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https://www.readbyqxmd.com/read/29209123/prediction-of-early-stage-hepatocellular-carcinoma-using-oncoscan-chromosomal-copy-number-aberration-data
#1
Ming-Chin Yu, Chao-Wei Lee, Yun-Shien Lee, Jang-Hau Lian, Chia-Lung Tsai, Yi-Ping Liu, Chun-Hsing Wu, Chi-Neu Tsai
AIM: To identify chromosomal copy number aberrations (CNAs) in early-stage hepatocellular carcinoma (HCC) and analyze whether they are correlated with patient prognosis. METHODS: One hundred and twenty patients with early-stage HCC were enrolled in our study, with the collection of formalin fixed, paraffin-embedded (FFPE) specimens and clinicopathological data. Tumor areas were marked by certified pathologists on a hematoxylin and eosin-stained slide, and cancer and adjacent non-cancerous tissues underwent extraction of DNA, which was analyzed with the Affymetrix OncoScan platform to assess CNAs and loss of heterozygosity (LOH)...
November 28, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/29203589/lymph-node-metastases-in-colon-cancer-are-polyclonal
#2
Peter J Ulintz, Joel K Greenson, Rong Wu, Eric R Fearon, Karin M Hardiman
PURPOSE:   Recent studies have highlighted the existence of sub-clones in tumors. Lymph nodes are generally the first location of metastasis for most solid epithelial tumors including colorectal cancer (CRC). We sought to understand the genetic origin of lymph node metastasis in CRC by evaluating the relationship between CRC tumor sub-clones present in primary tumors and lymph nodes. EXPERIMENTAL DESIGN:   A total of 33 samples from seven CRC's, including two or three spatially disparate regions from each primary tumor and one to four matched lymph nodes for each tumor, underwent next-generation whole-exome DNA sequencing, Affymetrix OncoScan SNP arrays, and targeted deep confirmatory sequencing...
December 4, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29169801/evaluating-melanocytic-lesions-with-single-nucleotide-polymorphism-snp-chromosomal-microarray
#3
Amin A Hedayat, Konstantinos Linos, Hou-Sung Jung, Laura J Tafe, Shaofeng Yan, Robert E LeBlanc, Joel A Lefferts
Histopathology is the gold standard for diagnosing melanocytic lesions; however, distinguishing benign versus malignant is not always clear histologically. Single nucleotide polymorphism (SNP) microarray analysis may help in making a definitive diagnosis. Here, we share our experience with the Oncoscan FFPE Assay and demonstrate its diagnostic utility in the context of ambiguous melanocytic lesions. Eleven archival melanocytic lesions, including three benign nevi, four melanomas, three BAP1-deficient Spitzoid nevi and one nevoid melanoma were selected for validation...
November 20, 2017: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/29156679/remote-intracranial-recurrence-of-idh-mutant-gliomas-is-associated-with-tp53-mutations-and-an-8q-gain
#4
Shunsuke Nakae, Takema Kato, Kazuhiro Murayama, Hikaru Sasaki, Masato Abe, Masanobu Kumon, Tadashi Kumai, Kei Yamashiro, Joji Inamasu, Mitsuhiro Hasegawa, Hiroki Kurahashi, Yuichi Hirose
Most IDH mutant gliomas harbor either 1p/19q co-deletions or TP53 mutation; 1p/19q co-deleted tumors have significantly better prognoses than tumors harboring TP53 mutations. To investigate the clinical factors that contribute to differences in tumor progression of IDH mutant gliomas, we classified recurrent tumor patterns based on MRI and correlated these patterns with their genomic characterization. Accordingly, in IDH mutant gliomas (N = 66), 1p/19 co-deleted gliomas only recurred locally, whereas TP53 mutant gliomas recurred both locally and in remote intracranial regions...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/28927094/genomic-markers-of-ovarian-adenocarcinoma-and-its-relevancy-to-the-effectiveness-of-chemotherapy
#5
Monika Englert-Golon, Bartosz Burchardt, Bartlomiej Budny, Szymon Dębicki, Blanka Majchrzycka, Elzbieta Wrotkowska, Piotr Jasiński, Katarzyna Ziemnicka, Radosław Słopień, Marek Ruchała, Stefan Sajdak
Ovarian cancer is the eighth most common cancer and the seventh highest cause of cancer-associated mortality in women worldwide. It is the second highest cause of mortality among female reproductive malignancies. The current standard first-line treatment for advanced ovarian cancer includes a combination of surgical debulking and standard systemic platinum-based chemotherapy with carboplatin and paclitaxel. Although a deeper understanding of this disease has been attained, relapse occurs in 70% of patients 18 months subsequent to the first-line treatment...
