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Whole genome sequencing pathology

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https://www.readbyqxmd.com/read/29159459/epg5-related-vici-syndrome-a-primary-defect-of-autophagic-regulation-with-an-emerging-phenotype-overlapping-with-mitochondrial-disorders
#1
Shanti Balasubramaniam, Lisa G Riley, Anand Vasudevan, Mark J Cowley, Velimir Gayevskiy, Carolyn M Sue, Caitlin Edwards, Edward Edkins, Reimar Junckerstorff, C Kiraly-Borri, P Rowe, J Christodoulou
Vici syndrome is a rare, under-recognised, relentlessly progressive congenital multisystem disorder characterised by five principal features of callosal agenesis, cataracts, cardiomyopathy, combined immunodeficiency and oculocutaneous hypopigmentation. In addition, three equally consistent features (profound developmental delay, progressive failure to thrive and acquired microcephaly) are highly supportive of the diagnosis. Since its recognition as a distinct entity in 1988, an extended phenotype with sensorineural hearing loss, skeletal myopathy and variable involvement of virtually any organ system, including the lungs, thyroid, liver and kidneys, have been described...
November 21, 2017: JIMD Reports
https://www.readbyqxmd.com/read/29153840/association-of-omics-features-with-histopathology-patterns-in-lung-adenocarcinoma
#2
Kun-Hsing Yu, Gerald J Berry, Daniel L Rubin, Christopher Ré, Russ B Altman, Michael Snyder
Adenocarcinoma accounts for more than 40% of lung malignancy, and microscopic pathology evaluation is indispensable for its diagnosis. However, how histopathology findings relate to molecular abnormalities remains largely unknown. Here, we obtained H&E-stained whole-slide histopathology images, pathology reports, RNA sequencing, and proteomics data of 538 lung adenocarcinoma patients from The Cancer Genome Atlas and used these to identify molecular pathways associated with histopathology patterns. We report cell-cycle regulation and nucleotide binding pathways underpinning tumor cell dedifferentiation, and we predicted histology grade using transcriptomics and proteomics signatures (area under curve >0...
November 13, 2017: Cell Systems
https://www.readbyqxmd.com/read/29152610/mutations-in-coagulation-factor-viii-are-associated-with-more-favorable-outcome-in-patients-with-cutaneous-melanoma
#3
Zheng Ping, Abha Soni, Lance A Williams, Huy P Pham, Malay K Basu, X Long Zheng
Coagulation factor VIII (FVIII), von Willebrand factor (VWF), and ADAMTS13 play an important role in regulation of normal hemostasis. However, little is known about their roles in patients with malignancy, particularly with cutaneous melanoma. Whole genome sequencing data are available for 25,719 cases in 126 cancer genomic studies for analysis. All sequencing data and corresponding pathology findings were obtained from The Cancer Genome Atlas. The cBioportal bioinformatics tools were used for the data analysis...
July 2017: TH Open
https://www.readbyqxmd.com/read/29138824/genetic-mutational-testing-of-chinese-children-with-familial-hematuria-with-biopsy%C3%A2-proven-fsgs
#4
Yongzhen Li, Ying Wang, Qingnan He, Xiqiang Dang, Yan Cao, Xiaochuan Wu, Shuanghong Mo, Xiaoxie He, Zhuwen Yi
Focal segmental glomerulosclerosis (FSGS) is a pathological lesion rather than a disease, with a diverse etiology. FSGS may result from genetic and non‑genetic factors. FSGS is considered a podocyte disease due to the fact that in the majority of patients with proven‑FSGS, the lesion results from defects in the podocyte structure or function. However, FSGS does not result exclusively from podocyte‑associated genes, however also from other genes including collagen IV‑associated genes. Patients who carry the collagen type IVA3 chain (COL4A3) or COL4A4 mutations usually exhibit Alport Syndrome (AS), thin basement membrane neuropathy or familial hematuria (FH)...
