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Eduardo Avila, Aline Brugnera Felkl, Pietra Graebin, Cláudia Paiva Nunes, Clarice Sampaio Alho
Use of Massive Parallel Sequencing (MPS) techniques has been investigated by forensic community aiming introduction of such methods in routine forensic casework analyses. Interesting features presented by MPS include high-throughput, ability to simultaneous genotyping of significant number of samples and forensic markers, workflow automation, among others. Emergence of single nucleotide polymorphism (SNP) as forensic relevant markers was facilitated in this process, since concurrent typing of larger marker sets is necessary for obtaining same levels of individual discrimination provided by other marker categories...
February 13, 2019: Forensic Science International. Genetics
Maria A Smolle, Karl Kashofer, Jakob M Riedl, Michael Stotz, Armin Gerger
BACKGROUND/AIM: Colorectal cancer (CRC) is the third most common cancer worldwide. The prognosis between left- and right-sided CRC differs, partly due to baseline differences as vascular supply. The purpose of the present study was to investigate whether there are genetic differences between left- and right-sided CRC. PATIENTS AND METHODS: Eighty-seven patients with CRC (mean age: 61 years) were retrospectively included in the study. Blood samples were used for genetic analysis, by applying the sequencing research panel Ion AmpliSeq Colon and Lung Cancer Research Panel V2...
February 2019: Anticancer Research
Zhi Long, Yinan Li, Yu Gan, Dongyu Zhao, Guangyu Wang, Ning Xie, Jessica M Lovnicki, Ladan Fazli, Qi Cao, Kaifu Chen, Xuesen Dong
Homeobox A10 (HOXA10) is an important transcription factor that regulates the development of the prostate gland. However, it remains unknown whether it modulates prostate cancer (PCa) progression into castrate-resistant stages. In this study, we have applied RNA in situ hybridization assays to demonstrate that downregulation of HOXA10 expression is associated with castrate-resistant PCa. These findings are supported by public RNA-seq data showing that reduced HOXA10 expression is correlated with poor patient survival...
March 1, 2019: Endocrine-related Cancer
Eric Strengman, Francoise A S Barendrecht-Smouter, Carmen de Voijs, Paula de Vree, Isaac J Nijman, Wendy W J de Leng
Next-generation sequencing (NGS) is rapidly becoming the method of choice for mutation analysis in both research and diagnostics. The benefit of targeted NGS compared to whole-genome and whole-exome sequencing is that smaller amounts of input material can be used as well as qualitatively suboptimal tissue samples, like formalin-fixed, paraffin-embedded archival tissue.Here, we describe the protocol for targeted next-generation sequencing using the Ion Torrent PGM platform in combination with Ion Ampliseq NGS gene panels for formalin-fixed, paraffin-embedded tissues...
2019: Methods in Molecular Biology
Hans M Albertsen, Charoula Matalliotaki, Michail Matalliotakis, Maria I Zervou, Ioannis Matalliotakis, Demetrios A Spandidos, Rakesh Chettier, Kenneth Ward, George N Goulielmos
Endometriosis is an enigmatic condition with an unknown etiology and a poorly understood pathogenesis. It is considered to appear from the interplay of many genetic and environmental factors, affecting up to 10% of women and represents a major cause of pain and infertility. The familial association of endometriosis, as demonstrated through monozygotic twin and family studies suggests a genetic contribution to the disease, with further case‑control and genome‑wide association studies (GWAS) detecting various endometriosis risk factors...
January 3, 2019: Molecular Medicine Reports
Tao Cui, Stefan Enroth, Adam Ameur, Inger Gustavsson, David Lindquist, Ulf Gyllensten
Invasive cervical cancer (ICC) with very low titer of high-risk human papillomavirus (HPV) has worse clinical outcome than cases with high titer, indicating a difference in molecular etiology. Fresh-frozen ICC tumors (n=49) were classified into high and low HPV titer cases using real-time PCR-based HPV genotyping. The mutation spectra were studied using the AmpliSeq Comprehensive Cancer Panel and the expression profiles using total RNA-sequencing, and the results validated using the AmpliSeq Transcriptome assay...
December 28, 2018: Carcinogenesis
Go Eun Bae, Nara Yoon, Eun Yoon Cho, Hyun-Soo Kim, Soo Youn Cho
BACKGROUND/AIM: Adenoid cystic carcinoma accounts for fewer than 1% of all breast malignancies. Herein, we describe the clinicopathological characteristics and immunophenotype of mammary adenoid cystic carcinoma that exhibited adipocytic differentiation. Furthermore, we aimed to identify mutations potentially associated with this rare tumor. CASE REPORT: A 52-year-old woman was referred to our Institution after detection of an incidental breast mass. The resected breast specimen contained a well-circumscribed, firm mass surrounded by ill-defined, soft, yellow bulging nodules and measured 2...
