Moving next-generation sequencing into the clinical realm: Detection of somatic mutations in cancer by targeted amplicon sequencing.

2012 ◽  
Vol 30 (30_suppl) ◽  
pp. 60-60
Author(s):  
Chih-Jian Lih ◽  
Thomas Forbes ◽  
Michele Mehaffey ◽  
Eric Sause ◽  
David Sims ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Next Generation Sequencing ◽  
Cancer Patients ◽  
Patient Selection ◽  
Somatic Mutations ◽  
Germ Line ◽  
Early Stage ◽  
Illumina Miseq ◽  
Next Generation ◽  
Generation Sequencing

60 Background: Molecular targeted therapies are increasingly important in treating cancer patients; robust analytically validated clinical assays are required for patient selection in early-stage clinical trials. The goal of Molecular Characterization Laboratory (MoCha) is to develop clinical diagnostic assays using next generation sequencing methods to support clinical studies in DCTD (CTEP). Methods: We developed a custom assay for somatic mutation detection using Fluidigm access array technology for amplicon generation followed by sequencing with the Illumina Miseq. A panel of 62 amplicons covering 6 Kb genomic regions was designed to detect 92 DNA loci, including common therapeutically actionable targets, in 37 genes. Analytical studies were performed using genomic DNA samples from fresh or formalin fixed cancer cell-lines and a normal hapmap individual (CEPH). We subsequently applied this assay to characterize DNA samples from both tumor tissues and blood specimens from ovarian cancer patients. Results: The assay detected known variants in both frozen and fixed DNA samples reproducibly with high sensitivity and specificity (<2%). Using a series of positive control plasmid spikes mixed into a normal reference CEPH DNA at pre-defined copy number ratios, we verified the assay is sensitive to detect variants at 5% allelic frequency with a minimum 400 X coverage. We identified somatic mutations in TP53 and PIK3CA in a few patients, and a germ-line variant D1583N in ATM genes occurring in one-third of tested patients. Conclusions: We developed and validated a next generation sequencing assay suitable for patient selection for clinical trials. Plans are to correlate sequencing and clinical results when clinical data are available.

scholarly journals NRAS germline variant G138R and multiple rare somatic mutations on APC in colorectal cancer patients in Taiwan by next generation sequencing

Oncotarget ◽  
2016 ◽  
Vol 7 (25) ◽  
pp. 37566-37580 ◽  
Author(s):  
Pi-Yueh Chang ◽  
Jinn-Shiun Chen ◽  
Nai-Chung Chang ◽  
Shih-Cheng Chang ◽  
Mei-Chia Wang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Next Generation Sequencing ◽  
Cancer Patients ◽  
Somatic Mutations ◽  
Next Generation ◽  
Germline Variant ◽  
Colorectal Cancer Patients ◽  
Generation Sequencing

Landscape of targetable alterations discovered by next generation sequencing demonstrates the role a community hospital can play in precision-guided oncology: Experience from Lenox Hill Hospital.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e19279-e19279
Author(s):  
Morana Vojnic ◽  
Jordan Steinberg ◽  
Igor Odintsov ◽  
Yonah Ziemba ◽  
Lindsay K Hill ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Next Generation Sequencing ◽  
Early Stage ◽  
Braf V600e ◽  
Egfr Mutations ◽  
Advanced Stage ◽  
Next Generation ◽  
Data Set ◽  
Number Of Patients ◽  
Generation Sequencing

