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Clinical whole genome sequencing

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https://www.readbyqxmd.com/read/28534044/hsp-and-deafness-neurocristopathy-caused-by-a-novel-mosaic-sox10-mutation
#1
Sandra Donkervoort, Diana Bharucha-Goebel, Pomi Yun, Ying Hu, Payam Mohassel, Ahmet Hoke, Wadih M Zein, Daniel Ezzo, Andrea M Atherton, Ann C Modrcin, Majed Dasouki, A Reghan Foley, Carsten G Bönnemann
OBJECTIVE: To identify the underlying genetic cause in 2 sisters affected with progressive lower extremity spasticity, neuropathy, and early-onset deafness. METHODS: Whole-exome sequencing was performed, and segregation testing of variants was investigated using targeted Sanger sequencing. An inherited paternal mosaic mutation was further evaluated through quantitative analysis of the ratio of mutant vs wild-type allele in genomic DNA from various tissues, including blood, dermal fibroblasts, and saliva...
June 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/28533336/a-coding-variant-in-the-gene-bardet-biedl-syndrome-4-bbs4-is-associated-with-a-novel-form-of-canine-progressive-retinal-atrophy
#2
Tracy Chew, Bianca Haase, Roslyn Bathgate, Cali E Willet, Maria K Kaukonen, Lisa J Mascord, Hannes T Lohi, Claire M Wade
Progressive retinal atrophy is a common cause of blindness in the dog and affects over 100 breeds. It is characterized by gradual vision loss that occurs due to the degeneration of photoreceptor cells in the retina. Similar to the human counterpart retinitis pigmentosa, the canine disorder is clinically and genetically heterogeneous and the underlying cause remains unknown for many cases. We use a positional candidate gene approach to identify putative variants in the Hungarian Puli breed using genotyping data of 14 family-based samples (CanineHD BeadChip array, Illumina) and whole genome sequencing data of two proband and two parental samples (Illumina HiSeq 2000)...
May 22, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28531216/impact-of-mutations-in-toll-like-receptor-pathway-genes-on-esophageal-carcinogenesis
#3
Daffolyn Rachael Fels Elliott, Juliane Perner, Xiaodun Li, Martyn F Symmons, Brett Verstak, Matthew Eldridge, Lawrence Bower, Maria O'Donovan, Nick J Gay, Rebecca C Fitzgerald
Esophageal adenocarcinoma (EAC) develops in an inflammatory microenvironment with reduced microbial diversity, but mechanisms for these influences remain poorly characterized. We hypothesized that mutations targeting the Toll-like receptor (TLR) pathway could disrupt innate immune signaling and promote a microenvironment that favors tumorigenesis. Through interrogating whole genome sequencing data from 171 EAC patients, we showed that non-synonymous mutations collectively affect the TLR pathway in 25/171 (14...
May 22, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28530888/genomic-relatedness-of-staphylococcus-pettenkoferi-isolates-of-different-origins
#4
Emeli Månsson, Bengt Hellmark, Marc Stegger, Paal Skytt Andersen, Martin Sundqvist, Bo Söderquist
PURPOSE: The aim of the study was to characterize clinical and environmental Staphylococcus pettenkoferi isolates with regard to genomic diversity and antibiotic susceptibility pattern. Repetitive-sequence-based PCR and core genome phylogenetic analysis of whole-genome sequencing (WGS) data verified the presence of distinct clades comprising closely related S. pettenkoferi isolates from different geographical locations and origins. METHODOLOGY: Phylogenetic relationships between 25 S...
