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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
Farah Jouali, Nabila Marchoudi, Salwa Talbi, Basma Bilal, Mohamed El Khasmi, Houria Rhaissi, Jamal Fekkak
BACKGROUND: Triple Negative Breast Cancer (TNBC) is an aggressive form of breast cancer, that represents 10-20% of all breast carcinomas and characterized by the lack of a specific cell surface marker compared to other breast cancer subtypes. Due to the absence of molecular markers for TNBC his treatment options remains limited, without proven targeted therapies, which emphasize the need for discovering molecular markers that could be targeted for patient treatment, An important number of TNBC cases harbor aberrations in the phosphoinositide 3-kinase (PI3K) pathway, leading to constitutive activation of the downstream signaling pathway...
September 18, 2018: BMC Cancer
Xin-Fu Lin, Jie-Wei Luo, Gui Liu, Yao-Bin Zhu, Zhao Jin, Xing Lin
Dilated cardiomyopathy (DCM) is a complex myocardial disease of multifactorial etiologies, including enlarged cardiac chambers and contractile dysfunction. It has been suggested that the inheritance of DCM‑associated mutations predominates its onset. Therefore, the present study investigated the pathogenesis of DCM via pedigree analysis and genetic diagnosis by massive whole‑exome screening, and targeted exon capture. To study the familial gene‑phenotype association, the exon and splice sites of 325 hereditary disease‑associated genes in the proband with familial dilated cardiomyopathy (FDC), including 61 cardiac disease‑associated genes, such as the lamins A/C (LMNA), were analyzed by ultra‑high multiplex polymerase chain reaction and the Ion AmpliSeq™ Inherited Disease Panel...
September 5, 2018: Molecular Medicine Reports
Hee Kyung Kim, Kyung Hee Park, Youjin Kim, Song Ee Park, Han Sang Lee, Sung Won Lim, Jang Ho Cho, Ji-Yeon Kim, Jeong Eon Lee, Jin Seok Ahn, Young-Hyuck Im, Jong Han Yu, Yeon Hee Park
Purpose: We aimed to analyze the discordance between immunohistochemistry (IHC)-based surrogate subtyping and PAM50 intrinsic subtypes and to assess overall survival (OS) according to discordance. Materials and Methods: A total of 607 patients were analyzed. Hormone receptor (HR) expression was evaluated by IHC, and human epidermal growth factor receptor 2 (HER2) expression was analyzed by IHC and/or fluorescence in situ hybridization. PAM50 intrinsic subtypes were determined according to 50 cancer genes using the NanoString nCounter Analysis System...
September 5, 2018: Cancer Research and Treatment: Official Journal of Korean Cancer Association
Ji Hyun Lee, Sohee Cho, Moon-Young Kim, Dong Hoon Shin, Allah Rakha, Vasant Shinde, Soong Deok Lee
Massively parallel sequencing (MPS) offers additional information in cases that lack reference samples for comparison. The HID-Ion AmpliSeq Ancestry Panel is a forensic multiplex platform consisting of 165 autosomal markers designed to provide biogeographic ancestry information. We analyzed seven different population groups from Asia to assess the accuracy and reliability of analysis, using this panel. In this study, we have designated 750 unrelated Asians, from southern China (n = 99), Beijing (n = 100), Japan (n = 101), Korea (n = 100), Vietnam (n = 100), Nepal (n = 100), India (n = 51), and Pakistan (n = 99)...
August 23, 2018: Legal Medicine
Viola Paradiso, Andrea Garofoli, Nadia Tosti, Manuela Lanzafame, Valeria Perrina, Luca Quagliata, Matthias S Matter, Stefan Wieland, Markus H Heim, Salvatore Piscuoglio, Charlotte K Y Ng, Luigi M Terracciano
Commercially available targeted panels miss genomic regions frequently altered in hepatocellular carcinoma (HCC). We sought to design and benchmark a sequencing assay for genomic screening in HCC. We designed an AmpliSeq custom panel targeting all exons of 33 protein-coding and two long noncoding RNA genes frequently mutated in HCC, TERT promoter, and nine genes with frequent copy number alterations. By using this panel, the profiling of DNA from fresh-frozen (n = 10, 1495×) and/or formalin-fixed, paraffin-embedded (FFPE) tumors with low-input DNA (n = 36, 530×) from 39 HCCs identified at least one somatic mutation in 90% of the cases...
