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Human Genomics

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https://www.readbyqxmd.com/read/28302172/transcriptome-analysis-of-bronchoalveolar-lavage-fluid-from-children-with-severe-mycoplasma-pneumoniae-pneumonia-reveals-novel-gene-expression-and-immunodeficiency
#1
Kuo Wang, Man Gao, Mingyue Yang, Fanzheng Meng, Deli Li, Ruihua Lu, Yan Wang, Huadong Zhuang, Mengyao Li, Genhong Cheng, Xiaosong Wang
BACKGROUND: A growing number of severe Mycoplasma pneumoniae pneumonia (MPP) cases have been reported recently. However, the pathogenesis of severe MPP is not clear. In the current study, transcriptome sequencing was used to identify gene expression and alternative splicing profiles to provide insights into the pathogenesis of severe MPP. METHODS: RNAs of bronchoalveolar lavage fluid (BALF) samples from three severe MPP children and three mild MPP children were analyzed respectively by deep sequencing followed by computational annotation and quantification...
March 16, 2017: Human Genomics
https://www.readbyqxmd.com/read/28302154/the-israeli-national-genetic-database-a-10-year-experience
#2
Joël Zlotogora, George P Patrinos
BACKGROUND: The Israeli National and Ethnic Mutation database ( http://server.goldenhelix.org/israeli ) was launched in September 2006 on the ETHNOS software to include clinically relevant genomic variants reported among Jewish and Arab Israeli patients. In 2016, the database was reviewed and corrected according to ClinVar ( https://www.ncbi.nlm.nih.gov/clinvar ) and ExAC ( http://exac.broadinstitute.org ) database entries. The present article summarizes some key aspects from the development and continuous update of the database over a 10-year period, which could serve as a paradigm of successful database curation for other similar resources...
March 16, 2017: Human Genomics
https://www.readbyqxmd.com/read/28257648/genetic-determinants-of-clinical-heterogeneity-of-the-coronary-artery-disease-in-the-population-of-hyderabad-india
#3
Rayabarapu Pranavchand, Arramraju Sreenivas Kumar, Battini Mohan Reddy
BACKGROUND: Genetic predisposition to the clinical categories of coronary artery disease (anatomical viz., insignificant, single, double, and triple vessel diseases and phenotypic severity categories viz., angina, acute coronary syndrome, and myocardial infarction) is poorly understood. Particularly, the apolipoprotein genes clustered at 11q23.3 chromosomal region play a vital role in cholesterol homeostasis, and a large number of SNPs identified in this region need to be explored for their association with the clinical categories of CAD...
March 4, 2017: Human Genomics
https://www.readbyqxmd.com/read/28219410/copy-number-variation-of-human-amy1-is-a-minor-contributor-to-variation-in-salivary-amylase-expression-and-activity
#4
Danielle Carpenter, Laura M Mitchell, John A L Armour
BACKGROUND: Salivary amylase in humans is encoded by the copy variable gene AMY1 in the amylase gene cluster on chromosome 1. Although the role of salivary amylase is well established, the consequences of the copy number variation (CNV) at AMY1 on salivary amylase protein production are less well understood. The amylase gene cluster is highly structured with a fundamental difference between odd and even AMY1 copy number haplotypes. In this study, we aimed to explore, in samples from 119 unrelated individuals, not only the effects of AMY1 CNV on salivary amylase protein expression and amylase enzyme activity but also whether there is any evidence for underlying difference between the common haplotypes containing odd numbers of AMY1 and even copy number haplotypes...
February 20, 2017: Human Genomics
https://www.readbyqxmd.com/read/28209183/variants-in-congenital-hypogonadotrophic-hypogonadism-genes-identified-in-an-indonesian-cohort-of-46-xy-under-virilised-boys
#5
Katie L Ayers, Aurore Bouty, Gorjana Robevska, Jocelyn A van den Bergen, Achmad Zulfa Juniarto, Nurin Aisyiyah Listyasari, Andrew H Sinclair, Sultana M H Faradz
BACKGROUND: Congenital hypogonadotrophic hypogonadism (CHH) and Kallmann syndrome (KS) are caused by disruption to the hypothalamic-pituitary-gonadal (H-P-G) axis. In particular, reduced production, secretion or action of gonadotrophin-releasing hormone (GnRH) is often responsible. Various genes, many of which play a role in the development and function of the GnRH neurons, have been implicated in these disorders. Clinically, CHH and KS are heterogeneous; however, in 46,XY patients, they can be characterised by under-virilisation phenotypes such as cryptorchidism and micropenis or delayed puberty...
