Establishment and validation of pdx model for human col openi. Co04647ion ampliseq cancer hotspot panel v2 flyerrevision. The cnvs were detected using the control sequence data provided by thermo fisher scientific as a control, including both copy number gains and losses. Illumina ampliseq, the perfect solution for targeted dna rna sequencing using one of the industrys leading ngs platform producers. The ion ampliseqcancer hotspot panel v2 is a single pool of primers used to perform multiplex pcr for preparation of amplicon libraries from genomic hot spot regions that are frequently mutated in human cancer genes download the list of targeted genes and mutations for the ion ampliseqcancer hotspot panel v2. The ampliseq for illumina cancer hotspot panel v2 is a targeted resequencing assay for researching somatic mutations across the hotspot regions of 50 genes with known associations to cancer, as identified in the catalogue of somatic mutations in cancer cosmic 1 database. Ion ampliseq cancer hotspot panel v2 primer pool 4475346 ion ampliseq custom panels can be ordered via ion ampliseq designer. Conversely, the ion ampliseq cancer hotspot panel v2 chpv2, which includes the genes most frequently mutated in thyroid neoplasms. Easy panel configuration starting with disease research area. One panel is the ion ampliseq cancer hotspot panel v2, which has been previously used for gc genotyping in a clinical cancer research 11. Co26706 ampliseq cancer appnote v12 thermo fisher scientific. How effective and reliable would ion ampliseq cancer hotspot panel v2 be for identifying variants of oncogenes and tumor suppressors genes in xenograft.
Cancer hotspot panel v2 targeted hot spot regions of 50 oncogenes and tumor suppressor genes, with whole exon coverage of kras, braf and egfr 98% detection rate for 5% variant frequency 1400x average depth of coverage with up to 16 samples on a single ion 318 chip. To characterize cancer at a molecular level, the use of formalinfixed paraffinembedded tissue is important. This may be due to the design of the primers used in the ampliseq cancer hotspot panel v2 or the location of the mutations. Ion ampliseq cancer hotspot panel v2 libre pathology. Ion ampliseq cancer hotspot panel v2 ion torrent was used to detect frequent somatic mutations and similarity of molecular characteristics between the 10 patient tumors and matched pdx.
Application note ion ampliseq technology sanger sequencing. Versatile ion s5xl sequencer for targeted next generation. Thirtyfive ffpe tumour samples with known mutational status were collected from four different hospitals and sequenced with chv2 using an ion chef system and ion s5 xl system. Examination of our data using the ion torrent in combination with the ampliseq cancer hotspot panel v2 did not reveal any homopolymerbased errors or any errors caused by mutation position in the amplicon. The ampliseq for illumina solution offers a highly multiplexed polymerase chain reaction pcrbased workflow for use with. Cancer research institute, college of medicine, the. Ion ampliseq cancer hotspot panel v2 thermo fisher bioz. Highthroughput sequencing and copy number variation. Ampliseq for illumina cancer hotspot panel v2 50 hotspot. Ion ampliseq colon and lung cancer research panel v2 figure 2. Illuminas ampliseq chemistry provides research teams the ability to sequence anywhere from a handful of genes to hundreds of genes simultaneously using ngs platforms commonly found in todays literature such as the illumina miseq, illumina hiseq, and the. Ion ampliseq rna cancer panel targets 50 oncogenes with detection of key genes kras, braf, and egfr.
The ion ampliseq cancer hotspot panel v2 targeting mutationhotspot region in 50 most common cancerassociated genes was utilized. Ion ampliseq rna cancer panel thermo fisher scientific. We conducted the ion ampliseq cancer hotspot panel v2 detecting 2,855 oncogenic mutations in 50 commonly mutated genes and ncounter copy number variation assay, which was designed with 21 genes based on available targeted agents, as a high throughput genomic platform in 14 patients with metastatic gepnets. Sep 22, 2015 as a result of its flexibility, ion ampliseq technology enables researchers to zoomin on specific hotspot mutation sites using a panel such as the ion ampliseq cancer hotsport panel v2 for rapid. The list of pthogenic or likely pathogenic muatations detected by ion ampliseq cancer hotspot panel v2. Use of the ion ampliseq cancer hotspot panel in clinical molecular. Consumables and equipment used with the ampliseq for illumina cancer hotspot panel v2. Can the ion ampliseq cancer hotspot panel v2 be used for nexta. How effective is ion ampliseq cancer hotspot panel v2. Ion ampliseq dna and rna library preparation user guide pn. From gene expression, to cancer research, to inherited disease research, or. Conversely, the ion ampliseq cancer hotspot panel v2 chpv2, which includes the genes most frequently mutated in thyroid neoplasms, is commercially available and may represent an alternative to thyroid. The ion ampliseq cancer hotspot panel v2 is a single pool of primers used to perform multiplex pcr for preparation of amplicon libraries from genomic hot spot regions that are frequently mutated in human cancer genes.
