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Whole genome sequencing pathology

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https://www.readbyqxmd.com/read/27912315/genetics-of-infectious-and-inflammatory-diseases-overlapping-discoveries-from-association-and-exome-sequencing-studies
#1
David Langlais, Nassima Fodil, Philippe Gros
Genome technologies have defined a complex genetic architecture in major infectious, inflammatory, and autoimmune disorders. High density marker arrays and Immunochips have powered genome-wide association studies (GWAS) that have mapped nearly 450 genetic risk loci in 22 major inflammatory diseases, including a core of common genes that play a central role in pathological inflammation. Whole-exome and whole-genome sequencing have identified more than 265 genes in which mutations cause primary immunodeficiencies and rare forms of severe inflammatory bowel disease...
December 1, 2016: Annual Review of Immunology
https://www.readbyqxmd.com/read/27889782/molecular-pathology-a-requirement-for-precision-medicine-in-cancer
#2
Manfred Dietel
The increasing importance of targeting drugs and check-point inhibitors in the treatment of several tumor entities (breast, colon, lung, malignant melanoma, lymphoma, etc.) and the necessity of a companion diagnostic (HER2, (pan)RAS, EGFR, ALK, BRAF, ROS1, MET, PD-L1, etc.) is leading to new challenges for surgical pathology. Since almost all the biomarkers to be specifically detected are tissue based, a precise and reliable diagnostic is absolutely crucial. To meet this challenge surgical pathology has adapted a number of molecular methods (semi-quantitative immunohistochemistry, fluorescence in situ hybridization, PCR and its multiple variants, (pyro/Sanger) sequencing, next generation sequencing (amplicon, whole exome, whole genome), DNA arrays, methylation analyses, etc...
2016: Oncology Research and Treatment
https://www.readbyqxmd.com/read/27862604/whole-genome-sequencing-of-cytogenetically-balanced-chromosome-translocations-identifies-potentially-pathological-gene-disruptions-and-highlights-the-importance-of-microhomology-in-the-mechanism-of-formation
#3
Daniel Nilsson, Maria Pettersson, Peter Gustavsson, Alisa Förster, Wolfgang Hofmeister, Josephine Wincent, Vasilios Zachariadis, Britt-Marie Anderlid, Ann Nordgren, Outi Mäkitie, Valtteri Wirta, Max Käller, Francesco Vezzi, James R Lupski, Magnus Nordenskjöld, Elisabeth Syk Lundberg, Claudia M B Carvalho, Anna Lindstrand
Most balanced translocations are thought to result mechanistically from nonhomologous end joining or, in rare cases of recurrent events, by nonallelic homologous recombination. Here, we use low-coverage mate pair whole-genome sequencing to fine map rearrangement breakpoint junctions in both phenotypically normal and affected translocation carriers. In total, 46 junctions from 22 carriers of balanced translocations were characterized. Genes were disrupted in 48% of the breakpoints; recessive genes in four normal carriers and known dominant intellectual disability genes in three affected carriers...
November 16, 2016: Human Mutation
https://www.readbyqxmd.com/read/27811364/erbb2-mutation-is-associated-with-a-worse-prognosis-in-patients-with-cdh1-altered-invasive-lobular-cancer-of-the-breast
#4
Zheng Ping, Gene P Siegal, Shuko Harada, Isam-Eldin Eltoum, Mariam Youssef, Tiansheng Shen, Jianbo He, Yingjie Huang, Dongquan Chen, Yiping Li, Kirby I Bland, Helena R Chang, Dejun Shen
E-cadherin (CDH1) is a glycoprotein that mediates adhesion between epithelial cells and also suppresses cancer invasion. Mutation or deletion of the CDH1 gene has been reported in 30-60% cases of invasive lobular carcinoma (ILC). However, little is known about genomic differences between ILC with and without a CDH1 alteration. Therefore, we analyzed whole genome sequencing data of 169 ILC cases from The Cancer Genome Atlas (TCGA) to address this deficiency. Our study shows that CDH1 gene was altered in 59.2% (100/169) of ILC...