January 2019: Anticancer Research
Ruiqi Chen, Haolong Li, Yinan Li, Ladan Fazli, Martin Gleave, Lucia Nappi, Xuesen Dong
Background: HOXA10 is a key transcriptional factor that regulates testis development as reported from previous transgenic mouse models and human inherited diseases. However, whether it also plays important roles in promoting the development of testicular cancer is not well-understood. Objective: To study the expression of HOXA10 and its regulated signaling pathways in testicular cancers. Design, Setting, and Participants: A tissue microarray was constructed with benign and cancerous testis. TCam2, NT-2, and NCCIT cell models were applied in this study...
2018: Frontiers in Oncology
Joshua D Smith, Andrew C Birkeland, Andrew J Rosko, Rebecca C Hoesli, Susan K Foltin, Paul Swiecicki, Michelle Mierzwa, Steven B Chinn, Andrew G Shuman, Kelly M Malloy, Keith A Casper, Scott A McLean, Gregory T Wolf, Carol R Bradford, Mark E Prince, John Chad Brenner, Matthew E Spector
BACKGROUND: We sought to describe targeted DNA sequencing data of persistent/recurrent laryngeal squamous cell carcinoma (LSCC) and to compare gene-specific alteration frequencies with that of primary, untreated LSCC specimens from The Cancer Genome Atlas (TCGA). METHODS: The tumors of 21 patients with persistent/recurrent LSCC were subjected to targeted DNA sequencing using the Ion AmpliSeq Comprehensive Cancer Panel. Gene-specific alteration frequencies were compared (Chi-Square test) to primary, untreated LSCC sequencing data from TCGA using the cBioPortal platform...
December 12, 2018: Head & Neck
Gyorgy Petrovics, Douglas K Price, Hong Lou, Yongmei Chen, Lisa Garland, Sara Bass, Kristine Jones, Indu Kohaar, Amina Ali, Lakshmi Ravindranath, Denise Young, Jennifer Cullen, Tiffany H Dorsey, Isabell A Sesterhenn, Stephen A Brassell, Inger L Rosner, Doug Ross, William Dahut, Stefan Ambs, William Douglas Figg, Shiv Srivastava, Michael Dean
BACKGROUND: Germline mutations in BRCA2 have been linked to a higher risk of prostate cancer (PCa), and high frequency of BRCA1 and BRCA2 (BRCA1/2) gene alterations was recently reported in metastatic castration-resistant PCa specimens. Mutations in BRCA2 vary in racial and ethnic groups including African-American (AA) and Caucasian-American (CA) populations. METHODS: BRCA1 and BRCA2 genes were sequenced (Ion AmpliSeq targeted sequencing) in archived blood DNA specimens in 1240 PCa patients, including 30% AA patients, in three different cohorts: localized early stage (T2) PCa (N = 935); advanced PCa (50% T3-4) (N = 189); and metastatic PCa (N = 116)...
December 12, 2018: Prostate Cancer and Prostatic Diseases
Jing Zhai, Gabriel Giannini, Mark D Ewalt, Elizabeth Y Zhang, Marta Invernizzi, Joyce Niland, Lily L Lai
Metaplastic breast carcinoma (MBC) is a rare subtype of breast cancer with variable morphology. MBC is more often triple negative (ER-, PR-, HER2-) and is associated with poorer clinical outcome when compared to infiltrating ductal carcinoma. The purpose of our study is to identify molecular alterations in MBC using next generation sequencing (NGS) which may aid chemotherapy selection and use of targeted therapy. A cohort of 18 patients with MBC yielded adequate DNA from microdissected formalin fixed and paraffin embedded (FFPE) tumor blocks...
December 8, 2018: Human Pathology
Ruchi Chaudhary, Luca Quagliata, Jermann Philip Martin, Ilaria Alborelli, Dinesh Cyanam, Vinay Mittal, Warren Tom, Janice Au-Young, Seth Sadis, Fiona Hyland
Background: Tumor mutational burden (TMB) is an increasingly important biomarker for immune checkpoint inhibitors. Recent publications have described strong association between high TMB and objective response to mono- and combination immunotherapies in several cancer types. Existing methods to estimate TMB require large amount of input DNA, which may not always be available. Methods: In this study, we develop a method to estimate TMB using the Oncomine Tumor Mutation Load (TML) Assay with 20 ng of DNA, and we characterize the performance of this method on various formalin-fixed, paraffin-embedded (FFPE) research samples of several cancer types...
December 2018: Translational Lung Cancer Research
Yasmin Soares de Lima, Marcela Chiabai, Jun Shen, Mara S Córdoba, Beatriz R Versiani, Rosenelle O A Benício, Robert Pogue, Regina Célia Mingroni-Netto, Karina Lezirovitz, Aline Pic-Taylor, Juliana F Mazzeu, Silviene F Oliveira
Syndromic hearing loss accounts for approximately 30% of all cases of hearing loss due to genetic causes. Mutation screening in known genes is important because it potentially sheds light on the genetic etiology of hearing loss and helps in genetic counseling of families. In this study, we describe a customized Ion AmpliSeq Panel, specifically designed for the investigation of syndromic hearing loss. The Ion AmpliSeq Panel was customized to cover the coding sequences of 52 genes. Twenty-four patients were recruited: 17 patients with a clinical diagnosis of a known syndrome, and seven whose clinical signs did not allow identification of a syndrome...