November 10, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29132146/identification-of-unique-neoantigen-qualities-in-long-term-survivors-of-pancreatic-cancer
#5
Vinod P Balachandran, Marta Łuksza, Julia N Zhao, Vladimir Makarov, John Alec Moral, Romain Remark, Brian Herbst, Gokce Askan, Umesh Bhanot, Yasin Senbabaoglu, Daniel K Wells, Charles Ian Ormsby Cary, Olivera Grbovic-Huezo, Marc Attiyeh, Benjamin Medina, Jennifer Zhang, Jennifer Loo, Joseph Saglimbeni, Mohsen Abu-Akeel, Roberta Zappasodi, Nadeem Riaz, Martin Smoragiewicz, Z Larkin Kelley, Olca Basturk, Mithat Gönen, Arnold J Levine, Peter J Allen, Douglas T Fearon, Miriam Merad, Sacha Gnjatic, Christine A Iacobuzio-Donahue, Jedd D Wolchok, Ronald P DeMatteo, Timothy A Chan, Benjamin D Greenbaum, Taha Merghoub, Steven D Leach
Pancreatic ductal adenocarcinoma is a lethal cancer with fewer than 7% of patients surviving past 5 years. T-cell immunity has been linked to the exceptional outcome of the few long-term survivors, yet the relevant antigens remain unknown. Here we use genetic, immunohistochemical and transcriptional immunoprofiling, computational biophysics, and functional assays to identify T-cell antigens in long-term survivors of pancreatic cancer. Using whole-exome sequencing and in silico neoantigen prediction, we found that tumours with both the highest neoantigen number and the most abundant CD8(+) T-cell infiltrates, but neither alone, stratified patients with the longest survival...
November 8, 2017: Nature
https://www.readbyqxmd.com/read/29128982/actionable-secondary-findings-from-whole-genome-sequencing-of-954-east-asians
#6
Clara Sze-Man Tang, Saloni Dattani, Man-Ting So, Stacey S Cherny, Paul K H Tam, Pak C Sham, Maria-Mercè Garcia-Barcelo
Recently, the American College of Medical Genetics (ACMG) recommended the return of actionable secondary findings detected from clinical sequencing. The reported frequency of secondary findings in Asian populations were highly variable and it is unclear whether the uniformity in coverage offered by whole-genome sequencing (WGS) may impact the estimate. In this analysis, we aimed to refine the rate of secondary findings on East Asians through a large-scale WGS study. We classified 1256 protein-altering or splicing variants of the 59 actionable genes detected from WGS of 954 East Asians in strict accordance with the ACMG and the Association for Molecular Pathology guidelines...
November 11, 2017: Human Genetics
https://www.readbyqxmd.com/read/29123202/potential-damaging-mutation-in-lrp5-from-genome-sequencing-of-the-first-reported-chimpanzee-with-the-chiari-malformation
#7
Manuel Solis-Moruno, Marc de Manuel, Jessica Hernandez-Rodriguez, Claudia Fontsere, Alba Gomara-Castaño, Cristina Valsera-Naranjo, Dietmar Crailsheim, Arcadi Navarro, Miquel Llorente, Laura Riera, Olga Feliu-Olleta, Tomas Marques-Bonet
The genus Pan is the closest related to humans (Homo sapiens) and it includes two species: Pan troglodytes (chimpanzees) and Pan paniscus (bonobos). Different characteristics, some of biomedical aspect, separate them from us. For instance, some common human medical conditions are rare in chimpanzees (menopause, Alzheimer disease) although it is unclear to which extent longevity plays an active role in these differences. However, both humans and chimpanzees present similar pathologies, thus, understanding traits in chimpanzees can help unravel the molecular basis of human conditions...
