Cancer Gene Sequencing. A poster describing a single assay capable of characterizing both the genome and the transcriptome of diverse tumor types using targeted, deep sequencing will improve the application of personalized medicine to cancer. Clarity LIMS Protocols Prepare Library. A targeted deep sequencing assay identifies multidrug-resistant tuberculosis strains responsible for silent outbreaks. T1 - Targeted deep sequencing of urothelial bladder cancers and associated urinary DNA. Department of Internal Medicine, Korea University Anam Hospital, Korea University College of … "Adverse variants/mutations" in PV included ASXL1, SRSF2, and IDH2 and in ET SH2B3, SF3B1, U2AF1, TP53, IDH2, and EZH2; combined prevalence was 15% and 15%, respectively. Robertson Mackenzie 1, Stefan Kommoss 2,3, Boris J. Winterhoff 4, Benjamin R. Kipp 4, Joaquin J. Garcia 4, Jesse Voss 4, Kevin Halling 4, Anthony Karnezis 2, Janine Senz 2, Winnie Yang 1, … 30 … Highly targeted single-gene sequencing is accurate, fast, and affordable with Sanger sequencing. The genomic landscape of the 49 patients with BTC … Successful sequencing was defined when there was at least 100x average depth of coverage for >80 % of amplicons sequenced. Integration of targeted DNA capture assays and next-generation deep resequencing improves the ability to identify clinically and biologically relevant mutations. S1). Targeted deep sequencing of fragmented DNA by TAm-Seq. 3.1. Author information. Gene sequencing can be accomplished using several different DNA sequencing methods, depending on the scale.Highly targeted single-gene sequencing is accurate, fast, and affordable with Sanger sequencing. 0000004265 00000 n
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A myeloid neoplasm-relevant 27-gene panel was used for next-generation sequencing of bone marrow or whole blood DNA and conventional tools were used for analysis. Terra L. Lasho, Terra L. Lasho Among 32 patients with stage IV and R2 resection (a non‑radical resection), 21 patients underwent conventional chemotherapy (mGEMOX), while the remaining 11 patients received a personalized targeted agent. It is useful in population genetics since it can target a large diversity of organisms. Draft sequences of the human genome (3000 Mb) were published in 2001 by a public consortium led by Eric Lander and Francis Collins and a private corporation led by Venter. 0000007034 00000 n
| Here, we present the first results from an ongoing study involving a prospectively accrued… We conclude that targeted deep sequencing in PV and ET allows for genetic risk stratification that is independent of clinically derived prognostic models. Please enable it to take advantage of the complete set of features! Off-target sites were validated by inducing double-strand break (DSB) of DNA in a cell and inspecting the DNA mutations at the potential off-target sites, which were obtained from Digenome-seq, using targeted deep sequencing (Cho, S. W. et al. They identify possible off-target … It also enables deeper analysis of results than WGS and other survey approaches. A panel of SMs was validated by targeted deep‐sequencing of tumour DNA from 956 patients with UBC. Loscocco GG, Guglielmelli P, Vannucchi AM. Featured Coronavirus NGS Workflows. 2017 Apr;31(4):837-845. doi: 10.1038/leu.2016.307. Targeted sequencing studies focus on a select set of genes or gene regions that have known associations with cancer. USA.gov. h�b```b``1d`e`��� ̀ �@16� Deep sequencing is useful for studies in cancer, microbiology, and other research involving analysis of rare cell populations. Therefore, pTMB could act as an invaluable biomarker in the setting of both clinical trials and practice outside of trials based on its reliable performance in mitigating the purity-related bias. Targeted sequencing is a rapid and cost-effective way to detect known and novel variants in selected sets of genes or genomic regions. National Center for Biotechnology Information, Unable to load your collection due to an error, Unable to load your delegates due to an error. Myllykangas S(1), Ji HP. Deep sequencing refers to sequencing a genomic region multiple times, sometimes hundreds or even thousands of times. AU - Ward, Douglas G. AU - Gordon, Naheema S. AU - Boucher, Rebecca H. AU - Pirrie, Sarah J. 2020 Dec 1;10(4):259. doi: 10.3390/jpm10040259. Using targeted deep sequencing, mutations in 29 genes associated with CLL and/or the BCR signaling pathway were assessed in patients with CLL who developed resistance to BTK inhibition with ibrutinib/acalabrutinib at a single institution. The study group included 29 patients with BTKi‐resistant CLL, 23 patients with disease progression, and 6 patients with Richter … Targeted deep sequencing of cell-free DNA in serous body cavity fluids with malignant, suspicious, and benign cytology. trailer
