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Journal articles on the topic 'Low-frequency variant detection'

Author: Grafiati

Published: 4 June 2021

Last updated: 14 February 2022

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1

Hermann, Bernd Timo, Sebastian Pfeil, Nicole Groenke, et al. "DEEPGENTM—A Novel Variant Calling Assay for Low Frequency Variants." Genes 12, no. 4 (2021): 507. http://dx.doi.org/10.3390/genes12040507.

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Detection of genetic variants in clinically relevant genomic hot-spot regions has become a promising application of next-generation sequencing technology in precision oncology. Effective personalized diagnostics requires the detection of variants with often very low frequencies. This can be achieved by targeted, short-read sequencing that provides high sequencing depths. However, rare genetic variants can contain crucial information for early cancer detection and subsequent treatment success, an inevitable level of background noise usually limits the accuracy of low frequency variant calling a

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Ura, Hiroki, Sumihito Togi, and Yo Niida. "Dual Deep Sequencing Improves the Accuracy of Low-Frequency Somatic Mutation Detection in Cancer Gene Panel Testing." International Journal of Molecular Sciences 21, no. 10 (2020): 3530. http://dx.doi.org/10.3390/ijms21103530.

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Cancer gene panel testing requires accurate detection of somatic mosaic mutations, as the test sample consists of a mixture of cancer cells and normal cells; each minor clone in the tumor also has different somatic mutations. Several studies have shown that the different types of software used for variant calling for next generation sequencing (NGS) can detect low-frequency somatic mutations. However, the accuracy of these somatic variant callers is unknown. We performed cancer gene panel testing in duplicate experiments using three different high-fidelity DNA polymerases in pre-capture amplif

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Weng, Li, Lin Wang, Xiao Chen, et al. "Detecting ultra low-frequency variants and gene fusions in lung cancer patients using an amplicon-based Firefly NGS method." Journal of Clinical Oncology 35, no. 15_suppl (2017): e23062-e23062. http://dx.doi.org/10.1200/jco.2017.35.15_suppl.e23062.

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e23062 Background: The analysis of EGFR, KRAS, and BRAF mutations and Alk fusion is critical for guiding targeted therapy selection, detecting drug resistance, and monitoring residual disease in patients with NSCLC. Designing next-generation sequencing (NGS) assays for detecting low-frequency variants, however, is an ongoing challenge. The limited availability of cfDNA combined with the breadth of coverage necessary to create meaningful, clinically-actionable results requires a solution with multiplex capacity which, in turn, requires greater technological sensitivity and specificity. Here we

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Sater, Vincent, Pierre-Julien Viailly, Thierry Lecroq, et al. "UMI-VarCal: a new UMI-based variant caller that efficiently improves low-frequency variant detection in paired-end sequencing NGS libraries." Bioinformatics 36, no. 9 (2020): 2718–24. http://dx.doi.org/10.1093/bioinformatics/btaa053.

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Abstract Motivation Next-generation sequencing has become the go-to standard method for the detection of single-nucleotide variants in tumor cells. The use of such technologies requires a PCR amplification step and a sequencing step, steps in which artifacts are introduced at very low frequencies. These artifacts are often confused with true low-frequency variants that can be found in tumor cells and cell-free DNA. The recent use of unique molecular identifiers (UMI) in targeted sequencing protocols has offered a trustworthy approach to filter out artefactual variants and accurately call low-f

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JARVI, S. I., M. E. FARIAS, D. A. LAPOINTE, M. BELCAID, and C. T. ATKINSON. "Next-generation sequencing reveals cryptic mtDNA diversity of Plasmodium relictum in the Hawaiian Islands." Parasitology 140, no. 14 (2013): 1741–50. http://dx.doi.org/10.1017/s0031182013000905.

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SUMMARYNext-generation 454 sequencing techniques were used to re-examine diversity of mitochondrial cytochrome b lineages of avian malaria (Plasmodium relictum) in Hawaii. We document a minimum of 23 variant lineages of the parasite based on single nucleotide transitional changes, in addition to the previously reported single lineage (GRW4). A new, publicly available portal (Integroomer) was developed for initial parsing of 454 datasets. Mean variant prevalence and frequency was higher in low elevation Hawaii Amakihi (Hemignathus virens) with Avipoxvirus-like lesions (P = 0·001), suggesting th

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Chien, Richard, Dumitru Brinza, Jian Gu, et al. "Comprehensive detection of ctDNA variants at 0.1% allelic frequency using a broad targeted NGS panel for liquid biopsy research." Journal of Clinical Oncology 35, no. 15_suppl (2017): e23065-e23065. http://dx.doi.org/10.1200/jco.2017.35.15_suppl.e23065.

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e23065 Background: Advances in non-invasive tumor biomarker research have shown that tumor cells release fragments of DNA called circulating tumor DNA (ctDNA) into peripheral blood. Somatic mutations representing the tumors could be successfully detected from isolated ctDNA, providing new potential for tumor sample assessment in addition to traditional tissue biopsy methods. However, the low amount of ctDNA in the blood, which can be less than 1% allelic frequency, presents significant challenges for reliable variant detection with NGS assays. Improvement of sequencing accuracy at low allelic

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Watson, Simon J., Matthijs R. A. Welkers, Daniel P. Depledge, et al. "Viral population analysis and minority-variant detection using short read next-generation sequencing." Philosophical Transactions of the Royal Society B: Biological Sciences 368, no. 1614 (2013): 20120205. http://dx.doi.org/10.1098/rstb.2012.0205.