November 2, 2016: Oncotarget
https://www.readbyqxmd.com/read/27799067/identification-of-a-rai1-associated-disease-network-through-integration-of-exome-sequencing-transcriptomics-and-3d-genomics
#5
Maria Nicla Loviglio, Christine R Beck, Janson J White, Marion Leleu, Tamar Harel, Nicolas Guex, Anne Niknejad, Weimin Bi, Edward S Chen, Isaac Crespo, Jiong Yan, Wu-Lin Charng, Shen Gu, Ping Fang, Zeynep Coban-Akdemir, Chad A Shaw, Shalini N Jhangiani, Donna M Muzny, Richard A Gibbs, Jacques Rougemont, Ioannis Xenarios, James R Lupski, Alexandre Reymond
BACKGROUND: Smith-Magenis syndrome (SMS) is a developmental disability/multiple congenital anomaly disorder resulting from haploinsufficiency of RAI1. It is characterized by distinctive facial features, brachydactyly, sleep disturbances, and stereotypic behaviors. METHODS: We investigated a cohort of 15 individuals with a clinical suspicion of SMS who showed neither deletion in the SMS critical region nor damaging variants in RAI1 using whole exome sequencing. A combination of network analysis (co-expression and biomedical text mining), transcriptomics, and circularized chromatin conformation capture (4C-seq) was applied to verify whether modified genes are part of the same disease network as known SMS-causing genes...
November 1, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27798646/independent-origin-and-global-distribution-of-distinct-plasmodium-vivax-duffy-binding-protein-gene-duplications
#6
Jessica B Hostetler, Eugenia Lo, Usheer Kanjee, Chanaki Amaratunga, Seila Suon, Sokunthea Sreng, Sivanna Mao, Delenasaw Yewhalaw, Anjali Mascarenhas, Dominic P Kwiatkowski, Marcelo U Ferreira, Pradipsinh K Rathod, Guiyun Yan, Rick M Fairhurst, Manoj T Duraisingh, Julian C Rayner
BACKGROUND: Plasmodium vivax causes the majority of malaria episodes outside Africa, but remains a relatively understudied pathogen. The pathology of P. vivax infection depends critically on the parasite's ability to recognize and invade human erythrocytes. This invasion process involves an interaction between P. vivax Duffy Binding Protein (PvDBP) in merozoites and the Duffy antigen receptor for chemokines (DARC) on the erythrocyte surface. Whole-genome sequencing of clinical isolates recently established that some P...
October 2016: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/27769649/knowledge-gaps-and-research-recommendations-for-essential-tremor
#7
Franziska Hopfner, Dietrich Haubenberger, Wendy R Galpern, Katrina Gwinn, Ashlee Van't Veer, Samantha White, Kailash Bhatia, Charles H Adler, David Eidelberg, William Ondo, Glenn T Stebbins, Caroline M Tanner, Rick C Helmich, Fred A Lenz, Roy V Sillitoe, David Vaillancourt, Jerrold L Vitek, Elan D Louis, Holly A Shill, Matthew P Frosch, Tatiana Foroud, Gregor Kuhlenbäumer, Andrew Singleton, Claudia M Testa, Mark Hallett, Rodger Elble, Günther Deuschl
Essential tremor (ET) is a common cause of significant disability, but its etiologies and pathogenesis are poorly understood. Research has been hampered by the variable definition of ET and by non-standardized research approaches. The National Institute of Neurological Disorders and Stroke (USA) invited experts in ET and related fields to discuss current knowledge, controversies, and gaps in our understanding of ET and to develop recommendations for future research. Discussion focused on phenomenology and phenotypes, therapies and clinical trials, pathophysiology, pathology, and genetics...
October 4, 2016: Parkinsonism & related Disorders
https://www.readbyqxmd.com/read/27769631/evolution-of-the-%C3%AE-adrenoreceptors-in-vertebrates
#8
Kattina Zavala, Michael W Vandewege, Federico G Hoffmann, Juan C Opazo
The study of the evolutionary history of genes related to human disease lies at the interface of evolution and medicine. These studies provide the evolutionary context on which medical researchers should work, and are also useful in providing information to suggest further genetic experiments, especially in model species where genetic manipulations can be made. Here we studied the evolution of the β-adrenoreceptor gene family in vertebrates with the aim of adding an evolutionary framework to the already abundant physiological information...
