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ffpe dna isolation

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https://www.readbyqxmd.com/read/29771965/evaluation-of-commercial-dna-and-rna-extraction-methods-for-high-throughput-sequencing-of-ffpe-samples
#1
Stine H Kresse, Heidi M Namløs, Susanne Lorenz, Jeanne-Marie Berner, Ola Myklebost, Bodil Bjerkehagen, Leonardo A Meza-Zepeda
Nucleic acid material of adequate quality is crucial for successful high-throughput sequencing (HTS) analysis. DNA and RNA isolated from archival FFPE material are frequently degraded and not readily amplifiable due to chemical damage introduced during fixation. To identify optimal nucleic acid extraction kits, DNA and RNA quantity, quality and performance in HTS applications were evaluated. DNA and RNA were isolated from five sarcoma archival FFPE blocks, using eight extraction protocols from seven kits from three different commercial vendors...
2018: PloS One
https://www.readbyqxmd.com/read/29600293/-usp8-mutations-in-pituitary-cushing-adenomas-targeted-analysis-by-next-generation-sequencing
#2
Cora Ballmann, Anne Thiel, Hannah E Korah, Anna-Carinna Reis, Wolfgang Saeger, Stefanie Stepanow, Karl Köhrer, Guido Reifenberger, Christiane B Knobbe-Thomsen, Ulrich J Knappe, Ute I Scholl
Gain-of-function somatic mutations in the ubiquitin specific protease 8 ( USP8 ) gene have recently been reported as a cause of pituitary adenomas in Cushing disease. Molecular diagnostic testing of tumor tissue may aid in the diagnosis of specimens obtained through therapeutic transsphenoidal surgery; however, for small tumors, availability of fresh tissue is limited, and contamination with normal tissue is frequent. We performed molecular testing of DNA isolated from single formalin-fixed and paraffin-embedded (FFPE) tissue sections of 42 pituitary adenomas from patients with Cushing disease (27 female patients and 15 male patients; mean age at surgery, 42...
March 1, 2018: Journal of the Endocrine Society
https://www.readbyqxmd.com/read/29568401/a-single-digital-droplet-pcr-assay-to-detect-multiple-kit-exon-11-mutations-in-tumor-and-plasma-from-patients-with-gastrointestinal-stromal-tumors
#3
Pieter A Boonstra, Arja Ter Elst, Marco Tibbesma, Lisette J Bosman, Ron Mathijssen, Florence Atrafi, Frits van Coevorden, Neeltje Steeghs, Sheima Farag, Hans Gelderblom, Winette T A van der Graaf, Ingrid M E Desar, Jacqueline Maier, Jelle Overbosch, Albert J H Suurmeijer, Jourik Gietema, Ed Schuuring, Anna K L Reyners
Background: Gastrointestinal stromal tumors (GISTs) are characterized by oncogenic KIT mutations that cluster in two exon 11 hotspots. The aim of this study was to develop a single, sensitive, quantitative digital droplet PCR (ddPCR) assay for the detection of common exon 11 mutations in both GIST tumor tissue and in circulating tumor DNA (ctDNA) isolated from GIST patients' plasma. Methods: A ddPCR assay was designed using two probes that cover both hotspots. Available archival FFPE tumor tissue from 27 consecutive patients with known KIT exon 11 mutations and 9 randomly selected patients without exon 11 mutations were tested...