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RNA viruses within infected individuals exist as a population of evolutionary-related variants. Owing to evolutionary change affecting the constitution of this population, the frequency and/or occurrence of individual viral variants can show marked or subtle fluctuations. Since the development of massively parallel sequencing platforms, such viral populations can now be investigated to unprecedented resolution. A critical problem with such analyses is the presence of sequencing-related errors that obscure the identification of true biological variants present at low frequency. Here, we report

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Huang, Jiaqi, Johannes-Matthias Löhr, Magnus Nilsson, et al. "Variant Profiling of Candidate Genes in Pancreatic Ductal Adenocarcinoma." Clinical Chemistry 61, no. 11 (2015): 1408–16. http://dx.doi.org/10.1373/clinchem.2015.238543.

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Abstract BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) has a poor prognosis. Variant profiling is crucial for developing personalized treatment and elucidating the etiology of this disease. METHODS Patients with PDAC undergoing surgery from 2007 to 2012 (n = 73) were followed from diagnosis until death or the end of the study. We applied an anchored multiplex PCR (AMP)-based next-generation sequencing (NGS) method to a panel of 65 selected genes and assessed analytical performance by sequencing a quantitative multiplex DNA reference standard. In clinical PDAC samples, detection of low-lev

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Verbist, Bie M. P., Kim Thys, Joke Reumers, et al. "VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering." Bioinformatics 31, no. 1 (2014): 94–101. http://dx.doi.org/10.1093/bioinformatics/btu587.

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Underhill, Hunter, David Nix, Christian Davidson, et al. "COMP-10. THE MUTATIONAL PROFILE OF GLIOBLASTOMA-DERIVED CELL-FREE DNA IN PLASMA REPRESENTS A DISTINCT SUBSET OF THE SOMATIC MUTATIONS PRESENT IN GLIOBLASTOMA SOLID TUMOR DNA." Neuro-Oncology 21, Supplement_6 (2019): vi63. http://dx.doi.org/10.1093/neuonc/noz175.253.

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Abstract Glioblastoma’s mutational landscape varies widely in the same tumor. Using conventional criteria to identify mutations from a focal tissue specimen (e.g., variant allele frequency > 5%) undersamples glioblastoma’s broad clonal diversity, which may limit detection of glioblastoma-derived circulating cell-free DNA in plasma (i.e., circulating tumor DNA; ctDNA). Here, we sought to enhance somatic variant identification in solid tumor DNA to improve detection and characterize glioblastoma-derived ctDNA. Tumor DNA and plasma cell-free DNA (collected < 24 hours prior to the surgical p

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Ciferska, H., K. Pavelcova, J. Vachek, and B. Stiburkova. "POS0354 DETECTION OF ABCG2 VARIANTS IN ENCODING OF URATE TRANSPORTERS ASSOCIATED WITH THE HYPERURICEMIA IN HAEMODIALYSIS PATIENTS." Annals of the Rheumatic Diseases 80, Suppl 1 (2021): 407.2–408. http://dx.doi.org/10.1136/annrheumdis-2021-eular.2084.

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Background:Hyperuricemia is associated with gout, hypertension, cardiovascular diseases and renal disease. The presence of chronic kidney disease (CKD) is associated with low excretion of the uric acid as the homeostasis in maintaining of serum levels of uric acid is impaired. Progression of CKD is connected to hyperuricemia and lowering levels of the uric acid is one of the most important goals in clinical treatment. Dysfunctional variants of ATP-binding cassette transporter subfamily G member 2 (ABCG2), a major urate transporter in the kidney and intestine, are the major causes of hyperurice

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Tiong, Ing Soo, Clarissa Wilson, Satwica Yerneni, et al. "Mutational and Copy Number Profiling of Circulating Tumor DNA in Acute Myeloid Leukemia Using Targeted Next Generation Sequencing." Blood 136, Supplement 1 (2020): 39–40. http://dx.doi.org/10.1182/blood-2020-138933.

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The assessment of circulating tumor DNA (ctDNA), released by tumor cells undergoing apoptosis or necrosis, has established utility in solid tumors due to the advantage of a non-invasive "liquid biopsy" replacing multiple site-specific biopsies. However, its role in acute myeloid leukemia (AML) is uncertain, where a significant proportion of variants detected in the bone marrow (BM) may not be detected in ctDNA (Short, Blood Adv 2020). We have previously demonstrated the possibility of comprehensive genomic characterization of lymphoid malignancy from ctDNA using a single targeted next generati

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Udar, Nitin, Robert Haigis, Thomas Gros, et al. "A novel approach to improve detection of somatic DNA variants in solid tumors by next-generation sequencing from FFPE samples." Journal of Clinical Oncology 31, no. 15_suppl (2013): e22177-e22177. http://dx.doi.org/10.1200/jco.2013.31.15_suppl.e22177.

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e22177 Background: Low frequency variant detection by sequencing is a highly desired goal for therapy selection in cancer especially the detection of actionable targets. The lower limit of detection using Sanger sequening is ~20% minor allele frequency (MAF). Deep sequencing of target genes using next generation sequencing (NGS) is gaining popularity. Formalin Fixed Paraffin Embedded (FFPE) tissue is the most common sample type in solid tumor histopathology. However, because the fixation process fragments DNA and damages it at varying frequencies, downstream processes can potentially misclassi

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Kim, Jerry H., Gail P. Jarvik, Brian L. Browning, et al. "Exome Sequencing Reveals Novel Rare Variants in the Ryanodine Receptor and Calcium Channel Genes in Malignant Hyperthermia Families." Anesthesiology 119, no. 5 (2013): 1054–65. http://dx.doi.org/10.1097/aln.0b013e3182a8a998.

