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10.1186/s13046-017-0591-4 http://scihub22266oqcxt.onion/10.1186/s13046-017-0591-4 C5590190!5590190 !28882180     free     free     free Warning: file_get_contents(https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=28882180 &cmd=llinks): Failed to open stream: HTTP request failed! 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High performance of targeted next generation sequencing on variance detection in clinical tumor specimens in comparison with current conventional methods |pdf=|usr=}}{{28882180 }} gab.com Text High performance of targeted next generation sequencing on variance detection in clinical tumor specimens in comparison with current conventional methods JO: J Exp Clin Cancer Res http://www.kidney.de/pget.php?&tw=1&pmid=28882180 #FOAvip BACKGROUND: Next generation sequencing (NGS) is being increasingly applied for assisting cancer molecular diagnosis. However, it is still needed to validate NGS accuracy on detection of DNA alternations based on a large number of clinical samples, especially for DNA rearrangements and copy number variations (CNVs). This study is to set up basic parameters of targeted NGS for clinical diagnosis and to understand advantage of targeted NGS in comparison with the conventional methods of molecular diagnosis. METHODS: Genomic DNA from 1000 Genomes Project and DNA from cancer cell lines have been used to establish the basic parameters for targeted NGS. The following confirmation was conducted by clinical samples. The multiple variants tested by amplification-refractory mutation system (ARMS), fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) were evaluated by targeted NGS to determine the sensitivity. Furthermore, the multiple variants detected by targeted NGS were confirmed by current conventional methods to elucidate the specificity. RESULTS: At sequencing depth of 500×, the maximal sensitivities on detecting single nucletic variances (SNVs) and small insertions/deletions (Indels) can reach 99% and 98.7% respectively, and in 20% of cancer cells, CNV detection can reach to the maximal level. The following confirmation of the sensitivity and specificity was conducted by a large cohort of clinical samples. For SNV and indel detection in clinical samples, targeted NGS can identify all hotspot mutations with 100% sensitivity and specificity. On ALK fusion detection, about 86% IHC-identified cases could be identified by targeted NGS and all ALK fusion detected by targeted NGS were confirmed by IHC. For HER2-amplification, 14 HER2-amplification cases identified by target NGS were all confirmed by FISH and about 93.3% of Her-2 IHC (3+) cases were identified by targeted NGS. Finally, the targeted NGS platform developed here has accurately detected EGFR hotspot mutations in 215 NSCLC patients. CONCLUSIONS: DNA from cancer cell lines is better than standard DNA as a reference to establish basic parameters for targeted NGS. Comparison of the conventional methods using a large cohort of patient samples confirmed the high preformance of targeted NGS on detecting DNA alterations. Twit Text FOAVip High performance of targeted next generation sequencing on variance detection in clinical tumor specimens in comparison with current conventional methods ????J Exp Clin Cancer Res http://www.kidney.de/pget.php?&tw=1&pmid=28882180 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=28882180 #FOAvip English Wikipedia <ref>{{Cite pmid|28882180 }}</ref> High performance of targeted next generation sequencing on variance detection in clinical tumor specimens in comparison with current conventional methods #MMPMID28882180 Su D ; Zhang D ; Chen K ; Lu J ; Wu J ; Cao X ; Ying L ; Jin Q ; Ye Y ; Xie Z ; Xiong L ; Mao W ; Li F J Exp Clin Cancer Res 2017[Sep]; 36 (1 ): 121 PMID28882180 show ga BACKGROUND: Next generation sequencing (NGS) is being increasingly applied for assisting cancer molecular diagnosis. However, it is still needed to validate NGS accuracy on detection of DNA alternations based on a large number of clinical samples, especially for DNA rearrangements and copy number variations (CNVs). This study is to set up basic parameters of targeted NGS for clinical diagnosis and to understand advantage of targeted NGS in comparison with the conventional methods of molecular diagnosis. METHODS: Genomic DNA from 1000 Genomes Project and DNA from cancer cell lines have been used to establish the basic parameters for targeted NGS. The following confirmation was conducted by clinical samples. The multiple variants tested by amplification-refractory mutation system (ARMS), fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) were evaluated by targeted NGS to determine the sensitivity. Furthermore, the multiple variants detected by targeted NGS were confirmed by current conventional methods to elucidate the specificity. RESULTS: At sequencing depth of 500×, the maximal sensitivities on detecting single nucletic variances (SNVs) and small insertions/deletions (Indels) can reach 99% and 98.7% respectively, and in 20% of cancer cells, CNV detection can reach to the maximal level. The following confirmation of the sensitivity and specificity was conducted by a large cohort of clinical samples. For SNV and indel detection in clinical samples, targeted NGS can identify all hotspot mutations with 100% sensitivity and specificity. On ALK fusion detection, about 86% IHC-identified cases could be identified by targeted NGS and all ALK fusion detected by targeted NGS were confirmed by IHC. For HER2-amplification, 14 HER2-amplification cases identified by target NGS were all confirmed by FISH and about 93.3% of Her-2 IHC (3+) cases were identified by targeted NGS. Finally, the targeted NGS platform developed here has accurately detected EGFR hotspot mutations in 215 NSCLC patients. CONCLUSIONS: DNA from cancer cell lines is better than standard DNA as a reference to establish basic parameters for targeted NGS. Comparison of the conventional methods using a large cohort of patient samples confirmed the high preformance of targeted NGS on detecting DNA alterations. |Anaplastic Lymphoma Kinase [MESH] |DNA Copy Number Variations/*genetics [MESH] |Female [MESH] |Gene Rearrangement/*genetics [MESH] |High-Throughput Nucleotide Sequencing [MESH] |Human Genome Project [MESH] |Humans [MESH] |INDEL Mutation/*genetics [MESH] |Immunohistochemistry [MESH] |In Situ Hybridization, Fluorescence [MESH] |Male [MESH] |Neoplasms/*genetics/pathology [MESH] |Oncogene Proteins, Fusion/genetics [MESH] |Receptor Protein-Tyrosine Kinases/genetics [MESH]High performance of targeted next generation sequencing on variance de(epmc).pdf DeepDyve Pubget Overpricing