September 2017: Oncology Letters
https://www.readbyqxmd.com/read/28899736/characterization-of-genome-wide-copy-number-aberrations-in-colonic-mixed-adenoneuroendocrine-carcinoma-and-neuroendocrine-carcinoma-reveals-recurrent-amplification-of-ptger4-and-myc-genes
#6
Namita Sinha, Daniel Gaston, Daniel Manders, Marissa Goudie, Makoto Matsuoka, Tao Xie, Weei-Yuarn Huang
Colonic Mixed adenoneuroendocrine Carcinoma (MANEC) is an aggressive neoplasm with worse prognosis compared to adenocarcinoma. To gain a better understanding of the molecular features of colonic MANEC, we characterized the genome-wide copy number aberrations (CNA) of 14 MANECs and 5 neuroendocrine carcinomas using the OncoScan FFPE assay. Compared to 269 colonic adenocarcinomas, 19 of 42 chromosomal arms of MANEC exhibited a similar frequency of major aberrant events as adenocarcinomas, and 13 chromosomal arms exhibited a higher frequency of copy number gains...
September 9, 2017: Human Pathology
https://www.readbyqxmd.com/read/28807814/development-of-a-chromosomal-microarray-test-for-the-detection-of-abnormalities-in-formalin-fixed-paraffin-embedded-products-of-conception-specimens
#7
Troy J Gliem, Umut Aypar
Testing the products of conception (POCs) provides information about the cause of fetal loss and helps determine the recurrence risk of future losses and chromosome abnormalities in subsequent pregnancies. Historically, the Mayo Clinic Cytogenetics Laboratory performed targeted fluorescent in situ hybridization (FISH) testing to identify aneuploidy of only certain chromosomes in formalin-fixed, paraffin-embedded (FFPE) POC samples. Chromosomal microarray studies using the Affymetrix OncoScan FFPE Assay can detect copy number changes across the genome...
August 12, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28697743/integrative-analysis-of-copy-number-and-gene-expression-in-breast-cancer-using-formalin-fixed-paraffin-embedded-core-biopsy-tissue-a-feasibility-study
#8
Mahesh Iddawela, Oscar Rueda, Jenny Eremin, Oleg Eremin, Jed Cowley, Helena M Earl, Carlos Caldas
BACKGROUND: An absence of reliable molecular markers has hampered individualised breast cancer treatments, and a major limitation for translational research is the lack of fresh tissue. There are, however, abundant banks of formalin-fixed paraffin-embedded (FFPE) tissue. This study evaluated two platforms available for the analysis of DNA copy number and gene expression using FFPE samples. METHODS: The cDNA-mediated annealing, selection, extension, and ligation assay (DASL™) has been developed for gene expression analysis and the Molecular Inversion Probes assay (Oncoscan™), were used for copy number analysis using FFPE tissues...
