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anchored molecular ngs

Kurtis D Davies, Aprille Lomboy, Carolyn A Lawrence, Michael Yourshaw, Gregary T Bocsi, D Ross Camidge, Dara L Aisner
INTRODUCTION: Genomic variants that lead to MET exon 14 skipping represent a potential targetable molecular abnormality in non-small cell lung cancer (NSCLC). Consequently, reliable molecular diagnostic approaches that detect these variants are vital for patient care. METHODS: We screened NSCLC patient tumor samples for MET exon 14 skipping via two distinct approaches: a DNA-based next-generation sequencing (NGS) assay that employs an amplicon-mediated target enrichment, and an RNA-based NGS assay that employs anchored multiplex PCR for target enrichment...
January 9, 2019: Journal of Thoracic Oncology
Wangzhao Song, Albert J H Suurmeijer, Stijn M Bollen, Anne-Marie Cleton-Jansen, Judith V M G Bovée, Herman M Kroon
OBJECTIVE: Aneurysmal bone cysts (ABC) rarely present in soft tissue locations (STABC). The 30 cases of STABC reported in the English literature were reviewed. Six new cases retrieved from the files of the Netherlands Committee on Bone Tumors were compared to the six cases described in the radiological literature. MATERIALS AND METHODS: Imaging studies and histopathology of six new STABC cases were reviewed. Follow-up was recorded with respect to local recurrence...
January 2, 2019: Skeletal Radiology
Suk Wai Lam, Anne-Marie Cleton-Jansen, Arjen H G Cleven, Dina Ruano, Tom van Wezel, Karoly Szuhai, Judith V M G Bovée
Molecular assays for translocation detection in bone and soft tissue tumors have gradually been incorporated into routine diagnostics. However, conventional methods such as fluorescence in situ hybridization (FISH) and reverse transcriptase-PCR come with several drawbacks. In this study, the applicability of a novel technique termed anchored multiplex PCR (AMP) for next-generation sequencing (NGS), using the Archer FusionPlex Sarcoma kit, aimed at 26 genes, was evaluated and compared with FISH and reverse transcriptase-PCR...
September 2018: Journal of Molecular Diagnostics: JMD
Kurtis D Davies, Anh T Le, Jamie Sheren, Hala Nijmeh, Katherine Gowan, Kenneth L Jones, Marileila Varella-Garcia, Dara L Aisner, Robert C Doebele
INTRODUCTION: ROS1 gene fusions are a well-characterized class of oncogenic driver found in approximately 1% to 2% of NSCLC patients. ROS1-directed therapy in these patients is more efficacious and is associated with fewer side effects compared to chemotherapy and is thus now considered standard-of-care for patients with advanced disease. Consequently, accurate detection of ROS1 rearrangements/fusions in clinical tumor samples is vital. In this study, we compared the performance of three common molecular testing approaches on a cohort of ROS1 rearrangement/fusion-positive patient samples...
October 2018: Journal of Thoracic Oncology
Matthew W Rosenbaum, Martin Jones, Jonathan C Dudley, Long P Le, A John Iafrate, Martha B Pitman
BACKGROUND: The diagnosis of a pancreatic cyst as mucinous or high-risk dictates the need for follow-up or surgery. Molecular analysis of aspirated pancreatic cyst fluid (PCF) can provide valuable information not obtained by carcinoembryonic antigen (CEA) analysis or cytology. METHODS: All patients who underwent molecular analysis of PCF between March 2013 and June 2015 were reviewed, including pathology, imaging, and follow-up. Molecular testing was performed using a patented, anchored multiplex polymerase chain reaction next-generation sequencing (NGS) platform, which sequenced numerous hotspots in 39 genes linked with malignancy...