e19279 Background: Next generation sequencing (NGS) has become standard of care in aiding diagnosis and treatment of advanced solid cancers, and in conducting clinical trials at large centers. It is imperative that this is expanded to other hospitals that care for the majority of cancer patients. We analyzed NGS reports from our hospital to assess the number of patients who can benefit from approved or investigational targeted therapies. Methods: We analyzed NGS data for 511 solid tumor samples sequenced between January 1, 2018 and December 31, 2019. NGS was performed by GenPath Dx (77%), Caris Life Sciences (16%) or Foundation Medicine (7%). Results: The majority of samples represented advanced stage malignancies and 21% were stage I or II. They originated from the following primaries: 195 lung (37%), 150 gastrointestinal (29%), 64 primary brain (12%), 20 gynecological (4%), 14 skin (3%), 13 head and neck (3%) and 11 sarcomas (1%). 72 samples had mutations in EGFR (14%), 170 in TP53 (33%), 124 in KRAS (24%), 28 in BRAF (6%), and 3 in RET (0.6%). 34/107 (32%) early stage samples harbored an actionable mutation (20 EGFR mutations, 1 MET exon 14 skipping, 4 KRAS G12C, 7 BRAF V600E, 1 FGFR3 amplification and 1 CD74/NRG1 fusion). In contrast, only 58/317 (18%) advanced stage samples had a targetable mutation (p-value = 0.02, χ² test). 76% of EGFR-mutated samples were lung adenocarcinomas, and 19% were primary brain tumors; 54% of these are targetable by FDA-approved EGFR inhibitors. KRAS mutations were found in gastrointestinal (54%), lung (37%) and pancreatic (5%) malignancies. 17 patients had a KRAS G12C mutation and, therefore, could benefit from one of the KRAS G12C inhibitors in early clinical trials. Four samples harbored crizotinib-sensitive mutations (2 MET amplifications and 2 MET exon 14 skipping mutations). Regarding gene fusions, one glioblastoma sample had a PTPRZ-MET fusion and one lung adenocarcinoma sample harbored a CD74-NRG1 fusion. Conclusions: We identified 92/511 samples (18%) with clinically actionable mutations; distributed in 32% early stage and 18% advanced stage disease, indicating that actionable mutations are present at an increased frequency in early stage solid malignancies in our data set and trials to investigate targeted therapy in such settings should be considered. Furthermore, we show that a community-based hospital can be a site for future clinical trials of small molecule inhibitors and bring precision-guided medicine to additional patients.

scholarly journals Panel of serum miRNAs as potential non-invasive biomarkers for pancreatic ductal adenocarcinoma

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Imteyaz Ahmad Khan ◽  
Safoora Rashid ◽  
Nidhi Singh ◽  
Sumaira Rashid ◽  
Vishwajeet Singh ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Pancreatic Ductal Adenocarcinoma ◽  
Early Stage ◽  
Ductal Adenocarcinoma ◽  
Next Generation ◽  
Serum Samples ◽  
Tissue Samples ◽  
Non Invasive ◽  
Specific Symptoms ◽  
Generation Sequencing

AbstractEarly-stage diagnosis of pancreatic ductal adenocarcinoma (PDAC) is difficult due to non-specific symptoms. Circulating miRNAs in body fluids have been emerging as potential non-invasive biomarkers for diagnosis of many cancers. Thus, this study aimed to assess a panel of miRNAs for their ability to differentiate PDAC from chronic pancreatitis (CP), a benign inflammatory condition of the pancreas. Next-generation sequencing was performed to identify miRNAs present in 60 FFPE tissue samples (27 PDAC, 23 CP and 10 normal pancreatic tissues). Four up-regulated miRNAs (miR-215-5p, miR-122-5p, miR-192-5p, and miR-181a-2-3p) and four down-regulated miRNAs (miR-30b-5p, miR-216b-5p, miR-320b, and miR-214-5p) in PDAC compared to CP were selected based on next-generation sequencing results. The levels of these 8 differentially expressed miRNAs were measured by qRT-PCR in 125 serum samples (50 PDAC, 50 CP, and 25 healthy controls (HC)). The results showed significant upregulation of miR-215-5p, miR-122-5p, and miR-192-5p in PDAC serum samples. In contrast, levels of miR-30b-5p and miR-320b were significantly lower in PDAC as compared to CP and HC. ROC analysis showed that these 5 miRNAs can distinguish PDAC from both CP and HC. Hence, this panel can serve as a non-invasive biomarker for the early detection of PDAC.

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