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Whole genome sequencing pathology

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https://www.readbyqxmd.com/read/28327926/genomic-characterisation-of-her2-positive-breast-cancer-and-response-to-neoadjuvant-trastuzumab-and-chemotherapy-results-from-the-acosog-z1041-alliance-trial
#1
R Lesurf, O L Griffith, M Griffith, J Hundal, L Trani, M A Watson, R Aft, M J Ellis, D Ota, V J Suman, F Meric-Bernstam, A M Leitch, J C Boughey, G Unzeitig, A U Buzdar, K K Hunt, E R Mardis
Background: HER2 ( ERBB2 ) gene amplification and its corresponding overexpression are present in 15-30% of invasive breast cancers. While HER2-targeted agents are effective treatments, resistance remains a major cause of death. The American College of Surgeons Oncology Group Z1041 trial (NCT00513292) was designed to compare the pathologic complete response (pCR) rate of distinct regimens of neoadjuvant chemotherapy and trastuzumab, but ultimately identified no difference [1]. Patients and methods: In supplement to tissues from 37 Z1041 cases, 11 similarly treated cases were obtained from a single institution study (NCT00353483)...
February 21, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28327142/exome-sequencing-identified-rare-variants-in-genes-hspg2-and-atp2b4-in-a-family-segregating-developmental-dysplasia-of-the-hip
#2
Sulman Basit, Alia M Albalawi, Essa Alharby, Khalid I Khoshhal
BACKGROUND: Developmental dysplasia of the hip (DDH) is a common pathological condition of the musculoskeletal system in infants which results in a congenital and developmental malformation of the hip joint. DDH is a spectrum of pathologies affecting the infant hip ranging from asymptomatic subtle radiographic signs through mild instability to frank dislocations with acetabular dysplasia. A Saudi family with three affected individuals with DDH was identified and genetic analysis was performed to detect the possible genetic defect(s) underlying DDH in the affected members of the family...
March 21, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28323122/exome-analysis-of-the-evolutionary-path-of-hepatocellular-adenoma-carcinoma-transition-vascular-invasion-and-brain-dissemination
#3
Sílvia Vilarinho, 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 17 cm heterogeneous mass in the left lobe of the liver. She underwent left hepatectomy and pathology revealed a 14 cm moderately differentiated hepatocellular carcinoma (HCC) arising in a shell of a HCA...
March 17, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28318500/mutations-in-tmem260-cause-a-pediatric-neurodevelopmental-cardiac-and-renal-syndrome
#4
Asaf Ta-Shma, Tahir N Khan, Asaf Vivante, Jason R Willer, Pavle Matak, Chaim Jalas, Ben Pode-Shakked, Yishay Salem, Yair Anikster, Friedhelm Hildebrandt, Nicholas Katsanis, Orly Elpeleg, Erica E Davis
Despite the accelerated discovery of genes associated with syndromic traits, the majority of families affected by such conditions remain undiagnosed. Here, we employed whole-exome sequencing in two unrelated consanguineous kindreds with central nervous system (CNS), cardiac, renal, and digit abnormalities. We identified homozygous truncating mutations in TMEM260, a locus predicted to encode numerous splice isoforms. Systematic expression analyses across tissues and developmental stages validated two such isoforms, which differ in the utilization of an internal exon...
March 11, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28292896/loss-of-lmod1-impairs-smooth-muscle-cytocontractility-and-causes-megacystis-microcolon-intestinal-hypoperistalsis-syndrome-in-humans-and-mice
#5
Danny Halim, Michael P Wilson, Daniel Oliver, Erwin Brosens, Joke B G M Verheij, Yu Han, Vivek Nanda, Qing Lyu, Michael Doukas, Hans Stoop, Rutger W W Brouwer, Wilfred F J van IJcken, Orazio J Slivano, Alan J Burns, Christine K Christie, Karen L de Mesy Bentley, Alice S Brooks, Dick Tibboel, Suowen Xu, Zheng Gen Jin, Tono Djuwantono, Wei Yan, Maria M Alves, Robert M W Hofstra, Joseph M Miano
Megacystis microcolon intestinal hypoperistalsis syndrome (MMIHS) is a congenital visceral myopathy characterized by severe dilation of the urinary bladder and defective intestinal motility. The genetic basis of MMIHS has been ascribed to spontaneous and autosomal dominant mutations in actin gamma 2 (ACTG2), a smooth muscle contractile gene. However, evidence suggesting a recessive origin of the disease also exists. Using combined homozygosity mapping and whole exome sequencing, a genetically isolated family was found to carry a premature termination codon in Leiomodin1 (LMOD1), a gene preferentially expressed in vascular and visceral smooth muscle cells...