March 2, 2018: Oncotarget
https://www.readbyqxmd.com/read/29523759/landscape-of-tumor-mutation-load-mismatch-repair-deficiency-and-pd-l1-expression-in-a-large-patient-cohort-of-gastrointestinal-cancers
#4
Mohamed E Salem, Alberto Puccini, Axel Grothey, Derek Raghavan, Richard M Goldberg, Joanne Xiu, W Michael Korn, Benjamin A Weinberg, Jimmy J Hwang, Anthony F Shields, John L Marshall, Philip A Philip, Heinz-Josef Lenz
The efficacy of immunotherapy varies widely among different gastrointestinal cancers. Response to immune checkpoint inhibitors is shown to correlate with tumor mutation load (TML), mismatch repair deficiency (dMMR) status, and programmed cell death-ligand 1 (PD-L1) expression. Herein, we quantify TML, dMMR, and PD-L1 expression and determine their interrelationship in gastrointestinal cancers. Here, a total of 4,125 tumors from 14 different gastrointestinal cancer sites were studied using validated assays. Next-generation sequencing was performed on genomic DNA isolated from formalin-fixed paraffin-embedded tumor specimens using the NextSeq platform...
May 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29471422/phylogenetic-analysis-of-histoplasma-capsulatum-var-duboisii-in-baboons-from-archived-formalin-fixed-paraffin-embedded-tissues
#5
M Hensel, A Rodrigues Hoffmann, M Gonzales, M A Owston, E J Dick
Histoplasma capsulatum var. duboisii (Hcd) infections have been well documented to cause chronic granulomatous disease, mainly involving the skin of baboons and humans in African countries primarily. This retrospective study classified the subspecies of Histoplasma and developed a phylogenetic tree utilizing DNA sequences extracted from formalin-fixed, paraffin embedded (FFPE) tissues from 9 baboons from a research colony in Texas histologically diagnosed with Hcd. Based on sequence analysis of ITS-2, Tub-1, and ARF, Hcd isolated from the archived samples closely aligns with the African clade and has 88% sequence homology with a sample isolated from an individual in Senegal...
February 16, 2018: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
https://www.readbyqxmd.com/read/29444723/evaluation-of-the-xpert-mtb-rif-performance-on-tissues-potential-impact-on-airborne-infection-isolation-at-a-tertiary-cancer-care-center
#6
Tracy McMillen, Shauna C Usiak, Liang Hua Chen, Luz Gomez, Peter Ntiamoah, Meera R Hameed, Indre Budvytiene, Niaz Banaei, Mini Kamboj, N Esther Babady
OBJECTIVES In this study, we sought to evaluate the performance of the Xpert MTB/RIF (Cepheid) assay for the detection of Mycobacterium tuberculosis (MTB) complex DNA on fresh and formalin-fixed, paraffin-embedded (FFPE) tissue specimens from oncology patients in an area with a low prevalence of tuberculosis. We also aimed to retrospectively assess the potential impact of Xpert MTB/RIF on the duration of airborne infection isolation (AII). SETTING A 473-bed, tertiary-care cancer center in New York City. DESIGN A total of 203 tissue samples (101 FFPE and 102 fresh) were tested using Xpert MTB/RIF, including 133 pulmonary tissue samples (65...
April 2018: Infection Control and Hospital Epidemiology
https://www.readbyqxmd.com/read/29344860/laser-microdissection-for-human-papillomavirus-hpv-genotyping-attribution-and-methylation-pattern-analyses-of-squamous-intraepithelial-lesions
#7
Monica Molano, Suzanne M Garland, Alyssa M Cornall
Human papillomavirus (HPV) is a nearly ubiquitous infectious organism. It is estimated that 80% of sexually active adults will be exposed to anogenital HPVs in their lifetime, and detection of multiple genotypes in an anogenital sample is common. Detection and genotyping of HPV is usually performed by DNA testing, and less frequently by mRNA testing. HPV genotype testing and characterization of DNA methylation patterns of HPV-related lesions can provide important biological, epidemiological, and potentially relevant clinical information in individuals and populations...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344856/next-generation-sequencing-analysis-of-laser-microdissected-formalin-fixed-and-paraffin-embedded-ffpe-tissue-specimens
#8
Lavinia Mägel, Stephan Bartels, Ulrich Lehmann