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Abstract Background: About half of malignant hyperthermia (MH) cases are associated with skeletal muscle ryanodine receptor 1 (RYR1) and calcium channel, voltage-dependent, L type, α1S subunit (CACNA1S) gene mutations, leaving many with an unknown cause. The authors chose to apply a sequencing approach to uncover causal variants in unknown cases. Sequencing the exome, the protein-coding region of the genome, has power at low sample sizes and identified the cause of over a dozen Mendelian disorders. Methods: The authors considered four families with multiple MH cases lacking mutations in RYR1 a

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van Schaik, Ron HN, Ilse P. van der Heiden, John N. van den Anker, and Jan Lindemans. "CYP3A5 Variant Allele Frequencies in Dutch Caucasians." Clinical Chemistry 48, no. 10 (2002): 1668–71. http://dx.doi.org/10.1093/clinchem/48.10.1668.

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Abstract Background: Enzymes of the cytochrome P450 3A (CYP3A) family are responsible for the metabolism of &gt;50% of currently prescribed drugs. CYP3A5 is expressed in a limited number of individuals. The absence of CYP3A5 expression in ∼70% of Caucasians was recently correlated to a genetic polymorphism (CYP3A5*3). Because CYP3A5 may represent up to 50% of total CYP3A protein in individuals polymorphically expressing CYP3A5, it may have a major role in variation of CYP3A-mediated drug metabolism. Using sequencing, have been identified (Hustert et al. Pharmacogenetics 2001;11:773–9; Kueh

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Šálek, Milan, and Beáta Szabó-Takács. "Comparison of SAFNWC/MSG Satellite Cloud Type with Vaisala CL51 Ceilometer-Detected Cloud Base Layer Using the Sky Condition Algorithm and Vaisala BL-View Software." Atmosphere 10, no. 6 (2019): 316. http://dx.doi.org/10.3390/atmos10060316.

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Ceilometer detection can be used to determine cloud type based on cloud layer height. Satellite observations provide images of clouds’ physical properties. During the summer and winter of 2017, Satellite Application Facility on support to Nowcasting/Very Short-Range Forecasting Meteosat Second Generation (SAFNWC/MSG) cloud type was compared to cloud base layers based upon a sky condition algorithm of Vaisala CL51 ceilometer and the BL-View applied range-variant smoothing backscatter profile at the National Atmospheric Observatory in Košetice, Czech Republic. This study investigated whether the

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DiNardo, Courtney D., Larissa A. Korde, and Matthew B. Yurgelun. "A Case-Based Approach to Understanding Complex Genetic Information in an Evolving Landscape." American Society of Clinical Oncology Educational Book, no. 41 (June 2021): e328-e338. http://dx.doi.org/10.1200/edbk_321041.

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The rapid integration of highly sensitive next-generation sequencing technologies into clinical oncology care has led to unparalleled progress, and yet these technological advances have also made genetic information considerably more complex. For instance, accurate interpretation of genetic testing for germline/inherited cancer predisposition syndromes and somatic/acquired pathogenic variants now requires a more nuanced understanding of the presence and incidence of clonal hematopoiesis and circulating tumor cells, with careful evaluation of pathogenic variants occurring at low variant allele

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Mansukhani, Sonia, Louise J. Barber, Dimitrios Kleftogiannis, et al. "Ultra-Sensitive Mutation Detection and Genome-Wide DNA Copy Number Reconstruction by Error-Corrected Circulating Tumor DNA Sequencing." Clinical Chemistry 64, no. 11 (2018): 1626–35. http://dx.doi.org/10.1373/clinchem.2018.289629.

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Abstract BACKGROUND Circulating free DNA sequencing (cfDNA-Seq) can portray cancer genome landscapes, but highly sensitive and specific technologies are necessary to accurately detect mutations with often low variant frequencies. METHODS We developed a customizable hybrid-capture cfDNA-Seq technology using off-the-shelf molecular barcodes and a novel duplex DNA molecule identification tool for enhanced error correction. RESULTS Modeling based on cfDNA yields from 58 patients showed that this technology, requiring 25 ng of cfDNA, could be applied to &gt;95% of patients with metastatic color

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Boulos, Hala, Robert Tell, Nike Beaubier, and Richard Blidner. "Greater than two coexisting mutations in KRAS and NRAS identified in the circulating tumor DNA fraction of liquid biopsies by NGS and confirmed with ddPCR." Journal of Clinical Oncology 38, no. 15_suppl (2020): e15563-e15563. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.e15563.

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e15563 Background: Liquid biopsies are increasingly utilized as a non-invasive tool in precision oncology to assess tumor mutational profiles in order to select targeted therapies, detect treatment resistance, and monitor disease progression in cancer patients. Additionally, liquid biopsies may provide a more comprehensive representation of tumor heterogeneity than standard tissue biopsies. However, limitations such as scarcity of circulating tumor DNA (ctDNA) and/or variants at low frequencies can be technically challenging to detect by next-generation sequencing (NGS) assays. Here, we use NG

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de Lima, Lucas F., André L. Ferreira, Marcelo D. T. Torres, William R. de Araujo, and Cesar de la Fuente-Nunez. "Minute-scale detection of SARS-CoV-2 using a low-cost biosensor composed of pencil graphite electrodes." Proceedings of the National Academy of Sciences 118, no. 30 (2021): e2106724118. http://dx.doi.org/10.1073/pnas.2106724118.