July 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28614790/genomic-landscape-and-evolution-of-metastatic-chromophobe-renal-cell-carcinoma
#9
Jozefina Casuscelli, Nils Weinhold, Gunes Gundem, Lu Wang, Emily C Zabor, Esther Drill, Patricia I Wang, Gouri J Nanjangud, Almedina Redzematovic, Amrita M Nargund, Brandon J Manley, Maria E Arcila, Nicholas M Donin, John C Cheville, R Houston Thompson, Allan J Pantuck, Paul Russo, Emily H Cheng, William Lee, Satish K Tickoo, Irina Ostrovnaya, Chad J Creighton, Elli Papaemmanuil, Venkatraman E Seshan, A Ari Hakimi, James J Hsieh
Chromophobe renal cell carcinoma (chRCC) typically shows ~7 chromosome losses (1, 2, 6, 10, 13, 17, and 21) and ~31 exonic somatic mutations, yet carries ~5%-10% metastatic incidence. Since extensive chromosomal losses can generate proteotoxic stress and compromise cellular proliferation, it is intriguing how chRCC, a tumor with extensive chromosome losses and a low number of somatic mutations, can develop lethal metastases. Genomic features distinguishing metastatic from nonmetastatic chRCC are unknown. An integrated approach, including whole-genome sequencing (WGS), targeted ultradeep cancer gene sequencing, and chromosome analyses (FACETS, OncoScan, and FISH), was performed on 79 chRCC patients including 38 metastatic (M-chRCC) cases...
June 15, 2017: JCI Insight
https://www.readbyqxmd.com/read/28417079/detection-of-copy-number-alterations-in-cell-free-tumor-dna-from-plasma
#10
Olga Østrup, Lise Barlebo Ahlborn, Ulrik Lassen, Morten Mau-Sørensen, Finn Cilius Nielsen
BACKGROUND: Somatic copy number alterations (SCNAs) occurring in tumors can provide information about tumor classification, patient's outcome or treatment targets. Liquid biopsies, incl. plasma samples containing circulating cell-free tumor DNA (ccfDNA) can be used to assess SCNAs for clinical purposes, however specify and reliability of methods have to be tested. METHODS: SNP microarrays (Affymetrix) were used to generate whole-genome copy number profiles from plasma ccfDNA (OncoScan) and paired tumor biopsies (CytoScan) from ten patients with metastatic cancers...
June 2017: BBA Clinical
https://www.readbyqxmd.com/read/28348108/comprehensive-somatic-genome-alterations-of-urachal-carcinoma
#11
Seungchul Lee, Jingu Lee, Sung Hoon Sim, Yeonghun Lee, Kyung Chul Moon, Cheol Lee, Woong-Yang Park, Nayoung Kd Kim, Se-Hoon Lee, Hyunju Lee
BACKGROUND: Urachal cancer is a rare cancer that develops in the urachus. Because of its rarity, standard treatment therapies for urachal cancer are not established, and chemotherapeutic regimens for bladder cancer have been unsuccessful for patients with urachal cancer. Hence, we aim to understand a systematic molecular characterisation of urachal cancer. METHODS: We identified somatic single-nucleotide variations (SNVs)/indels and somatic copy number aberrations (SCNAs) in the 17 patients by using whole-exome sequencing (WES) and OncoScan platform (Affymetrix) as follows: tumour-normal paired sequencing (WES, n=10), tumour-only sequencing (WES, n=1; targeted deep sequencing, n=16), and OncoScan (n=17)...
March 27, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/28315634/comparing-mutation-calls-in-fixed-tumour-samples-between-the-affymetrix-oncoscan%C3%A2-array-and-pcr-based-next-generation-sequencing
#12
COMPARATIVE STUDY
Henry M Wood, Joseph M Foster, Morag Taylor, Emma Tinkler-Hundal, Fiona S Togneri, Paula Wojtowicz, Assa Oumie, Karen G Spink, Fiona Brew, Philip Quirke
BACKGROUND: The importance of accurate and affordable mutation calling in fixed pathology samples is becoming increasingly important as we move into the era of personalised medicine. The Affymetrix OncoScan® Array platform is designed to produce actionable mutation calls in archival material. METHODS: We compared calls made using the OncoScan platform with calls made using a custom designed PCR panel followed by next-generation sequencing (NGS), in order to benchmark the sensitivity and specificity of the OncoScan calls in a large cohort of fixed tumour samples...