January 2017: Cancer Cytopathology
Danielle A Murphy, Heather A Ely, Robert Shoemaker, Aaron Boomer, Brady P Culver, Ian Hoskins, Josh D Haimes, Ryan D Walters, Diane Fernandez, Joshua A Stahl, Jeeyun Lee, Kyoung-Mee Kim, Jennifer Lamoureux, Jason Christiansen
Targeted therapy combined with companion diagnostics has led to the advancement of next-generation sequencing (NGS) for detection of molecular alterations. However, using a diagnostic test to identify patient populations with low prevalence molecular alterations, such as gene rearrangements, poses efficiency, and cost challenges. To address this, we have developed a 2-step diagnostic test to identify NTRK1, NTRK2, NTRK3, ROS1, and ALK rearrangements in formalin-fixed paraffin-embedded clinical specimens. This test is comprised of immunohistochemistry screening using a pan-receptor tyrosine kinase cocktail of antibodies to identify samples expressing TrkA (encoded by NTRK1), TrkB (encoded by NTRK2), TrkC (encoded by NTRK3), ROS1, and ALK followed by an RNA-based anchored multiplex polymerase chain reaction NGS assay...
August 2017: Applied Immunohistochemistry & Molecular Morphology: AIMM
Xiaodong Li, Mona Anand, Josh D Haimes, Namitha Manoj, Aaron M Berlin, Brian A Kudlow, Marisa R Nucci, Tony L Ng, Colin J R Stewart, Cheng-Han Lee
AIMS: Endometrial stromal sarcomas (ESSs) are divided into low-grade and high-grade subtypes, with the latter showing more aggressive clinical behaviour. Although histology and immunophenotype can aid in the diagnosis of these tumours, genetic studies can provide additional diagnostic insights, as low-grade ESSs frequently harbour fusions involving JAZF1/SUZ12 and/or JAZF1/PHF1, whereas high-grade ESSs are defined by YWHAE-NUTM2A/B fusions. The aim of this study was to evaluate the utility of a next-generation sequencing (NGS)-based assay in identifying ESS fusions in archival formalin-fixed paraffin-embedded tumour samples...
October 2016: Histopathology
Sara Ruane, Christopher J Raxworthy, Alan R Lemmon, Emily Moriarty Lemmon, Frank T Burbrink
BACKGROUND: Using molecular data generated by high throughput next generation sequencing (NGS) platforms to infer phylogeny is becoming common as costs go down and the ability to capture loci from across the genome goes up. While there is a general consensus that greater numbers of independent loci should result in more robust phylogenetic estimates, few studies have compared phylogenies resulting from smaller datasets for commonly used genetic markers with the large datasets captured using NGS...
October 12, 2015: BMC Evolutionary Biology
Yu Liu, Mehmet Koyutürk, Sean Maxwell, Min Xiang, Martina Veigl, Richard S Cooper, Bamidele O Tayo, Li Li, Thomas LaFramboise, Zhenghe Wang, Xiaofeng Zhu, Mark R Chance
BACKGROUND: Sequences up to several megabases in length have been found to be present in individual genomes but absent in the human reference genome. These sequences may be common in populations, and their absence in the reference genome may indicate rare variants in the genomes of individuals who served as donors for the human genome project. As the reference genome is used in probe design for microarray technology and mapping short reads in next generation sequencing (NGS), this missing sequence could be a source of bias in functional genomic studies and variant analysis...
2014: BMC Genomics
Oscar Campuzano, Catarina Allegue, Georgia Sarquella-Brugada, Monica Coll, Jesus Mates, Mireia Alcalde, Carles Ferrer-Costa, Anna Iglesias, Josep Brugada, Ramon Brugada
Sudden infant death syndrome (SIDS) is the leading cause of death in the first year of life. Several arrhythmogenic genes have been associated with cardiac pathologies leading to infant sudden cardiac death (SCD). Our aim was to take advantage of next generation sequencing (NGS) technology to perform a thorough genetic analysis of a SIDS case. A SIDS case was referred to our institution after negative autopsy. We performed a genetic analysis of 104 SCD-related genes using a custom panel. Confirmed variants in index case were also analyzed in relatives...