March 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28236343/tarseqqc-quality-control-on-targeted-sequencing-experiments-in-r
#6
Gabriela A Merino, Yanina A Murua, Cristóbal Fresno, Juan M Sendoya, Mariano Golubicki, Soledad Iseas, Mariana Coraglio, Osvaldo L Podhajcer, Andrea S Llera, Elmer A Fernández
Targeted sequencing is growing as a screening methodology used in research and medical genetics to identify genomic alterations causing human diseases. In general, a list of possible genomic variants is derived from mapped reads through a variant calling step. This processing step is usually based on variant coverage, although it may be affected by several factors. Therefore, under-covered relevant clinical variants may not be reported, impacting on pathology diagnosis or treatment. Thus, a prior quality control of the experiment is critical to determine variant detection accuracy and to avoid erroneous medical conclusions...
February 24, 2017: Human Mutation
https://www.readbyqxmd.com/read/28235824/a-nonsense-variant-in-the-st14-gene-in-akhal-teke-horses-with-naked-foal-syndrome
#7
Anina Bauer, Theresa Hiemesch, Vidhya Jagannathan, Markus Neuditschko, Iris Bachmann, Stefan Rieder, Sofia Mikko, M Cecilia Penedo, Nadja Tarasova, Martina Vitková, Nicolò Sirtori, Paola Roccabianca, Tosso Leeb, Monika M Welle
Naked foal syndrome (NFS) is a genodermatosis in the Akhal-Teke horse breed. We provide the first scientific description of this phenotype. Affected horses had almost no hair and showed a mild ichthyosis. So far, all known NFS affected horses died between a few weeks and 3 years of age. It is not clear whether a specific pathology caused the premature deaths. NFS is inherited as a monogenic autosomal recessive trait. We mapped the disease causing genetic variant to two segments on chromosomes 7 and 27 in the equine genome...
February 24, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28228131/whole-genome-sequencing-of-one-complex-pedigree-illustrates-challenges-with-genomic-medicine
#8
Han Fang, Yiyang Wu, Hui Yang, Margaret Yoon, Laura T Jiménez-Barrón, David Mittelman, Reid Robison, Kai Wang, Gholson J Lyon
BACKGROUND: Human Phenotype Ontology (HPO) has risen as a useful tool for precision medicine by providing a standardized vocabulary of phenotypic abnormalities to describe presentations of human pathologies; however, there have been relatively few reports combining whole genome sequencing (WGS) and HPO, especially in the context of structural variants. METHODS: We illustrate an integrative analysis of WGS and HPO using an extended pedigree, which involves Prader-Willi Syndrome (PWS), hereditary hemochromatosis (HH), and dysautonomia-like symptoms...
February 23, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28126467/mixed-hepatocellular-cholangiocarcinoma-tumors-cholangiolocellular-carcinoma-is-a-distinct-molecular-entity
#9
Agrin Moeini, Daniela Sia, Zhongyang Zhang, Genis Camprecios, Ashley Stueck, Hui Dong, Robert Montal, Laura Torrens, Iris Martinez-Quetglas, M Isabel Fiel, Ke Hao, Augusto Villanueva, Swan N Thung, Myron E Schwartz, Josep M Llovet
BACKGROUND AND AIMS: Mixed hepatocellular-cholangiocarcinoma (HCC-CCA) is a rare and poorly understood type of primary liver cancer. We aimed to perform a comprehensive molecular characterization of this malignancy. METHODS: We performed gene expression profiling, DNA copy number detection, and exome sequencing using formalin-fixed samples from 18 patients with mixed HCC-CCA encompassing the whole histological spectrum of the disease. Comparative genomic analysis was performed with independent datasets of HCC (n=164) and iCCA (n=149)...