March 18, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28247034/genomic-characteristics-of-trastuzumab-resistant-her2-positive-metastatic-breast-cancer
#13
Mateus de Oliveira Taveira, Sheida Nabavi, Yuker Wang, Peter Tonellato, Francisco J Esteva, Lewis C Cantley, Gerburg M Wulf
PURPOSE: Resistance to trastuzumab therapy is linked to phosphoinositol 3-kinase (PI3K) pathway activation. One key downstream effector and regulator of this pathway is the mechanistic target of rapamycin (mTOR). In 2011, a phase I/II study evaluated the combination of trastuzumab and everolimus (a mTOR inhibitor) for treatment of Her2-positive metastatic breast cancer (MBC) for patients who had progressed on trastuzumab-based therapy. METHODS: We retrospectively analyzed GeneChip microarray data from 22 of 47 patients included in the study...
July 2017: Journal of Cancer Research and Clinical Oncology
https://www.readbyqxmd.com/read/28184012/chromosome-20q-amplification-defines-a-subtype-of-microsatellite-stable-left-sided-colon-cancers-with-wild-type-ras-raf-and-better-overall-survival
#14
Ryan N Ptashkin, Carlos Pagan, Rona Yaeger, Sumit Middha, Jinru Shia, Kevin P O'Rourke, Michael F Berger, Lu Wang, Robert Cimera, Jiajing Wang, David S Klimstra, Leonard Saltz, Marc Ladanyi, Ahmet Zehir, Jaclyn F Hechtman
Here, comprehensive analysis was performed on the molecular and clinical features of colorectal carcinoma harboring chromosome 20q amplification. Tumor and normal DNA from patients with advanced colorectal carcinoma underwent next-generation sequencing via MSK-IMPACT, and a subset of case samples was subjected to high-resolution microarray (Oncoscan). Relationships between genomic copy number and transcript expression were assessed with The Cancer Genome Atlas (TCGA) colorectal carcinoma data. Of the colorectal carcinoma patients sequenced (n = 401) with MSK-IMPACT, 148 (37%) had 20q gain, and 30 (7%) had 20q amplification...
June 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28181325/recurrent-copy-number-alterations-in-low-grade-and-anaplastic-pleomorphic-xanthoastrocytoma-with-and-without-braf-v600e-mutation
#15
Rachael A Vaubel, Alissa A Caron, Seiji Yamada, Paul A Decker, Jeanette E Eckel Passow, Fausto J Rodriguez, Amulya A Nageswara Rao, Daniel Lachance, Ian Parney, Robert Jenkins, Caterina Giannini
Pleomorphic xanthoastrocytoma (PXA) is a rare localized glioma characterized by frequent BRAF V600E mutation and CDKN2A/B deletion. We explored the association of copy-number variants (CNVs) with BRAF mutations, tumor grade, and patient survival in a cohort of 41 PXA patients using OncoScan chromosomal microarray. Primary resection specimens were available in 38 cases, including 24 PXA and 14 anaplastic PXA (A-PXA), 23 BRAF V600E mutant tumors (61%). CNVs were identified in all cases and most frequently involved chromosome 9 with homozygous CDKN2A/B deletion (n = 33, 87%), a higher proportion than previously detected by comparative genomic hybridization (50%-60%) (37)...
February 9, 2017: Brain Pathology
https://www.readbyqxmd.com/read/28059097/fibrous-hamartoma-of-infancy-a-clinicopathologic-study-of-145-cases-including-2-with-sarcomatous-features
#16
Alyaa Al-Ibraheemi, Anthony Martinez, Sharon W Weiss, Harry P Kozakewich, Antonio R Perez-Atayde, Henry Tran, David M Parham, William R Sukov, Karen J Fritchie, Andrew L Folpe
Fibrous hamartoma of infancy is a rare soft tissue lesion of infants and young children with characteristic triphasic morphology, which typically occurs in the axilla and less commonly in other locations. We reviewed 145 cases of fibrous hamartoma of infancy from our consultation archives. Cases occurred in 106 males and 39 females (mean age-15 months; range-birth to 14 years), and involved both typical sites (eg, axilla/back/upper arm) (n=69) and unusual locations (n=76). Six were congenital. The tumors presented as subcutaneous masses and ranged from 0...