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In both Mayo Clinic and Italian cohorts, leukemic or fibrotic progression was also predicted by adverse variants/mutations. Targeted deep sequencing approach. Targeted deep sequencing in primary myelofibrosis Clinical Trials & Observations. Yang SR (1), Mooney KL (1), Libiran P (1), Jones CD (1), Joshi R (1), Lau HD (1), Stehr H (1), Berry GJ (1), Zehnder JL (1), Long SR (1), Kong CS (1), Kunder CA (1). Hematology Am Soc Hematol Educ Program. This method generally requires less sample input and produces a smaller amount of data than WGS, making analyses more manageable. Deep sequencing has enabled both the large‐scale identification of somatic mutations (SMs) in UBC 6 and the sensitive detection of SMs in urinary DNA 7-11. Clinical Application of Targeted Deep Sequencing in Metastatic Colorectal Cancer Patients: Actionable Genomic Alteration in K-MASTER Project Youngwoo Lee , 1 Soohyeon Lee , 1 Jae Sook Sung , 2 Hee-Joon Chung , 2 Ah-reum Lim , 1 Ju Won Kim , 1 Yoon Ji Choi , 1 Kyong Hwa Park , 1 and Yeul Hong Kim 1, 2 According to our previous study (19), this panel of targeted deep sequencing consisted of 4,557 exons of 365 tumor‑associated genes, and 45 introns from 25 genes where frequent gene fusions could be captured in cancer (Table SIII). J Pers Med. Here, we used targeted strain-level deep sequencing to uncover the strain dynamics within a host-associated microbial community using the honey bee gut microbiome as a model system. Polycythemia vera (PV) is characterized by JAK2 and essential thrombocythemia (ET) by JAK2, calreticulin (CALR), and myeloproliferative leukemia virus oncogene (MPL) mutations; we describe the occurrence and prognostic relevance of DNA sequence variants/mutations other than JAK2/CALR/MPL. See this image and copyright information in PMC. Conventional targeted sequencing methods eliminate many of the benefits of nanopore sequencing, such as the ability to accurately detect structural variants or epigenetic modifications. Conflict-of-interest disclosure: The authors declare no competing financial interests. | Targeted deep resequencing of the human cancer genome using next-generation technologies. Topics: dna, leukemia, massively-parallel genome sequencing, mutation, myelofibrosis, polycythemia vera, thrombocythemia, hemorrhagic, protein p53, asxl1 gene, idh2 … Clipboard, Search History, and several other advanced features are temporarily unavailable. Lighezan DL, Bojan AS, Iancu M, Pop RM, Gligor-Popa Ș, Tripon F, Cosma AS, Tomuleasa C, Dima D, Zdrenghea M, Fetica B, Ioniță I, Gaál IO, Vișan S, Mirea AM, Popp RA, Florea M, Araniciu C, Petrescu L, Pop IV, Bănescu C, Trifa AP. HHS TruSight Tumor 15. Kinome Revealed through Targeted Deep Sequencing Zhi Jiang Zang1,2, Choon Kiat Ong3, Ioana Cutcutache4, Willie Yu3, Shen Li Zhang2, Dachuan Huang 3, Lian Dee Ler , Karl Dykema5, Anna Gan3, Jiong Tao2,6, Siyu Lim7, Yujing Liu2,8, P. Andrew Futreal9, Heike Grabsch10, Kyle A. Furge5, Liang Kee Goh2, Steve Rozen4, Bin Tean Teh3,11, and Patrick Tan1,2,12,13 Abstract Genetic … Enables deep sequencing at high coverage levels for rare variant identification; Compared to broader approaches, such as whole-genome sequencing, targeted sequencing is a more cost-effective method for investigating areas of interest. Performing single-plex amplification with each of these primer pairs would … This webinar is brought to you by the Science/AAAS Custom Publishing Office. Targeted deep sequencing 2021 Jan;133(1-2):52-61. doi: 10.1007/s00508-020-01761-3. We undertook hotspot sequencing of 50 genes PubMed. 2020 Dec 4;2020(1):440-449. doi: 10.1182/hematology.2020000129. NextSeq 550 NextSeq … Candidate sites were amplified using Phusion polymerase (New England Biolabs) then … Illumina Stranded Total RNA Prep with Ribo-Zero Plus Sequence. 55 0 obj
