ArticleGenes, chromosomes & cancer2018
Copy number variant analysis using genome-wide mate-pair sequencing.
Article in Genes, chromosomes & cancer, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
31 citing papers in PubMed.
- Functional impact of the hyperduplication genomophenotype in high copy number endometrial cancer.iScience · 2025Article
- Tumor ploidy determination in low-pass whole genome sequencing and allelic copy number visualization using the Constellation Plot.Genome biology · 2025Article
- Article
- Constitutional Chromothripsis on Chromosome 2: A Rare Case with Severe Presentation.Case reports in genetics · 2024Article
- Mate Pair Sequencing: Next-Generation Sequencing for Structural Variant Detection.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Optimization of the "Ecology and evolution · 2023Article
- Characterization of unusual iAMP21 B-lymphoblastic leukemia (iAMP21-ALL) from the Mayo Clinic and Children's Oncology Group.Genes, chromosomes & cancer · 2022Article
- Analysis of autosomal dominant genes impacted by copy number loss in 24,844 fetuses without structural abnormalities.BMC genomics · 2022Article
- Patient-Specific Assays Based on Whole-Genome Sequencing Data to Measure Residual Disease in Children With Acute Lymphoblastic Leukemia: A Proof of Concept Study.Frontiers in oncology · 2022Article
- The Prognostic Role of MYC Structural Variants Identified by NGS and FISH in Multiple Myeloma.Clinical cancer research : an official journal of the American Association for Cancer Research · 2021Article
- Increased complexity of t(11;14) rearrangements in plasma cell neoplasms compared with mantle cell lymphoma.Genes, chromosomes & cancer · 2021Article
- Next-generation sequencing for constitutional variants in the clinical laboratory, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG).Genetics in medicine : official journal of the American College of Medical Genetics · 2021Article
- Detection of a mosaic CDKL5 deletion and inversion by optical genome mapping ends an exhaustive diagnostic odyssey.Molecular genetics & genomic medicine · 2021Article
- Theragnostic chromosomal rearrangements in treatment-naive pancreatic ductal adenocarcinomas obtained via endoscopic ultrasound.Journal of cellular and molecular medicine · 2021Article
- Prenatal characterization of a novel invertedClinical case reports · 2021Article
- Personalized tumor-specific DNA junctions to detect circulating tumor in patients with endometrial cancer.PloS one · 2021Article
- Biliary tract cancer patient-derived xenografts: Surgeon impact on individualized medicine.JHEP reports : innovation in hepatology · 2020Article
- Integration of Comprehensive Genomic Analysis and Functional Screening of Affected Molecular Pathways to Inform Cancer Therapy.Mayo Clinic proceedings · 2020Article
- Mate pair sequencing outperforms fluorescence in situ hybridization in the genomic characterization of multiple myeloma.Blood cancer journal · 2019Article
- An intragenic duplication ofCold Spring Harbor molecular case studies · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors.
Funding
Abstract
Copy number variation (CNV) is a common form of structural variation detected in human genomes, occurring as both constitutional and somatic events. Cytogenetic techniques like chromosomal microarray (CMA) are widely used in analyzing CNVs. However, CMA techniques cannot resolve the full nature of these structural variations (i.e. the orientation and location of associated breakpoint junctions) and must be combined with other cytogenetic techniques, such as karyotyping or FISH, to do so. This makes the development of a next-generation sequencing (NGS) approach capable of resolving both CNVs and breakpoint junctions desirable. Mate-pair sequencing (MPseq) is a NGS technology designed to find large structural rearrangements across the entire genome. Here we present an algorithm capable of performing copy number analysis from mate-pair sequencing data. The algorithm uses a step-wise procedure involving normalization, segmentation, and classification of the sequencing data. The segmentation technique combines both read depth and discordant mate-pair reads to increase the sensitivity and resolution of CNV calls. The method is particularly suited to MPseq, which is designed to detect breakpoint junctions at high resolution. This allows for the classification step to accurately calculate copy number levels at the relatively low read depth of MPseq. Here we compare results for a series of hematological cancer samples that were tested with CMA and MPseq. We demonstrate comparable sensitivity to the state-of-the-art CMA technology, with the benefit of improved breakpoint resolution. The algorithm provides a powerful analytical tool for the analysis of MPseq results in cancer.
Indexed as
Identifiers
What OpenQuestion holds
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.