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Multiplex PCR

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https://www.readbyqxmd.com/read/28211539/genetic-analysis-of-19-x-chromosome-str-loci-for-forensic-purposes-in-four-chinese-ethnic-groups
#1
Xingyi Yang, Xiaofang Zhang, Junyong Zhu, Linli Chen, Changhui Liu, Xingling Feng, Ling Chen, Huijun Wang, Chao Liu
A new 19 X- short tandem repeat (STR) multiplex PCR system has recently been developed, though its applicability in forensic studies has not been thoroughly assessed. In this study, 932 unrelated individuals from four Chinese ethnic groups (Han, Tibet, Uighur and Hui) were successfully genotyped using this new multiplex PCR system. Our results showed significant linkage disequilibrium between markers DXS10103 and DXS10101 in all four ethnic groups; markers DXS10159 and DXS10162, DXS6809 and DXS6789, and HPRTB and DXS10101 in Tibetan populations; and markers DXS10074 and DXS10075 in Uighur populations...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28208239/narcissus-yellow-stripe-virus-and-narcissus-mosaic-virus-detection-in-narcissus-via-multiplex-taqman-based-reverse-transcription-pcr-assay
#2
Jing Jin, Jianguo Shen, Wei Cai, Xie Guohui, Furong Liao, Fangluan Gao, Junfeng Ma, Xihong Chen, Zujian Wu
AIMS: Development of a multiplex TaqMan RT-qPCR assay to simultaneously detect Narcissus yellow stripe virus (NYSV) and Narcissus mosaic virus (NMV), frequently causing mixed narcissus infection. Feasibility verification was confirmed in natural samples. METHODS AND RESULTS: Primers and probes were designed based on the conserved CP gene regions of NYSV or NMV and their suitability for singleplex and multiplex TaqMan RT-qPCR assays as well as for conventional RT-PCR...
February 16, 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/28205274/genetic-variants-rs1994016-and-rs3825807-in-adamts7-affect-its-mrna-expression-in-atherosclerotic-occlusive-peripheral-arterial-disease
#3
Burcu Bayoglu, Caner Arslan, Cigdem Tel, Turgut Ulutin, Ahmet Dirican, Serkan Burc Deser, Mujgan Cengiz
AIM: Peripheral artery disease (PAD) is a vascular disease affecting peripheral circulation. Recently, genome-wide association studies revealed a relationship between single nucleotide polymorphisms (SNPs) in ADAMTS7 (a disintegrin and metalloprotease with thrombospondin motif 7) and atherosclerosis. In this study, we aimed to determine ADAMTS7 expression in peripheral blood mononuclear cells (PBMCs) and the frequency of ADAMTS7 rs1994016 and rs3825807 polymorphisms in a sample of Turkish patients with PAD, and to evaluate the association of matrix metalloproteinase (MMP) levels with PAD development...
February 15, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28202789/use-of-multiplex-real-time-pcr-to-diagnose-scrub-typhus
#4
Wiwit Tantibhedhyangkul, Ekkarat Wongsawat, Saowaluk Silpasakorn, Duangdao Waywa, Nuttawut Saenyasiri, Jintapa Suesuay, Wilawan Thipmontree, Yupin Suputtamongkol
Scrub typhus, caused by Orientia tsutsugamushi, is a common cause of acute undifferentiated febrile illness in the Asia--Pacific region. However, its non-specific clinical manifestation often prevents early diagnosis. We propose the use of PCR and serologic tests as diagnostic tools. Here, we developed a multiplex real-time PCR assay using hydrolysis (Taqman) probes targeting O. tsutsugamushi47-kDa, groEL, and human IFNB genes to improve early diagnosis of scrub typhus. The amplification efficiency was higher than 94%, and the lower detection limit was 10 copies per reaction...
February 15, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28202084/aprepitant-limits-in-vivo-neuroinflammatory-responses-in-a-rhesus-model-of-lyme-neuroborreliosis
#5
Alejandra N Martinez, Amanda R Burmeister, Geeta Ramesh, Lara Doyle-Meyers, Ian Marriott, Mario T Philipp
BACKGROUND: Substance P (SP) is produced at high levels in the central nervous system (CNS), and its target receptor, neurokinin 1 receptor (NK-1R), is expressed by glia and leukocytes. This tachykinin functions to exacerbate inflammatory responses at peripheral sites. Moreover, SP/NK-1R interactions have recently been associated with severe neuroinflammation and neuronal damage. We have previously demonstrated that NK-1R antagonists can limit neuroinflammatory damage in a mouse model of bacterial meningitis...
