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https://www.readbyqxmd.com/read/28539665/copy-number-variants-and-candidate-gene-mutations-in-isolated-split-hand-foot-malformation
#1
Tonia C Carter, Robert J Sicko, Denise M Kay, Marilyn L Browne, Paul A Romitti, Zoё L Edmunds, Aiyi Liu, Ruzong Fan, Charlotte M Druschel, Michele Caggana, Lawrence C Brody, James L Mills
Split hand/foot malformation (SHFM) is a congenital limb deficiency with missing or shortened central digits. Some SHFM genes have been identified but the cause of many SHFM cases is unknown. We used single-nucleotide polymorphism (SNP) microarray analysis to detect copy-number variants (CNVs) in 25 SHFM cases without other birth defects from New York State (NYS), prioritized CNVs absent from population CNV databases, and validated these CNVs using quantitative real-time polymerase chain reaction (qPCR). We tested for the validated CNVs in seven cases from Iowa using qPCR, and also sequenced 36 SHFM candidate genes in all the subjects...
May 25, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28539377/dietary-starch-intake-modifies-the-relation-between-copy-number-variation-in-the-salivary-amylase-gene-and-bmi
#2
Gull Rukh, Ulrika Ericson, Johanna Andersson-Assarsson, Marju Orho-Melander, Emily Sonestedt
Background: Studies have shown conflicting associations between the salivary amylase gene (AMY1) copy number and obesity. Salivary amylase initiates starch digestion in the oral cavity; starch is a major source of energy in the diet.Objective: We investigated the association between AMY1 copy number and obesity traits, and the effect of the interaction between AMY1 copy number and starch intake on these obesity traits.Design: We first assessed the association between AMY1 copy number (genotyped by digital droplet polymerase chain reaction) and obesity traits in 4800 individuals without diabetes (mean age: 57 y; 60% female) from the Malmö Diet and Cancer Cohort...
May 24, 2017: American Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/28537806/analytic-and-clinical-validation-of-an-ultrasensitive-quantitative-polymerase-chain-reaction-assay-for-egfr-mutation-analysis-with-circulating-tumor-dna
#3
Xiaowei Wang, Yunhua Gao, Bei Wang, Zhenrong Zhang, Chaoyang Liang, Hongxiang Feng, Yongqing Guo, Jiping Da, Minli Mo, Mengyun Zhang, Feng Ding, Zhao Chen, Hui Li, Deruo Liu
CONTEXT: - The mutation analysis of epidermal growth factor receptor (EGFR) has become a common test to guide therapeutic decision making for lung cancer. Molecular testing with circulating tumor DNA in plasma allows diagnosis of mutations when tumor tissue is not available as well as monitoring treatment response with repeat biopsies. OBJECTIVES: - To develop a timely and cost-effective assay that can accurately detect EGFR mutations in circulating tumor DNA and to evaluate the analytic and clinical performance of the assay...
May 24, 2017: Archives of Pathology & Laboratory Medicine
https://www.readbyqxmd.com/read/28535331/computer-and-mobile-technology-interventions-for-self-management-in-chronic-obstructive-pulmonary-disease
#4
REVIEW
Catherine McCabe, Margaret McCann, Anne Marie Brady
BACKGROUND: Chronic obstructive pulmonary disease (COPD) is characterised by airflow obstruction due to an abnormal inflammatory response of the lungs to noxious particles or gases, for example, cigarette smoke. The pattern of care for people with moderate to very severe COPD often involves regular lengthy hospital admissions, which result in high healthcare costs and an undesirable effect on quality of life. Research over the past decade has focused on innovative methods for developing enabling and assistive technologies that facilitate patient self-management...
May 23, 2017: Cochrane Database of Systematic Reviews
https://www.readbyqxmd.com/read/28522907/droplet-digital-pcr-for-quantification-of-itga6-in-a-stool-mrna-assay-for-the-detection-of-colorectal-cancers
#5
Elizabeth Herring, Shigeru Kanaoka, Éric Tremblay, Jean-François Beaulieu
AIM: To investigate the use of droplet digital polymerase chain reaction (ddPCR) for detecting host mRNA markers in stools as a non-invasive test for colorectal cancer screening. METHODS: ddPCR and quantitative PCR were compared side by side for their performance in the detection of ITGA6 and ITGA6A transcripts in stool samples obtained from patients with various types of colorectal lesions (advanced adenomas and stage II-IV colorectal cancers) and control (patients displaying no pathological findings) using duplex TaqMan reactions for both methods...