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According to our previous study (19), this panel of targeted deep sequencing consisted of 4,557 exons of 365 tumor‑associated genes, and 45 introns from 25 genes where frequent gene fusions could be captured in cancer (Table SIII). Standard Agilent protocols were used to design the target capture for a total of ~105 kb of sequence representing the four interferon pathway … Targeted sequencing is more cost-effective than whole genome sequencing (WGS). The Oncologist is committed to helping physicians excel in the constantly changing fields of oncology and hematology through the publication of timely reviews, original studies, and commentaries on important developments. NCI CPTC Antibody Characterization Program. Targeted deep sequencing that can achieve high sequencing depth is crucial to accurately identify genomic variants in formalin-fixed paraffin-embedded samples with low tumor cell content and high heterogeneity (32–34), and has also been recognized as a practical method for clinical genetic alteration detection in many types of cancers (35–37). 2020. For SNV calling, we report EBCall, Mutect, Virmid and Strelka to be the most reliable somatic variant callers for both exome sequencing and targeted deep sequencing. Ayalew Tefferi, Ayalew Tefferi 1 Division of Hematology, Department of Internal Medicine, Search for other works by this author on: This Site. The TAS approach incorporates bioinformatics techniques to produce a large amount of data at a fraction of the … Targeted deep sequencing (>40x) of 4 prioritized genes in the interferon pathway was performed on an Illumina HiSeq2000 at the Center for Inherited Disease Research (CIDR) at Johns Hopkins University (see Supplementary methods). The deep coverage offered by targeted resequencing allows for higher sensitivity to call variants in rare tumor subclones accurately. AU - Baxter, Laura. Results. We conclude that targeted deep sequencing in PV and ET allows for genetic risk stratification that is independent of clinically derived prognostic models. In both Mayo Clinic and Italian cohorts, leukemic or fibrotic progression was also predicted by adverse variants/mutations. 0000001509 00000 n
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Targeted deep sequencing helps distinguish independent primary tumors from intrapulmonary metastasis for lung cancer diagnosis. The specific … Our results revealed that amplicon sequencing of conserved protein-coding gene regions using species-specific primers is a cost-effective and accurate method for exploring strain-level … The experimental design of TDS can be schematically divided into five steps: (i) selection of the target sequence; (ii) template quantitation; (iii) library preparation; (iv) sequencing; and (v) data analysis. To amplify and sequence fragmented DNA, we designed primers to generate amplicons that tile regions of interest in short segments of about 150 to 200 bases (Fig. We conclude that targeted deep sequencing in PV and ET allows for genetic risk stratification that is independent of clinically derived prognostic models. Gene sequencing can be accomplished using several different DNA sequencing methods, depending on the scale. 0000001626 00000 n
The most popular … The experimental design of TDS can be schematically divided into five steps: (i) selection of the target sequence; (ii) template quantitation; (iii) library preparation; (iv) sequencing; and (v) data analysis. AU - Whalley, Celina M. In 1995, Craig Venter reported the sequence of Hemophilus influenza , a bacterial genome containing 1.8 Mb (million DNA bases). Targeted sequencing uses deep sequencing to detect known and novel variants within your region of interest. For example, deep sequencing is required to identify mutations within tumors, because normal cell contamination is common in cancer samples, and the tumors themselves likely contain multiple sub-clones of cancer cells. The sequencing workflow included a first study at diagnosis and a second study at follow-up. Deep coverage across the 15 genes most commonly mutated in solid tumors to detect rare variants. Computed tomographic images and histological staining were also used to validate tumor relationships. Targeted deep sequencing The characterization of mixed HIV-1 populations is a key question in clinical and basic research settings. Using targeted deep sequencing, mutations in 29 genes associated with CLL and/or the BCR signaling pathway were assessed in patients with CLL who developed resistance to BTK inhibition with ibrutinib/acalabrutinib at a single institution. Using this … 7 authors. 0000016881 00000 n
In brief, indexed sequencing libraries were prepared from 120 ng of sheared supernatant cfDNA. 0000101708 00000 n
Next-generation sequencing technologies have revolutionized … Kim SY, Bae SH, Bang SM, Eom KS, Hong J, Jang S, Jung CW, Kim HJ, Kim HY, Kim MK, Kim SJ, Mun YC, Nam SH, Park J, Won JH, Choi CW. 0000004240 00000 n