January 1, 2017: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/27747882/gene-regulation-and-genetics-in-neurochemistry-past-to-future
#9
Steven W Barger
Ask any neuroscientist to name the most profound discoveries in the field in the past 60 years, and at or near the top of the list will be a phenomenon or technique related to genes and their expression. Indeed, our understanding of genetics and gene regulation has ushered in whole new systems of knowledge and new empirical approaches, many of which could not have even been imagined prior to the molecular biology boon of recent decades. Neurochemistry, in the classic sense, intersects with these concepts in the manifestation of neuropeptides, obviously dependent upon the central dogma (the established rules by which DNA sequence is eventually converted into protein primary structure) not only for their conformation but also for their levels and locales of expression...
October 17, 2016: Journal of Neurochemistry
https://www.readbyqxmd.com/read/27742377/whole-genome-sequencing-discriminates-hepatocellular-carcinoma-with-intrahepatic-metastasis-from-multi-centric-tumors
#10
Mayuko Furuta, Masaki Ueno, Akihiro Fujimoto, Shinya Hayami, Satoru Yasukawa, Fumiyoshi Kojima, Koji Arihiro, Yoshiiku Kawakami, Christopher P Wardell, Yuichi Shiraishi, Hiroko Tanaka, Kaoru Nakano, Kazuhiro Maejima, Aya Sasaki-Oku, Naoki Tokunaga, Keith A Boroevich, Tetsuo Abe, Hiroshi Aikata, Hideki Ohdan, Kunihito Gotoh, Michiaki Kubo, Tatsuhiko Tsunoda, Satoru Miyano, Kazuaki Chayama, Hiroki Yamaue, Hidewaki Nakagawa
BACKGROUND & AIMS: Patients with hepatocellular carcinoma (HCC) have a high-risk of multi-centric (MC) tumor occurrence due to a strong carcinogenic background in the liver. In addition, they have a high risk of intrahepatic metastasis (IM). Liver tumors withIM or MC are profoundly different in their development and clinical outcome. However, clinically or pathologically discriminating between IM and MC can be challenging. This study investigated whether IM or MC could be diagnosed at the molecular level...
October 11, 2016: Journal of Hepatology
https://www.readbyqxmd.com/read/27688977/chromosomal-rearrangements-and-protein-globularity-changes-in-mycobacterium-tuberculosis-isolates-from-cerebrospinal-fluid
#11
Seow Hoon Saw, Joon Liang Tan, Xin Yue Chan, Kok Gan Chan, Yun Fong Ngeow
BACKGROUND: Meningitis is a major cause of mortality in tuberculosis (TB). It is not clear what factors promote central nervous system invasion and pathology but it has been reported that certain strains of Mycobacterium tuberculosis (Mtb) might have genetic traits associated with neurotropism. METHODS: In this study, we generated whole genome sequences of eight clinical strains of Mtb that were isolated from the cerebrospinal fluid (CSF) of patients presenting with tuberculous meningitis (TBM) in Malaysia, and compared them to the genomes of H37Rv and other respiratory Mtb genomes either downloaded from public databases or extracted from local sputum isolates...
2016: PeerJ
https://www.readbyqxmd.com/read/27658539/the-genetics-of-nonsyndromic-bilateral-duane-retraction-syndrome
#12
Khaled K Abu-Amero, Arif O Khan, Darren T Oystreck, Altaf A Kondkar, Thomas M Bosley
PURPOSE: To assess the importance of monogenic mutations and chromosomal copy number variants (CNVs) in the occurrence of nonsyndromic bilateral Duane retraction syndrome (bilateral nsDRS). METHODS: The medical records of 12 patients with bilateral nsDRS were reviewed. Genes associated with DRS and associated congenital cranial dysinnervation disorders (SALL4, CHN1, HOXA1, TUBB3, and KIF21A) were sequenced in the standard fashion in each patient. Array comparative genomic hybridization (array CGH) was performed using Affymetrix Cytogenetics Whole-Genome 2...