January 23, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28067894/unexpected-uvr-and-non-uvr-mutation-burden-in-some-acral-and-cutaneous-melanomas
#10
Robert V Rawson, Peter A Johansson, Nicholas K Hayward, Nicola Waddell, Ann-Marie Patch, Serigne Lo, John V Pearson, John F Thompson, Graham J Mann, Richard A Scolyer, James S Wilmott
Ultraviolet radiation (UVR) mutagenesis causes nearly all cutaneous melanomas, however, since UVR signatures are largely absent in acral melanoma, as well as melanoma in sun-protected sites, the cause of these melanomas is unknown. Whole-genome sequencing data generated as part of the Australian Melanoma Genome Project was supplemented with a detailed histopathological assessment with the melanomas then classified as UVR or non-UVR related, based on their mutation signatures. The clinicopathological characteristics of melanomas with mutation signatures for their subtype were compared...
January 9, 2017: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/28057588/global-gene-expression-patterns-and-somatic-mutations-in-sporadic-intracranial-aneurysms
#11
Zhili Li, Haibin Tan, Yi Shi, Guangfu Huang, Zhenyu Wang, Ling Liu, Cheng Yin, Qi Wang
BACKGROUND: High-throughput sequencing technologies can expand our understanding of the pathological basis of intracranial aneurysms (IAs). Our study was aimed to decipher the gene expression signature and genetic factors associated with IAs. METHODS: We determined the gene expression levels of three cases of IAs by RNA sequencing. Bioinformatics analysis was conducted to identify the differentially expressed genes (DEGs) and uncover their biological function. Moreover, whole genome sequencing (WGS) on additional six cases of IAs was performed to detect the potential somatic alterations in DEGs...
January 2, 2017: World Neurosurgery
https://www.readbyqxmd.com/read/28046008/cell-free-dna-provides-a-good-representation-of-the-tumor-genome-despite-its-biased-fragmentation-patterns
#12
Xiangyuan Ma, Liangjun Zhu, Xue Wu, Hua Bao, Xiaonan Wang, Zhili Chang, Yang W Shao, Zhenxin Wang
Cell-free DNA (cfDNA) is short, extracellular, fragmented double-stranded DNA found in plasma. Plasma of patients with solid tumor has been found to show significantly increased quantities of cfDNA. Although currently poorly understood, the mechanism of cfDNA generation is speculated to be a product of genomic DNA fragmentation during cellular apoptosis and necrosis. Sequencing of cfDNA with tumor origin has identified tumor biomarkers, elucidating molecular pathology and assisting in accurate diagnosis. In this study, we performed whole-genome sequencing ofcfDNA samples with matching tumor and whole blood samples from five patients diagnosed with stage IV gastric or lung cancer...
2017: PloS One
https://www.readbyqxmd.com/read/28041643/comprehensive-rare-variant-analysis-via-whole-genome-sequencing-to-determine-the-molecular-pathology-of-inherited-retinal-disease
#13
Keren J Carss, Gavin Arno, Marie Erwood, Jonathan Stephens, Alba Sanchis-Juan, Sarah Hull, Karyn Megy, Detelina Grozeva, Eleanor Dewhurst, Samantha Malka, Vincent Plagnol, Christopher Penkett, Kathleen Stirrups, Roberta Rizzo, Genevieve Wright, Dragana Josifova, Maria Bitner-Glindzicz, Richard H Scott, Emma Clement, Louise Allen, Ruth Armstrong, Angela F Brady, Jenny Carmichael, Manali Chitre, Robert H H Henderson, Jane Hurst, Robert E MacLaren, Elaine Murphy, Joan Paterson, Elisabeth Rosser, Dorothy A Thompson, Emma Wakeling, Willem H Ouwehand, Michel Michaelides, Anthony T Moore, Andrew R Webster, F Lucy Raymond
Inherited retinal disease is a common cause of visual impairment and represents a highly heterogeneous group of conditions. Here, we present findings from a cohort of 722 individuals with inherited retinal disease, who have had whole-genome sequencing (n = 605), whole-exome sequencing (n = 72), or both (n = 45) performed, as part of the NIHR-BioResource Rare Diseases research study. We identified pathogenic variants (single-nucleotide variants, indels, or structural variants) for 404/722 (56%) individuals. Whole-genome sequencing gives unprecedented power to detect three categories of pathogenic variants in particular: structural variants, variants in GC-rich regions, which have significantly improved coverage compared to whole-exome sequencing, and variants in non-coding regulatory regions...