December 2018: Hearing Research
Xiangpei Zeng, Kyleen Elwick, Carrie Mayes, Maiko Takahashi, Jonathan L King, David Gangitano, Bruce Budowle, Sheree Hughes-Stamm
Skeletal remains recovered from missing persons' cases are often exposed to harsh environmental conditions resulting in the DNA being damaged, degraded, and/or the samples containing PCR inhibitors. In this study, the efficacy of common extraction methods was evaluated to remove high levels of PCR inhibitors commonly encountered with human remains, and their downstream compatibility with the two leading sequencing chemistries and platforms for human identification purposes. Blood, hair, and bone samples were spiked with high levels of inhibitors commonly identified in each particular substrate in order to test the efficiency of various DNA extraction methods prior to sequencing...
October 19, 2018: International Journal of Legal Medicine
Miho Kono, Takeo Fujii, Naoko Matsuda, Kenichi Harano, Huiqin Chen, Chetna Wathoo, Aron Y Joon, Debu Tripathy, Funda Meric-Bernstam, Naoto T Ueno
Background: Bone is the most common site of metastasis of breast cancer. Biological mechanisms of metastasis to bone may be different from mechanisms of metastasis to non-bone sites, and identification of distinct signaling pathways and somatic mutations may provide insights on biology and rational targets for treatment and prevention of bone metastasis. The aims of this study were to compare and contrast somatic mutations, clinicopathologic characteristics, and survival in breast cancer patients with bone-only versus non-bone sites of first metastasis...
2018: Journal of Cancer
Dario Kringel, Mari A Kaunisto, Catharina Lippmann, Eija Kalso, Jörn Lötsch
Background: Many gene variants modulate the individual perception of pain and possibly also its persistence. The limited selection of single functional variants is increasingly being replaced by analyses of the full coding and regulatory sequences of pain-relevant genes accessible by means of next generation sequencing (NGS). Methods: An NGS panel was created for a set of 77 human genes selected following different lines of evidence supporting their role in persisting pain. To address the role of these candidate genes, we established a sequencing assay based on a custom AmpliSeqTM panel to assess the exomic sequences in 72 subjects of Caucasian ethnicity...
2018: Frontiers in Pharmacology
Rosa Doñate Puertas, Gilles Millat, Isabelle Ernens, Vincent Gache, Samuel Chauveau, Elodie Morel, Emilie Christin, Nathalie Couturier, Yvan Devaux, Philippe Chevalier
Atrial fibrillation (AF) is a common arrhythmia for which the genetic studies mainly focused on the genes involved in electrical remodeling, rather than left atrial muscle remodeling. To identify rare variants involved in atrial myopathy using mutational screening, a high-throughput next-generation sequencing (NGS) workflow was developed based on a custom AmpliSeq™ panel of 55 genes potentially involved in atrial myopathy. This workflow was applied to a cohort of 94 patients with AF, 76 with atrial dilatation and 18 without...
2018: BioMed Research International
Omar Youssef, Aija Knuuttila, Päivi Piirilä, Tom Böhling, Virinder Sarhadi, Sakari Knuutila
BACKGROUND: Genetic alterations occurring in lung cancer are the basis for defining molecular subtypes and essential for targeted therapies. Exhaled breath condensate (EBC) is a form of non-invasive sample that, amongst components, contains DNA from pulmonary tissue. Next-generation sequencing (NGS) was herein used to analyze mutations in EBC from patients with lung cancer. MATERIALS AND METHODS: EBC was collected from 26 patients with cancer and 20 healthy controls...
October 2018: Anticancer Research
Ryan Poplin, Pi-Chuan Chang, David Alexander, Scott Schwartz, Thomas Colthurst, Alexander Ku, Dan Newburger, Jojo Dijamco, Nam Nguyen, Pegah T Afshar, Sam S Gross, Lizzie Dorfman, Cory Y McLean, Mark A DePristo
Despite rapid advances in sequencing technologies, accurately calling genetic variants present in an individual genome from billions of short, errorful sequence reads remains challenging. Here we show that a deep convolutional neural network can call genetic variation in aligned next-generation sequencing read data by learning statistical relationships between images of read pileups around putative variant and true genotype calls. The approach, called DeepVariant, outperforms existing state-of-the-art tools...
November 2018: Nature Biotechnology
Anna Kluska, Maria Kulecka, Tomasz Litwin, Karolina Dziezyc, Aneta Balabas, Magdalena Piatkowska, Agnieszka Paziewska, Michalina Dabrowska, Michal Mikula, Diana Kaminska, Anna Wiernicka, Piotr Socha, Anna Czlonkowska, Jerzy Ostrowski
BACKGROUND & AIMS: Wilson's disease (WD) is an autosomal recessive disorder associated with disease-causing alterations across the ATP7B gene, with highly variable symptoms and age of onset. We aimed to assess whether the clinical variability of WD relates to modifier genes. METHODS: A total of 248 WD patients were included, of whom 148 were diagnosed after age of 17. Human exome libraries were constructed using AmpliSeq technology and sequenced using the IonProton platform...
September 19, 2018: Liver International: Official Journal of the International Association for the Study of the Liver
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