February 16, 2017: Human Genomics
https://www.readbyqxmd.com/read/28031051/the-status-of-her2-amplification-and-kras-mutations-in-mucinous-ovarian-carcinoma
#6
LETTER
Kuang-Leei Chang, Ming-Yung Lee, Wan-Ru Chao, Chih-Ping Han
Jayson GC et al. remarked in Lancet that nearly 100% of mucinous ovarian cancer cases have Kras mutation as well as a high frequency of Her2 amplification. Using the Abbott PathVysion Her2 DNA Probe Kit and Kras mutant-enriched PCR Kits (FemtoPath®), 21 samples of primary ovarian mucinous cystadenocarcinomas from Taiwanese patients were examined to determine the status of Her2 amplification and Kras mutations. Our results showed the Her2 amplification rates were 33.33%, while the Kras mutation rates were 61...
December 28, 2016: Human Genomics
https://www.readbyqxmd.com/read/27894333/head-and-neck-squamous-cell-carcinoma-risk-in-smokers-no-association-detected-between-phenotype-and-ahr-cyp1a1-cyp1a2-or-cyp1b1-genotype
#7
Lucia F Jorge-Nebert, Ge Zhang, Keith M Wilson, Zhengwen Jiang, Randall Butler, Jack L Gluckman, Susan M Pinney, Daniel W Nebert
BACKGROUND: Head-and-neck squamous cell carcinoma (HNSCC) differs between smokers and nonsmokers in etiology and clinical presentation. Because of demonstrated unequivocal involvement in smoking-induced cancer in laboratory animals, four candidate genes--AHR, CYP1A1, CYP1A2, and CYP1B1--were selected for a clinical genotype-phenotype association study of HNSCC risk in smokers. Thirty-six single-nucleotide variants (mostly tag-SNPs) within and near these four genes [16 (AHR), 4 (CYP1A1), 4 (CYP1A2), and 12 (CYP1B1)] were chosen...
November 28, 2016: Human Genomics
https://www.readbyqxmd.com/read/27881154/targeted-next-generation-sequencing-identifies-novel-notch3-gene-mutations-in-cadasil-diagnostics-patients
#8
Neven Maksemous, Robert A Smith, Larisa M Haupt, Lyn R Griffiths
BACKGROUND: Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a monogenic, hereditary, small vessel disease of the brain causing stroke and vascular dementia in adults. CADASIL has previously been shown to be caused by varying mutations in the NOTCH3 gene. The disorder is often misdiagnosed due to its significant clinical heterogeneic manifestation with familial hemiplegic migraine and several ataxia disorders as well as the location of the currently identified causative mutations...
November 24, 2016: Human Genomics
https://www.readbyqxmd.com/read/27871310/transcriptome-analysis-reveals-manifold-mechanisms-of-cyst-development-in-adpkd
#9
Rita M C de Almeida, Sherry G Clendenon, William G Richards, Michael Boedigheimer, Michael Damore, Sandro Rossetti, Peter C Harris, Britney-Shea Herbert, Wei Min Xu, Angela Wandinger-Ness, Heather H Ward, James A Glazier, Robert L Bacallao
BACKGROUND: Autosomal dominant polycystic kidney disease (ADPKD) causes progressive loss of renal function in adults as a consequence of the accumulation of cysts. ADPKD is the most common genetic cause of end-stage renal disease. Mutations in polycystin-1 occur in 87% of cases of ADPKD and mutations in polycystin-2 are found in 12% of ADPKD patients. The complexity of ADPKD has hampered efforts to identify the mechanisms underlying its pathogenesis. No current FDA (Federal Drug Administration)-approved therapies ameliorate ADPKD progression...
November 21, 2016: Human Genomics
https://www.readbyqxmd.com/read/27863505/a-genomic-case-study-of-desmoplastic-small-round-cell-tumor-comprehensive-analysis-reveals-insights-into-potential-therapeutic-targets-and-development-of-a-monitoring-tool-for-a-rare-and-aggressive-disease
#10
Elisa Napolitano Ferreira, Bruna Durães Figueiredo Barros, Jorge Estefano de Souza, Renan Valieris Almeida, Giovana Tardin Torrezan, Sheila Garcia, Ana Cristina Victorino Krepischi, Celso Abdon Lopes de Mello, Isabela Werneck da Cunha, Clóvis Antonio Lopes Pinto, Fernando Augusto Soares, Emmanuel Dias-Neto, Ademar Lopes, Sandro José de Souza, Dirce Maria Carraro
BACKGROUND: Genome-wide profiling of rare tumors is crucial for improvement of diagnosis, treatment, and, consequently, achieving better outcomes. Desmoplastic small round cell tumor (DSRCT) is a rare type of sarcoma arising from mesenchymal cells of abdominal peritoneum that usually develops in male adolescents and young adults. A specific translocation, t(11;22)(p13;q12), resulting in EWS and WT1 gene fusion is the only recurrent molecular hallmark and no other genetic factor has been associated to this aggressive tumor...
