Probe-free allele-specific copy number detection and analysis of tumors
| Autor: | Xiaowei Guan, Guiqin Xie, Ailin Zhu, Xinbin Gu |
|---|---|
| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
DNA Copy Number Variations Genotyping Techniques Gene Dosage Biophysics Copy number analysis Single-nucleotide polymorphism Diamines Biology Nucleic Acid Denaturation Real-Time Polymerase Chain Reaction Polymorphism Single Nucleotide Biochemistry Melting curve analysis Mice 03 medical and health sciences Cell Line Tumor Neoplasms Animals Humans Benzothiazoles Copy-number variation Organic Chemicals Molecular Biology Genotyping Alleles Fluorescent Dyes Genetics PTEN Phosphohydrolase DNA Cell Biology genomic DNA 030104 developmental biology Quinolines Variants of PCR |
| Zdroj: | Analytical Biochemistry. 497:95-102 |
| ISSN: | 0003-2697 |
| DOI: | 10.1016/j.ab.2015.12.012 |
| Popis: | Cancer development and progression frequently involve nucleotide mutations as well as amplifications and deletions of genomic segments. Quantification of allele-specific copy number is an important step in characterizing tumor genomes for precision medicine. Despite advances in approaches to high-throughput genomic DNA analysis, inexpensive and simple methods for analyzing complex nucleotide and copy number variants are still needed. Real-time polymerase chain reaction (PCR) methods for discovering and genotyping single nucleotide polymorphisms are becoming increasingly important in genetic analysis. In this study, we describe a simple, single-tube, probe-free method that combines SYBR Green I-based quantitative real-time PCR and quantitative melting curve analysis both to detect specific nucleotide variants and to quantify allele-specific copy number variants of tumors. The approach is based on the quantification of the targets of interest and the relative abundance of two alleles in a single tube. The specificity, sensitivity, and utility of the assay were demonstrated in detecting allele-specific copy number changes critical for carcinogenesis and therapeutic intervention. Our approach would be useful for allele-specific copy number analysis or precise genotyping. |
| Databáze: | OpenAIRE |
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