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COVID-19 has led to over 3.47 million deaths worldwide and continues to devastate primarily middle- and low-income countries. High-frequency testing has been proposed as a potential solution to prevent outbreaks. However, current tests are not sufficiently low-cost, rapid, or scalable to enable broad COVID-19 testing. Here, we describe LEAD (Low-cost Electrochemical Advanced Diagnostic), a diagnostic test that detects severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within 6.5 min and costs $1.50 per unit to produce using easily accessible and commercially available materials. LEAD

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Gan, Qiang, Zhen Cui, Simin Tang, Michael Joseph Powell, Aiguo Zhang, and Michael Y. Sha. "A novel XNA-based NGS panel for cancer diagnostics." Journal of Clinical Oncology 38, no. 15_suppl (2020): e16142-e16142. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.e16142.

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e16142 Background: Identification of genetic variants with low allelic frequency using NGS method is confounded by the complexity of the human genome sequence and by bias and errors that arise during library preparation, sequencing and analysis. To overcome this, we developed a novel NGS approach employing a modified backbone nucleic acid molecule, Xenonucleic Acid (XNA) to enrich the target mutant before the sequencing. XNA enables to efficiently and selectively suppress wild type targeted DNA amplification but amplify targeted mutant alleles. Methods: We developed this XNA-based NGS for dete

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Kurtz, David M., Joanne Soo, Stefan Alig, et al. "Phased Variant Enrichment for Enhanced Minimal Residual Disease Detection from Cell-Free DNA." Blood 134, Supplement_1 (2019): 552. http://dx.doi.org/10.1182/blood-2019-131267.

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Background: Circulating tumor DNA (ctDNA) is an emerging biomarker in non-Hodgkin lymphomas (NHLs). Current methods for ctDNA minimal residual disease (MRD) are limited by two factors - low input DNA amounts and high background error rates. VDJ sequencing (i.e., IgHTS) has low background but is limited by low cell-free DNA (cfDNA). Tracking multiple mutations via CAPP-Seq improves sensitivity, but detection is limited by background errors. Clustered mutations have been described in multiple cancers including NHLs and potentially have lower error rates. We explored clustered mutations from whol

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Tahir, Muhammad, Mingchu Li, Naeem Ayoub, and Muhammad Aamir. "Efficacy Improvement of Anomaly Detection by Using Intelligence Sharing Scheme." Applied Sciences 9, no. 3 (2019): 364. http://dx.doi.org/10.3390/app9030364.

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Computer networks are facing threats of ever-increasing frequency and sophistication. Encryption is becoming the norm in both legitimate and malicious network traffic. Therefore, intrusion detection systems (IDSs) are now required to work efficiently regardless of the encryption. In this study, we propose two new methods to improve the efficacy of the Cisco Cognitive Threat Analytics (CTA) system. In the first method, the efficacy of CTA is improved by sharing of intelligence information across a large number of enterprise networks. In the second method, a four variant-based global reputation

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Blesa, Sebastian, Ana Barbara Garcia-Garcia, Sergio Martinez-Hervas, et al. "Analysis of Sequence Variations in the LDL Receptor Gene in Spain: General Gene Screening or Search for Specific Alterations?" Clinical Chemistry 52, no. 6 (2006): 1021–25. http://dx.doi.org/10.1373/clinchem.2006.067645.

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Abstract Background: Familial hypercholesterolemia (FH) is a frequent form of autosomal-dominant hypercholesterolemia that predisposes to premature coronary atherosclerosis. FH is caused by sequence variations in the gene coding for the LDL receptor (LDLR). This gene has a wide spectrum of sequence variations, and genetic diagnosis can be performed by 2 strategies. Methods: Point variations and large rearrangements were screened along all the LDLR gene (promoter, exons, and flanking intron sequences). Results: We screened a sample of 129 FH probands from the Valencian Community, Spain, and ide

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de Deus, Danielle Rodrigues, Dielle Monteiro Teixeira, Jainara Cristina dos Santos Alves, et al. "Occurrence of norovirus genogroups I and II in recreational water from four beaches in Belém city, Brazilian Amazon region." Journal of Water and Health 17, no. 3 (2019): 442–54. http://dx.doi.org/10.2166/wh.2019.304.

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Abstract This study aimed to investigate the presence of norovirus (NoV) in recreational waters of four estuarine beaches located in Mosqueiro Island, Belém city, Brazilian Amazon, during two years of monitoring (2012 and 2013). NoV particles were concentrated on filtering membrane by the adsorption-elution method and detected by semi-nested RT-PCR (reverse transcription polymerase chain reaction) and sequencing. NoV positivity was observed in 37.5% (39/104) of the surface water samples, with genogroup GI (69.2%) occurring at a higher frequency than GII (25.7%), with a cocirculation of both ge

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Basu, Gargi D., Janine LoBello, and Audrey Ozols. "Employing RNA sequencing to enhance treatment options for cancer patients." Journal of Clinical Oncology 38, no. 15_suppl (2020): 3628. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.3628.