Ampliseq for illumina is a suite of ampliseq chemistry products that are compatible with illumina nextgeneration sequencing platforms. Conversely, the ion ampliseq cancer hotspot panel v2 chpv2, which includes the genes most frequently mutated in thyroid neoplasms, is commercially. Histologic and immunohistochemical analyses revealed a high degree of pathologic similarity including histologic architecture and expression of cea, ck7, and. Ion ampliseq cancer hotspot panel v2 thermo fisher. Performance characteristics of the ampliseq cancer hotspot. Ion ampliseq panel primer pairspool description of change ion ampliseq pharmacogenomics research panel cat. From gene expression, to cancer research, to inherited disease research, or even human identification. In the era of targeted therapy, mutation profiling of cancer is a crucial aspect of making therapeutic decisions.
The ion ampliseqcancer hotspot panel v2 is designed to amplify 207 amplicons covering approximately 2,800 cosmic mutations from 50 oncogenes and. Ion ampliseq cancer hotspot panel v2 hide panel description. Table 1 shows the high level of accuracy observed across three typical data sets obtained using the ion ampliseq cancer panel v1, ion ampliseq library kit 2. Ion ampliseq cancer hotspot panel v2, supplied by thermo fisher, used in various techniques. We evaluated the applicability of the ion ampliseq cancer hotspot panel v2 chv2 using formalinfixed, paraffinembedded ffpe tissue of clinical specimens. Working with key cancer researchers and incorporating information from literature. Download this form to a preferred location before using it. The ion ampliseq sample id panel requires the use of the ion ampliseq library kit 2. The ion ampliseq cancer hotspot panel v2 is now expanded to allow translational and disease researchers to fasttrack oncology research by surveying hotspot regions of 50 oncogenes and tumor suppressor genes, with wide coverage of the kras, braf, and. Ion ampliseq cancer hotspot panel v2 is an off the shelf pcr panel to look for mutation hotspots in cancer. The ion ampliseq cancer hot spot panel v2 chpv2 250 amplicons thermofisher scientific, waltham, ma covers mutations in hotspot regions of 50 genes in one prime pool and requires 10ng of genomic dna for library preparation and sequencing on the ion pgm sequencer life technologies. We tested the ion ampliseq cancer hotspot panel v2 and ncounter copy number variation assay in 89 formalinfixed paraffinembedded gastric cancer samples to determine.
High coverage uniformity demonstrated with the ion ampliseq colon and lung cancer research panel v2 using applied biosystems acrometrix kras ffpe process controls cat. Clinical relevance of somatic mutations in main driver genes. The ion ampliseq cancer hotspot panel v2 is 207 primer pairs, the comprehensive cancer panel is 4,000 primer pairspool, and. Ampliseq for illumina cancer hotspot panel v2 consumables. The ion ampliseq rna cancer panel is a screening tool designed against 50 oncogenestumor suppressor genes found in the cosmic database. Typical ion ampliseq cancer panel sequencing coverage on ion 314 chip. Pdf use of the ion ampliseq cancer hotspot panel in. Now that you know a little bit about what ion ampliseq targeted sequencing has to offer and how it works, feel free to play with our design tool after all it is completely free to try. The ion ampliseq cancer hotspot panel v2 allows translational and disease researchers to fasttrack oncology research by surveying hotspot regions of 50 oncogenes and tumor suppressor genes, with wide coverage of the kras, braf and egfr genes. Ion ampliseq rna cancer panel was developed as an rna complement to the ion ampliseq cancer hotspot panel v2. The ampliseq for illumina solution offers a highly multiplexed polymerase chain reaction pcrbased workflow for use with targets ranging from a few to hundreds in a single run. The ion ampliseq cancer hotspot panel v2 is a single pool of primers used to perform multiplex pcr for preparation of amplicon libraries from genomic hot spot regions that are frequently mutated in human cancer genes download the list of targeted genes and mutations for the ion ampliseq cancer hotspot panel v2. Ion ampliseq direct ffpe dna kit ion torrent dual barcode kit 196. A29251 119 add 2 amplification cycles 20 cycles instead of 18 cycles for highquality dna ion ampliseq comprehensive cancer panel cat.
Interactive list of consumables and equipment used with the ampliseq for illumina cancer hotspot panel v2. In addition, we tested 24 ion ampliseq panel targets covering the exons of the human tp53 gene. The ion ampliseq cancer hotspot panel v2 is designed to amplify 207 amplicons covering approximately 2,800 cosmic mutations from 50 oncogenes and tumor suppressor genes. Ion ampliseq colon and lung cancer research panel v2 and. Mutations in cancerassociated genes were detected using ion ampliseq cancer hotspot panel v2. Depth of sequencing coverage 100x 500x average depth of coverage all mutations 96. We evaluated two next generation sequencing assays from ion torrent, the ampliseq cancer hotspot panel v2 and the ampliseq lung and colon cancer panel, capable of identifying, in a single assay, multiple somatic mutations in 50 and 22 genes respectively. Flexible design customization with madetoorder configuration. Ion ampliseq cancer hotspot panel v2 thermo fisher scientific.