January 5, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28028040/whole-genome-expression-analysis-of-mammalian-wide-interspersed-repeat-elements-in-human-cell-lines
#14
Davide Carnevali, Anastasia Conti, Matteo Pellegrini, Giorgio Dieci
With more than 500,000 copies, mammalian-wide interspersed repeats (MIRs), a sub-group of SINEs, represent ∼2.5% of the human genome and one of the most numerous family of potential targets for the RNA polymerase (Pol) III transcription machinery. Since MIR elements ceased to amplify ∼130 myr ago, previous studies primarily focused on their genomic impact, while the issue of their expression has not been extensively addressed. We applied a dedicated bioinformatic pipeline to ENCODE RNA-Seq datasets of seven human cell lines and, for the first time, we were able to define the Pol III-driven MIR transcriptome at single-locus resolution...
December 27, 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/27982025/morphological-characterization-of-colorectal-cancers-in-the-cancer-genome-atlas-reveals-distinct-morphology-molecular-associations-clinical-and-biological-implications
#15
Jinru Shia, Nikolaus Schultz, Deborah Kuk, Efsevia Vakiani, Sumit Middha, Neil H Segal, Jaclyn F Hechtman, Michael F Berger, Zsofia K Stadler, Martin R Weiser, Jedd D Wolchok, C Richard Boland, Mithat Gönen, David S Klimstra
The Cancer Genome Atlas data on colorectal carcinoma have provided a comprehensive view of the tumor's genomic alterations and their tumorigenic roles. Tumor morphology, however, has not been fully integrated into the analysis. The aim of this study was to explore relevant associations between tumor morphology and the newly characterized genomic alterations in colorectal carcinoma. Two hundred and seven colorectal carcinomas that had undergone whole-exome sequencing as part of The Cancer Genome Atlas project and had adequate virtual images in the cBioPortal for Cancer Genomics constituted our study population...
December 16, 2016: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/27959926/predictors-of-chemosensitivity-in-triple-negative-breast-cancer-an-integrated-genomic-analysis
#16
Tingting Jiang, Weiwei Shi, Vikram B Wali, Lőrinc S Pongor, Charles Li, Rosanna Lau, Balázs Győrffy, Richard P Lifton, William F Symmans, Lajos Pusztai, Christos Hatzis
BACKGROUND: Triple negative breast cancer (TNBC) is a highly heterogeneous and aggressive disease, and although no effective targeted therapies are available to date, about one-third of patients with TNBC achieve pathologic complete response (pCR) from standard-of-care anthracycline/taxane (ACT) chemotherapy. The heterogeneity of these tumors, however, has hindered the discovery of effective biomarkers to identify such patients. METHODS AND FINDINGS: We performed whole exome sequencing on 29 TNBC cases from the MD Anderson Cancer Center (MDACC) selected because they had either pCR (n = 18) or extensive residual disease (n = 11) after neoadjuvant chemotherapy, with cases from The Cancer Genome Atlas (TCGA; n = 144) and METABRIC (n = 278) cohorts serving as validation cohorts...