May 2017: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/28522256/sporadic-early-onset-diffuse-gastric-cancers-have-high-frequency-of-somatic-cdh1-alterations-but-low-frequency-of-somatic-rhoa-mutations-compared-with-late-onset-cancers
#5
Soo Young Cho, Jun Won Park, Yang Liu, Young Soo Park, Ju Hee Kim, Hanna Yang, Hyejin Um, Woo Ri Ko, Byung Il Lee, Sun Young Kwon, Seung Wan Ryu, Chae Hwa Kwon, Do Youn Park, Jae-Hyuk Lee, Sang Il Lee, Kyu Sang Song, Hoon Hur, Sang-Uk Han, Heekyung Chang, Su-Jin Kim, Byung-Sik Kim, Jeong-Hwan Yook, Moon-Won Yoo, Beom-Su Kim, In-Seob Lee, Myeong-Cherl Kook, Nina Thiessen, An He, Chip Stewart, Andrew Dunford, Jaegil Kim, Juliann Shih, Gordon Saksena, Andrew D Cherniack, Steven Schumacher, Amaro-Taylor Weiner, Mara Rosenberg, Gad Getz, Eun Gyeong Yang, Min Hee Ryu, Adam J Bass, Hark Kyun Kim
BACKGROUND & AIMS: Early-onset gastric cancer, which develops in younger patients than most gastric cancers, is usually detected at advanced stages, has diffuse histologic features, and occurs more frequently in women. We investigated somatic genomic alterations associated with the unique characteristics of sporadic diffuse gastric cancers (DGCs) from younger patients. METHODS: We conducted whole exome and RNA sequence analyses of 80 resected DGC samples from patients 45 years old or younger in Korea...
May 15, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28518168/using-high-resolution-variant-frequencies-to-empower-clinical-genome-interpretation
#6
Nicola Whiffin, Eric Minikel, Roddy Walsh, Anne H O'Donnell-Luria, Konrad Karczewski, Alexander Y Ing, Paul J R Barton, Birgit Funke, Stuart A Cook, Daniel MacArthur, James S Ware
PurposeWhole-exome and whole-genome sequencing have transformed the discovery of genetic variants that cause human Mendelian disease, but discriminating pathogenic from benign variants remains a daunting challenge. Rarity is recognized as a necessary, although not sufficient, criterion for pathogenicity, but frequency cutoffs used in Mendelian analysis are often arbitrary and overly lenient. Recent very large reference datasets, such as the Exome Aggregation Consortium (ExAC), provide an unprecedented opportunity to obtain robust frequency estimates even for very rare variants...
May 18, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28516087/dna-sequence-analysis-in-clinical-medicine-proceeding-cautiously
#7
REVIEW
Moyra Smith
Delineation of underlying genomic and genetic factors in a specific disease may be valuable in establishing a definitive diagnosis and may guide patient management and counseling. In addition, genetic information may be useful in identification of at risk family members. Gene mapping and initial genome sequencing data enabled the development of microarrays to analyze genomic variants. The goal of this review is to consider different generations of sequencing techniques and their application to exome sequencing and whole genome sequencing and their clinical applications...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28514307/exome-sequencing-identifies-a-de-novo-mutation-of-ctnnb1-gene-in-a-patient-mainly-presented-with-retinal-detachment-lens-and-vitreous-opacities-microcephaly-and-developmental-delay-case-report-and-literature-review
#8
Niu Li, Yufei Xu, Guoqiang Li, Tingting Yu, Ru-En Yao, Xiumin Wang, Jian Wang
RATIONALE: The CTNNB1 (β-catenin) gene is well known for its crucial role in cell adhesion and the Wnt-signaling pathway. Previous studies have shown that gain-of-function mutations in the CTNNB1 gene contribute to the occurrence and development of a variety of carcinomas in humans. Recently, de novo, heterozygous, loss-of-function mutations of the CTNNB1 gene were found that partially explain intellectual disability in some patients. Other major clinical symptoms in these patients included microcephaly, abnormal facial features, motor delays, speech impairments, and deformities of the hands and feet...