April 28, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28506959/health-related-internet-use-in-people-with-cancer-results-from-a-cross-sectional-study-in-two-outpatient-clinics-in-sweden
#6
Susanne Mattsson, Erik Martin Gustaf Olsson, Birgitta Johansson, Maria Carlsson
BACKGROUND: The access to various forms of support during the disease trajectory is crucial for people with cancer. The provision and use of Internet health services is increasing, and it is important to further investigate the preferences and demographical characteristics of its users. Investigating the uptake and perceived value of Internet health services is a prerequisite to be able to meet the needs in the targeted group. OBJECTIVE: The objective of this study was to investigate health-related Internet use among people with cancer...
May 15, 2017: Journal of Medical Internet Research
https://www.readbyqxmd.com/read/28502728/technical-validation-of-a-next-generation-sequencing-assay-for-detecting-clinically-relevant-levels-of-breast-cancer-related-single-nucleotide-variants-and-copy-number-variants-using-simulated-cell-free-dna
#7
Xin Yang, Yuxing Chu, Rui Zhang, Yanxi Han, Lucheng Zhang, Yu Fu, Dan Li, Rongxue Peng, Dongdong Li, Jiansheng Ding, Ziyang Li, Meiru Zhao, Kuo Zhang, Tian Lu, Lang Yi, Qisheng Wu, Guigao Lin, Jiehong Xie, Tao Liu, Ling Yang, Xin Yi, Jinming Li
Next-generation sequencing (NGS) is commonly used in a clinical setting for diagnostic and prognostic testing of genetic mutations to select optimal targeted therapies. Herein, we describe the development of a custom NGS assay for detecting single-nucleotide variants (SNVs) and copy number variations (CNVs) in a panel of 51 genes related to breast cancer. We designed and implemented a validation strategy in accordance with principles and guidelines developed by the Next-Generation Sequencing: Standardization of Clinical Testing work group using artificial, cell-free DNA (cfDNA) with mutant fragments prepared in a simple, rapid, and cost-effective manner...
May 11, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28499138/human-pegivirus-1-in-the-csf-of-patients-with-hiv-associated-neurocognitive-disorder-hand-may-be-derived-from-blood-in-highly-viraemic-patients
#8
Diana Hardie, Heidi Smuts
BACKGROUND: Human pegivirus-1 (HPgV-1) infection in the brain has not been extensively examined and its association with disease remains unconfirmed. In a high throughput sequencing study to look for infectious agents that could play a role in HIV-associated neurocognitive disorder (HAND), this virus was detected in 3 of 8 CSF samples. OBJECTIVES: To determine the significance of this finding, additional patients were screened and the viral load and viral diversity in blood and CSF were examined...
April 6, 2017: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://www.readbyqxmd.com/read/28483527/immuno-pcr-with-digital-readout
#9
Hendrik Schröder, Maximilian Grösche, Michael Adler, Mark Spengler, Christof M Niemeyer
Immuno-PCR (IPCR) combines the versatile ELISA antigen detection with ultrasensitive PCR signal amplification, thereby enabling the highly sensitive detection of a broad range of targets with a typically very large dynamic detection range. The quantification of the antigen is usually achieved by real-time PCR, which provides a correlation between the target concentration and amplified DNA marker. We here report on the implementation of digital droplet PCR as a means for direct quantification of DNA copies to enable the highly sensitive detection of protein biomarkers...
May 5, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28481899/lumican-and-versican-protein-expression-are-associated-with-colorectal-adenoma-to-carcinoma-progression
#10
Meike de Wit, Beatriz Carvalho, Pien M Delis-van Diemen, Carolien van Alphen, Jeroen A M Beliën, Gerrit A Meijer, Remond J A Fijneman
BACKGROUND: One prominent event associated with colorectal adenoma-to-carcinoma progression is genomic instability. Approximately 85% of colorectal cancer cases exhibit chromosomal instability characterized by accumulation of chromosome copy number aberrations (CNAs). Adenomas with gain of chromosome 8q, 13q, and/or 20q are at high risk of progression to cancer. Tumor progression is also associated with expansion of the extracellular matrix (ECM) and the activation of non-malignant cells within the tumor stroma...