In recent years, next-generation sequencing (NGS) became widely used in molecular pathology. Comprehensive mutational profiling improved diagnosis and prognosis, as well as the identification of therapeutically relevant genetic alterations. However, the vast majority of studies analyzing tissue samples use DNA extracted from bulk tissue or only manually microdissected specimens. Laser-assisted microdissection offers the possibility of isolating morphologically defined small tissue compartments (like individual glands) or even of single cells for further molecular analysis...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29120619/a-rapid-throughput-method-to-extract-dna-from-formalin-fixed-paraffin-embedded-tissues-for-biomonitoring-carcinogenic-dna-adducts
#9
Byeong Hwa Yun, Shun Xiao, Lihua Yao, Sesha Krishnamachari, Thomas A Rosenquist, Kathleen G Dickman, Arthur P Grollman, Paari Murugan, Christopher J Weight, Robert J Turesky
Formalin-fixed paraffin-embedded (FFPE) tissues are rarely used for screening DNA adducts of carcinogens because the harsh conditions required to reverse the formaldehyde-mediated DNA cross-links can destroy DNA adducts. We recently adapted a commercial silica-based column kit used in genomics to manually isolate DNA under mild conditions from FFPE tissues of rodents and humans and successfully measured DNA adducts of several carcinogens including aristolochic acid I (AA-I), 4-aminobiphenyl (4-ABP), and 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) (Yun et al...
December 18, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/29024035/the-role-of-human-papillomavirus-in-p16-positive-oral-cancers
#10
Simone Belobrov, Alyssa M Cornall, Richard J Young, Kendrick Koo, Christopher Angel, David Wiesenfeld, Danny Rischin, Suzanne M Garland, Michael McCullough
BACKGROUND: The aim of this study was to identify the presence and frequency of human papillomavirus (HPV) nucleic acid in p16-positive oral squamous cell carcinomas (OSCCs), to assess whether the virus was transcriptionally active and to assess the utility of p16 overexpression as a surrogate marker for HPV in OSCC. METHODS: Forty-six OSCC patients treated between 2007 and 2011 with available formalin-fixed paraffin-embedded (FFPE) specimens were included. Twenty-three patients were positive for p16 by immunohistochemistry (IHC) and these were matched with 23 patients with p16-negative tumours...
January 2018: Journal of Oral Pathology & Medicine
https://www.readbyqxmd.com/read/28952562/human-papillomavirus-investigation-in-head-and-neck-squamous-cell-carcinoma-initial-report-from-the-low-risk-hpv-types-associations
#11
Mohammad Hadi Karbalaie Niya, Fahimeh Safarnezhad Tameshkel, Mahshid Panahi, Farah Bokharaei Salim, Seyed Hamid Reza Monavari, Hossein Keyvani
Background: Head and neck squamous cell carcinomas (HNSCC) are a major health issue in many parts of the world. Recently, attention has focused on the human papilloma virus (HPV) as a potential causative agent for HNSCC. This study aimed to survey HPV occurrence in HNSCCs as part of a comprehensive molecular epidemiology approach. Methods: In this retrospective study, patients were recruited from hospitals affiliated to the Iran University of Medical Sciences, Tehran, Iran. Formalin-fixed paraffin-embedded (FFPE) blocks were subjected to DNA isolation by QIAamp® DNA FFPE Tissue Kit and nested PCR, HPV-16 specific conventional PCR, and extra INNO-LiPA HPV genotyping assays were subsequently performed...
September 27, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/28900470/mutational-frequency-of-kras-nras-idh2-pik3ca-and-egfr-in-north-indian-gallbladder-cancer-patients
#12
Aarti Sharma, Ashok Kumar, Niraj Kumari, Narendra Krishnani, Neeraj Rastogi
BACKGROUND: Gallbladder cancer (GBC) has a peculiar geographical distinction, with a high prevalence seen in North India and Chile. There are various aetiopathogenetic mechanisms of GBC causation; one of them is a series of pathogenic mutations, which is responsible for the malignant transformation of gallbladder epithelium. Therefore, the present study aimed to find out cancer-specific hot spot mutations in five major cancer-related genes KRAS exon1 &2, NRAS exon1, IDH2 exon, PIK3CA exon 20, IDH2 exon 4 and EGFR exon 20 in North Indian GBC patients and their association with clinicopathological variables...