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3628 Background: Fusions and translocations account for 20% of cancer mortality globally. Maximizing their detection enhances the utility of precision medicine for various solid and hematologic cancers. Practice guidelines stress the importance of RNA sequencing. Novel assay techniques employing a comprehensive genomic profiling approach, including RNA sequencing, yield information beyond conventional DNA next generation sequencing (NGS) alone. Methods: Tumor samples (N = 1517) were assayed combining whole transcriptome (RNA) sequencing, whole exome (DNA) sequencing, and comparison of tumor se

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Yao, Yu, Xuan Li, and Lenan Wu. "Cognitive Frequency-Hopping Waveform Design for Dual-Function MIMO Radar-Communications System." Sensors 20, no. 2 (2020): 415. http://dx.doi.org/10.3390/s20020415.

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A frequency-hopping (FH)-based dual-function multiple-input multiple-output (MIMO) radar communications system enables implementation of a primary radar operation and a secondary communication function simultaneously. The set of transmit waveforms employed to perform the MIMO radar task is generated using FH codes. For each transmit antenna, the communication operation can be realized by embedding one phase symbol during each FH interval. However, as the radar channel is time-variant, it is necessary for a successive waveform optimization scheme to continually obtain target feature information

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Gaag, Kristiaan J. van der, Stijn Desmyter, Sophie Smit, Lourdes Prieto, and Titia Sijen. "Reducing the Number of Mismatches between Hairs and Buccal References When Analysing mtDNA Heteroplasmic Variation by Massively Parallel Sequencing." Genes 11, no. 11 (2020): 1355. http://dx.doi.org/10.3390/genes11111355.

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In forensics, mitochondrial DNA (mtDNA) analysis is foremost applied to rootless hairs often lacking detectable nuclear DNA. Sanger sequencing is the routine mtDNA method in most forensic laboratories, even though interpretation of mixed samples and heteroplasmic sites can be challenging. Individuals may hold cells with low-level heteroplasmy variants below the detection threshold and other cells where this minor variant is the major one. This difference may be interpreted as a mismatch between reference and evidentiary trace samples, such as buccal specimens and rootless hairs. Such mismatche

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Przychodzen, Bartlomiej P., Andres Jerez, Hideki Makishima, Kathryn M. Guinta, and Peter Chomczynski. "Mass Screening for Non-Synonymous SNPs Using Custom Cancer Microarrays Directly Reveals Possible Pathogenic Predisposition Factors in AA." Blood 118, no. 21 (2011): 1333. http://dx.doi.org/10.1182/blood.v118.21.1333.1333.

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Abstract Abstract 1333 While immune mechanisms are involved in the pathogenesis of idiopathic aplastic anemia (AA), identification of heritable predisposition/susceptibility traits has been difficult due to the impact of exogenous factors and the low prevalence of AA. The seemingly sporadic and likely complex and heterogeneous traits leading to AA are not easily amenable to genetic studies. With the advent of whole genome scanning (WGS) technologies such as single nucleotide polymorphism arrays (SNP-A), large scale investigations in various disorders have been conducted. A systems level unders

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Prieto-Potin, Iván, Nerea Carvajal, Jenifer Plaza-Sánchez, et al. "Validation and clinical application of a targeted next-generation sequencing gene panel for solid and hematologic malignancies." PeerJ 8 (October 6, 2020): e10069. http://dx.doi.org/10.7717/peerj.10069.

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Background Next-generation sequencing (NGS) is a high-throughput technology that has become widely integrated in molecular diagnostics laboratories. Among the large diversity of NGS-based panels, the Trusight Tumor 26 (TsT26) enables the detection of low-frequency variants across 26 genes using the MiSeq platform. Methods We describe the inter-laboratory validation and subsequent clinical application of the panel in 399 patients presenting a range of tumor types, including gastrointestinal (GI, 29%), hematologic (18%), lung (13%), gynecological and breast (8% each), among others. Results The p

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Hosseeini, Soudabeh, Ebrahim Kalantari, Akbar Dorgalaleh, Taregh Bamedi, Massomeh Farzi, and Dorgalele Saeed. "Thalassemia and Hemoglobinopathy Screening By HPLC Method and Comparison With Conventional Methods." Blood 122, no. 21 (2013): 4709. http://dx.doi.org/10.1182/blood.v122.21.4709.4709.

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Background Thalassemia and hemoglobinopathies are heterogeneous group of inherited disorders that affects men and women equally. HPLC is a valuable method for hemoglobinopathy and/or thalassemia carrier screening. This study evaluate the role of cation exchange HPLC along with adjunctive tests as needed in the diagnosis of thalassaemias/haemoglobinopathies and to see the frequency of these disorders in the Iranian population. Methods This five-year study was conducted on 3780 patients. Initially complete blood count was done by autoanalyzer and then for detection of abnormal hemoglobins HPLC a

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Patel, R., P. McGinty, V. Cuthill, M. Hawkins, S. K. Clark, and A. Latchford. "Risk of colorectal adenomas and cancer in monoallelic carriers of MUTYH pathogenic variants: a single-centre experience." International Journal of Colorectal Disease 36, no. 10 (2021): 2199–204. http://dx.doi.org/10.1007/s00384-021-03983-x.

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Abstract Purpose The carrier frequency of MUTYH pathogenic variants in the population may be as high as one in 45. Some studies have found an increased risk of colorectal cancer (CRC) in monoallelic carriers of MUTYH pathogenic variants, but the role of early surveillance colonoscopy is not conclusive. This study aimed to assess the outcomes of colonoscopy surveillance in MUTYH carriers. Methods Patients, with a monoallelic pathogenic variant in MUTYH, found at cascade testing, were identified from the St Mark’s Hospital Polyposis Registry database. Findings at surveillance colonoscopy were re

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Erbilgin, Yucel, Ahmet Emre Eskazan, Ozden Hatirnaz Ng, et al. "Next-Generation Sequencing Of The BCR-ABL1 Kinase Domain May Be Beneficial In Decision Making Among Chronic Myeloid Leukemia Patients With Tyrosine Kinase Inhibitor Resistance." Blood 122, no. 21 (2013): 384. http://dx.doi.org/10.1182/blood.v122.21.384.384.

