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Clinical whole genome sequencing

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https://www.readbyqxmd.com/read/29332568/fgf-21-as-a-potential-biomarker-for-mitochondrial-diseases
#1
Leila Motlagh Scholle, Diana Lehmann, Marcus Deschauer, Torsten Kraya, Stephan Zierz
The diagnosis of mitochondrial diseases is still challenging due to clinical and genetical heterogeneity. The development of advanced technologies including Whole-Exome-Sequencing (WES) and Whole-Genome-Sequencing (WGS) have led to improvements in genetic diagnosis. However, a reliable biomarker in serum could enhance and ease the diagnosis and indeed reduce the need for muscle biopsy. Several studies suggest Fibroblast growth factor 21 (FGF-21) as a biomarker for diagnosis in mitochondrial disorders. It is known, that in patients with mitochondrial disorders, the expression of FGF-21 gets elevated in an effort to counteract the underlying metabolic deficiency...
January 10, 2018: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/29330334/detection-of-heterozygous-mutation-in-hook-microtubule-tethering-protein-1-in-three-patients-with-decapitated-and-decaudated-spermatozoa-syndrome
#2
Huixing Chen, Yong Zhu, Zijue Zhu, Erlei Zhi, Keming Lu, Xiaobo Wang, Feng Liu, Zheng Li, Weiliang Xia
BACKGROUND: The mechanism of intramanchette transport is crucial to the transformation of sperm tail and the nuclear condensation during spermiogenesis. Although few dysfunctional proteins could result in abnormal junction between the head and tail of spermatozoon, little is known about the genetic cues in this process. OBJECTIVE: Based on patients with severe decapitated and decaudated spermatozoa (DDS) syndrome, the study aimed to validate whether new mutation exists on their Hook microtubule-tethering protein 1 (HOOK1) genes and follow their results of assisted reproduction treatment (ART)...
January 12, 2018: Journal of Medical Genetics
https://www.readbyqxmd.com/read/29329757/challenges-of-francisella-classification-exemplified-by-an-atypical-clinical-isolate
#3
L M Matz, K Y Kamdar, M E Holder, G A Metcalf, G M Weissenberger, Q Meng, V Vee, Y Han, D M Muzny, R A Gibbs, C L Johnson, P A Revell, J F Petrosino
The accumulation of sequenced Francisella strains has made it increasingly apparent that the 16S rRNA gene alone is not enough to stratify the Francisella genus into precise and clinically useful classifications. Continued whole-genome sequencing of isolates will provide a larger base of knowledge for targeted approaches with broad applicability. Additionally, examination of genomic information on a case-by-case basis will help resolve outstanding questions regarding strain stratification. We report the complete genome sequence of a clinical isolate, designated here as F...
December 6, 2017: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/29328368/identification-of-significant-biomarkers-and-pathways-associated-with-gastric-carcinogenesis-by-whole-genome-wide-expression-profiling-analysis
#4
Hong-Jun Fei, Song-Chang Chen, Jun-Yu Zhang, Shu-Yuan Li, Lan-Lan Zhang, Yi-Yao Chen, Chun-Xin Chang, Chen-Ming Xu
The incidence of gastric cancer (GC) is extremely high in East Asia. GC is also one of the most common and lethal forms of cancer from a global perspective. However, to date, we have not been able to determine one or several genes as biomarkers in the diagnosis of GC and have also been unable to identify the genes which are important in the therapy of GC. In this study, we analyzed all genome-wide expression profiling arrays uploaded onto the Gene Expression Omnibus (GEO) database to filtrate the differentially expressed genes (DEGs) between normal stomach tissues and GC tissues...
January 11, 2018: International Journal of Oncology
https://www.readbyqxmd.com/read/29326010/genomics-of-corynebacterium-striatum-an-emerging-multi-drug-resistant-pathogen-of-immunocompromised-patients
#5
Kathleen Nudel, Xiaomin Zhao, Sankha Basu, Xiaoxi Dong, Maria Hoffmann, Michael Feldgarden, Marc Allard, Michael Klompas, Lynn Bry
OBJECTIVES: Corynebacterium striatum is an emerging multi-drug resistant (MDR) pathogen of immunocompromised and chronically ill patients. The objective of these studies was to provide a detailed genomic analysis of disease causing C. striatum and determine the genomic drivers of resistance and resistance-gene transmission. METHODS: A multi-institutional and prospective pathogen genomics program flagged seven MDR C. striatum infections occurring close in time, and specifically in immunocompromised patients with underlying respiratory diseases...