February 15, 2017: Journal of Neuroinflammation
https://www.readbyqxmd.com/read/28199413/low-prevalence-of-human-papillomavirus-in-head-and-neck-squamous-cell-carcinoma-in-the-northwest-region-of-the-philippines
#6
Pia Marie Albano, Dana Holzinger, Christianne Salvador, Jose Orosa, Sheryl Racelis, Modesty Leaño, Danilo Sanchez, Lara Mae Angeles, Gordana Halec, Markus Schmitt, John Donnie Ramos, Michael Pawlita
BACKGROUND: Geographic heterogeneity of human papillomavirus (HPV) involvement in head and neck squamous cell carcinoma (HNSCC) has been observed over the last few years. This trend has not been evaluated in the Philippines. Hence, this study aims to provide for the first time a data on the prevalence of HPV in HNSCC in the northwestern region of the Philippines. METHODS: Two hundred one (201) biopsy samples (179 formalin fixed paraffin embedded and 22 fresh frozen) from 163 Filipino HNSCC cases (oral cavity = 88; larynx = 60; oropharynx = 15) diagnosed between 2003 to 2013 were initially included in this study...
2017: PloS One
https://www.readbyqxmd.com/read/28198978/high-prevalence-of-human-papillomavirus-hpv-in-oral-mucosal-lesions-of-patients-at-the-ambulatory-of-oral-diagnosis-of-the-federal-university-of-sergipe-northeastern-brazil
#7
Mariana Goveia Melo Ribeiro, Larissa Doddi Marcolino, Bruna Ribeiro de Andrade Ramos, Elaine Alves Miranda, Cleverson Luciano Trento, Sona Jain, Ricardo Queiroz Gurgel, Márcia Guimarães da Silva, Silvio Santana Dolabella
Objective: The aim of this study was to evaluate the frequency of HPV infection and its genotypes in patients with oral lesions at the Ambulatory of Oral Diagnosis of the Federal University of Sergipe, Brazil. Material and Methods: We conducted a molecular study with 21 patients (15 females) aged from two to 83 years with clinically detectable oral lesions. Samples were collected through exfoliation of lesions and HPV-DNA was identified using MY09/11 and GP5+/6+ primers...
January 2017: Journal of Applied Oral Science: Revista FOB
https://www.readbyqxmd.com/read/28198726/community-acquired-pneumonia-requiring-hospitalization-rational-decision-making-and-interpretation-of-guidelines
#8
Douwe F Postma, Cornelis H van Werkhoven, Jan Jelrik Oosterheert
PURPOSE OF REVIEW: This review focuses on the evidence base for guideline recommendations on the diagnosis, the optimal choice, timing and duration of empirical antibiotic therapy, and the use of microbiological tests for patients hospitalized with community-acquired pneumonia (CAP): issues for which guidelines are frequently used as a quick reference. Furthermore, we will discuss possibilities for future research in these topics. RECENT FINDINGS: Many national and international guideline recommendations, even on critical elements of CAP management, are based on low-to-moderate quality evidence...
February 13, 2017: Current Opinion in Pulmonary Medicine
https://www.readbyqxmd.com/read/28197340/phenotypic-and-genotypic-analysis-of-multidrug-resistant-mycobacterium-tuberculosis-isolates-from-sudanese-patients
#9
Solima M A Sabeel, Mohamed Ahmed Salih, Manasik Ali, Salah-Eldin El-Zaki, Nadir Abuzeid, Zeinab Abubaker Mohammed Elgadi, Hisham N Altayb, Asrar M A Elegail, Nuha Y Ibrahim, Bahaeldin K Elamin
Background. Currently, mutations in rpoB, KatG, and rrs genes and inhA promoter were considered to be involved in conferring resistance to rifampicin, isoniazid, and streptomycin in Mycobacterium tuberculosis (MTB). Objective. The aims of this study were to detect the prevalence of first-line tuberculosis (TB) drug resistance among a group of previously treated and newly detected TB patients, to determine the association between prevalence of multidrug resistance (MDR) and demographic information (age and sex), to explain genes correlated with MDR Mycobacterium tuberculosis, and to characterize MTB via 16S ribosomal RNA (16S rRNA) analysis...
2017: Tuberculosis Research and Treatment
https://www.readbyqxmd.com/read/28196921/noninvasive-prenatal-screening-of-fetal-aneuploidy-without-massively-parallel-sequencing
#10
Chenming Xu, Ting Wang, Chao Liu, Hong Li, Xiaoyan Chen, Huanhuan Zhu, Songchang Chen, Qiuhong Xin, Jing Tao, Liming Huang, Zhengwen Jiang
BACKGROUND: Noninvasive prenatal screening (NIPS) using plasma cell-free DNA has gained tremendous popularity in the clinical assessment of fetal aneuploidy. Most, if not all, of these tests rely on complex and expensive massively parallel sequencing (MPS) techniques, hindering the use of NIPS as a common screening procedure. METHODS: We have developed and optimized an MPS-independent noninvasive genetic test that can rapidly detect fetal aneuploidy at considerably lower costs...
