scholarly journals Next generation sequencing is a highly reliable method to analyze exon 7 deletion of survival motor neuron 1 (SMN1) gene

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Sumin Zhao ◽  
Yaoshen Wang ◽  
Xiuqing Xin ◽  
Zhonghai Fang ◽  
Linlin Fan ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Copy Number ◽  
Reliable Method ◽  
Quantitative Polymerase Chain Reaction ◽  
Gene Copy Number ◽  
Carrier Screening ◽  
Gene Copy ◽  
Next Generation ◽  
Expanded Carrier Screening ◽  
Generation Sequencing

AbstractSpinal muscular atrophy (SMA) is one of the most common and severe genetic diseases. SMA carrier screening is an effective way to identify couples at risk of having affected children. Next-generation sequencing (NGS)-based expanded carrier screening could detect SMN1 gene copy number without extra experiment and with high cost performance. However, its performance has not been fully evaluated. Here we conducted a systematic comparative study to evaluate the performance of three common methods. 478 samples were analyzed with multiplex ligation probe amplification (MLPA), real-time quantitative polymerase chain reaction (qPCR) and NGS, simultaneously. Taking MLPA-based results as the reference, for 0 copy, 1 copy and ≥ 2 copy SMN1 analysis with NGS, the sensitivity, specificity and precision were all 100%. Using qPCR method, the sensitivity was 100%, 97.52% and 94.30%, respectively; 98.63%, 95.48% and 100% for specificity; and 72.72%, 88.72% and 100% for precision. NGS repeatability was higher than that of qPCR. Moreover, among three methods, NGS had the lowest retest rate. Thus, NGS is a relatively more reliable method for SMN1 gene copy number detection. In expanded carrier screening, compared with the combination of multiple methods, NGS method could reduce the test cost and simplify the screening process.

Targeted Amplicon Based Next-Generation Sequencing Facilitates Detection of KMT2A/MLL Gene Copy Number Changes

2017 ◽  
Vol 214-215 ◽  
pp. 41-42
Author(s):  
Rashmi Kanagal-Shamanna ◽  
Xinyan Lu ◽  
Wei Chen ◽  
Mark Routbort ◽  
Bedia Barkoh ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Copy Number ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Next Generation ◽  
Mll Gene ◽  
Copy Number Changes ◽  
Generation Sequencing

scholarly journals MET amplification identified by next-generation sequencing and its clinical relevance for MET inhibitors

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Lun-Xi Peng ◽  
Guang-Ling Jie ◽  
An-Na Li ◽  
Si-Yang Liu ◽  
Hao Sun ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Copy Number ◽  
Kinase Inhibitor ◽  
De Novo ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Precision Oncology ◽  
Next Generation ◽  
Driver Genes ◽  
Generation Sequencing

Abstract Background MET amplification plays an important role in the development of non-small-cell lung cancer (NSCLC) either de novo or in resistance to epidermal growth factor receptor tyrosine–kinase inhibitor (EGFR-TKI) settings. Fluorescence in situ hybridization (FISH) is the standard method for MET amplification. With more and more discoveries of oncogenic driver genes, next-generation sequencing (NGS) plays a significant role in precision oncology. Meanwhile, the role of NGS in MET amplification remains uncertain. Methods Forty patients diagnosed with advanced NSCLC were included. FISH and NGS were conducted prior to MET inhibitors treatment. MET amplification by FISH was defined as a MET/CEP7 ratio of  >  2.0 and/or copy number (CN)  >  5. MET amplification by NGS was defined as gene copy number (GCN)  ≥  5. Results The concordance rate among FISH and NGS was 62.5% (25/40). MET amplification identified by FISH showed the optimal predictive value. The partial response (PR) rate was 68.0% (17/25 with MET amplification) vs. 6.7% (1/15 without MET amplification); the median progression-free survival (PFS) was 5.4 months versus 1.0 months (P  < 0.001). MET amplification identified by NGS failed to distinguish significant clinical outcomes. The PR rate was 60.0% (6/10, with MET GCN  ≥ 5) vs. 40.0% (12/30, with MET GCN  < 5); the median PFS was 4.8 months vs. 2.2 months (P  = 0.357). The PR rate was 68.8% (11/16) and the median PFS was 4.8 months in patients with focal amplification by NGS. Conclusions MET amplification identified by FISH remains the optimal biomarker to identify suitable candidates for MET-TKI therapy. In comparison, amplification identified by NGS seems not as robust to be effective predictive biomarker. Further exploration is needed regarding the focal amplification by NGS in predicting the efficacy.