September 20, 2016: Journal of AAPOS: the Official Publication of the American Association for Pediatric Ophthalmology and Strabismus
https://www.readbyqxmd.com/read/27646943/genetic-determinants-of-cisplatin-resistance-in-patients-with-advanced-germ-cell-tumors
#13
Aditya Bagrodia, Byron H Lee, William Lee, Eugene K Cha, John P Sfakianos, Gopa Iyer, Eugene J Pietzak, Sizhi Paul Gao, Emily C Zabor, Irina Ostrovnaya, Samuel D Kaffenberger, Aijazuddin Syed, Maria E Arcila, Raju S Chaganti, Ritika Kundra, Jana Eng, Joseph Hreiki, Vladimir Vacic, Kanika Arora, Dayna M Oschwald, Michael F Berger, Dean F Bajorin, Manjit S Bains, Nikolaus Schultz, Victor E Reuter, Joel Sheinfeld, George J Bosl, Hikmat A Al-Ahmadie, David B Solit, Darren R Feldman
PURPOSE: Owing to its exquisite chemotherapy sensitivity, most patients with metastatic germ cell tumors (GCTs) are cured with cisplatin-based chemotherapy. However, up to 30% of patients with advanced GCT exhibit cisplatin resistance, which requires intensive salvage treatment, and have a 50% risk of cancer-related death. To identify a genetic basis for cisplatin resistance, we performed whole-exome and targeted sequencing of cisplatin-sensitive and cisplatin-resistant GCTs. METHODS: Men with GCT who received a cisplatin-containing chemotherapy regimen and had available tumor tissue were eligible to participate in this study...
September 19, 2016: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/27626165/mutational-burdens-and-evolutionary-ages-of-thyroid-follicular-adenoma-are-comparable-to-those-of-follicular-carcinoma
#14
Seung-Hyun Jung, Min Sung Kim, Chan Kwon Jung, Hyun-Chun Park, So Youn Kim, Jieying Liu, Ja-Seong Bae, Sung Hak Lee, Tae-Min Kim, Sug Hyung Lee, Yeun-Jun Chung
Follicular thyroid adenoma (FTA) precedes follicular thyroid carcinoma (FTC) by definition with a favorable prognosis compared to FTC. However, the genetic mechanism of FTA to FTC progression remains unknown. For this, it is required to disclose FTA and FTC genomes in mutational and evolutionary perspectives. We performed whole-exome sequencing and copy number profiling of 14 FTAs and 13 FTCs, which exhibited previously-known gene mutations (NRAS, HRAS, BRAF, TSHR and EIF1AX) and copy number alterations (CNAs) (22q loss and 1q gain) in follicular tumors...
September 9, 2016: Oncotarget
https://www.readbyqxmd.com/read/27616680/intra-familial-variability-associated-with-recessive-ryr1-mutation-diagnosed-prenatally-by-exome-sequencing
#15
Jillian Casey, Karen Flood, Sean Ennis, Emma Doyle, Michael Farrell, Sally Ann Lynch
OBJECTIVE: To determine the underlying molecular aetiology in a non-consanguineous Irish family who have had three fetal losses because of a primary myopathy characterised by fetal akinesia, arthrogryposis multiplex, bilateral pulmonary hypoplasia and reduced muscle bulk. METHODS: Fetal DNA extracted from amniotic cells was whole genome amplified and subjected to whole exome sequencing. RESULTS: Whole exome sequencing identified compound heterozygous variants in RYR1 as the cause of the lethal myopathy in this family...
November 2016: Prenatal Diagnosis
https://www.readbyqxmd.com/read/27600764/type-ii-enteropathy-associated-t-cell-lymphoma-features-a-unique-genomic-profile-with-highly-recurrent-setd2-alterations
#16
Annalisa Roberti, Maria Pamela Dobay, Bettina Bisig, David Vallois, Cloé Boéchat, Evripidis Lanitis, Brigitte Bouchindhomme, Marie-Cécile Parrens, Céline Bossard, Leticia Quintanilla-Martinez, Edoardo Missiaglia, Philippe Gaulard, Laurence de Leval
Enteropathy-associated T-cell lymphoma (EATL), a rare and aggressive intestinal malignancy of intraepithelial T lymphocytes, comprises two disease variants (EATL-I and EATL-II) differing in clinical characteristics and pathological features. Here we report findings derived from whole-exome sequencing of 15 EATL-II tumour-normal tissue pairs. The tumour suppressor gene SETD2 encoding a non-redundant H3K36-specific trimethyltransferase is altered in 14/15 cases (93%), mainly by loss-of-function mutations and/or loss of the corresponding locus (3p21...
