Genetic analyses of earlyonset alzheimers disease using. The ion proton 409 gene panel detected all expected snvs in the samples with itpgm 46 gene panel sequencing results unless there was amplicon failure in the 409 gene panel. The cdna synthesis protocol can be completed in five. The ion ampliseq exome rdy panel also offers a comprehensive view of 20,000 genes, encompassing approximately 1% of the genome yet containing approximately 85% of diseasecausing mutations in disease research. Rnaseq panels choose from over 20,000 genes to survey gene expression fold changes starting with as little as 500 pg of unfixed rna or 5 ng of ffpe rna. Targeted gene sequencing panels are useful tools for analyzing specific mutations in a given sample. Description cystic fibrosis is one of the most common, fatal genetic diseases in the united states and is caused by mutations in the cystic fibrosis transmembrane regulator cftr gene. Jun 26, 2015 dna samples 10 ng of each were treated to obtain the ion proton ampliseq library for one of the gene panels as appropriate. Dna samples 10 ng of each were treated to obtain the ion proton ampliseq library for one of the gene panels as appropriate. The accuracy for homopolymer repeats of 5 repeats in length was 98%. Genetic profiling as a clinical tool in advanced parathyroid. The panel facilitates the detection of actionable and targetable mutations in lung, colorectal, thyroid, brain and skin cancer melanomafor appropriate. Since all diseasespecific gene panels were designed for iontorrent.
Apr 07, 2015 we first analyzed the uniformity of each mps run and sample. Ion xpress barcode adapters life technologies were ligated to the amplicons. The initial 614 sequential clinical samples were tested over a 2. A comparison of illumina and ion torrent sequencing platforms. This panel uses archers proprietary anchored multiplex pcr ampbased enrichment to detect all fusions associated with the genes in a single sequencing assay, even without prior. The first version of the panel, the ion ampliseq colon and lung cancer research panel, was tested and verified by the onconetwork consortium, with 155 unique ffpe samples. Nov 21, 2016 mutation analysis with a 7 gene mutation panel using realtime pcr and thyroseq v2 on the ion torrent pgm sequencer showed that. Analyzing fusion genes using nextgeneration sequencing.
Sequencing gene panels with ion torrent technology is complete. In our lab, two ngs panels on ion torrent are in daily use in nsclc patients. It comprises a 50 gene hotspot panel for the ion torrent platform with an average coverage depth of x that was well able to derive informative data from dna extracted from ffpe tissue. Ion ampliseq colon and lung cancer research panel v2 and ion. Ion ampliseq rna cancer panel thermo fisher scientific. The panel facilitates the detection of actionable and targetable mutations in lung, colon, rectum, thyroid, brain and. The ion ampliseq colon and lung cancer research panel v2 is readytouse and optimized for data analysis with torrent suite and ion reporter software. Methods the ion torrent panel was first verified on cell lines and on control samples and then prospectively applied to routine specimens n114, with sanger sequencing as reference.
The panel facilitates the detection of actionable and targetable mutations in lung, colorectal, thyroid, brain and skin cancer. In 10% of samples, automated analysis identified a. The personal genetic information era dawned when james watson, who discovered the structure of dna, was recorded as the first person to analyze personal. Ampliseq for illumina cancer hotspot panel v2 50 hotspot cancer. With allexon coverage of 409 genes, the ion ampliseq comprehensive cancer panel delivers fast, ffpecompatible, target selection for a broad survey of key genes. Accelamplicon ngs panels utilize multiple amplicons in a single tube, using a rapid, 2hour workflow to prepare readytosequence libraries, they combine the easiest, fastest workflow with flexible content to accelerate your variant discovery and screening. 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. The ion one touch and one touch es were used to prepare and enrich templates and enable testing via ion sphere particles on a semi conductor chip. The ion ampliseqcancer hotspot panel v2 is a single pool of primers used to perform multiplex pcr. Nextgeneration sequencing was conducted using an ion torrent cancer 50 gene mutation testing panel.
