scholarly journals Clinical evaluation of panel testing by next-generation sequencing (NGS) for gene mutations in myeloid neoplasms

2016 ◽  
Vol 11 (1) ◽  
Author(s):  
Chun Hang Au ◽  
Anna Wa ◽  
Dona N. Ho ◽  
Tsun Leung Chan ◽  
Edmond S. K. Ma
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Evaluation ◽  
Gene Mutations ◽  
Next Generation ◽  
Panel Testing ◽  
Myeloid Neoplasms ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

scholarly journals Next-Generation Sequencing Improves Diagnosis, Prognosis and Clinical Management of Myeloid Neoplasms

Cancers ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 1364 ◽  
Author(s):  
Diego Carbonell ◽  
Julia Suárez-González ◽  
María Chicano ◽  
Cristina Andrés-Zayas ◽  
Juan Carlos Triviño ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Copy Number Variants ◽  
Genetic Alterations ◽  
Next Generation ◽  
Pathogenic Variants ◽  
Myeloid Neoplasms ◽  
Diagnostic Samples ◽  
Gene Panels ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Molecular diagnosis of myeloid neoplasms (MN) is based on the detection of multiple genetic alterations using various techniques. Next-generation sequencing (NGS) has been proved as a useful method for analyzing many genes simultaneously. In this context, we analyzed diagnostic samples from 121 patients affected by MN and ten relapse samples from a subset of acute myeloid leukemia patients using two enrichment-capture NGS gene panels. Pathogenicity classification of variants was enhanced by the development and application of a custom onco-hematology score. A total of 278 pathogenic variants were detected in 84% of patients. For structural alterations, 82% of those identified by cytogenetics were detected by NGS, 25 of 31 copy number variants and three out of three translocations. The detection of variants using NGS changed the diagnosis of seven patients and the prognosis of 15 patients and enabled us to identify 44 suitable candidates for clinical trials. Regarding AML, six of the ten relapsed patients lost or gained variants, comparing with diagnostic samples. In conclusion, the use of NGS panels in MN improves genetic characterization of the disease compared with conventional methods, thus demonstrating its potential clinical utility in routine clinical testing. This approach leads to better-adjusted treatments for each patient.

scholarly journals Liquid Biopsy Using Ascites and Pleural Effusion Supernatant for Genomic Profiling in Gastrointestinal and Lung Cancers

2021 ◽  
Author(s):  
Hui-Ta Wu ◽  
Hao-Nan Ji ◽  
Wen-Hui Yang ◽  
Min Zhang ◽  
Yi-Fang Guo ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Next Generation Sequencing ◽  
Pleural Effusion ◽  
Mutation Rate ◽  
Gene Mutations ◽  
Specific Gene ◽  
Genomic Profiling ◽  
Next Generation ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Background: Precision medicine highlights the importance of incorporating molecular genetic testing into standard clinical care. Next-generation sequencing (NGS) can detect cancer-specific gene mutations, and molecular targeted drugs can be designed to be effective for one or more specific gene mutations. For patients with special site metastasis, it is particularly important to use appropriate samples for genetic profiling test.Methods: Tissues, plasma, ascites (ASC) supernatants, pleural effusion (PE) samples from gastrointestinal (GI) patients with peritoneal metastasis and lung cancer patients with pleural metastasis were collected for comprehensive genomic profiling. The sample were performed on next-generation sequencing (NGS) using 59 or 1021 cancer-relevant genes panel. Results: The study enrolled 156 tissues, 188 plasma, 45 ascites supernatants, and 1 pleural effusion in 304 GI group and 446 pleural effusion supernatants, 122 tissues, 389 plasma, 45 pleural effusion sediments in 407 lung cancer group. The MSAF were significantly higher in ASC and PE supernatant than plasma ctDNA (50.18% ± 32.03% vs 12.31% ± 19.90%, p < 0.0001 and 33.74% ± 28.34% vs 6.28% ± 12.17%, p < 0.0001, respectively). ASC supernatant had a higher actionable mutation rate than plasma. ASC supernatant accounts for more actionable alterations than plasma ctDNA in 26 paired samples. PE supernatant had higher total actionable mutation rate than plasma (80.3% vs 48.4%, p < 0.05). PE supernatant had a higher frequency of uncommon variations than plasma no matter had distant organ metastasis. Conclusion: ASC and PE supernatants could be better alternatives when tumor tissues are not available in the real world, especially in patients who have only peritoneal or pleural metastases.

scholarly journals Less frequently mutated genes in colorectal cancer: evidences from next-generation sequencing of 653 routine cases

2016 ◽  
Vol 69 (9) ◽  
pp. 767-771 ◽  
Author(s):  
Umberto Malapelle ◽  
Pasquale Pisapia ◽  
Roberta Sgariglia ◽  
Elena Vigliar ◽  
Maria Biglietto ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Next Generation Sequencing ◽  
Somatic Mutations ◽  
Gene Mutations ◽  
Next Generation ◽  
Genomic Landscape ◽  
Next Generation Sequencing Ngs ◽  
Pcr Targeting ◽  
Diagnostic Setting ◽  
Generation Sequencing