November 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29113995/time-for-change-a-new-training-programme-for-morpho-molecular-pathologists
#8
REVIEW
David A Moore, Caroline A Young, Hayley T Morris, Karin A Oien, Jessica L Lee, J Louise Jones, Manuel Salto-Tellez
The evolution of cellular pathology as a specialty has always been driven by technological developments and the clinical relevance of incorporating novel investigations into diagnostic practice. In recent years, the molecular characterisation of cancer has become of crucial relevance in patient treatment both for predictive testing and subclassification of certain tumours. Much of this has become possible due to the availability of next-generation sequencing technologies and the whole-genome sequencing of tumours is now being rolled out into clinical practice in England via the 100 000 Genome Project...
November 7, 2017: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/29112122/identification-and-antimicrobial-susceptibility-testing-of-anaerobic-bacteria-rubik-s-cube-of-clinical-microbiology
#9
REVIEW
Márió Gajdács, Gabriella Spengler, Edit Urbán
Anaerobic bacteria have pivotal roles in the microbiota of humans and they are significant infectious agents involved in many pathological processes, both in immunocompetent and immunocompromised individuals. Their isolation, cultivation and correct identification differs significantly from the workup of aerobic species, although the use of new technologies (e.g., matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, whole genome sequencing) changed anaerobic diagnostics dramatically...
November 7, 2017: Antibiotics
https://www.readbyqxmd.com/read/29100084/profiling-of-short-tandem-repeat-disease-alleles-in-12-632-human-whole-genomes
#10
Haibao Tang, Ewen F Kirkness, Christoph Lippert, William H Biggs, Martin Fabani, Ernesto Guzman, Smriti Ramakrishnan, Victor Lavrenko, Boyko Kakaradov, Claire Hou, Barry Hicks, David Heckerman, Franz J Och, C Thomas Caskey, J Craig Venter, Amalio Telenti
Short tandem repeats (STRs) are hyper-mutable sequences in the human genome. They are often used in forensics and population genetics and are also the underlying cause of many genetic diseases. There are challenges associated with accurately determining the length polymorphism of STR loci in the genome by next-generation sequencing (NGS). In particular, accurate detection of pathological STR expansion is limited by the sequence read length during whole-genome analysis. We developed TREDPARSE, a software package that incorporates various cues from read alignment and paired-end distance distribution, as well as a sequence stutter model, in a probabilistic framework to infer repeat sizes for genetic loci, and we used this software to infer repeat sizes for 30 known disease loci...
November 2, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29099283/lowly-methylated-region-analysis-identifies-ebf1-as-a-potential-epigenetic-modifier-in-breast-cancer
#11
Nora Fernandez-Jimenez, Athena Sklias, Szilvia Ecsedi, Vincent Cahais, Davide Degli-Esposti, Antonin Jay, Pierre Benoit Ancey, Hae Dong Woo, Hector Hernandez-Vargas, Zdenko Herceg
Breast cancer (BC) encompasses heterogeneous pathologies with different subtypes exhibiting distinct molecular changes, including those related to DNA methylation. However, the role of these changes in mediating BC heterogeneity is poorly understood. Lowly methylated regions (LMRs), non-CpG island loci that usually contain transcription factor (TF) binding sites, have been suggested to act as regulatory elements that define cellular identity. In this study, we aimed to identify the key subtype-specific TFs that may lead to LMR generation and shape the BC methylome and transcription program...
November 3, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29075935/novel-gfm2-variants-associated-with-early-onset-neurological-presentations-of-mitochondrial-disease-and-impaired-expression-of-oxphos-subunits
#12
Ruth I C Glasgow, Kyle Thompson, Inês A Barbosa, Langping He, Charlotte L Alston, Charu Deshpande, Michael A Simpson, Andrew A M Morris, Axel Neu, Ulrike Löbel, Julie Hall, Holger Prokisch, Tobias B Haack, Maja Hempel, Robert McFarland, Robert W Taylor
Mitochondrial diseases are characterised by clinical, molecular and functional heterogeneity, reflecting their bi-genomic control. The nuclear gene GFM2 encodes mtEFG2, a protein with an essential role during the termination stage of mitochondrial translation. We present here two unrelated patients harbouring different and previously unreported compound heterozygous (c.569G>A, p.(Arg190Gln); c.636delA, p.(Glu213Argfs*3)) and homozygous (c.275A>C, p.(Tyr92Ser)) recessive variants in GFM2 identified by whole exome sequencing (WES) together with histochemical and biochemical findings to support the diagnoses of pathological GFM2 variants in each case...