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Abstract Background and Aim BCR-ABL1 mutation testing is recommended for chronic myeloid leukemia (CML) patients who have suboptimal response and/or treatment failure with tyrosine kinase inhibitor (TKI) therapy. BCR-ABL1 mutations in the kinase domain (KD) of ABL1 account for at least 40-50% of all TKI resistant cases. Thus, detection of low-level mutations after development of resistance may offer critical information to guide subsequent therapy selection. The current gold standard for BCR-ABL1 mutation detection is Sanger sequencing (SS), which has an analytical sensitivity of approximately

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Cher, Chae Yin, Zi Yi Lim, Daryl Tan, et al. "An ultrasensitive amplicon-based sequencing panel for noninvasive molecular testing of hematological malignancies using blood." Journal of Clinical Oncology 38, no. 15_suppl (2020): e19511-e19511. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.e19511.

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e19511 Background: Hematological malignancies, especially acute myeloid leukemia, myeloproliferative neoplasms, and myelodysplastic syndromes (MDS), present with distinct genomic alterations relevant to prognosis. Bone marrow (BM) is the primary sample source for genetic testing, but is obtained by an invasive biopsy procedure which carries risk of infection. An alternative non-invasive sample type to profile disease-relevant genomic alterations at diagnosis and subsequently, is desired for clinical decision making. An ultrasensitive sequencing panel was applied to peripheral blood (PB) as an

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HELAMA, S., J. K. NIELSEN, M. MACIAS FAURIA, and I. VALOVIRTA. "A fistful of shells: amplifying sclerochronological and palaeoclimate signals from molluscan death assemblages." Geological Magazine 146, no. 6 (2009): 917–30. http://dx.doi.org/10.1017/s0016756809990033.

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AbstractA growing body of literature is using sclerochronological information to infer past climates. Sclerochronologies are based on series of skeletal growth records of molluscs that have been correctly aligned in time. Incremental series are obtained from a number of shells to assess the temporal control and improve the climate signal in the final chronology. Much of the sclerochronological theory has been adopted from tree-ring science, due to the longer tradition and more firmly established concepts of chronology construction in dendrochronology. Compared to tree-ring studies, however, sc

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Tamura, Daisuke, Margaret Okomo-Adhiambo, Vasiliy P. Mishin, et al. "Application of a Seven-Target Pyrosequencing Assay To Improve the Detection of Neuraminidase Inhibitor-Resistant Influenza A(H3N2) Viruses." Antimicrobial Agents and Chemotherapy 59, no. 4 (2015): 2374–79. http://dx.doi.org/10.1128/aac.04939-14.

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ABSTRACTNational U.S. influenza antiviral surveillance incorporates data generated by neuraminidase (NA) inhibition (NI) testing of isolates supplemented with NA sequence analysis and pyrosequencing analysis of clinical specimens. A lack of established correlates for clinically relevant resistance to NA inhibitors (NAIs) hinders interpretation of NI assay data. Nonetheless, A(H3N2) viruses are commonly monitored for moderately or highly reduced inhibition in the NI assay and/or for the presence of NA markers E119V, R292K, and N294S. In 2012 to 2013, three drug-resistant A(H3N2) viruses were de

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Taylor, Cassandra R., Kevin M. Kiesler, Kimberly Sturk-Andreaggi, et al. "Platinum-Quality Mitogenome Haplotypes from United States Populations." Genes 11, no. 11 (2020): 1290. http://dx.doi.org/10.3390/genes11111290.

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A total of 1327 platinum-quality mitochondrial DNA haplotypes from United States (U.S.) populations were generated using a robust, semi-automated next-generation sequencing (NGS) workflow with rigorous quality control (QC). The laboratory workflow involved long-range PCR to minimize the co-amplification of nuclear mitochondrial DNA segments (NUMTs), PCR-free library preparation to reduce amplification bias, and high-coverage Illumina MiSeq sequencing to produce an average per-sample read depth of 1000 × for low-frequency (5%) variant detection. Point heteroplasmies below 10% frequency were con

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Deiana, Michela, Antonio Mori, Chiara Piubelli, et al. "Impact of Full Vaccination with mRNA BNT162b2 on SARS-CoV-2 Infection: Genomic and Subgenomic Viral RNAs Detection in Nasopharyngeal Swab and Saliva of Health Care Workers." Microorganisms 9, no. 8 (2021): 1738. http://dx.doi.org/10.3390/microorganisms9081738.

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SARS-CoV-2 infection was monitored in 1898 health care workers (HCWs) after receiving full vaccination with BNT162b2. Untill 30 June 2021, 10 HCWs tested positive for SARS-CoV-2 using real time RT-PCR, resulting in a 4-month cumulative incidence of 0.005%. The infection was mildly symptomatic in six (60%) and asymptomatic in four (40%) individuals. Among the infected HCWs, eight consenting individuals provided paired NPS and saliva during the course of infection, for the purpose of the analysis performed in the present study. Genomic and subgenomic viral RNAs were investigated using real-time

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Przychodzen, Bartlomiej P., Monika Jasek, Sandra P. Smieszek, et al. "GWAS Indicates the Presence of Rare Immunogenetic Polymorphisms as Possible Predisposition Factors in Aplastic Anemia." Blood 114, no. 22 (2009): 1093. http://dx.doi.org/10.1182/blood.v114.22.1093.1093.