AimsThe incidence of RAS/RAF/PI3KA and TP53 gene mutations in colorectal cancer (CRC) is well established. Less information, however, is available on other components of the CRC genomic landscape, which are potential CRC prognostic/predictive markers.MethodsFollowing a previous validation study, ion-semiconductor next-generation sequencing (NGS) was employed to process 653 routine CRC samples by a multiplex PCR targeting 91 hotspot regions in 22 CRC significant genes.ResultsA total of 796 somatic mutations in 499 (76.4%) tumours were detected. Besides RAS/RAF/PI3KA and TP53, other 12 genes showed at least one mutation including FBXW7 (6%), PTEN (2.8%), SMAD4 (2.1%), EGFR (1.2%), CTNNB1 (1.1%), AKT1 (0.9%), STK11 (0.8%), ERBB2 (0.6%), ERBB4 (0.6%), ALK (0.2%), MAP2K1 (0.2%) and NOTCH1 (0.2%).ConclusionsIn a routine diagnostic setting, NGS had the potential to generate robust and comprehensive genetic information also including less frequently mutated genes potentially relevant for prognostic assessments or for actionable treatments.

Coverage analysis in a targeted amplicon-based next-generation sequencing panel for myeloid neoplasms

2016 ◽  
Vol 69 (9) ◽  
pp. 801-804 ◽  
Author(s):  
Benedict Yan ◽  
Yongli Hu ◽  
Christopher Ng ◽  
Kenneth H K Ban ◽  
Tin Wee Tan ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Gc Content ◽  
Read Depth ◽  
Next Generation ◽  
Diagnostic Assays ◽  
Amplification Bias ◽  
Lower Performance ◽  
Myeloid Neoplasms ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

AimsPCR amplicon-based next-generation sequencing (NGS) panels are increasingly used for clinical diagnostic assays. Amplification bias is a well-known limitation of PCR amplicon-based approaches. We sought to characterise lower-performance amplicons in an off-the-shelf NGS panel (TruSight Myeloid Sequencing Panel) for myeloid neoplasms and attempted to patch the low read depth for one of the affected genes, CEBPA.MethodsWe performed targeted NGS of 158 acute myeloid leukaemia samples and analysed the amplicon read depths across 568 amplicons to identify lower-performance amplicons. We also correlated the amplicon read depths with the template GC content. Finally, we attempted to patch the low read depth for CEBPA using a parallel library preparation (Nextera XT) workflow.ResultsWe identified 16 lower-performance amplicons affecting nine genes, including CEBPA. There was a slight negative correlation between the amplicon read depths and template GC content. Addition of the separate CEBPA library generated a minimum read depth per base across the CEBPA gene ranging from 268x to 758x across eight samples.ConclusionsThe identification of lower-performance amplicons will be informative to laboratories intending to use this panel. We have also demonstrated proof-of-concept that different libraries (TruSight Myeloid and Nextera XT) can be combined and sequenced on the same flow cell to generate additional reads for CEBPA.

Utility of multi-gene panel testing with next generation sequencing in women with endometrial cancer.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. 5588-5588
Author(s):  
Jing-Yi Chern ◽  
Nigel Madden ◽  
Jessica Lee ◽  
Deanna Gerber ◽  
Anna Cantor ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Family History ◽  
Gynecologic Cancer ◽  
Gene Mutations ◽  
Gene Panel ◽  
Next Generation ◽  
Mmr Genes ◽  
Panel Testing ◽  
Gene Panel Testing ◽  
Generation Sequencing

5588 Background: Lynch syndrome (LS) accounts for 2-6% of all endometrial cancers (EC), and women with a germline mutation in the mismatch repair (MMR) genes ( MLH1, MSH2, MSH6, and PMS2) have an average lifetime risk of EC of 40%. As with breast and ovarian cancer syndromes, there are likely other genes implicated in the development of EC outside of the MMR genes. Multi-gene panel testing (MGPT) with next generation sequencing (NGS) allows for simultaneous analysis of numerous genes.We sought to evaluate the characteristics and incidence of gene mutations in women with newly diagnosed EC. Methods: We conducted a review of EC patients diagnosed from 6/2013 to 12/2016 who had MGPT at our institution. Demographics, family history, genetic testing results, and tumor characteristics were collected and analyzed using χ2 tests. Results: Of the 129 patients who had MGPT, 13 (10%) had a mutation and only 5 (38%) were in patients < 50 years old. The median age of EC diagnosis is 55 (31-100) years and median BMI = 27.5 (21-59). Majority were stage 1, 76 (59%) and grade 1, 50 (39%). Patients with additional primary cancers, breast or colon were not more likely to have a mutation. However, patients with a family history of gynecologic cancer were more likely to have a mutation identified, 10 (77%) mutation vs no mutation 34 (29%), p = 0.003. Among all patients tested, 8 (6%) had a mutation in LS genes, and 6 (5%) had mutations in other genes ( BRCA1, BRCA2, RAD51C, MUTYH, CHEK2); 1 (0.8%) had both MSH2 and CHEK2 mutation. Three patients had prior testing for breast cancer; 2 were found to have a BRCA1/ 2 mutation and the other was on Tamoxifen and BRCA negative. IHC was performed on 7 of 13 patients, and 5 (71%) had a loss of MMR protein expression. Variants of uncertain significance were noted in 35/129 (27%) of patients tested. Conclusions: Majority of EC patients with a mutation detected with NGS were > age 50. We identified additional new mutations in non-LS genes including, CHEK2, RAD51C, and MUYTH with MGPT. These accounted for 29% of the mutations and would have not been not detected using classic LS gene testing. These genes are implicated in breast, ovary or colon cancer. MGPT testing is feasible and useful in identifying additional actionable gene mutations.

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