October 26, 2017: Neurogenetics
https://www.readbyqxmd.com/read/29027470/next-generation-sequencing-applications-for-cardiovascular-disease
#13
Samira Kalayinia, Hamidreza Goodarzynejad, Majid Maleki, Nejat Mahdieh
The Human Genome Project (HGP), as the primary sequencing of the human genome, lasted more than one decade to be completed using the traditional Sanger's method. At present, next-generation sequencing (NGS) technology could provide the genome sequence data in hours. NGS has also decreased the expense of sequencing; therefore, nowadays it is possible to carry out both whole-genome (WGS) and whole-exome sequencing (WES) for the variations detection in patients with rare genetic diseases as well as complex disorders such as common cardiovascular diseases (CVDs)...
October 13, 2017: Annals of Medicine
https://www.readbyqxmd.com/read/29025399/plasmodium-falciparum-epcr-binding-pfemp1-expression-increases-with-malaria-disease-severity-and-is-elevated-in-retinopathy-negative-cerebral-malaria
#14
Estela Shabani, Benjamin Hanisch, Robert O Opoka, Thomas Lavstsen, Chandy C John
BACKGROUND: Expression of group A and the A-like subset of group B Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) is associated with severe malaria (SM). The diversity of var sequences combined with the challenges of distinct classification of patient pathologies has made studying the role of distinct PfEMP1 variants on malaria disease severity challenging. The application of retinopathy in the recent years has provided a further method to clinically evaluate children with cerebral malaria (CM)...
October 13, 2017: BMC Medicine
https://www.readbyqxmd.com/read/28974544/tert-structural-rearrangements-in-metastatic-pheochromocytomas
#15
Trisha Dwight, Aidan Flynn, Kaushalya Amarasinghe, Diana E Benn, Richard Lupat, Jason Li, Daniel Cameron, Annette Hogg, Shiva Balachander, Ida Lm Candiloro, Stephen Wong, Bruce G Robinson, Anthony T Papenfuss, Anthony J Gill, Alexander Dobrovic, Rodney J Hicks, Roderick Clifton-Bligh, Richard William Tothill
Pheochromocytomas (PC) and paragangliomas (PGL) are endocrine tumors for which the genetic and clinico-pathological features of metastatic progression remain incompletely understood. As a result, the risk of metastasis from a primary tumor cannot be predicted. Early diagnosis of individuals at high risk of developing metastases is clinically important and the identification of new biomarkers that are predictive of metastatic potential is of high value. Activation of TERT has been associated with a number of malignant tumors, including PC/PGL...
October 3, 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28974240/association-of-a-novel-point-mutation-in-msh2-gene-with-familial-multiple-primary-cancers
#16
Hai Hu, Hong Li, Feng Jiao, Ting Han, Meng Zhuo, Jiujie Cui, Yixue Li, Liwei Wang
BACKGROUND: Multiple primary cancers (MPC) have been identified as two or more cancers without any subordinate relationship that occur either simultaneously or metachronously in the same or different organs of an individual. Lynch syndrome is an autosomal dominant genetic disorder that increases the risk of many types of cancers. Lynch syndrome patients who suffer more than two cancers can also be considered as MPC; patients of this kind provide unique resources to learn how genetic mutation causes MPC in different tissues...