November 18, 2016: Human Genomics
https://www.readbyqxmd.com/read/27793185/navigating-the-dynamic-landscape-of-long-noncoding-rna-and-protein-coding-gene-annotations-in-gencode
#11
Saakshi Jalali, Shrey Gandhi, Vinod Scaria
BACKGROUND: Our understanding of the transcriptional potential of the genome and its functional consequences has undergone a significant change in the last decade. This has been largely contributed by the improvements in technology which could annotate and in many cases functionally characterize a number of novel gene loci in the human genome. Keeping pace with advancements in this dynamic environment and being able to systematically annotate a compendium of genes and transcripts is indeed a formidable task...
October 28, 2016: Human Genomics
https://www.readbyqxmd.com/read/27836013/novel-genetic-risk-variants-for-pediatric-celiac-disease
#12
Angeliki Balasopoulou, Biljana Stanković, Angeliki Panagiotara, Gordana Nikčevic, Brock A Peters, Anne John, Effrosyni Mendrinou, Apostolos Stratopoulos, Aigli Ioanna Legaki, Vasiliki Stathakopoulou, Aristoniki Tsolia, Nikolaos Govaris, Sofia Govari, Zoi Zagoriti, Konstantinos Poulas, Maria Kanariou, Nikki Constantinidou, Maro Krini, Kleopatra Spanou, Nedeljko Radlovic, Bassam R Ali, Joseph Borg, Radoje Drmanac, George Chrousos, Sonja Pavlovic, Eleftheria Roma, Branka Zukic, George P Patrinos, Theodora Katsila
BACKGROUND: Celiac disease is a complex chronic immune-mediated disorder of the small intestine. Today, the pathobiology of the disease is unclear, perplexing differential diagnosis, patient stratification, and decision-making in the clinic. METHODS: Herein, we adopted a next-generation sequencing approach in a celiac disease trio of Greek descent to identify all genomic variants with the potential of celiac disease predisposition. RESULTS: Analysis revealed six genomic variants of prime interest: SLC9A4 c...
October 24, 2016: Human Genomics
https://www.readbyqxmd.com/read/27678214/an-efficient-method-for-protein-function-annotation-based-on-multilayer-protein-networks
#13
Bihai Zhao, Sai Hu, Xueyong Li, Fan Zhang, Qinglong Tian, Wenyin Ni
BACKGROUND: Accurate annotation of protein functions is still a big challenge for understanding life in the post-genomic era. Many computational methods based on protein-protein interaction (PPI) networks have been proposed to predict the function of proteins. However, the precision of these predictions still needs to be improved, due to the incompletion and noise in PPI networks. Integrating network topology and biological information could improve the accuracy of protein function prediction and may also lead to the discovery of multiple interaction types between proteins...
September 27, 2016: Human Genomics
https://www.readbyqxmd.com/read/27671536/a-first-line-diagnostic-assay-for-limb-girdle-muscular-dystrophy-and-other-myopathies
#14
Dorota Monies, Hindi N Alhindi, Mohamed A Almuhaizea, Mohamed Abouelhoda, Anas M Alazami, Ewa Goljan, Banan Alyounes, Dyala Jaroudi, Abdulelah AlIssa, Khalid Alabdulrahman, Shazia Subhani, Mohamed El-Kalioby, Tariq Faquih, Salma M Wakil, Nada A Altassan, Brian F Meyer, Saeed Bohlega
BACKGROUND: Fifty random genetically unstudied families (limb-girdle muscular dystrophy (LGMD)/myopathy) were screened with a gene panel incorporating 759 OMIM genes associated with neurological disorders. Average coverage of the CDS and 10 bp flanking regions of genes was 99 %. All families were referred to the Neurosciences Clinic of King Faisal Specialist Hospital and Research Centre, Saudi Arabia. Patients presented with muscle weakness affecting the pelvic and shoulder girdle. Muscle biopsy in all cases showed dystrophic or myopathic changes...
September 27, 2016: Human Genomics
https://www.readbyqxmd.com/read/27608623/micrornas-in-acute-kidney-injury
#15
REVIEW
Pei-Chun Fan, Chia-Chun Chen, Yung-Chang Chen, Yu-Sun Chang, Pao-Hsien Chu
Acute kidney injury (AKI) is an important clinical issue that is associated with significant morbidity and mortality. Despite research advances over the past decades, the complex pathophysiology of AKI is not fully understood. The regulatory mechanisms underlying post-AKI repair and fibrosis have not been clarified either. Furthermore, there is no definitively effective treatment for AKI. MicroRNAs (miRNAs) are endogenous single-stranded noncoding RNAs of 19~23 nucleotides that have been shown to be crucial to the post-transcriptional regulation of various cellular biological functions, including proliferation, differentiation, metabolism, and apoptosis...