2017: Ecancermedicalscience
https://www.readbyqxmd.com/read/28838400/emergence-of-fgfr3-tacc3-fusions-as-a-potential-by-pass-resistance-mechanism-to-egfr-tyrosine-kinase-inhibitors-in-egfr-mutated-nsclc-patients
#13
Sai-Hong Ignatius Ou, Leora Horn, Marcelo Cruz, Davood Vafai, Christine M Lovly, Allison Spradlin, Michael J Williamson, Ibiayi Dagogo-Jack, Adrienne Johnson, Vincent A Miller, Shirish Gadgeel, Siraj M Ali, Alexa B Schrock
Resistance to EGFR tyrosine kinase inhibitors (TKIs) in non-small cell lung cancers (NSCLCs) with activating EGFR mutations generally involve development of acquired secondary or tertiary EGFR mutations, such as T790M or C797S. However, case reports have demonstrated that actionable receptor tyrosine kinase fusions such as EML4-ALK, CCDC6-RET, and FGFR3-TACC3 can potentially confer resistance to EGFR TKIs. We seeked to identify the prevalence of FGFR3-TACC3 fusion transcripts as resistance mechanism to EGFR TKIs...
September 2017: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/28783138/flow-cytometric-sorting-coupled-with-exon-capture-sequencing-identifies-somatic-mutations-in-archival-lymphoma-tissues
#14
Nenggang Jiang, Christopher Chen, Qiang Gong, Kristen Shields, Yuping Li, YuanYuan Chen, Joo Song, Timothy W McKeithan, Wing C Chan
The enormous number of archived formalin-fixed paraffin-embedded (FFPE) tissues available are a valuable resource of material for research. However, the use of such tissues poses many challenges, among which is the difficulty of isolating different cell populations within the tissue. In this study, we used tissue from two types of non-Hodgkin lymphoma as a model to demonstrate a method we have established and optimized to separate FFPE samples into distinct tumor and nonmalignant populations. Using FFPE reactive tonsil sections, various approaches for antigen retrieval and labeling, and the effectiveness of flow cytometric sorting were tested...
November 2017: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/28705719/prevalence-of-ebv-hpv-and-mmtv-in-pakistani-breast-cancer-patients-a-possible-etiological-role-of-viruses-in-breast-cancer
#15
Wasifa Naushad, Orooj Surriya, Hajra Sadia
BACKGROUND: Breast cancer being a multifactorial disease, the role of infectious agent in development of disease is of great interest. The high incidence of breast cancer around the world has woken the interest in a viral etiology of breast cancer. Despite decades of research, no etiologic factor(s) for human breast cancer has been known and the quest for a contributing cause has all but been abandoned during the past years. Recent investigations have linked breast cancer to viral infections, such as Epstein-Barr virus (EBV), Human papillomavirus (HPV) and mouse mammary tumor virus...
July 10, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28588314/frequency-of-gnas-r201h-substitution-mutation-in-polyostotic-fibrous-dysplasia-pyrosequencing-analysis-in-tissue-samples-with-or-without-decalcification
#16
Su-Jin Shin, Seok Joo Lee, Sang Kyum Kim
Guanine nucleotide-binding protein/α-subunit (GNAS) mutations are involved in fibrous dysplasia (FD) pathogenesis. Here, we analyzed GNAS mutations in FD which were performed by pyrosequencing DNA isolated from formalin-fixed paraffin-embedded (FFPE) tissue. The mutation detection rate was determined in FD specimens with and without decalcification. GNAS mutation was identified in 28 cases out of 87 FDs (32.18%) [p.R201C (N = 14) and p.R201H (N = 14)]. GNAS mutation was more likely to occur in polyostotic FD (7/28, 25...