October 3, 2017: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/28939077/genomic-characterization-of-tobacco-nut-chewing-hpv-negative-early-stage-tongue-tumors-identify-mmp10-asa-candidate-to-predict-metastases
#17
Pawan Upadhyay, Nilesh Gardi, Sanket Desai, Pratik Chandrani, Asim Joshi, Bhaskar Dharavath, Priyanca Arora, Munita Bal, Sudhir Nair, Amit Dutt
OBJECTIVES: Nodal metastases status among early stage tongue squamous cell cancer patients plays a decisive role in the choice of treatment, wherein about 70% patients can be spared from surgery with an accurate prediction of negative pathological lymph node status. This underscores an unmet need for prognostic biomarkers to stratify the patients who are likely to develop metastases. MATERIALS AND METHODS: We performed high throughput sequencing of fifty four samples derived from HPV negative early stage tongue cancer patients habitual of chewing betel nuts, areca nuts, lime or tobacco using whole exome (n=47) and transcriptome (n=17) sequencing that were analyzed using in-house computational tools...
October 2017: Oral Oncology
https://www.readbyqxmd.com/read/28924022/pan-genomic-analyses-identify-key-helicobacter-pylori-pathogenic-loci-modified-by-carcinogenic-host-microenvironments
#18
Jennifer M Noto, Abha Chopra, John T Loh, Judith Romero-Gallo, M Blanca Piazuelo, Mark Watson, Shay Leary, Amber C Beckett, Keith T Wilson, Timothy L Cover, Simon Mallal, Dawn A Israel, Richard M Peek
OBJECTIVE: Helicobacter pylori is the strongest risk factor for gastric cancer; however, the majority of infected individuals do not develop disease. Pathological outcomes are mediated by complex interactions among bacterial, host and environmental constituents, and two dietary factors linked with gastric cancer risk are iron deficiency and high salt. We hypothesised that prolonged adaptation of H. pylori to in vivo carcinogenic microenvironments results in genetic modification important for disease...
September 18, 2017: Gut
https://www.readbyqxmd.com/read/28894165/evolution-analysis-of-heterogeneous-non-small-cell-lung-carcinoma-by-ultra-deep-sequencing-of-the-mitochondrial-genome
#19
Wafa Amer, Csaba Toth, Erik Vassella, Jeannine Meinrath, Ulrike Koitzsch, Anne Arens, Jia Huang, Hannah Eischeid, Alexander Adam, Reinhard Buettner, Andreas Scheel, Stephan C Schaefer, Margarete Odenthal
Accurate assessment of tumour heterogeneity is an important issue that influences prognosis and therapeutic decision in molecular pathology. Due to the shortage of protective histones and a limited DNA repair capacity, the mitochondrial (mt)-genome undergoes high variability during tumour development. Therefore, screening of mt-genome represents a useful molecular tool for assessing precise cell lineages and tracking tumour history. Here, we describe a highly specific and robust multiplex PCR-based ultra-deep sequencing technology for analysis of the whole mt-genome (wmt-seq) on low quality-DNA from formalin-fixed paraffin-embedded tissues...
September 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28884746/inflammatory-leiomyosarcoma-is-a-distinct-tumor-characterized-by-near-haploidization-few-somatic-mutations-and-a-primitive-myogenic-gene-expression-signature
#20
Elsa Arbajian, Jan Köster, Fredrik Vult von Steyern, Fredrik Mertens
Inflammatory leiomyosarcoma is a soft-tissue tumor resembling conventional leiomyosarcoma, but with a prominent intrinsic inflammatory component. Previous studies have suggested that inflammatory leiomyosarcoma differs genetically from leiomyosarcoma, but in-depth analyses are lacking. Here we provide a comprehensive picture of the genome and transcriptome of inflammatory leiomyosarcoma by combining cytogenetic, single-nucleotide polymorphism array, mRNA-sequencing, and whole-exome sequencing data. The results show that inflammatory leiomyosarcoma has a specific genetic profile characterized by near-haploidization with or without subsequent whole-genome doubling...
September 8, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
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