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Abstract Abstract 1093 Poster Board I-115 While immune mechanisms are involved in the pathogenesis of idiopathic aplastic anemia (AA), due to the impact of exogenous factors and the low prevalence of AA, this disease is not easily amenable to genetic studies. With the advent of whole genome scanning (WGS) technologies such as single nucleotide polymorphism arrays (SNP-A), large scale investigations in various disorders have been conducted. A systems level understanding of particular disease can allows for identification of candidate genetic variants as prognostic and diagnostic markers. We hav

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Kim, Leeseul, Young Kwang Chae, Chan Mi Jung, Alice Daeun Lee, and Emma Yu. "Addition of selpercatinib to overcome osimertinib resistance in non-small cell lung cancer (NSCLC) with acquired RET fusion detected in ctDNA at very low allele frequency." Journal of Clinical Oncology 39, no. 15_suppl (2021): 3046. http://dx.doi.org/10.1200/jco.2021.39.15_suppl.3046.

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3046 Background: Osimertinib, a highly selective third generation EGFR tyrosine kinase inhibitor (TKI) became the standard front-line therapy for EGFR-mutant NSCLC. However, therapeutic options are limited for TKI resistance which commonly occurs. Therefore, overcoming acquired resistance to osimertinib remains an important high unmet need in the field of precision oncology. Herein, we present the first case of advanced adenocarcinoma of the lung that showed notable response with the addition of selpercatinib after acquired resistance to osimertinib monotherapy. Methods: Case presentation. Res

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Higgins, Jacob, Gabriel Pratt, Charles C. Valentine, Lindsey N. Williams, and Jesse J. Salk. "Redefining "Gold Standard": Ultra-Sensitive Characterization of Commercial DNA Standards with Duplex Sequencing." Blood 134, Supplement_1 (2019): 2093. http://dx.doi.org/10.1182/blood-2019-131428.

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DNA standards are a critical resource in diagnostic and research labs. Positive and negative controls are essential for validating the sensitivity and specificity of next generation sequencing (NGS) and other genetic assays. Several commercial DNA standards have been widely used to validate clinical oncology assays. However, as genomic technologies have become more sensitive, the metrics defining what a "gold standard" entails have not been carefully re-evaluated. Cell culture and synthetic chemical means of generating DNA standards have the potential to artificially introduce mutations. Cell

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Szentirmay, Zoltán, Judit Kurcsics, Erzsébet Csernák, Ildikó Tándor, and Erika Tóth. "Vastagbélrák-hajlamosító DNS-szekvencia-variációk tumormentes és vastagbél-daganatos populációban Magyarországon. Az egyedi daganathajlam becslése." Orvosi Hetilap 159, no. 40 (2018): 1614–23. http://dx.doi.org/10.1556/650.2018.31129.

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Abstract: Genome-wide association studies (GWAS) using population-based designs have identified many genetic loci, at which common variants can influence the risk of developing the sporadic colon cancers. These are single nucleotide polymorphisms (SNPs) located on different chromosomes, close to genes involved in cancer developing process, and the SNPs modify their functions, and as a consequence the cancer risk is increased. Our aim was to provide frequency distributions data of variable (risk) allele of six independent SNPs in patients with colorectal cancers and in control Hungarian populat

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Jacobs, Miriam T., Nisha A. Mohindra, Lindsey Shantzer, et al. "Use of Low-Frequency Driver Mutations Detected by Cell-Free Circulating Tumor DNA to Guide Targeted Therapy in Non–Small-Cell Lung Cancer: A Multicenter Case Series." JCO Precision Oncology, no. 2 (November 2018): 1–10. http://dx.doi.org/10.1200/po.17.00318.

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Purpose To evaluate the clinical outcome of patients with non–small-cell lung cancer treated by targeting low variant allelic frequency (VAF) driver mutations identified through cell-free DNA (cfDNA) next-generation sequencing (NGS). Detection of driver mutations in cancer is critically important in the age of targeted therapy, where both tumor-based as well as cfDNA sequencing methods have been used for therapeutic decision making. We hypothesized that VAF should not be predictive of response and that low VAF alterations detected by cfDNA NGS can respond to targeted therapy. Patients and Meth

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Cutts, Anthony, Edward Wilson, Pek Sang Tang, et al. "Interim Cell-Free Circulating Lymphoma DNA Analysis of the Phase 2 Accept Trial." Blood 136, Supplement 1 (2020): 24–25. http://dx.doi.org/10.1182/blood-2020-137439.

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Introduction Plasma cell-free DNA (cfDNA) and circulating tumor DNA (ctDNA) genotyping in Diffuse Large B-cell Lymphoma (DLBCL) holds great promise for early detection and response prediction. DLBCL is a highly heterogenous disease with diverse tumor behaviour and outcomes, yet the delineation of poor- risk groups remains challenging. Genomically driven molecular risk stratification, using ultradeep next generation sequencing (NGS) provides a comprehensive view of the mutational landscape of lymphoma and enables ultrasensitive disease detection. Here, we present an interim analysis of ctDNA ki

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Gutierrez-Rodrigues, Fernanda, Isabel Beerman, Emma M. Groarke, et al. "Clinical Utility of Plasma Cell-Free DNA for Detection and Quantification of Clonal Hematopoiesis." Blood 136, Supplement 1 (2020): 4–5. http://dx.doi.org/10.1182/blood-2020-139874.