2017: PloS One
https://www.readbyqxmd.com/read/28477149/current-and-emerging-applications-of-droplet-digital-pcr-in-oncology
#11
REVIEW
Susana Olmedillas-López, Mariano García-Arranz, Damián García-Olmo
The clinical management of cancer has evolved in recent years towards more personalized strategies that require a comprehensive knowledge of the complex molecular features involved in tumor growth and evolution, and the development of drug resistance mechanisms leading to disease progression. Droplet digital PCR (ddPCR) has become one of the most accurate and reliable tools for the examination of genetic alterations in a wide variety of cancers because of its high sensitivity and specificity. ddPCR is currently being applied for absolute allele quantification, rare mutation detection, analysis of copy number variations, DNA methylation, and gene rearrangements in different kinds of clinical samples...
May 5, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28472366/androgen-receptor-gene-status-in-plasma-dna-associates-with-worse-outcome-on-enzalutamide-or-abiraterone-for-castration-resistant-prostate-cancer-a-multi-institution-correlative-biomarker-study
#12
V Conteduca, D Wetterskog, M T A Sharabiani, E Grande, M P Fernandez-Perez, A Jayaram, S Salvi, D Castellano, A Romanel, C Lolli, V Casadio, G Gurioli, D Amadori, A Font, S Vazquez-Estevez, A González Del Alba, B Mellado, O Fernandez-Calvo, M J Méndez-Vidal, M A Climent, I Duran, E Gallardo, A Rodriguez, C Santander, M I Sáez, J Puente, D Gasi Tandefelt, A Wingate, D Dearnaley, F Demichelis, U De Giorgi, E Gonzalez-Billalabeitia, G Attard
Background: There is an urgent need to identify biomarkers to guide personalized therapy in castration-resistant prostate cancer (CRPC). We aimed to clinically qualify androgen receptor (AR) gene status measurement in plasma DNA using multiplex droplet digital PCR (ddPCR) in pre- and post-chemotherapy CRPC. Methods: We optimized ddPCR assays for AR copy number and mutations and retrospectively analyzed plasma DNA from patients recruited to one of the three biomarker protocols with prospectively collected clinical data...
May 3, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28466553/autopsy-fingerprint-technique-using-fingerprint-powder
#13
Lee O Morgan, Marty Johnson, Jered B Cornelison, Carolyn V Isaac, Joyce L deJong, Joseph A Prahlow
The collection of high-quality fingerprints is an important component of routine forensic autopsies and represents one of the several potential methods for identifying a decedent. Fingerprint collection at autopsy frequently employs a manual method using fingerprint ink and cards, although some offices use digital-scanning equipment. While these methodologies are adequate in most circumstances, this study introduces an alternative method using fingerprint powder and adhesive labels. The method is quick, easy to perform, and cost-effective and provides the additional advantage of an adhesive label that easily conforms to the finger, palm, or foot which reduces smudging of prints in individuals with rigor mortis, skin slippage, or decomposition compared to more traditional autopsy fingerprint collection techniques...
May 3, 2017: Journal of Forensic Sciences
https://www.readbyqxmd.com/read/28456859/a-comparison-of-visual-recognition-of-the-laryngopharyngeal-structures-between-high-and-standard-frame-rate-videos-of-the-fiberoptic-endoscopic-evaluation-of-swallowing
#14
Mehran Alizadeh Aghdam, Makoto Ogawa, Toshihiko Iwahashi, Kiyohito Hosokawa, Chieri Kato, Hidenori Inohara
The purpose of this study was to assess whether or not high frame rate (HFR) videos recorded using high-speed digital imaging (HSDI) improve the visual recognition of the motions of the laryngopharyngeal structures during pharyngeal swallow in fiberoptic endoscopic evaluation of swallowing (FEES). Five healthy subjects were asked to swallow 0.5 ml water under fiberoptic nasolaryngoscopy. The endoscope was connected to a high-speed camera, which recorded the laryngopharyngeal view throughout the swallowing process at 4000 frames/s (fps)...
April 29, 2017: Dysphagia
https://www.readbyqxmd.com/read/28448765/digital-assays-part-i-partitioning-statistics-and-digital-pcr
#15
Amar S Basu
A digital assay is one in which the sample is partitioned into many small containers such that each partition contains a discrete number of biological entities (0, 1, 2, 3, …). A powerful technique in the biologist's toolkit, digital assays bring a new level of precision in quantifying nucleic acids, measuring proteins and their enzymatic activity, and probing single-cell genotypes and phenotypes. Part I of this review begins with the benefits and Poisson statistics of partitioning, including sources of error...