April 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/27974698/genome-wide-copy-number-analyses-of-superficial-esophageal-squamous-cell-carcinoma-with-and-without-metastasis
#17
Pengjiao Wang, Ling Shan, Liyan Xue, Bo Zheng, Jianming Ying, Ning Lu
Superficial esophageal squamous cell carcinoma (ESCC) is generally considered a subtype of less invasive ESCC. Yet a subset of these superficial ESCC would have metastasis after esophagostomy or endoscopic resection and lead to poor prognosis. The objective of this study is to determine biomarkers that can identify such subset of superficial ESCC that would have metastasis after surgery using genome wide copy number alteration (CNA) analyses. The CNAs of 38 cases of superficial ESCCs originated from radical surgery, including 19 without metastasis and 19 with metastasis within 5 years' post-surgery, were analyzed using Affymetrix OncoScan™ FFPE Assay...
January 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/27818284/cardiac-angiosarcoma-histopathologic-immunohistochemical-and-cytogenetic-analysis-of-10-cases
#18
Charles Leduc, Sarah M Jenkins, William R Sukov, Jeannette G Rustin, Joseph J Maleszewski
Angiosarcoma (AS) is the most common cardiac sarcoma with differentiation, and is poorly characterized from a molecular genetic standpoint. Prognosis remains poor, owing to several factors including aggressive tumor biology, poor response to adjuvant therapy, and lack of targeted therapy. The clinical, pathologic and molecular cytogenetic features were studied in ten cardiac AS surgically resected at Mayo Clinic (1994-2015) using a whole-genome, single-nucleotide polymorphism-based platform (OncoScan). Mean patient age was 47...
February 2017: Human Pathology
https://www.readbyqxmd.com/read/27716627/precise-erbb2-copy-number-assessment-in-breast-cancer-by-means-of-molecular-inversion-probe-array-analysis
#19
Matthias Christgen, Jana L van Luttikhuizen, Mieke Raap, Peter Braubach, Lars Schmidt, Danny Jonigk, Friedrich Feuerhake, Ulrich Lehmann, Brigitte Schlegelberger, Hans H Kreipe, Doris Steinemann
HER2/ERBB2 amplification/overexpression determines the eligibility of breast cancer patients to HER2-targeted therapy. This study evaluates the agreement between ERBB2 copy number assessment by fluorescence in situ hybridization, a standard method recommended by the American Society of Clinical Oncology/College of American Pathologists (ASCO/CAP), and newly available DNA extraction-based methods. A series of n=29 formalin-fixed paraffin-embedded breast cancers were subjected to ERBB2 copy number assessment by fluorescence in situ hybridization (FISH, Vysis, Abbott)...
December 13, 2016: Oncotarget
https://www.readbyqxmd.com/read/27683181/patient-derived-xenograft-establishment-from-human-malignant-pleural-mesothelioma
#20
Licun Wu, Ghassan Allo, Thomas John, Ming Li, Tetsuzo Tagawa, Isabelle Opitz, Masaki Anraku, Zhihong Yun, Melania Pintilie, Bethany Pitcher, Geoffrey Liu, Ron Feld, Michael R Johnston, Marc de Perrot, Ming-Sound Tsao
PURPOSE: Malignant pleural mesothelioma (MPM) is a rare but aggressive disease with few therapeutic options. The tumor-stromal interface is important in MPM, but this is lost in cell lines, the main model used for preclinical studies. We sought to characterize MPM patient-derived xenografts (PDX) to determine their suitability as preclinical models and whether tumors that engraft reflect a more aggressive biological phenotype. EXPERIMENTAL DESIGN: Fresh tumors were harvested from extrapleural pneumonectomy, decortication, or biopsy samples of 50 MPM patients and implanted subcutaneously into immunodeficient mice and serially passaged for up to five generations...
September 28, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
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