Targeted next generation sequencing as a reliable diagnostic. Based on the results of the mutations and changes identified, targetted therapy may. Ion ampliseq cancer hotspot panel v2 thermo fisher scientific. This includes the 739 cosmic mutations from 46 genes in the first ion ampliseqcancer panel along with added hotspot mutations from significant cancer genes. Aug 29, 2014 a new gene panel validation control workflow supports several types of data sets, including ion torrent ampliseq comprehensive cancer panel, illumina trusight cancer panel, as well as custom. You have the ion ampliseq gene selection technology, the ion pgm sequencing system and also the ion reporter analysis software. Ion ampliseq transcriptome human gene expression kit 384 rxns a26327 ion xpress barcode adapters 116 kit 1 kit 4471250 includes ion ampliseq transcriptome human gene expression core panel, ion ampliseq library plus kit, and invitrogen superscript vilo cdna synthesis kit. We also participated in thermo fisher scientifics international validation program for the final version of this fusion panel. The ion ampliseq cancer hotspot panel v2 is a multiplex pcrbased library preparation method by which 207 amplicons covering approximately 2,800 cosmic mutations from 50 oncogenes and tumor suppressor genes are selectively analyzed. Ngs and the ion ampliseq cancer hot spot panel v2 by ion torrent life technologies. Comprehensive gene panels provide advantages over clinical. A new gene panel validation control workflow supports several types of data sets, including ion torrent ampliseq comprehensive cancer panel, illumina trusight cancer panel, as well as custom. The ion ampliseqcancer hotspot panel v2 is designed to amplify 207 amplicons covering approximately 2,800 cosmic mutations from 50 oncogenes and tumor suppressor genes.
Targeted ngs platforms for genetic screening and gene discovery. This assay was performed with 10 ng of dna using the ion ampliseq cancer hotspot panel v2 chpv2 ampliseq, life technologies on the ion torrent pgm platform. Aug 10, 2017 though illumina has largely dominated the rnaseq field, the simultaneous availability of ion torrent has left scientists wondering which platform is most effective for differential gene expression dge analysis. Recently, we implemented the multiplex pcrbased ion ampliseq cancer hotspot panel 200 amplicons in 50 genes to evaluate egfr, kras, and braf in lung and colorectal adenocarcinomas. Sarscov2 gene variants provide clues to coronavirus. Clinical application of a custom ampliseq library and ion. Ion training courses cover library preparation, template preparation, sequence generation, and data analysis and are offered at the training centers in carlsbad, california and frederick. Ion ampliseq predesigned panels for inherited disease research. Nextgeneration sequencing in thyroid cancer journal of. Levy, md, discusses the mutations that are tested in nonsquamous nonsmall cell lung cancer and the role of pdl1 testing. Myh7, mybpc3, myl2, lmna, scn5a, tnnt2, tnni3 and tpm1. The readytouse panel saves you the time and effort of identifying targets, designing primers, and optimizing panels. Panel optimization for genexus system underway to further expedite ngs analysis of sarscov2 and to help meet growing customer demand, thermo fisher has begun to optimize the ion ampliseq sarscov2 research panel for the ion torrent genexus system.
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. Results the ion torrent panel detected mutant alleles at the 5% level on cell lines and correctly classified all control tissues. Many mutations in the amyloid precursor protein app and. The archer fusionplex solid tumor panel is a robust targeted sequencing assay to simultaneously detect and identify fusions and other mutations associated with over 50 genes linked to various carcinomas. Targeted gene sequencing focused panels targeting key genes. Cancer 50 gene panel test for cancer dr lal pathlabs.
Nextgeneration sequencing shows great promise by allowing rapid mutational analysis of multiple genes in human cancers. Accurate gene expression fold changes between samples leveraging the highly reproducible ion ampliseq technology to selectively amplify ion ampliseq rna cancer panel was developed as an rna complement to the ion ampliseq cancer hotspot panel v2. Clinical massively parallel nextgeneration sequencing. Dna was amplified using gene panel primer pools, ampliseq hifi mix thermo fisher, carlsbad, ca, usa and 1015 amplification cycles. The panel, created using the ion ampliseq designer software, was designed to identify diseasecausing mutations in the following genes. Added value of 50gene panel sequencing to distinguish. Ion ampliseq ngs panels thermo fisher scientific us. The uniformity of the read number for each mps run was. The ion ampliseq cftr panel is a 2 pool panel with 102 amplicons used for reamplification and analysis of the coding region of the cftr gene.