May 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28513873/myxoid-fibroadenomas-differ-from-conventional-fibroadenomas-a-hypothesis-generating-study
#9
John R Lozada, Kathleen A Burke, Aoife Maguire, Fresia Pareja, Raymond S Lim, Jisun Kim, Rodrigo Gularte-Merida, Melissa P Murray, Edi Brogi, Britta Weigelt, Jorge S Reis-Filho, Felipe C Geyer
AIMS: Breast myxoid fibroadenomas (MFAs) are characterized by a distinctive hypocellular myxoid stroma, and occur sporadically or in the context of Carney Complex, an inheritable condition caused by PRKAR1A inactivating germline mutations. Conventional fibroadenomas (FAs) are underpinned by recurrent MED12 mutations in the stromal components of the lesions. We sought to investigate the genomic landscape of MFAs and compare it to that of conventional FAs. METHODS AND RESULTS: Eleven MFAs from patients without clinical and/or genetic evidence of Carney Complex were retrieved...
May 17, 2017: Histopathology
https://www.readbyqxmd.com/read/28513417/carriage-of-extended-spectrum-beta-lactamase-producing-enterobacteriaceae-in-hiv-infected-children-in-zimbabwe
#10
S M S Wilmore, K Kranzer, A Williams, B Makamure, A F Nhidza, J Mayini, T Bandason, J Metcalfe, M P Nicol, I Balakrishnan, M J Ellington, N Woodford, S Hopkins, T D McHugh, R A Ferrand
BACKGROUND: Antimicrobial resistance is an emerging global health issue. Data on the epidemiology of multidrug-resistant organisms are scarce for Africa, especially in HIV-infected individuals who often have frequent contact with healthcare. We investigated the prevalence of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) carriage in stool among HIV-infected children attending an HIV outpatient department in Harare, Zimbabwe. METHODS: We recruited children who were stable on antiretroviral therapy (ART) attending a HIV clinic from August 2014 to June 2015...
May 2017: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/28512736/cagi4-sickkids-clinical-genomes-challenge-a-pipeline-for-identifying-pathogenic-variants
#11
Lipika R Pal, Kunal Kundu, Yizhou Yin, John Moult
Compared with earlier more restricted sequencing technologies, identification of rare disease variants using whole genome sequence has the possibility of finding all causative variants, but issues of data quality and an overwhelming level of background variants complicate the analysis. The CAGI4 SickKids clinical genome challenge provided an opportunity to assess the landscape of variants found in a difficult set of 25 unsolved rare disease cases. To address the challenge, we developed a three-stage pipeline, first carefully analyzing data quality, then classifying high quality gene specific variants into seven categories, and finally examining each candidate variant for compatibility with the often complex phenotypes of these patients for final prioritization...
May 16, 2017: Human Mutation
https://www.readbyqxmd.com/read/28512290/evolution-of-drug-resistant-acinetobacter-baumannii-after-dcd-renal-transplantation
#12
Hong Jiang, Luxi Cao, Lihui Qu, Tingting Qu, Guangjun Liu, Rending Wang, Bingjue Li, Yuchen Wang, Chaoqun Ying, Miao Chen, Yingying Lu, Shi Feng, Yonghong Xiao, Junwen Wang, Jianyong Wu, Jianghua Chen
Infection after renal transplantation remains a major cause of morbidity and death, especially infection from the extensively drug-resistant bacteria, A. baumannii. A total of fourteen A. baumannii isolates were isolated from the donors' preserved fluid from DCD (donation after cardiac death) renal transplantation and four isolates in the recipients' draining liquid at the Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, from March 2013 to November 2014. An outbreak of A...
May 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28512093/population-genomic-analysis-of-1-777-extended-spectrum-beta-lactamase-producing-klebsiella-pneumoniae-isolates-houston-texas-unexpected-abundance-of-clonal-group-307
#13
S Wesley Long, Randall J Olsen, Todd N Eagar, Stephen B Beres, Picheng Zhao, James J Davis, Thomas Brettin, Fangfang Xia, James M Musser
Klebsiella pneumoniae is a major human pathogen responsible for high morbidity and mortality rates. The emergence and spread of strains resistant to multiple antimicrobial agents and documented large nosocomial outbreaks are especially concerning. To develop new therapeutic strategies for K. pneumoniae, it is imperative to understand the population genomic structure of strains causing human infections. To address this knowledge gap, we sequenced the genomes of 1,777 extended-spectrum beta-lactamase-producing K...