June 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28432562/increased-expression-of-the-microrna-106b-25-cluster-and-its-host-gene-mcm7-in-corticotroph-pituitary-adenomas-is-associated-with-tumor-invasion-and-crooke-s-cell-morphology
#17
Filip Garbicz, Dawid Mehlich, Beata Rak, Emir Sajjad, Maria Maksymowicz, Wiktor Paskal, Grzegorz Zieliński, Paweł K Włodarski
PURPOSE: MCM7 (minichromosome maintenance complex component 7), a DNA replication licensing factor, is a host gene for the oncogenic miR-106b~25 cluster. It has been recently revealed as a relevant prognostic biomarker in a variety of cancers, including pituitary adenomas. The purpose of this study was to assess whether miR-106b~25 and MCM7 levels correlate with tumor invasiveness in a cohort of ACTH-immunopositive adenomas. METHODS: Tissue samples were obtained intraoperatively from 25 patients with pituitary adenoma...
August 2017: Pituitary
https://www.readbyqxmd.com/read/28351563/sensitivity-of-tumor-surface-brushings-to-detect-human-papilloma-virus-dna-in-head-and-neck-cancer
#18
Barbara Kofler, Wegene Borena, Claudia Manzl, Jozsef Dudas, Anne-Sophie Wegscheider, Pidder Jansen-Dürr, Volker Schartinger, Herbert Riechelmann
OBJECTIVE: Human papilloma virus (HPV) induced head and neck squamous cell carcinoma (HNSCC) represents a distinct tumor subset. We questioned how accurately a brushing from the tumor surface detects HPV in patients with HNSCC. MATERIALS AND METHODS: Brushings from the tumor surface were compared with HPV DNA isolation from formalin-fixed and paraffin-embedded (FFPE) tumor biopsies, which served as the reference standard. In both matrices, HPV DNA was detected using a commercially available test kit...
April 2017: Oral Oncology
https://www.readbyqxmd.com/read/28346123/panfungal-polymerase-chain-reaction-for-identification-of-fungal-pathogens-in-formalin-fixed-animal-tissues
#19
Courtney Meason-Smith, Erin E Edwards, Caitlin E Older, Mackenzie Branco, Laura K Bryan, Sara D Lawhon, Jan S Suchodolski, Gabriel Gomez, Joanne Mansell, Aline Rodrigues Hoffmann
Identification of fungal organisms often poses a problem for pathologists because the histomorphology of some fungal organisms is not specific, fresh tissues may not be available, and isolation and identification in culture may take a long time. The purpose of this study was to validate the use of panfungal polymerase chain reaction (PCR) to identify fungal organisms from formalin-fixed paraffin-embedded (FFPE) tissues. Formalin-fixed paraffin-embedded curls were tested from 128 blocks containing canine, feline, equine, and bovine tissues with cutaneous, nasal, pulmonary, and systemic fungal infections, identified by the presence of fungi in histologic sections...
July 2017: Veterinary Pathology
https://www.readbyqxmd.com/read/28323122/exome-analysis-of-the-evolutionary-path-of-hepatocellular-adenoma-carcinoma-transition-vascular-invasion-and-brain-dissemination
#20
Sílvia Vilarinho, E Zeynep Erson-Omay, Kisha Mitchell-Richards, Charles Cha, Carol Nelson-Williams, Akdes Serin Harmancı, Katsuhito Yasuno, Murat Günel, Tamar H Taddei
Hepatocellular adenoma (HCA) is a rare benign liver tumor, predominantly seen in young women. Its major complications are malignant transformation, spontaneous hemorrhage, and rupture. We describe a case of a young female with no underlying liver disease who presented with acute abdominal pain and was found to have a 17cm heterogeneous mass in the left lobe of the liver. She underwent left hepatectomy and pathology revealed a 14cm moderately differentiated hepatocellular carcinoma (HCC) arising in a shell of a HCA...
July 2017: Journal of Hepatology
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