Personal genome business division the field of personal genetics is receiving attention as a core factor of the future medical paradigm such as precision medicine and preventive medicine. Each assay includes both a dna and rna panel, enabling detection of key cancer driver variations such as egfr, alk, ros1, braf, kras, ret, erbb2, and many others. Additionally, this panel targets the 50 genes selected in the focused ion ampliseq. The 541cancer gene panel includes the desired genes from every nccc investigator, which covers a broad spectrum of cancers and signaling pathways. Microsoft word faq cancer gene mutation panel 50 genes 121814. Tumor profiling gene mutation panel using realtime pcr and thyroseq v2 on the ion torrent pgm sequencer showed that. The distribution of the read numbers produced by each sequence run is shown in figure 1. The results revealed the complexity of tp53 mutations.
Dilutions 50, 10, 3, and 1% of dna extracted from ffpe cell line. Ion ampliseq cancer hotspot panel v2 just one tube. Distinguish multiple primary lung cancers from pulmonary metastases. 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. The panel facilitates the detection of actionable and targetable mutations in lung, colon, rectum, thyroid, brain and skin cancer for appropriate. The average length of the amplicons is 198 bp ranging from 124 bp to 255 bp. Gene panels can be purchased with preselected content or custom designed to include genomic regions. Targeted research panel investigating hotspot regions of 50 genes with known associations to cancer. The readlength as of february 2011 was 100 base pairs. Ampliseq for illumina cancer hotspot panel v2 50 hotspot. The panel contains 2 pools, containing a total of 247 amplicons 242 unique ones to detect 237 viral specific sarscov2 targets and 5 human gene expression controls to assess presence of the virus in a variety of sample types isolates, throat and nasal swabs and will cover all potential serotypes to help better understand epidemiology outbreaks. All patients with advanced pc were tested for hotspot panels using ngs panels including a 50 gene panel, a 409 gene panel if the standard 50 gene panel ion torrent, life technology was negative or a foundationone panel. The requirements for input material are relatively minor 20 ng dna from samples with at least 10% tumour cell percentage generating reproducible data with. Can the ion ampliseq cancer hotspot panel v2 be used for nexta.
The panel facilitates the detection of actionable and targetable mutations in lung, colorectal, thyroid, brain and skin cancer melanomafor appropriate diagnosis, prognosis and selection of therapy. Evaluation of a new ngs method based on a custom ampliseq. The panel contains 2 pools, containing a total of 247 amplicons 242 unique ones to detect 237 viral specific sarscov2 targets and 5 human gene expression controls to assess presence of the virus in a variety of sample types isolates, throat and nasal swabs and will cover all potential serotypes to help better understand epidemiology. Tp53 remains as the most frequently altered gene in high grade serous ovarian cancer and ion torrent personal genome machine pgm in combination with ion ampliseq cancer hotspot panel v2 were proven to be instrumental in identifying a wide range of genetic alterations simultaneously from a minute amount of dna.
This panel uses archers proprietary anchored multiplex pcr ampbased enrichment to detect all fusions associated with the genes in a single. Encompassing over 50% of the wellcome trust sanger institute cancer gene census, this is the most comprehensive cancer gene panel available. A total of 1,022 clinical samples were analyzed using the ion torrent pgm with the ion ampliseq cancer hotspot panel v2 50 gene hotspot panel. Focused panels contain a select set of genes or gene regions that have known or suspected associations with the disease or phenotype under study. Ion ampliseq panel genes covered average gene coverage panel. The amplicons were digested, barcoded and amplified using the ion ampliseq library kit 2. The ion torrent systems combine semiconductor sequencing technology with natural biochemistry to directly translate chemical information into digital data. Validation from a pool of 120 routine tumour samples characterised with a 50 gene mutation panel ion torrent pgm2 and confirmed by sanger sequencing andor cobas roche qpcr, 24 ffpe cases were selected representing colorectal cancer and 4 other solid tumour types. Sequencing initiative at the norris cotton cancer center.