May 16, 2017: MBio
https://www.readbyqxmd.com/read/28510723/decreased-azithromycin-susceptibility-of-neisseria-gonorrhoeae-isolates-in-patients-recently-treated-with-azithromycin
#14
Carolien M Wind, Esther de Vries, Maarten F Schim van der Loeff, Martijn S van Rooijen, Alje P van Dam, Walter H B Demczuk, Irene Martin, Henry J C de Vries
Background.: Increasing azithromycin usage and resistance in Neisseria gonorrhoeae threatens current dual treatment. Because antimicrobial exposure influences resistance, we analyzed the association between azithromycin exposure and decreased susceptibility of N. gonorrhoeae. Methods.: We included N. gonorrhoeae isolates of patients who visited the Amsterdam STI Clinic between 1999 and 2013 (t0), with another clinic visit in the previous 60 days (t-1). Exposure was defined as the prescription of azithromycin at t-1...
March 24, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28509084/whole-exome-sequencing-identifies-a-novel-homozygous-frameshift-mutation-in-the-mtmr2-gene-as-a-causative-mutation-in-a-patient-with-charcot-marie-tooth-disease-type-4b1
#15
Tameemi Abdalla-Moady, Amir Peleg, Orit Sadeh, Khader Badarneh, Fuad Fares
Charcot-Marie-Tooth (CMT) disease refers to a heterogeneous group of axonal and demyelinating polyneuropathies, characterized by chronic motor and sensory dysfunction. CMT is the most common genetic cause of neuropathy. The present study aimed to identify the gene mutation responsible for CMT in Ashkenazi Jew (AJ) patient. Genomic DNA was extracted from whole blood leukocytes of affected family and normal subject. Whole-exome sequencing was performed using the Illumina HiSeq2500. The DNA region containing the identified mutation was amplified by PCR and sequenced using dye-terminator chemistry and the forward primer...
May 16, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28506673/high-frequency-of-silver-resistance-genes-in-invasive-isolates-of-enterobacter-and-klebsiella-species
#16
S Sütterlin, M Dahlö, C Tellgren-Roth, W Schaal, Å Melhus
BACKGROUND: Silver-based products have been marketed as an alternative to antibiotics, and their consumption has increased. Bacteria may, however, develop resistance to silver. AIM: To study the presence of genes encoding silver resistance (silE, silP, silS) over time in three clinically important Enterobacteriaceae genera. METHODS: Using polymerase chain reaction (PCR), 752 bloodstream isolates from the years 1990-2010 were investigated. Age, gender, and ward of patients were registered, and the susceptibility to antibiotics and silver nitrate was tested...
April 26, 2017: Journal of Hospital Infection
https://www.readbyqxmd.com/read/28504856/cell-free-dna-copy-number-variations-in-plasma-from-colorectal-cancer-patients
#17
Jian Li, Rachel L Dittmar, Shu Xia, Huijuan Zhang, Meijun Du, Chiang-Ching Huang, Brooke R Druliner, Lisa Boardman, Liang Wang
To evaluate clinical utility of cell free DNA (cfDNA), we performed whole genome sequencing to systematically examine plasma cfDNA copy number variations (CNVs) in a cohort of patients with colorectal cancer (CRC, n=80), polyps (n=20) and healthy controls (n=35). We initiallycompared cfDNA yield in 20 paired serum-plasma samples and observed significantly higher cfDNA concentration in serum (median=81.20ng, range 7.18-500ng/ml) than in plasma (median=5.09ng, range 3.76-62.8ng/ml) (p<0.0001). However, tumor-derived cfDNA content was significantly lower in serum than in matched plasma samples tested...