2016: Nature Communications
https://www.readbyqxmd.com/read/27596100/the-role-of-mitochondrial-genomics-in-patients-with-non-alcoholic-steatohepatitis-nash
#17
Rohini Mehta, Kianoush Jeiran, Aaron B Koenig, Munkzhul Otgonsuren, Zachary Goodman, Ancha Baranova, Zobair Younossi
BACKGROUND: Visceral obesity and metabolic syndrome are commonly associated with non-alcoholic fatty liver disease (NAFLD). The progression of steatosis to NASH depends on a number of metabolic and patient-related factors. The mechanisms of genetic predisposition towards the development of NASH and related fibrosis remain unclear. In this study, our aim was to utilize mitotyping and identify mitochondrial haplotypes that may be associated with NAFLD. METHODS: We examined mitochondrial haplotypes along with patatin-like phospholipase domain containing 3 (PNPLA3) rs738409 genotype to determine their association with NAFLD phenotypes...
2016: BMC Medical Genetics
https://www.readbyqxmd.com/read/27590805/copy-number-variation-contributes-to-cryptic-genetic-variation-in-outbreak-lineages-of-cryptococcus-gattii-from-the-north-american-pacific-northwest
#18
Jacob L Steenwyk, John S Soghigian, John R Perfect, John G Gibbons
BACKGROUND: Copy number variants (CNVs) are a class of structural variants (SVs) and are defined as fragments of DNA that are present at variable copy number in comparison with a reference genome. Recent advances in bioinformatics methodologies and sequencing technologies have enabled the high-resolution quantification of genome-wide CNVs. In pathogenic fungi SVs have been shown to alter gene expression, influence host specificity, and drive fungicide resistance, but little attention has focused specifically on CNVs...
2016: BMC Genomics
https://www.readbyqxmd.com/read/27567950/colorectal-cancer-with-residual-polyp-of-origin-a-model-of-malignant-transformation
#19
Brooke R Druliner, Shahrooz Rashtak, Xiaoyang Ruan, Taejeong Bae, Nikolaos Vasmatzis, Daniel O'Brien, Ruth Johnson, Donna Felmlee-Devine, Jill Washechek-Aletto, Nivedita Basu, Hongfang Liu, Thomas Smyrk, Alexej Abyzov, Lisa A Boardman
The majority of colorectal cancers (CRCs) arise from adenomatous polyps. In this study, we sought to present the underrecognized CRC with the residual polyp of origin (CRC RPO+) as an entity to be utilized as a model to study colorectal carcinogenesis. We identified all subjects with biopsy-proven CRC RPO+ that were evaluated over 10 years at Mayo Clinic, Rochester, MN, and compared their clinical and pathologic characteristics to CRC without remnant polyps (CRC RPO-). Overall survival and disease-free survival overlap with an equivalent hazard ratio between CRC RPO+ and RPO- cases when age, stage, and grade are adjusted...
August 2016: Translational Oncology
https://www.readbyqxmd.com/read/27493451/inflammation-thread-runs-across-medical-laboratory-specialities
#20
REVIEW
Urs Nydegger, Thomas Lung, Lorenz Risch, Martin Risch, Pedro Medina Escobar, Thomas Bodmer
We work on the assumption that four major specialities or sectors of medical laboratory assays, comprising clinical chemistry, haematology, immunology, and microbiology, embraced by genome sequencing techniques, are routinely in use. Medical laboratory markers for inflammation serve as model: they are allotted to most fields of medical lab assays including genomics. Incessant coding of assays aligns each of them in the long lists of big data. As exemplified with the complement gene family, containing C2, C3, C8A, C8B, CFH, CFI, and ITGB2, heritability patterns/risk factors associated with diseases with genetic glitch of complement components are unfolding...
2016: Mediators of Inflammation
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