December 2016: PLoS Medicine
https://www.readbyqxmd.com/read/27942904/whole-genome-sequencing-reveals-a-potential-causal-mutation-for-dwarfism-in-the-miniature-shetland-pony
#17
Julia Metzger, Alana Christina Gast, Rahel Schrimpf, Janina Rau, Deborah Eikelberg, Andreas Beineke, Maren Hellige, Ottmar Distl
The Miniature Shetland pony represents a horse breed with an extremely small body size. Clinical examination of a dwarf Miniature Shetland pony revealed a lowered size at the withers, malformed skull and brachygnathia superior. Computed tomography (CT) showed a shortened maxilla and a cleft of the hard and soft palate which protruded into the nasal passage leading to breathing difficulties. Pathological examination confirmed these findings but did not reveal histopathological signs of premature ossification in limbs or cranial sutures...
December 9, 2016: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/27940213/whole-genome-sequencing-of-fowl-aviadenovirus-a-a-causative-agent-of-gizzard-erosion-and-ulceration-in-adult-laying-hens
#18
Anna K Matczuk, Jowita S Niczyporuk, Maciej Kuczkowski, Grzegorz Woźniakowski, Marcin Nowak, Alina Wieliczko
Gizzard erosion and ulceration (GEU) caused by fowl aviadenovirus serotype 1 (FAdV-1) of the species Fowl aviadenovirus A (FAdV-A) represents an economically important problem in poultry production. The disease affects mostly young chicken broilers or layers before production. In this study, an unusual GEU outbreak in a flock of laying hens at 38weeks of age is described. The affected flock showed elevated mortality rates, with the highest number of dead birds appearing between the 39th and 40th week of life, with a subsequent reduction in laying performance and decreased total egg weight...
December 8, 2016: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/27939373/molecular-classification-of-hepatocellular-adenoma-associates%C3%A2-with-risk-factors-bleeding-and-malignant-transformation
#19
Jean Charles Nault, Gabrielle Couchy, Charles Balabaud, Guillaume Morcrette, Stefano Caruso, Jean-Frederic Blanc, Yannick Bacq, Julien Calderaro, Valérie Paradis, Jeanne Ramos, Jean-Yves Scoazec, Viviane Gnemmi, Nathalie Sturm, Catherine Guettier, Monique Fabre, Eric Savier, Laurence Chiche, Philippe Labrune, Janick Selves, Dominique Wendum, Camilla Pilati, Alexis Laurent, Anne De Muret, Brigitte Le Bail, Sandra Rebouissou, Sandrine Imbeaud, Paulette Bioulac-Sage, Eric Letouzé, Jessica Zucman-Rossi
BACKGROUND & AIMS: Hepatocellular adenomas (HCAs) are benign liver tumors that can be assigned to molecular subtypes based on inactivating mutations in hepatocyte nuclear factor 1A, activating mutations in β-catenin, or activation of inflammatory signaling pathways. We aimed to update the classification system for HCA and associate the subtypes with disease risk factors and complications. METHODS: We analyzed expression levels of 20 genes and sequenced exon regions of 8 genes (HNF1A, IL6ST, CTNNB1, FRK, STAT3, GNAS, JAK1, and TERT) in 607 samples of 533 HCAs from 411 patients, collected from 28 centers mainly in France from 2000 and 2014...
December 7, 2016: Gastroenterology
https://www.readbyqxmd.com/read/27935972/distinct-epigenetic-effects-of-tobacco-smoking-in-whole-blood-and-among-leukocyte-subtypes
#20
Dan Su, Xuting Wang, Michelle R Campbell, Devin K Porter, Gary S Pittman, Brian D Bennett, Ma Wan, Neal A Englert, Christopher L Crowl, Ryan N Gimple, Kelly N Adamski, Zhiqing Huang, Susan K Murphy, Douglas A Bell
Tobacco smoke exposure dramatically alters DNA methylation in blood cells and may mediate smoking-associated complex diseases through effects on immune cell function. However, knowledge of smoking effects in specific leukocyte subtypes is limited. To better characterize smoking-associated methylation changes in whole blood and leukocyte subtypes, we used Illumina 450K arrays and Reduced Representation Bisulfite Sequencing (RRBS) to assess genome-wide DNA methylation. Differential methylation analysis in whole blood DNA from 172 smokers and 81 nonsmokers revealed 738 CpGs, including 616 previously unreported CpGs, genome-wide significantly associated with current smoking (p <1...
2016: PloS One
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