scholarly journals Estimating copy number using next-generation sequencing to determine ERBB2 amplification status

2021 ◽  
Vol 38 (4) ◽  
Author(s):  
Kohei Nakamura ◽  
Eriko Aimono ◽  
Junna Oba ◽  
Hideyuki Hayashi ◽  
Shigeki Tanishima ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Next Generation Sequencing ◽  
Copy Number ◽  
The United States ◽  
Gene Copy ◽  
Cancer Tissue ◽  
Next Generation ◽  
Federal Drug Administration ◽  
Generation Sequencing ◽  
Erbb2 Amplification

AbstractAssessing Erb-b2 receptor tyrosine kinase 2 (ERBB2) amplification status in breast and gastric cancer is necessary for deciding the best therapeutic strategy. Immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) are currently used for assessing protein levels and gene copy number (CN), respectively. The use of next-generation sequencing (NGS) to measure ERBB2 CN in breast cancer is approved by the United States Federal Drug Administration as a companion diagnostic. However, a CN of less than 8 is evaluated as “equivocal”, which means that some ERBB2 amplification cases diagnosed as “HER2 negative” might be false-negative cases. We reviewed the results of gene profiling targeting 160 cancer-related genes in breast (N = 90) and non-breast (N = 19) cancer tissue, and compared the ERBB2 CN results with the IHC/FISH scores. We obtained an estimated CN from the measured CN by factoring in the histological proportion of tumor cells and found that an ERBB2-estimated CN of 3.2 or higher was concordant with the combined IHC/FISH outcome in 98.4% (88/90) of breast cancer cases, while this was not always evident among non-breast cancer cases. Therefore, NGS-estimated ERBB2 CN could be considered a diagnostic test for anti-HER2 therapy after the completion of adequate prospective clinical trials.

International Harmonization of Provisional Diagnostic Criteria for ERBB2-Amplified Metastatic Colorectal Cancer Allowing for Screening by Next-Generation Sequencing Panel

2020 ◽  
pp. 6-19 ◽  
Author(s):  
Satoshi Fujii ◽  
Anthony M. Magliocco ◽  
Jihun Kim ◽  
Wataru Okamoto ◽  
Jeong Eun Kim ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Next Generation Sequencing ◽  
Metastatic Colorectal Cancer ◽  
Diagnostic Criteria ◽  
Copy Number ◽  
Cross Validation ◽  
Gene Copy ◽  
Her2 Status ◽  
Next Generation ◽  
Generation Sequencing

PURPOSE ERBB2 amplification (human epidermal growth factor receptor 2 positivity [HER2+]) in metastatic colorectal cancer (mCRC) has important therapeutic implications that necessitate the need for accurate diagnostics. The study purpose was to establish and validate harmonized diagnostic criteria for HER2+ mCRC among 3 groups (GI-SCREEN-Japan, NCTN-SWOG-USA, and Korea). PATIENTS AND METHODS We assessed HER2 status by immunohistochemistry (IHC), ERBB2/CEP17 ratio, gene copy number (GCN) by fluorescence in situ hybridization (FISH), and copy number variation (CNV) using two targeted next-generation sequencing (NGS) panels. Tumor samples from 475 and 16 patients with mCRC in exploratory and validation cohorts, respectively, were used for cross-validation of the NGS panels. RESULTS Consensus diagnostic criteria among the 3 groups for HER2+ mCRC were established as follows: IHC 3+ or IHC 2+ and ERBB2/CEP17 ratio by FISH ≥ 2.0, tumor content > 10% for surgically resected specimens, and necessary tumor content not defined for biopsy specimens. The median GCN and CNV for HER2+ patients were 10.9 and 27.7 compared with 2.5 ( P < .0001) and 3.5 ( P < .0001), respectively, in HER2-negative patients. These findings were validated in a validation cohort (GCN, 16.2 v 2.4 [ P = .0002]; CNV, 42.5 v 2.0 [ P = .0003]). GCN correlated with CNV in both cohorts (exploratory, r = 0.90; validation, r = 0.97; P < .0001). CNV in cross-validation of the 2 NGS panels also showed a strong correlation ( r = 0.98; P < .0001). CNV in patients who fulfilled the consensus criteria was > 4.0 in all, which demonstrates the accuracy of the IHC/FISH criteria and cross-validation of NGS panels. CONCLUSION We have established and verified harmonized diagnostic criteria for HER2+ and demonstrated consistency between IHC/FISH and CNV determined by NGS in mCRC.

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