Low cost sequencing of bac clones and other constructs e. Ion ampliseq inherited disease panel target gene list symbol disease col5a1 ehlersdanlos syndrome, classic type col5a2 ehlersdanlos syndrome, classic type col7a1 epidermolysis bullosa simplex col9a1 stickler syndrome crb1 leber congenital amaurosis crx retinitis pigmentosa ctdp1 congenital cataracts, facial dysmorphism, and neuropathy ctns. Mutation analysis with a 7 gene mutation panel using realtime pcr and thyroseq v2 on the ion torrent pgm sequencer showed that. Oct 14, 2014 the ion proton 409 gene panel detected all expected snvs in the samples with itpgm 46 gene panel sequencing results unless there was amplicon failure in the 409 gene panel. Molecular characterization of serous ovarian carcinoma using. The new ion torrent ampliseq rna fusion lung cancer research panel allows simultaneous sequencing of 70 alk, ret, ros1, and ntrk1 fusion transcripts associated with lung cancer as well as 5 and 3 alk gene expression.
The panel is a single pool of primers targeting 50 oncogenes and tumor suppressor. Molecular response to neoadjuvant chemotherapy in high. Multicenter validation of cancer gene panelbased nextgeneration. For me, it is important to have a whole integrated. Matthew keyser a next gen sequencing software workflow for. Sample to insight product offerings 38 rnascan o cataloged o custom o extended illumina o 12index o 96index 4 sets, for up to 384plex ion torrent o 12index o 96index panels indices at a glance analyzing fusion genes with nextgeneration sequencing technology, 11. In 64 sequence runs using the ion torrent pgm sequencer with ion 318chips, the mean number standard deviation of reads was 3. Sequencing data processing, alignment versus hg19, and. I on ampliseq panels for i nherited disease research. The panel facilitates the detection of actionable and targetable mutations in lung, colon, rectum, thyroid, brain and skin cancer for appropriate diagnosis, prognosis and selection of therapy.
Ion ampliseq ondemand panels enable custom panel design in smaller pack sizes from pretested genes for practical customization that helps reduce upfront cost and risk. Ion ampliseq transcriptome human gene expression kit. Alzheimers disease ad is the most common type of neurodegenerative dementia, but the cause of ad remained poorly understood. Ion ampliseq colon and lung cancer research panel v2 and. Identification of factors affecting the success of nextgeneration sequencing testing in solid tumors rashmi s. Ion torrent gene target library preparation and ngs sequencing. Previous investigations of this question have typically used reference samples derived from cell lines and brain tissue, and do not involve biological variability. Encompassing over 50 % of the wellcome trust sanger institute cancer gene census, this is the most comprehensive cancer gene panel available. False positives in multiplex pcrbased nextgeneration.
The myeloid panel is part of an integrated workflow that includes ampliseq for illumina polymerase chain reaction pcrbased library preparation, illumina sequencing by synthesis sbs, ngs technology, and automated analysis. Tumor profiling inherited disease panel target gene list symbol disease col5a1 ehlersdanlos syndrome, classic type col5a2 ehlersdanlos syndrome, classic type col7a1 epidermolysis bullosa simplex col9a1 stickler syndrome crb1 leber congenital amaurosis crx retinitis pigmentosa ctdp1 congenital cataracts, facial dysmorphism, and neuropathy. Hot spot cancer panels next generation sequencing genewiz. Ion ampliseq inherited disease panel target gene list. Automate data analysis with torrent suite software and find the biological meaning of your data with ion reporter software. Next generation bidirectional sequencing was performed on the ion torrent personal genome machine and analyzed with the torrent suite software. Apr 26, 2020 ion ampliseq technology delivers simple and fast library construction for affordable targeted sequencing of specific genes or genomic regions. The panel is optimized to run on the ion genestudio s5 systems. Based on ultrahighmultiplex pcr, ion ampliseq technology requires as little as 1 ng of input dna to target sets of genes, making sequencing of ffpe samples routine on ion pgm or ion s5 systems. Ion torrent offers an ampliseq cancer panel of 50 most common cancer genes with 2,800 cosmic mutations.
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