February 14, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28194914/genetic-diversity-and-antimicrobial-resistance-profiles-of-campylobacter-coli-and-campylobacter-jejuni-isolated-from-broiler-chicken-in-farms-and-at-slaughter-in-central-italy
#11
S Pergola, M P Franciosini, F Comitini, M Ciani, S De Luca, S Bellucci, L Menchetti, P Casagrande Proietti
AIMS: Genetic diversity and antimicrobial resistance of C. coli and C. jejuni were investigated along the broiler chicken production chain in central Italy. METHODS AND RESULTS: Campylobacter spp. isolated from cloacal swabs in farms (n = 116) and from neck skin of chilled and eviscerated carcasses at slaughter (n = 24) were identified as C. coli (n = 99) and C. jejuni (n = 41) by multiplex PCR. Characterisation by s-AFLP revealed a specific genotype of Campylobacter for each farm...
February 14, 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/28194411/antibiotic-resistance-of-campylobacter-recovered-from-faeces-and-carcasses-of-healthy-livestock
#12
Akosua B Karikari, Kwasi Obiri-Danso, Enoch H Frimpong, Karen A Krogfelt
Campylobacter is of major significance in food safety and human and veterinary medicine. This study highlighted resistance situation in the area of veterinary public health in Ghana. Using selective mCCDA agar, isolates were confirmed phenotypically on API CAMPY and genotypically by multiplex PCR of IpxA gene. The susceptibility profile of species to common and relevant antibiotics was determined by the Kirby-Bauer disk diffusion method. Cattle, sheep, goat, and pig faecal samples analysed, respectively, yielded 13...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28191309/co-existence-of-blaoxa-23-and-blandm-1-genes-of-acinetobacter-baumannii-isolated-from-nepal-antimicrobial-resistance-and-clinical-significance
#13
Prabhu Raj Joshi, Mahesh Acharya, Trishna Kakshapati, Udomluk Leungtongkam, Rapee Thummeepak, Sutthirat Sitthisak
BACKGROUND: Molecular analysis of carbapenem-resistant genes in Acinetobacter baumannii, an emerging pathogen, is less commonly reported from Nepal. In this study we determined the antibiotic susceptibility profile and genetic mechanism of carbapenem resistance in clinical isolates of A. baumannii. METHODS: A. baumannii were isolated from various clinical specimens and identified based on Gram staining, biochemical tests, and PCR amplification of organism specific 16S rRNA and blaOXA-51 genes...
2017: Antimicrobial Resistance and Infection Control
https://www.readbyqxmd.com/read/28190609/evaluation-of-a-new-real-time-pcr-assay-for-the-direct-detection-of-diarrheagenic-escherichia-coli-in-stool-specimens
#14
U Eigner, A Hiergeist, A Veldenzer, M Rohlfs, R Schwarz, M Holfelder
Diarrheagenic E. coli (DEC) are one of the most common causes for diarrhea worldwide, especially in children. We evaluated the rapid RIDA ® GENE (RG) real-time multiplex PCR assays (R-Biopharm, Darmstadt, Germany) for the detection of the most important diarrheagenic E. coli. Three hundred fifteen liquid or non-formed stool specimens were examined. The results of the RG multiplex assays were compared to specific PCR methods. The sensitivity and specificity of the RG PCRs were as follows, 100%/100% for the detection of EHEC, 96...
February 1, 2017: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/28190461/detection-of-mycobacterium-chelonae-mycobacterium-abscessus-group-and-mycobacterium-fortuitum-complex-by-a-multiplex-real-time-pcr-directly-from-clinical-samples-using-the-bd-max-system
#15
Talita T Rocchetti, Suzane Silbert, Alicia Gostnell, Carly Kubasek, Antonio C Campos Pignatari, Raymond Widen
A new multiplex PCR test was designed to detect Mycobacterium chelonae, Mycobacterium abscessus group, and Mycobacterium fortuitum complex on the BD MAX System. A total of 197 clinical samples previously submitted for mycobacterial culture were tested using the new protocol. Samples were first treated with proteinase K, and then each sample was inoculated into the BD MAX Sample Buffer Tube. Extraction and multiplex PCR were performed by the BD MAX System, using the BD MAX ExK TNA-3 extraction kit and BD TNA Master Mix, along with specific in-house designed primers and probes for each target...