May 15, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28502397/performance-of-the-check-points-check-mdr-ct103xl-assay-utilizing-the-cdc-fda-antimicrobial-resistance-isolate-bank
#18
Eleanor A Powell, David Haslam, Joel E Mortensen
The Check-MDR CT103XL beta-lactamase assay was validated for use in the clinical microbiology laboratory using two CDC-FDA Antimicrobial Resistant Isolate Bank panels (133 gram-negative bacilli known beta-lactamase genes). The CT103XL detected most reported resistance genes (123 of 136 genes) and additionally identified several resistance genes not reported by the CDC. Discrepant results were confirmed via whole genome sequencing.
April 28, 2017: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/28502045/a-clinical-and-molecular-genetic-study-of-50-families-with-autosomal-recessive-parkinsonism-revealed-known-and-novel-gene-mutations
#19
Shaghayegh Taghavi, Rita Chaouni, Abbas Tafakhori, Luis J Azcona, Saghar Ghasemi Firouzabadi, Mir Davood Omrani, Javad Jamshidi, Babak Emamalizadeh, Gholam Ali Shahidi, Mona Ahmadi, Seyed Amir Hassan Habibi, Azadeh Ahmadifard, Atena Fazeli, Marzieh Motallebi, Peyman Petramfar, Saeed Askarpour, Shiva Askarpour, Hossein Ali Shahmohammadibeni, Neda Shahmohammadibeni, Hajar Eftekhari, Amir Ehtesham Shafiei Zarneh, Saeed Mohammadihosseinabad, Mehdi Khorrami, Safa Najmi, Ahmad Chitsaz, Parasto Shokraeian, Hossein Ehsanbakhsh, Jalal Rezaeidian, Reza Ebrahimi Rad, Faranak Madadi, Monavvar Andarva, Elham Alehabib, Minoo Atakhorrami, Seyed Erfan Mortazavi, Zahra Azimzadeh, Mahdis Bayat, Amir Mohammad Besharati, Mohammad Ali Harati-Ghavi, Samareh Omidvari, Zahra Dehghani-Tafti, Faraz Mohammadi, Banafsheh Mohammad Hossein Pour, Hamid Noorollahi Moghaddam, Ehsan Esmaili Shandiz, Arman Habibi, Zahra Taherian-Esfahani, Hossein Darvish, Coro Paisán-Ruiz
In this study, the role of known Parkinson's disease (PD) genes was examined in families with autosomal recessive (AR) parkinsonism to assist with the differential diagnosis of PD. Some families without mutations in known genes were also subject to whole genome sequencing with the objective to identify novel parkinsonism-related genes. Families were selected from 4000 clinical files of patients with PD or parkinsonism. AR inheritance pattern, consanguinity, and a minimum of two affected individuals per family were used as inclusion criteria...
May 13, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28499446/genome-sequence-of-shigella-flexneri-strain-sp1-a-diarrheal-isolate-that-encodes-an-extended-spectrum-%C3%AE-lactamase-esbl
#20
Ping Shen, Jianzhong Fan, Lihua Guo, Jiahua Li, Ang Li, Jing Zhang, Chaoqun Ying, Jinru Ji, Hao Xu, Beiwen Zheng, Yonghong Xiao
BACKGROUND: Shigellosis is the most common cause of gastrointestinal infections in developing countries. In China, the species most frequently responsible for shigellosis is Shigella flexneri. S. flexneri remains largely unexplored from a genomic standpoint and is still described using a vocabulary based on biochemical and serological properties. Moreover, increasing numbers of ESBL-producing Shigella strains have been isolated from clinical samples. Despite this, only a few cases of ESBL-producing Shigella have been described in China...
May 12, 2017: Annals of Clinical Microbiology and Antimicrobials
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