Onco Targets Ther. Targeted deep sequencing approach. Paired … Researchers in the UK have developed a targeted sequencing approach to detect mutations in circulating tumor DNA that they believe could eventually be developed as a clinical assay for early cancer diagnosis or to monitor disease progression and treatment response.. Their strategy, tagged-amplicon deep sequencing, or TAm-Seq, is a two-step amplification process that combines the … However, whole genome sequencing at sufficient depth to detect SMs at low mutant allele frequencies (MAFs) remains expensive; thus, to make a test affordable and interpretable, targeted sequencing of the … Subjects: Clinical Trials and Observations, Myeloid Neoplasia. … Targeted Deep Sequencing Reveals Clinically Relevant Subclonal IgHV Rearrangements in Chronic Lymphocytic Leukemia. Mucinous ovarian tumors represent a distinct histotype of epithelial ovarian cancer. Targeted deep sequencing for 48 tumor‐related genes was applied to 153 samples from 55 lung cancer patients obtained from six sources: Formalin‐fixed paraffin‐embedded (FFPE) tumor tissues, pleural effusion supernatant (PES) and pleural effusion cell sediments (PEC), white blood cells (WBCs), oral epithelial cells (OECs), and plasma. Targeted resequencing enables researchers to focus on regions that are most likely to be involved in the phenotype under study, conserving … 0000005410 00000 n
Individual cases were manually reviewed to evaluate overall sequencing quality (e.g., the number of variant calls due to sequencing artifacts [ 26 ], percentage of reads mapping to target region, etc. Google Scholar. Deep sequencing refers to the general concept of aiming for high number of unique reads of each region of a sequence. 0000004809 00000 n
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The used protocol is detailed in Section 2, and below are distinguished aspects of each step. Open Access; Published: 05 February 2016 Chronic lymphocytic leukemia. Targeted analysis sequencing (sometimes called target amplicon sequencing) (TAS) is a next-generation DNA sequencing technique focusing on amplicons and specific genes. Targeted deep sequencing and variant calling. "Adverse variants/mutations" were identified by age-adjusted multivariable analysis of impact on overall, leukemia-free, or myelofibrosis-free survival. The sequencing technology that enabled these accomplishments was based on a primer extension method invented by Nobel Laureate … PerkinElmer offers a complete line of NEXTFLEX ® library preparation kits to meet your targeted sequencing needs. 0000000956 00000 n
Buxhofer-Ausch V, Heibl S, Sliwa T, Beham-Schmid C, Wolf D, Geissler K, Krauth MT, Krippl P, Petzer A, Wölfler A, Melchardt T, Gisslinger H. Wien Klin Wochenschr. 0000044339 00000 n
This site needs JavaScript to work properly. MiniSeq Benchtop Sequencer. Coverage in DNA sequencing is the number of unique reads that include a given nucleotide in the reconstructed sequence. with targeted deep sequencing might have potential strength in predicting ICI responsiveness due to its enhanced sensitivity for hard-to-detect variants at low- allele fraction. Mutational profile screening at diagnosis was done with a customized NGS myeloid panel of 32 genes frequently mutated in myeloid diseases,13 (Online Supplementary Table S2) and NPM1 analysis was carried out with qPCR.14. Targeted deep sequencing was performed on 49 patients with BTC, to whom biologic agents were recommended. Targeted deep sequencing and variant calling. �����. 0000008319 00000 n
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Concept of aiming for high number of mutations did not provide additional prognostic information on the Management of Neoplasms... Like email updates of new Search results the authors declare no competing financial interests the of. Blood samples clipboard, Search History, and the depth of coverage helps in false! And Observations, myeloid Neoplasia known associations with cancer the scale kits to meet your sequencing! Detailed in Section 2, and benign cytology single-gene sequencing is more cost-effective than whole sequencing! Lymphocytic leukemia chemotherapy before surgery, there is an unmet need for noninvasive predictive biomarkers of response the (. Of sheared supernatant cfDNA … coverage in DNA sequencing is a key in. Body cavity fluids with malignant, suspicious, and other research involving analysis of rare populations. Cost-Effective than whole genome sequencing ( WGS ) panel was used for next-generation sequencing of bone marrow or blood! 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