September 2014: Forensic Science International
Huaan Yang, Ye Tao, Zequn Zheng, Qisen Zhang, Gaofeng Zhou, Mark W Sweetingham, John G Howieson, Chengdao Li
Lupin (Lupinus angustifolius L.) is the most recently domesticated crop in major agricultural cultivation. Its seeds are high in protein and dietary fibre, but low in oil and starch. Medical and dietetic studies have shown that consuming lupin-enriched food has significant health benefits. We report the draft assembly from a whole genome shotgun sequencing dataset for this legume species with 26.9x coverage of the genome, which is predicted to contain 57,807 genes. Analysis of the annotated genes with metabolic pathways provided a partial understanding of some key features of lupin, such as the amino acid profile of storage proteins in seeds...
2013: PloS One
Alex R Hastie, Lingli Dong, Alexis Smith, Jeff Finklestein, Ernest T Lam, Naxin Huo, Han Cao, Pui-Yan Kwok, Karin R Deal, Jan Dvorak, Ming-Cheng Luo, Yong Gu, Ming Xiao
Next-generation sequencing (NGS) technologies have enabled high-throughput and low-cost generation of sequence data; however, de novo genome assembly remains a great challenge, particularly for large genomes. NGS short reads are often insufficient to create large contigs that span repeat sequences and to facilitate unambiguous assembly. Plant genomes are notorious for containing high quantities of repetitive elements, which combined with huge genome sizes, makes accurate assembly of these large and complex genomes intractable thus far...
2013: PloS One
Lijia Huang, Katarzyna Szymanska, Victor L Jensen, Andreas R Janecke, A Micheil Innes, Erica E Davis, Patrick Frosk, Chunmei Li, Jason R Willer, Bernard N Chodirker, Cheryl R Greenberg, D Ross McLeod, Francois P Bernier, Albert E Chudley, Thomas Müller, Mohammad Shboul, Clare V Logan, Catrina M Loucks, Chandree L Beaulieu, Rachel V Bowie, Sandra M Bell, Jonathan Adkins, Freddi I Zuniga, Kevin D Ross, Jian Wang, Matthew R Ban, Christian Becker, Peter Nürnberg, Stuart Douglas, Cheryl M Craft, Marie-Andree Akimenko, Robert A Hegele, Carole Ober, Gerd Utermann, Hanno J Bolz, Dennis E Bulman, Nicholas Katsanis, Oliver E Blacque, Dan Doherty, Jillian S Parboosingh, Michel R Leroux, Colin A Johnson, Kym M Boycott
Joubert syndrome related disorders (JSRDs) have broad but variable phenotypic overlap with other ciliopathies. The molecular etiology of this overlap is unclear but probably arises from disrupting common functional module components within primary cilia. To identify additional module elements associated with JSRDs, we performed homozygosity mapping followed by next-generation sequencing (NGS) and uncovered mutations in TMEM237 (previously known as ALS2CR4). We show that loss of the mammalian TMEM237, which localizes to the ciliary transition zone (TZ), results in defective ciliogenesis and deregulation of Wnt signaling...
December 9, 2011: American Journal of Human Genetics
Jeffrey G Reid, Ankur K Nagaraja, Francis C Lynn, Rafal B Drabek, Donna M Muzny, Chad A Shaw, Michelle K Weiss, Arash O Naghavi, Mahjabeen Khan, Huifeng Zhu, Jayantha Tennakoon, Gemunu H Gunaratne, David B Corry, Jonathan Miller, Michael T McManus, Michael S German, Richard A Gibbs, Martin M Matzuk, Preethi H Gunaratne
Massively parallel sequencing of millions of < 30-nt RNAs expressed in mouse ovary, embryonic pancreas (E14.5), and insulin-secreting beta-cells (betaTC-3) reveals that approximately 50% of the mature miRNAs representing mostly the mmu-let-7 family display internal insertion/deletions and substitutions when compared to precursor miRNA and the mouse genome reference sequences. Approximately, 12%-20% of species associated with mmu-let-7 populations exhibit sequence discrepancies that are dramatically reduced in nucleotides 3-7 (5'-seed) and 10-15 (cleavage and anchor sites)...
October 2008: Genome Research
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