January 8, 2018: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/29325629/bioinformatics-and-genomic-databases
#6
Jason Chen, Giovanni Coppola
High-throughput, low-cost sequencing technologies have begun to yield new insights into biology and medicine. New data enable the interrogation of the molecular biology of disease from DNA to RNA to protein, charting the central dogma. This chapter reviews some of the key advances and resources in the application of bioinformatics to understanding, and ultimately diagnosing and treating, diseases of the nervous system. Array genotyping, exome sequencing, and whole-genome sequencing, in both disease and healthy populations, have enabled the interpretation of new genetic data...
2018: Handbook of Clinical Neurology
https://www.readbyqxmd.com/read/29325576/reanalysis-of-chinese-treponema-pallidum-samples-all-chinese-samples-cluster-with-ss14-like-group-of-syphilis-causing-treponemes
#7
Michal Strouhal, Jan Oppelt, Lenka Mikalová, Natasha Arora, Kay Nieselt, Fernando González-Candelas, David Šmajs
OBJECTIVE: Treponema pallidum subsp. pallidum (TPA) is the causative agent of syphilis. Genetic analyses of TPA reference strains and human clinical isolates have revealed two genetically distinct groups of syphilis-causing treponemes, called Nichols-like and SS14-like groups. So far, no genetic intermediates, i.e. strains containing a mixed pattern of Nichols-like and SS14-like genomic sequences, have been identified. Recently, Sun et al. (Oncotarget 2016. https://doi.org/10.18632/oncotarget...
January 11, 2018: BMC Research Notes
https://www.readbyqxmd.com/read/29325031/use-of-deep-whole-genome-sequencing-data-to-identify-structure-risk-variants-in-breast-cancer-susceptibility-genes
#8
Xingyi Guo, Jiajun Shi, Qiuyin Cai, Xiao-Ou Shu, Jing He, Wanqing Wen, Jamie Allen, Paul Pharoah, Alison Dunning, David J Hunter, Peter Kraft, Douglas F Easton, Wei Zheng, Jirong Long
Functional disruptions of susceptibility genes by large genomic structure variant (SV) deletions in germlines are known to be associated with cancer risk. However, few studies have been conducted to systematically search for SV deletions in breast cancer susceptibility genes. We analyzed deep (> 30x) whole genome sequencing (WGS) data generated in blood samples from 128 breast cancer patients of Asian and European descent with either a strong family history of breast cancer or early cancer onset disease...
January 8, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29323667/making-new-genetic-diagnoses-with-old-data-iterative-reanalysis-and-reporting-from-genome-wide-data-in-1-133-families-with-developmental-disorders
#9
Caroline F Wright, Jeremy F McRae, Stephen Clayton, Giuseppe Gallone, Stuart Aitken, Tomas W FitzGerald, Philip Jones, Elena Prigmore, Diana Rajan, Jenny Lord, Alejandro Sifrim, Rosemary Kelsell, Michael J Parker, Jeffrey C Barrett, Matthew E Hurles, David R FitzPatrick, Helen V Firth
PurposeGiven the rapid pace of discovery in rare disease genomics, it is likely that improvements in diagnostic yield can be made by systematically reanalyzing previously generated genomic sequence data in light of new knowledge.MethodsWe tested this hypothesis in the United Kingdom-wide Deciphering Developmental Disorders study, where in 2014 we reported a diagnostic yield of 27% through whole-exome sequencing of 1,133 children with severe developmental disorders and their parents. We reanalyzed existing data using improved variant calling methodologies, novel variant detection algorithms, updated variant annotation, evidence-based filtering strategies, and newly discovered disease-associated genes...
January 11, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29323230/developing-an-in-silico-minimum-inhibitory-concentration-panel-test-for-klebsiella-pneumoniae
#10
Marcus Nguyen, Thomas Brettin, S Wesley Long, James M Musser, Randall J Olsen, Robert Olson, Maulik Shukla, Rick L Stevens, Fangfang Xia, Hyunseung Yoo, James J Davis
Antimicrobial resistant infections are a serious public health threat worldwide. Whole genome sequencing approaches to rapidly identify pathogens and predict antibiotic resistance phenotypes are becoming more feasible and may offer a way to reduce clinical test turnaround times compared to conventional culture-based methods, and in turn, improve patient outcomes. In this study, we use whole genome sequence data from 1668 clinical isolates of Klebsiella pneumoniae to develop a XGBoost-based machine learning model that accurately predicts minimum inhibitory concentrations (MICs) for 20 antibiotics...