September 8, 2016: Human Genomics
https://www.readbyqxmd.com/read/27329102/amd-and-the-alternative-complement-pathway-genetics-and-functional-implications
#16
REVIEW
Perciliz L Tan, Catherine Bowes Rickman, Nicholas Katsanis
Age-related macular degeneration (AMD) is an ocular neurodegenerative disorder and is the leading cause of legal blindness in Western societies, with a prevalence of up to 8 % over the age of 60, which continues to increase with age. AMD is characterized by the progressive breakdown of the macula (the central region of the retina), resulting in the loss of central vision including visual acuity. While its molecular etiology remains unclear, advances in genetics and genomics have illuminated the genetic architecture of the disease and have generated attractive pathomechanistic hypotheses...
June 21, 2016: Human Genomics
https://www.readbyqxmd.com/read/27108086/multiplex-snapshot-a-new-simple-and-efficient-cyp2d6-and-adrb1-genotyping-method
#17
Songtao Ben, Rhonda M Cooper-DeHoff, Hanna K Flaten, Oghenero Evero, Tracey M Ferrara, Richard A Spritz, Andrew A Monte
BACKGROUND: Reliable, inexpensive, high-throughput genotyping methods are required for clinical trials. Traditional assays require numerous enzyme digestions or are too expensive for large sample volumes. Our objective was to develop an inexpensive, efficient, and reliable assay for CYP2D6 and ADRB1 accounting for numerous polymorphisms including gene duplications. MATERIALS AND METHODS: We utilized the multiplex SNaPshot® custom genotype method to genotype CYP2D6 and ADRB1...
April 23, 2016: Human Genomics
https://www.readbyqxmd.com/read/27098205/organization-evolution-and-functions-of-the-human-and-mouse-ly6-upar-family-genes
#18
REVIEW
Chelsea L Loughner, Elspeth A Bruford, Monica S McAndrews, Emili E Delp, Sudha Swamynathan, Shivalingappa K Swamynathan
Members of the lymphocyte antigen-6 (Ly6)/urokinase-type plasminogen activator receptor (uPAR) superfamily of proteins are cysteine-rich proteins characterized by a distinct disulfide bridge pattern that creates the three-finger Ly6/uPAR (LU) domain. Although the Ly6/uPAR family proteins share a common structure, their expression patterns and functions vary. To date, 35 human and 61 mouse Ly6/uPAR family members have been identified. Based on their subcellular localization, these proteins are further classified as GPI-anchored on the cell membrane, or secreted...
April 21, 2016: Human Genomics
https://www.readbyqxmd.com/read/27044517/three-hour-analysis-of-non-invasive-foetal-sex-determination-application-of-plexor-chemistry
#19
LETTER
Adalgisa Pietropolli, Maria Vittoria Capogna, Raffaella Cascella, Chiara Germani, Valentina Bruno, Claudia Strafella, Simona Sarta, Carlo Ticconi, Giusy Marmo, Sara Gallaro, Giuliana Longo, Luigi Tonino Marsella, Antonio Novelli, Giuseppe Novelli, Emilio Piccione, Emiliano Giardina
BACKGROUND: The knowledge of the individual genetic "status" in the prenatal era is particularly relevant in the case of positive family history for genetic diseases, in advanced maternal age and in the general screening for foetal abnormalities. In this context, here, we report an innovative molecular assay which utilizes the cell-free foetal DNA (cffDNA) as a source for the early and fast detection of the foetal sex. The study involved 132 pregnant women in their first 3 months of pregnancy, who agreed to give a blood sample...
April 4, 2016: Human Genomics
https://www.readbyqxmd.com/read/26936456/the-impact-of-common-polymorphisms-in-cetp-and-abca1-genes-with-the-risk-of-coronary-artery-disease-in-saudi-arabians
#20
Cyril Cyrus, Chittibabu Vatte, Awatif Al-Nafie, Shahanas Chathoth, Rudaynah Al-Ali, Abdullah Al-Shehri, Mohammed Shakil Akhtar, Mohammed Almansori, Fahad Al-Muhanna, Brendan Keating, Amein Al-Ali
BACKGROUND: Coronary artery disease (CAD) is a leading cause of morbidity and mortality worldwide. Many genetic and environmental risk factors including atherogenic dyslipidemia contribute towards the development of CAD. Functionally relevant mutations in the dyslipidemia-related genes and enzymes involved in the reverse cholesterol transport system are associated with CAD and contribute to increased susceptibility of myocardial infarction (MI). METHOD: Blood samples from 990 angiographically confirmed Saudi CAD patients with at least one event of myocardial infarction were collected between 2012 and 2014...
March 2, 2016: Human Genomics
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