallel sequencing data using kmers.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 94 papers.
What it found
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Who cites it
94 citing papers in PubMed, 222 citations in OpenAlex.
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- Targeting RAF1 gene fusions with MEK inhibition in metastatic melanoma.The oncologist · 2025Article
- Integrating genetic subtypes with PET scan monitoring to predict outcome in diffuse large B-cell lymphoma.Nature communications · 2025Article
- Molecular profiling of 888 pediatric tumors informs future precision trials and data-sharing initiatives in pediatric cancer.Nature communications · 2024Article
- Article
- MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads.Genome biology · 2023Article
- Ultrafast prediction of somatic structural variations by filtering out reads matched to pan-genome k-mer sets.Nature biomedical engineering · 2023Article
- Development and evaluation of INTFrontiers in oncology · 2023Article
- Clinicopathologic and molecular spectrum of testicular sex cord-stromal tumors not amenable to specific histopathologic subclassification.Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2022Article
- Rare FGFR Oncogenic Alterations in Sequenced Pediatric Solid and Brain Tumors Suggest FGFR Is a Relevant Molecular Target in Childhood Cancer.JCO precision oncology · 2022Article
- Clinical and molecular validation of BAP1, MTAP, P53, and Merlin immunohistochemistry in diagnosis of pleural mesothelioma.Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2022Article
- Genomic and microenvironmental landscape of stage I follicular lymphoma, compared with stage III/IV.Blood advances · 2022Article
- Genomic and biological study of fusion genes as resistance mechanisms to EGFR inhibitors.Nature communications · 2022Article
- Molecular profiling identifies targeted therapy opportunities in pediatric solid cancer.Nature medicine · 2022Observational
- Molecular assessment of testicular adult granulosa cell tumor demonstrates significant differences when compared to ovarian counterparts.Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2022Article
34 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genomic structural variation (SV), a common hallmark of cancer, has important predictive and therapeutic implications. However, accurately detecting SV using high-throughput sequencing data remains challenging, especially for 'targeted' resequencing efforts. This is critically important in the clinical setting where targeted resequencing is frequently being applied to rapidly assess clinically actionable mutations in tumor biopsies in a cost-effective manner. We present BreaKmer, a novel approach that uses a 'kmer' strategy to assemble misaligned sequence reads for predicting insertions, deletions, inversions, tandem duplications and translocations at base-pair resolution in targeted resequencing data. Variants are predicted by realigning an assembled consensus sequence created from sequence reads that were abnormally aligned to the reference genome. Using targeted resequencing data from tumor specimens with orthogonally validated SV, non-tumor samples and whole-genome sequencing data, BreaKmer had a 97.4% overall sensitivity for known events and predicted 17 positively validated, novel variants. Relative to four publically available algorithms, BreaKmer detected SV with increased sensitivity and limited calls in non-tumor samples, key features for variant analysis of tumor specimens in both the clinical and research settings.
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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.