January 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29322253/identification-of-a-mutation-in-cnnm4-by-whole-exome-sequencing-in-an-amish-family-and-functional-link-between-cnnm4-and-iqcb1
#11
Sisi Li, Quansheng Xi, Xiaoyu Zhang, Dong Yu, Lin Li, Zhenyang Jiang, Qiuyun Chen, Qing K Wang, Elias I Traboulsi
We investigated an Amish family in which three siblings presented with an early-onset childhood retinal dystrophy inherited in an autosomal recessive fashion. Genome-wide linkage analysis identified significant linkage to marker D2S2216 on 2q11 with a two-point LOD score of 1.95 and a multi-point LOD score of 3.76. Whole exome sequencing was then performed for the three affected individuals and identified a homozygous nonsense mutation (c.C1813T, p.R605X) in the cyclin and CBS domain divalent metal cation transport mediator 4 (CNNM4) gene located within the 2p14-2q14 Jalili syndrome locus...
January 10, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29321523/integrative-genomic-and-transcriptomic-analysis-of-leiomyosarcoma
#12
Priya Chudasama, Sadaf S Mughal, Mathijs A Sanders, Daniel Hübschmann, Inn Chung, Katharina I Deeg, Siao-Han Wong, Sophie Rabe, Mario Hlevnjak, Marc Zapatka, Aurélie Ernst, Kortine Kleinheinz, Matthias Schlesner, Lina Sieverling, Barbara Klink, Evelin Schröck, Remco M Hoogenboezem, Bernd Kasper, Christoph E Heilig, Gerlinde Egerer, Stephan Wolf, Christof von Kalle, Roland Eils, Albrecht Stenzinger, Wilko Weichert, Hanno Glimm, Stefan Gröschel, Hans-Georg Kopp, Georg Omlor, Burkhard Lehner, Sebastian Bauer, Simon Schimmack, Alexis Ulrich, Gunhild Mechtersheimer, Karsten Rippe, Benedikt Brors, Barbara Hutter, Marcus Renner, Peter Hohenberger, Claudia Scholl, Stefan Fröhling
Leiomyosarcoma (LMS) is an aggressive mesenchymal malignancy with few therapeutic options. The mechanisms underlying LMS development, including clinically actionable genetic vulnerabilities, are largely unknown. Here we show, using whole-exome and transcriptome sequencing, that LMS tumors are characterized by substantial mutational heterogeneity, near-universal inactivation of TP53 and RB1, widespread DNA copy number alterations including chromothripsis, and frequent whole-genome duplication. Furthermore, we detect alternative telomere lengthening in 78% of cases and identify recurrent alterations in telomere maintenance genes such as ATRX, RBL2, and SP100, providing insight into the genetic basis of this mechanism...
January 10, 2018: Nature Communications
https://www.readbyqxmd.com/read/29321190/genomic-landscape-of-pancreatic-neuroendocrine-tumours-the-international-cancer-genome-consortium
#13
Andrea Mafficini, Aldo Scarpa
Neuroendocrine tumours (NETs) may arise throughout the body and are a highly heterogeneous, relatively rare class of neoplasms difficult to study also for the lack of disease models. Despite this, knowledge on their molecular alterations has expanded in the latest years, also building from genetic syndromes causing their onset. Pancreatic NETs (PanNETs) have been among the most studied, and research so far has outlined a series of recurring features, as inactivation of MEN1, VHL, TSC1/2 genes, and hyperactivation of the PI3K/mTOR pathway...
January 10, 2018: Journal of Endocrinology
https://www.readbyqxmd.com/read/29320804/misidentification-of-genome-assemblies-in-public-databases-the-case-of-naumovozyma-dairenensis-and-proposal-of-a-protocol-to-correct-misidentifications
#14
Aimilia A Stavrou, Verónica Mixão, Teun Boekhout, Toni Gabaldón
Online sequence databases such as NCBI GenBank serve as a tremendously useful platform for researchers to share and reuse published data. However, submission systems lack control for errors such as organism misidentification, which once entered in the database can be propagated and mislead downstream analyses. Here we present an illustrating case of misidentification of Candida albicans from a clinical sample as Naumovozyma dairenensis based on whole-genome shotgun data. Analyses of phylogenetic markers, read mapping and single nucleotide polymorphisms (SNP) served to correct the identification...
January 10, 2018: Yeast
https://www.readbyqxmd.com/read/29311090/investigation-of-multiple-resistance-mechanisms-in-voriconazole-resistant-aspergillus-flavus-clinical-isolates-from-a-chest-hospital-surveillance-in-delhi-india
#15
Cheshta Sharma, Rakesh Kumar, Nitin Kumar, Aradhana Masih, Dinesh Gupta, Anuradha Chowdhary
Invasive and allergic infections by Aspergillus flavus are more common in tropical and subtropical countries. The emergence of voriconazole (VRC) resistance in A. flavus impacts the management of aspergillosis as azoles are used as the first line and empiric therapy. We screened molecularly confirmed 120 A. flavus isolates obtained from respiratory and sino-nasal specimens in a chest hospital in Delhi for azole resistance using CLSI BMD method. Overall, 2.5% (n=3/120) of A. flavus isolates had VRC MICs above epidemiological cutoff values (>1μg/ml)...