Validating auroras ngs library preparation instrument on clinical samples with ion ampliseq cancer hotspot panel v2 chp2 assay. The panel should be used with the ion ampliseq library kit 2. Ion ampliseq colon and lung cancer research panel v2 and ion. Herein, we evaluated the applicability of the ion ampliseq cancer hotspot panel v2 in clinical molecular diagnostics using the ion s5 xl system for the detection of somatic driver mutations in ffpe clinical samples, comparing the results with relevant molecular pathology tests and another ngs panel of the oncomine focus assay. Conversely, the ion ampliseq cancer hotspot panel v2 chpv2, which includes the genes most frequently mutated in thyroid neoplasms, is commercially available and may represent an alternative to thyroidspecific panels. Ampliseq for illumina cancer hotspot panel v2 documentation. The ampliseq for illumina cancer hotspot panel v2 is a targeted resequencing assay for researching somatic mutations across the hotspot regions of 50 genes. For interpretation of the references to colour in the table, the reader is referred to the. Mutations in cancer associated genes were detected using ion ampliseq cancer hotspot panel v2. Plasma cellfree circulating tumor dna ctdna has the potential to serve as a noninvasive surrogate to determine tumor genotype and monitor treatment response. The ion ampliseq cancer hotspot panel v2 allows translational and disease researchers to fasttrack oncology research by surveying hotspot regions of 50 oncogenes and tumor suppressor genes, with wide coverage of the kras, braf and. A total of 20 variants were identified in 12 genes. The interactivity in this form is not designed for use in a browser window.
This research panel, with improved primer design, contains 207 primer pairs in a. Ion ampliseq ngs panels by thermo fisher and the ion s5 xl system provide the ability to create custom gene panels. This panel has been developed as an rna complement to the dna focused ion ampliseq cancer hotspot panel v2. Ion ampliseq comprehensive cancer panel facilitates broad oncology surveys using only 40 ng of dna with 16,000 primer pairs multiplexed into just 4 pools. Percent mutant allelic frequencies are also listed. Pannello cancer hotspot ampliseq for illumina download. Molecular characterization of serous ovarian carcinoma using.
Building on the mutations included in our original ion ampliseq cancer. Ampliseq for illumina cancer hotspot panel v2 reference guide comprehensive information on the ampliseq for illumina cancer hotspot panel v2, including a detailed protocol. The nebnext direct cancer hotspot panel is designed to enrich for dna fragments across 190 common cancer targets from 50 genes, encompassing approximately 40 kb of sequence and including over 18,000 cosmic features. Baseline noise levels using the ion ampliseq cancer panel.
Eleven 55% were silent alterations and nine 45% were missense mutations. How effective and reliable would ion ampliseq cancer hotspot panel v2 be for identifying variants of oncogenes and tumor suppressors genes in xenograft tumor. Here we report the analytical validation of the ion ampliseq v2 cancer panel acp in plasma ctdna samples. Validating ngs library preparation with ion ampliseq kit. Ion ampliseq dna and rna library preparation user guide. Targeted nextgeneration sequencing of 50 cancerrelated. Download ampliseq for illumina direct ffpe dna kit reference guide.
Ion ampliseq sample id panel thermo fisher scientific. Use of the ion ampliseq cancer hotspot panel in clinical. The cnvs were detected using the control sequence data provided by thermo fisher scientific as a. Jan 16, 2020 one panel is the ion ampliseq cancer hotspot panel v2, which has been previously used for gc genotyping in a clinical cancer research 11. As a result of its flexibility, ion ampliseq technology enables researchers to zoomin on specific hotspot mutation sites using a panel such as the. The reads were mapped to the hg19 homo sapiens reference genome and adjusted to the specific amplicon target regions of the ion ampliseq cancer hotspot panel v2 deposited in the chp2. The ion ampliseq cancer hotspot panel v2 allows translational and disease researchers to fasttrack oncology research by surveying hotspot regions of 50. Ampliseq for illumina cancer hotspot panel v2 50 hotspot cancer. Validation of two nextgeneration sequencing cancer panels. Ion ampliseq direct ffpe dna kit ion torrent dual barcode kit 196 ioncode barcode adapters 84 kit ion xpress barcode adapters kits ion library equalizer kit ion ampliseq readytouse panels ion ampliseq madetoorder and community panels. Using this panel, we identified 11 mutations in 8 of the. Aug 26, 2015 now that you know a little bit about what ion ampliseq targeted sequencing has to offer and how it works, feel free to play with our design tool after all it is completely free to try. The ion ampliseq cancer hotspot panel v2 is a single pool of primers used to perform multiplex pcr for preparation of amplicon.
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