March 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28188172/t-cell-repertoires-in-refractory-coeliac-disease
#16
Julia Ritter, Karin Zimmermann, Korinna Jöhrens, Stefanie Mende, Anke Seegebarth, Britta Siegmund, Steffen Hennig, Kremena Todorova, Andreas Rosenwald, Severin Daum, Michael Hummel, Michael Schumann
OBJECTIVE: Refractory coeliac disease (RCD) is a potentially hazardous complication of coeliac disease (CD). In contrast to RCD type I, RCD type II is a precursor entity of enteropathy-associated T-cell lymphoma (EATL), which is associated with clonally expanding T-cells that are also found in the sequentially developing EATL. Using high-throughput sequencing (HTS), we aimed to establish the small-intestinal T-cell repertoire (TCR) in CD and RCD to unravel the role of distinct T-cell clonotypes in RCD pathogenesis...
February 10, 2017: Gut
https://www.readbyqxmd.com/read/28187714/tipmt-identification-of-pcr-based-taxon-specific-markers
#17
Gabriela F Rodrigues-Luiz, Mariana S Cardoso, Hugo O Valdivia, Edward V Ayala, Célia M F Gontijo, Thiago de S Rodrigues, Ricardo T Fujiwara, Robson S Lopes, Daniella C Bartholomeu
BACKGROUND: Molecular genetic markers are one of the most informative and widely used genome features in clinical and environmental diagnostic studies. A polymerase chain reaction (PCR)-based molecular marker is very attractive because it is suitable to high throughput automation and confers high specificity. However, the design of taxon-specific primers may be difficult and time consuming due to the need to identify appropriate genomic regions for annealing primers and to evaluate primer specificity...
February 11, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28187065/clinical-course-of-enterovirus-d68-in-hospitalized-children
#18
Jennifer E Schuster, Rangaraj Selvarangan, Ferdaus Hassan, Kayla B Briggs, Lindsay Hays, Jenna O Miller, Barbara Pahud, Henry T Puls, Mary Ann Queen, Marita T Thompson, Gina Weddle, Mary Anne Jackson
BACKGROUND: Enterovirus D68 (EV-D68) has been sporadically reported as a cause of respiratory tract infections. In 2014, an international outbreak of EV-D68 occurred and caused severe respiratory disease in the pediatric population. METHODS: A retrospective chart review was performed of children admitted to Children's Mercy Hospital from August 1-September 15, 2014 with positive multiplex PCR testing for enterovirus/rhinovirus (EV/RV). Specimens were subsequently tested for EV-D68, and clinical data were obtained from the medical records...
December 13, 2016: Pediatric Infectious Disease Journal
https://www.readbyqxmd.com/read/28187034/detection-of-novel-t-12-17-p12-p13-in-relapsed-refractory-acute-myeloid-leukemia-by-anchored-multiplex-pcr-amp-based-next-generation-sequencing
#19
Talha Badar, Laura Johnson, Katelyn Trifilo, Helen Wang, Brian A Kudlow, Eric Padron, Peter R Pappenhausen, Mohammad O Hussaini
Although several technologies can be used to detect gene fusions, anchored multiplex PCR next-generation sequencing (AMP-NGS) offers the advantage of novel fusion detection and the ability to multiplex multitudinous genes. We applied AMP-NGS technology in the evaluation of a 56-year-old gentleman with myelodysplastic syndrome transformed acute myeloid leukemia (AML). Patient was initially diagnosed with low-risk myelodysplastic syndrome-refractory cytopenias and multilineage dysplasia (MDS-RCMD), progressed to AML after failing hypomethylating agent therapy...
February 9, 2017: Applied Immunohistochemistry & Molecular Morphology: AIMM
https://www.readbyqxmd.com/read/28185831/use-of-dual-priming-oligonucleotide-system-based-multiplex-rt-pcr-combined-with-high-performance-liquid-chromatography-assay-for-simultaneous-detection-of-five-enteric-viruses-associated-with-acute-enteritis
#20
Wen-Lu Fan, Zi-Wei Wang, Yue Qin, Chao Sun, Zhong-Mei Liu, Yan-Ping Jiang, Xin-Yuan Qiao, Li-Jie Tang, Yi-Jing Li, Yi-Gang Xu
In this study, a specific and sensitive method for simultaneous detection of human astrovirus, human rotavirus, norovirus, sapovirus and enteric adenovirus associated with acute enteritis was developed, based on the specific dual priming oligonucleotide (DPO) system and the sensitive high-performance liquid chromatography (HPLC) analysis. The DPO system-based multiplex reverse transcription-polymerase chain reaction (RT-PCR) combined with HPLC assay was more sensitive than agarose gel electrophoresis analysis and real-time SYBR Green PCR assay, and showed a specificity of 100% and sensitivity of 96%-100%...
February 6, 2017: Journal of Virological Methods
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