January 8, 2018: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29311074/molecular-epidemiology-and-mechanism-of-sulbactam-resistance-in-acinetobacter-baumannii-isolates-with-diverse-genetic-background-in-china
#16
Yunxing Yang, Ying Fu, Peng Lan, Qingye Xu, Yan Jiang, Yan Chen, Zhi Ruan, Shujuan Ji, Xiaoting Hua, Yunsong Yu
Sulbactam is a plausible option for treating Acinetobacter infection because of its intrinsic antibacterial activity against the Acinetobacter genus, but the mechanisms of sulbactam resistance have not been studied fully in Acinetobacter baumannii In this study, a total of 2197 clinical A. baumannii isolates were collected from 27 provinces in China. Eighty-eight isolates with various minimal inhibitory concentrations (MICs) for sulbactam were selected based on their diverse clonality and underwent multilocus sequence typing, antimicrobial-susceptibility testing and resistance gene screening...
January 8, 2018: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29310751/multi-clonal-evolution-of-multi-drug-resistant-extensively-drug-resistant-mycobacterium-tuberculosis-in-a-high-prevalence-setting-of-papua-new-guinea-for-over-three-decades
#17
Arnold Bainomugisa, Evelyn Lavu, Stenard Hiashiri, Suman Majumdar, Alice Honjepari, Rendi Moke, Paison Dakulala, Grant A Hill-Cawthorne, Sushil Pandey, Ben J Marais, Chris Coulter, Lachlan Coin
An outbreak of multi-drug resistant (MDR) tuberculosis (TB) has been reported on Daru Island, Papua New Guinea. Mycobacterium tuberculosis strains driving this outbreak and the temporal accrual of drug resistance mutations have not been described. Whole genome sequencing of 100 of 165 clinical isolates referred from Daru General Hospital to the Supranational reference laboratory, Brisbane, during 2012-2015 revealed that 95 belonged to a single modern Beijing sub-lineage strain. Molecular dating suggested acquisition of streptomycin and isoniazid resistance in the 1960s, with potentially enhanced virulence mediated by an mycP1 mutation...
January 4, 2018: Microbial Genomics
https://www.readbyqxmd.com/read/29310750/integrating-patient-and-whole-genome-sequencing-data-to-provide-insights-into-the-epidemiology-of-seasonal-influenza-a-h3n2-viruses
#18
Emily J Goldstein, William T Harvey, Gavin S Wilkie, Samantha J Shepherd, Alasdair R MacLean, Pablo R Murcia, Rory N Gunson
Genetic surveillance of seasonal influenza is largely focused on sequencing of the haemagglutinin gene. Consequently, our understanding of the contribution of the remaining seven gene segments to the evolution and epidemiological dynamics of seasonal influenza is relatively limited. The increased availability of next-generation sequencing technologies allows rapid and economic whole-genome sequencing (WGS) of influenza virus. Here, 150 influenza A(H3N2) positive clinical specimens with linked epidemiological data, from the 2014/15 season in Scotland, were sequenced directly using both Sanger sequencing of the HA1 region and WGS using the Illumina MiSeq platform...
December 21, 2017: Microbial Genomics
https://www.readbyqxmd.com/read/29310749/culture-independent-approaches-to-chlamydial-genomics
#19
Alyce Taylor-Brown, Danielle Madden, Adam Polkinghorne
The expanding field of bacterial genomics has revolutionized our understanding of microbial diversity, biology and phylogeny. For most species, DNA extracted from culture material is used as the template for genome sequencing; however, the majority of microbes are actually uncultivable, and others, such as obligate intracellular bacteria, require laborious tissue culture to yield sufficient genomic material for sequencing. Chlamydiae are one such group of obligate intracellular microbes whose characterization has been hampered by this requirement...
January 3, 2018: Microbial Genomics
https://www.readbyqxmd.com/read/29306563/yield-rate-of-chromosomal-microarray-analysis-in-fetuses-with-congenital-heart-defects
#20
Sifa Turan, Mehmet Resit Asoglu, Rinat Gabbay Benziv, Lauren Doyle, Christopher Harman, Ozhan M Turan
OBJECTIVE: The purpose of this study was to calculate the yield rates of CMA in fetuses diagnosed with various CHDs in a tertiary center. STUDY DESIGN: This cohort study collected prenatal genetic test results of 145 fetuses diagnosed with CHD. All 145 cases underwent Conventional karyotype (CK), followed by CMA in cases of negative CK result. "Detection rate" of genetic abnormalities was calculated as the percentage of cases with genetic abnormalities identified...
December 12, 2017: European Journal of Obstetrics, Gynecology, and Reproductive Biology
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