August 22, 2018: Journal of Molecular Diagnostics: JMD
Amikar Sehdev, Olumide Gbolahan, Brad A Hancock, Melissa Stanley, Safi Shahda, Jun Wan, Howard H Wu, Milan Radovich, Bert H O'Neil
Purpose: Pancreatic ductal adenocarcinoma (PDAC) is a lethal cancer with lack of predictive biomarkers. We conducted a study to assess DNA damage repair (DDR) gene mutations as a predictive biomarker in PDAC patients treated with FOLFIRINOX. Experimental Design: Indiana University Simon Cancer Center pancreatic cancer database was used to identify patients with metastatic PDAC, treated with FOLFIRINOX and had tissue available for DNA sequencing. Baseline demographic, clinical, and pathologic information was gathered...
August 21, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Christina Demuth, Anne Winther-Larsen, Anne Tranberg Madsen, Peter Meldgaard, Boe Sandahl Sorensen
Background: The potentials of circulating tumour DNA (ctDNA) have been studied for non-invasive disease monitoring in patients with targetable mutations. However, the majority of cancer patients harbour no targetable mutations. A workflow including targeted next-generation sequencing (NGS) and droplet digital PCR (ddPCR) could be used for monitoring treatment in these patients. Thus, our aim was to evaluate the workflow for ctDNA monitoring in a cohort of non-small cell lung cancer patients...
July 24, 2018: Oncotarget
Cecily P Vaughn, José Luis Costa, Harriet E Feilotter, Rosella Petraroli, Varun Bagai, Anna Maria Rachiglio, Federica Zito Marino, Bastiaan Tops, Henriette M Kurth, Kazuko Sakai, Andrea Mafficini, Roy R L Bastien, Anne Reiman, Delphine Le Corre, Alexander Boag, Susan Crocker, Michel Bihl, Astrid Hirschmann, Aldo Scarpa, José Carlos Machado, Hélène Blons, Orla Sheils, Kelli Bramlett, Marjolijn J L Ligtenberg, Ian A Cree, Nicola Normanno, Kazuto Nishio, Pierre Laurent-Puig
BACKGROUND: Gene fusion events resulting from chromosomal rearrangements play an important role in initiation of lung adenocarcinoma. The recent association of four oncogenic driver genes, ALK, ROS1, RET, and NTRK1, as lung tumor predictive biomarkers has increased the need for development of up-to-date technologies for detection of these biomarkers in limited amounts of material. METHODS: We describe here a multi-institutional study using the Ion AmpliSeq™ RNA Fusion Lung Cancer Research Panel to interrogate previously characterized lung tumor samples...
August 16, 2018: BMC Cancer
Ahn R Lee, Yu Gan, Yuxin Tang, Xuesen Dong
BACKGROUND: Prostate adenocarcinoma (AdPC) cells can undergo lineage switching to neuroendocrine cells and develop into therapy-resistant neuroendocrine prostate cancer (NEPC). While genomic/epigenetic alterations are shown to induce neuroendocrine differentiation via an intermediate stem-like state, RNA splicing factor SRRM4 can transform AdPC cells into NEPC xenografts through a direct neuroendocrine transdifferentiation mechanism. Whether SRRM4 can also regulate a stem-cell gene network for NEPC development remains unclear...
August 10, 2018: EBioMedicine
Lisett Contreras, Ruben I Calderon, Armando Varela-Ramirez, Hong-Yu Zhang, Yuan Quan, Umashankar Das, Jonathan R Dimmock, Rachid Skouta, Renato J Aguilera
PURPOSE: Previously, compounds containing a piperidone structure have been shown to be highly cytotoxic to cancer cells. Recently, we found that the piperidone compound P2 exhibits a potent anti-neoplastic activity against human breast cancer-derived cells. Here, we aimed to evaluate two piperidone compounds, P1 and P2, for their potential anti-neoplastic activity against human leukemia/lymphoma-derived cells. METHODS: Cytotoxicity and apoptosis induction were evaluated using MTS, annexin V-FITC/PI and mitochondrial membrane potential polychromatic assays to confirm the mode of action of the piperidone compounds...
December 2018: Cellular Oncology (Dordrecht)
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