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Cell-free DNA (cfDNA) extracted from peripheral blood plasma has been increasingly used as a non-invasive approach for diagnosis and surveillance of solid and hematologic malignancies. Somatic variants associated with clonal hematopoiesis of indeterminate potential (CHIP) are commonly detected in such liquid biopsies, suggesting that cfDNA may be useful for their detection. CHIP has emerged as a predictor of progression to hematological malignancies; however, clones are still largely detected using peripheral blood (PB) and bone marrow (BM) cells. In this study, we investigated the performance

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Wen, Yu-Ye, Erica Fang, Yanchun Li, Condie Edwin Carmack, and Marilyn M. Li. "The efficacy of targeted next-generation sequencing for detection of clinically actionable mutations in cancer." Journal of Clinical Oncology 30, no. 15_suppl (2012): 10598. http://dx.doi.org/10.1200/jco.2012.30.15_suppl.10598.

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10598 Background: The emergence of next-generation sequencing (NGS) technologies has significantly accelerated the identification of cancer-causing mutations and the development of personalized cancer care. However, the clinical application of these technologies to detect cancer gene mutations has been extremely limited due to the long turn around time, the high cost, and large amount of input DNA required by existing NGS-based tests. Methods: We have assessed the performance of a novel NGS technology that merges multiplex PCR with ion semiconductor sequencing (AmpliSeq, Life Technologies, Inc

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Barnell, Erica Kay, Yiming Kang, Katie Marie Campbell, Andrew Ross Barnell, Kimberly Ray Kruse, and Elizabeth Marie Wurtzler. "Prospective clinical study using expressed sequencing variants on stool-derived eukaryotic RNA transcripts (seRNA) for colorectal cancer screening." Journal of Clinical Oncology 37, no. 4_suppl (2019): 516. http://dx.doi.org/10.1200/jco.2019.37.4_suppl.516.

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516 Background: Colorectal cancer (CRC) is the second leading cause of cancer related deaths in the United States. The high mortality rate is largely attributable to the high frequency of late-stage diagnoses, caused by low patient compliance with screening guidelines. A reliable and noninvasive screening alternative is needed for the 40 million noncompliant patients. The development of a novel nucleic acid extraction method to isolate stool-derived eukaryotic RNA (seRNA) permits reliable and noninvasive evaluation of biomarkers derived from the gastrointestinal (GI) epithelium. This method en

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Han, Tiancheng, Jianing Yu, Xiaojing Lin, et al. "A new method towards calculating the cancer cell fraction in cell-free DNA." Journal of Clinical Oncology 37, no. 15_suppl (2019): e13053-e13053. http://dx.doi.org/10.1200/jco.2019.37.15_suppl.e13053.

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e13053 Background: Circulating tumor DNA (ctDNA) has been applied and showed potential in cancer early/late-stage detection, tumor genotyping and post-operation recurrence monitoring. The fraction of ctDNA in cell-free DNA (noted as ccf hereby), in addition to standard SNV/INDEL/CNV analysis, has also been showed to associate with the tumor progression and prognosis. In theory, accurate ccf can further be useful in correcting and improving given SNV/INDEL/CNV results. Existing tools capable for calculating ccf (PureCN, FACETS, Sequenza, etc.) use coverage data in targeted regions and SNP allel

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Poh, Jonathan, Kao Chin Ngeow, Michelle Pek, Daniel Tan, Jing Shan Lim, and Yukti Choudhury. "Comprehensive molecular profiling of advanced cancers in a real-world setting using an ultrasensitive amplicon-based next-generation sequencing (NGS) liquid biopsy assay." Journal of Clinical Oncology 39, no. 15_suppl (2021): 3062. http://dx.doi.org/10.1200/jco.2021.39.15_suppl.3062.

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3062 Background: Molecular profiling of circulating tumor DNA (ctDNA) by NGS has demonstrated the value of liquid biopsy in informing treatment decisions and monitoring disease progression in cancer patients. Here we report results from the real-world clinical application of an ultrasensitive amplicon-based NGS liquid biopsy assay for advanced cancers. Methods: Plasma cell-free DNA (cfDNA) from 1,338 consecutive samples (51.3% lung, 15.6% breast, 8.4% colorectal, 26.8% from 18 other cancer types; 86.3% of cancer samples were metastatic) underwent real-world testing in a Singapore-based, CAP-ac

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Ding, Elizabeth, Zhilong Zhao, Hongsheng Xue, et al. "CancerScreen: A novel ultrasensitive liquid biopsy for early-stage cancer detection by ctDNA Duplex Sequencing and Tissue of Origin identification with supervised machine learning." Journal of Global Oncology 5, suppl (2019): 60. http://dx.doi.org/10.1200/jgo.2019.5.suppl.60.

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60 Background: Circulating tumor DNA (ctDNA) in blood holds promise as a cancer-specific biomarker for early-stage cancer diagnosis. However, detection of ultra-low mutation allelic frequency (MAF) of ctDNA at early stages of cancer is infeasible by conventional next generation sequencing (NGS). Using duplex sequencing with unique molecular identifiers (UMIs) and custom-designed probes, we tested the hypothesis that ctDNA duplex sequencing with UMIs was able to detect ultra-low MAF of ctDNA in patients with early-stage cancers. Methods: A 128-gene panel that contains probes targeted to clinica

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