April 1, 2017: SLAS Technology
https://www.readbyqxmd.com/read/28446770/instability-of-8e5-calibration-standard-revealed-by-digital-pcr-risks-inaccurate-quantification-of-hiv-dna-in-clinical-samples-by-qpcr
#16
Eloise Busby, Alexandra S Whale, R Bridget Ferns, Paul R Grant, Gary Morley, Jonathan Campbell, Carole A Foy, Eleni Nastouli, Jim F Huggett, Jeremy A Garson
Establishing a cure for HIV is hindered by the persistence of latently infected cells which constitute the viral reservoir. Real-time qPCR, used for quantification of this reservoir by measuring HIV DNA, requires external calibration; a common choice of calibrator is the 8E5 cell line, which is assumed to be stable and to contain one HIV provirus per cell. In contrast, digital PCR requires no external calibration and potentially provides 'absolute' quantification. We compared the performance of qPCR and dPCR in quantifying HIV DNA in 18 patient samples...
April 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28441604/digital-quantitative-analysis-of-microrna-in-single-cell-based-on-ligation-depended-polymerase-colony-polony
#17
Hui Wang, Honghong Wang, Xinrui Duan, Chenghui Liu, Zhengping Li
The ability to dissect cell-to-cell variations of microRNA (miRNA) expression with single-cell resolution has become a powerful tool to investigate the regulatory function of miRNAs in biological processes and the pathogenesis of miRNA-related diseases. Herein, we have developed a novel scheme for digital detection of miRNA in single cell by using the ligation-depended DNA polymerase colony (polony). Firstly, two simply designed target-specific DNA probes were ligated by using individual miRNA as the template...
September 15, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28422522/molecular-genetic-characterization-of-a-chinese-family-with-severe-split-hand-foot-malformation
#18
Lihua Cao, Wei Yang, Shusen Wang, Chen Chen, Xue Zhang, Yang Luo
AIMS: Split hand/foot malformation (SHFM) is a congenital limb malformation characterized by underdeveloped or absent central digital rays, clefts of the hands and feet, and variable syndactyly of the remaining digits. SHFM is a genetically heterogeneous disease; the aim of this study was to identify pathogenic variations in a Chinese family with SHFM. MATERIALS AND METHODS: Haplotype analyses with microsatellite markers covering the five SHFM loci were performed to localize the causative locus...
April 19, 2017: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/28414286/-pcr-analysis-of-the-absolute-number-of-copies-of-human-chromosome-18-transcripts-in-liver-and-hepg2-cells
#19
Y Y Kiseleva, K G Ptitsyn, O V Tikhonova, S P Radko, L K Kurbatov, I V Vakhrushev, V G Zgoda, E A Ponomarenko, A V Lisitsa, A I Archakov
Using reverse transcription in conjunction with the quantitative real-time PCR or digital droplet PCR, the transcriptome profiling of human chromosome 18 has been carried out in liver hepatocytes and hepatoblastoma cells (HepG2 cell line) in terms of the absolute number of each transcript per cell. The transcript abundance varies within the range of 0.006 to 9635 and 0.011 to 4819 copies per cell for HepG2 cell line and hepatocytes, respectively. The expression profiles for genes of chromosome 18 in hepatocytes and HepG2 cells were found to significantly correlate: the Spearman's correlation coefficient was equal to 0...
March 2017: Biomedit︠s︡inskai︠a︡ Khimii︠a︡
https://www.readbyqxmd.com/read/28414163/droplet-digital-pcr-ddpcr-vs-quantitative-real-time-pcr-qpcr-approach-for-detection-and-quantification-of-merkel-cell-polyomavirus-mcpyv-dna-in-formalin-fixed-paraffin-embedded-ffpe-cutaneous-biopsies
#20
Rosaria Arvia, Mauro Sollai, Federica Pierucci, Carmelo Urso, Daniela Massi, Krystyna Zakrzewska
BACKGROUND: Merkel cell polyomavirus (MCPyV) is associated with Merkel cell carcinoma and high viral load in the skin was proposed as a risk factor for the occurrence of this tumour. MCPyV DNA was detected, with lower frequency, in different skin cancers but since the viral load was usually low, the real prevalence of viral DNA could be underestimated. OBJECTIVE: To evaluate the performance of two assays (qPCR and ddPCR) for MCPyV detection and quantification in formalin fixed paraffin embedded (FFPE) tissue samples...
April 14, 2017: Journal of Virological Methods
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