Motivation: The ability to detect copy-number variation (CNV) and loss of heterozygosity (LOH) from exome sequencing data extends the utility of this powerful approach that has mainly been used for point or small insertion/deletion detection.
Results: We present ExomeCNV, a statistical method to detect CNV and LOH using depth-of-coverage and B-allele frequencies, from mapped short sequence reads, and we assess both the method's power and the effects of confounding variables. We apply our method to a cancer exome resequencing dataset. As expected, accuracy and resolution are dependent on depth-of-coverage and capture probe design.
Availability: CRAN package 'ExomeCNV'.
Contact: fsathira@fas.harvard.edu; snelson@ucla.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179661 | PMC |
| http://dx.doi.org/10.1093/bioinformatics/btr462 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Changes in the copy number of large genomic regions, termed copy number variations (CNVs), contribute to important phenotypes in many organisms. CNVs are readily identified using conventional approaches when present in a large fraction of the cell population. However, CNVs that are present in only a few genomes across a population are often overlooked but important; if beneficial under specific conditions, a de novo CNV that arises in a single genome can expand during selection to create a larger population of cells with novel characteristics.
View Article and Find Full Text PDFIntroduction: Structural variants (SVs) of the nebulin gene ( ), including intragenic duplications, deletions, and copy number variation of the triplicate region, are an established cause of recessively inherited nemaline myopathies and related neuromuscular disorders. Large deletions have been shown to cause dominantly inherited distal myopathies. Here we provide an overview of 35 families with muscle disorders caused by such SVs in .
View Article and Find Full Text PDFFamilial hypercholesterolemia - Targeted whole gene sequencing as a diagnostic approach.
Atheroscler Plus
March 2025
Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
Background And Aims: Familial hypercholesterolemia (FH) and other disorders with similar features are common genetic disorders that remain underdiagnosed and undertreated, due in part to the cost of screening. The aim of this study was to design and implement a whole gene targeted NGS panel for the molecular diagnosis of FH and statin intolerance with an emphasis on high quality variant calling, including copy number analysis.
Methods: A whole gene panel for hybridisation-based short read NGS was designed for the dominant FH-genes low density lipoprotein receptor (), apolipoprotein B (APOB), proproteinconvertas subtilisin/kexin type 9 (PCSK9), apolipoprotein E (APOE) and the recessive FH-genes low density lipoprotein receptor adaptor protein 1 (), ATP binding cassette subfamily member 5/8 (ABCG5/8) and lipase A, lysosomal acid type (), as well as solute carrier organic anion transporter family member 1B1 (), not an FH gene but linked to statin intolerance.
Real time-PCR a diagnostic tool for reporting copy number variation and relative gene-expression changes in pediatric B-cell acute lymphoblastic leukemia-a pilot study.
Biol Methods Protoc
December 2024
Division of Molecular Medicine, St John's Research Institute, St John's National Academy of Health Sciences (a Unit of CBCI Society for Medical Education), Bangalore 560034, Karnataka, India.
Real time-polymerase chain reaction (RT-PCR) is used routinely in clinical practice as a cost-effective method for molecular diagnostics. Research in pediatric B-cell Acute Lymphoblastic Leukemia (ped B-ALL) suggests that apart from cytogenetics and clinical features, there is a need to include Copy number variation (CNV) in select genes at diagnosis, for upfront stratification of patients. Using ped B-ALL as a model, we have developed a RT-PCR-based iterative probability scoring method for reporting CNVs, and relative gene-expression changes.
View Article and Find Full Text PDFWhole-Exome Sequencing: Discovering Genetic Causes of Granulomatous Mastitis.
Int J Mol Sci
January 2025
Department of Molecular Medicine, Aziz Sancar Institute of Experimental Medicine, Istanbul University, 34093 Istanbul, Türkiye.
Granulomatous mastitis (GM) is a rare, benign, but chronic and recurrent inflammatory breast disease that significantly impacts physical and psychological well-being. It often presents symptoms such as pain, swelling, and discharge, leading to diagnostic confusion with malignancy. The etiology of GM remains unclear, though autoimmune and multifactorial components are suspected.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!