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Human Genomics

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https://www.readbyqxmd.com/read/28031051/the-status-of-her2-amplification-and-kras-mutations-in-mucinous-ovarian-carcinoma
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
https://www.readbyqxmd.com/read/26842383/a-review-of-the-new-hgnc-gene-family-resource
#16
REVIEW
Kristian A Gray, Ruth L Seal, Susan Tweedie, Mathew W Wright, Elspeth A Bruford
The HUGO Gene Nomenclature Committee (HGNC) approves unique gene symbols and names for human loci. As well as naming genomic loci, we manually curate genes into family sets based on shared characteristics such as function, homology or phenotype. Each HGNC gene family has its own dedicated gene family report on our website, www.genenames.org . We have recently redesigned these reports to support the visualisation and browsing of complex relationships between families and to provide extra curated information such as family descriptions, protein domain graphics and gene family aliases...
February 3, 2016: Human Genomics
https://www.readbyqxmd.com/read/26772741/the-clinical-trial-landscape-in-oncology-and-connectivity-of-somatic-mutational-profiles-to-targeted-therapies
#17
Sara E Patterson, Rangjiao Liu, Cara M Statz, Daniel Durkin, Anuradha Lakshminarayana, Susan M Mockus
BACKGROUND: Precision medicine in oncology relies on rapid associations between patient-specific variations and targeted therapeutic efficacy. Due to the advancement of genomic analysis, a vast literature characterizing cancer-associated molecular aberrations and relative therapeutic relevance has been published. However, data are not uniformly reported or readily available, and accessing relevant information in a clinically acceptable time-frame is a daunting proposition, hampering connections between patients and appropriate therapeutic options...
January 16, 2016: Human Genomics
https://www.readbyqxmd.com/read/26747084/genetic-studies-of-polish-migraine-patients-screening-for-causative-mutations-in-four-migraine-associated-genes
#18
Izabela Domitrz, Michalina Kosiorek, Cezary Żekanowski, Anna Kamińska
BACKGROUND AND AIM: Migraine is the most common neurological disorder, affecting approximately 12 % of the adult population worldwide, caused by both environmental and genetic factors. Three causative genes have been identified in familial hemiplegic migraine (FHM) families: CACNA1A, ATP1A2, and SCNA1A. Recently, several mutations in KCNK18 have also been found as causative factors in migraine development. The aim of our study was to identify the genetic background of migraine in the Polish population...
January 8, 2016: Human Genomics
https://www.readbyqxmd.com/read/26744305/whole-exome-sequencing-identifies-novel-candidate-genes-that-modify-chronic-obstructive-pulmonary-disease-susceptibility
#19
Shannon Bruse, Michael Moreau, Yana Bromberg, Jun-Ho Jang, Nan Wang, Hongseok Ha, Maria Picchi, Yong Lin, Raymond J Langley, Clifford Qualls, Julia Klensney-Tait, Joseph Zabner, Shuguang Leng, Jenny Mao, Steven A Belinsky, Jinchuan Xing, Toru Nyunoya
BACKGROUND: Chronic obstructive pulmonary disease (COPD) is characterized by an irreversible airflow limitation in response to inhalation of noxious stimuli, such as cigarette smoke. However, only 15-20 % smokers manifest COPD, suggesting a role for genetic predisposition. Although genome-wide association studies have identified common genetic variants that are associated with susceptibility to COPD, effect sizes of the identified variants are modest, as is the total heritability accounted for by these variants...
January 7, 2016: Human Genomics
https://www.readbyqxmd.com/read/26742487/intragraft-transcriptional-profiling-of-renal-transplant-patients-with-tubular-dysfunction-reveals-mechanisms-underlying-graft-injury-and-recovery
#20
Hátylas Azevedo, Paulo Guilherme Renesto, Rogério Chinen, Erika Naka, Ana Cristina Carvalho de Matos, Marcos Antônio Cenedeze, Carlos Alberto Moreira-Filho, Niels Olsen Saraiva Câmara, Alvaro Pacheco-Silva
BACKGROUND: Proximal tubular dysfunction (PTD) is associated with a decreased long-term graft survival in renal transplant patients and can be detected by the elevation of urinary tubular proteins. This study investigated transcriptional changes in biopsies from renal transplant patients with PTD to disclose molecular mechanisms underlying graft injury and functional recovery. METHODS: Thirty-three renal transplant patients with high urinary levels of retinol-binding protein, a biomarker of PTD, were enrolled in the study...
January 7, 2016: Human Genomics
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