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Human Genomics

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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
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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/27663310/major-influence-of-repetitive-elements-on-disease-associated-copy-number-variants-cnvs
#11
Ana R Cardoso, Manuela Oliveira, Antonio Amorim, Luisa Azevedo
Copy number variants (CNVs) are important contributors to the human pathogenic genetic diversity as demonstrated by a number of cases reported in the literature. The high homology between repetitive elements may guide genomic stability which will give rise to CNVs either by non-allelic homologous recombination (NAHR) or non-homologous end joining (NHEJ). Here, we present a short guide based on previously documented cases of disease-associated CNVs in order to provide a general view on the impact of repeated elements on the stability of the genomic sequence and consequently in the origin of the human pathogenic variome...
2016: Human Genomics
https://www.readbyqxmd.com/read/27663196/variation-of-global-dna-methylation-levels-with-age-and-in-autistic-children
#12
Shui-Ying Tsang, Tanveer Ahmad, Flora W K Mat, Cunyou Zhao, Shifu Xiao, Kun Xia, Hong Xue
BACKGROUND: The change in epigenetic signatures, in particular DNA methylation, has been proposed as risk markers for various age-related diseases. However, the course of variation in methylation levels with age, the difference in methylation between genders, and methylation-disease association at the whole genome level is unclear. In the present study, genome-wide methylation levels in DNA extracted from peripheral blood for 2116 healthy Chinese in the 2-97 age range and 280 autistic trios were examined using the fluorescence polarization-based genome-wide DNA methylation quantification method developed by us...
2016: Human Genomics
https://www.readbyqxmd.com/read/27531006/transcriptome-sequencing-of-gingival-biopsies-from-chronic-periodontitis-patients-reveals-novel-gene-expression-and-splicing-patterns
#13
Yong-Gun Kim, Minjung Kim, Ji Hyun Kang, Hyo Jeong Kim, Jin-Woo Park, Jae-Mok Lee, Jo-Young Suh, Jae-Young Kim, Jae-Hyung Lee, Youngkyun Lee
BACKGROUND: Periodontitis is the most common chronic inflammatory disease caused by complex interaction between the microbial biofilm and host immune responses. In the present study, high-throughput RNA sequencing was utilized to systemically and precisely identify gene expression profiles and alternative splicing. METHODS: The pooled RNAs of 10 gingival tissues from both healthy and periodontitis patients were analyzed by deep sequencing followed by computational annotation and quantification of mRNA structures...
2016: Human Genomics
https://www.readbyqxmd.com/read/27519266/mutation-analysis-of-the-col1a1-and-col1a2-genes-in-vietnamese-patients-with-osteogenesis-imperfecta
#14
Binh Ho Duy, Lidiia Zhytnik, Katre Maasalu, Ivo Kändla, Ele Prans, Ene Reimann, Aare Märtson, Sulev Kõks
BACKGROUND: The genetics of osteogenesis imperfecta (OI) have not been studied in a Vietnamese population before. We performed mutational analysis of the COL1A1 and COL1A2 genes in 91 unrelated OI patients of Vietnamese origin. We then systematically characterized the mutation profiles of these two genes which are most commonly related to OI. METHODS: Genomic DNA was extracted from EDTA-preserved blood according to standard high-salt extraction methods. Sequence analysis and pathogenic variant identification was performed with Mutation Surveyor DNA variant analysis software...
2016: Human Genomics
https://www.readbyqxmd.com/read/27461468/the-up-regulation-of-myb-may-help-mediate-egcg-inhibition-effect-on-mouse-lung-adenocarcinoma
#15
Hong Zhou, Joseph Manthey, Ekaterina Lioutikova, William Yang, Kenji Yoshigoe, Mary Qu Yang, Hong Wang
BACKGROUND: Green tea polyphenol epigallocatechin-3-gallate (EGCG) has been demonstrated to inhibit cancer in experimental studies through its antioxidant activity and modulations on cellular functions by binding specific proteins. By means of computational analysis and functional genomic approaches, we previously identified a set of protein coding genes and microRNAs whose expressions were significantly modulated in response to the EGCG treatment in tobacco carcinogen-induced lung adenocarcinoma in A/J mice...
2016: Human Genomics
https://www.readbyqxmd.com/read/27461342/hypomethylation-coordinates-antagonistically-with-hypermethylation-in-cancer-development-a-case-study-of-leukemia
#16
Garima Kushwaha, Mikhail Dozmorov, Jonathan D Wren, Jing Qiu, Huidong Shi, Dong Xu
BACKGROUND: Methylation changes are frequent in cancers, but understanding how hyper- and hypomethylated region changes coordinate, associate with genomic features, and affect gene expression is needed to better understand their biological significance. The functional significance of hypermethylation is well studied, but that of hypomethylation remains limited. Here, with paired expression and methylation samples gathered from a patient/control cohort, we attempt to better characterize the gene expression and methylation changes that take place in cancer from B cell chronic lymphocyte leukemia (B-CLL) samples...
2016: Human Genomics
https://www.readbyqxmd.com/read/27461247/the-clinical-significance-of-snail-protein-expression-in-gastric-cancer-a-meta-analysis
#17
Xiaoya Chen, Jinjun Li, Ling Hu, William Yang, Lili Lu, Hongyan Jin, Zexiong Wei, Jack Y Yang, Hamid R Arabnia, Jun S Liu, Mary Qu Yang, Youping Deng
BACKGROUND: Snail is a typical transcription factor that could induce epithelial-mesenchymal transition (EMT) and cancer progression. There are some related reports about the clinical significance of snail protein expression in gastric cancer. However, the published results were not completely consistent. This study was aimed to investigate snail expression and clinical significance in gastric cancer. RESULTS: A systematic review of PubMed, CNKI, Weipu, and Wanfang database before March 2015 was conducted...
2016: Human Genomics
https://www.readbyqxmd.com/read/27461193/identification-of-protein-complexes-from-multi-relationship-protein-interaction-networks
#18
Xueyong Li, Jianxin Wang, Bihai Zhao, Fang-Xiang Wu, Yi Pan
BACKGROUND: Protein complexes play an important role in biological processes. Recent developments in experiments have resulted in the publication of many high-quality, large-scale protein-protein interaction (PPI) datasets, which provide abundant data for computational approaches to the prediction of protein complexes. However, the precision of protein complex prediction still needs to be improved due to the incompletion and noise in PPI networks. RESULTS: There exist complex and diverse relationships among proteins after integrating multiple sources of biological information...
2016: Human Genomics
https://www.readbyqxmd.com/read/27461106/a-comparative-study-of-k-spectrum-based-error-correction-methods-for-next-generation-sequencing-data-analysis
#19
Isaac Akogwu, Nan Wang, Chaoyang Zhang, Ping Gong
BACKGROUND: Innumerable opportunities for new genomic research have been stimulated by advancement in high-throughput next-generation sequencing (NGS). However, the pitfall of NGS data abundance is the complication of distinction between true biological variants and sequence error alterations during downstream analysis. Many error correction methods have been developed to correct erroneous NGS reads before further analysis, but independent evaluation of the impact of such dataset features as read length, genome size, and coverage depth on their performance is lacking...
2016: Human Genomics
https://www.readbyqxmd.com/read/27461004/association-of-six-cpg-snps-in-the-inflammation-related-genes-with-coronary-heart-disease
#20
Xiaomin Chen, Xiaoying Chen, Yan Xu, William Yang, Nan Wu, Huadan Ye, Jack Y Yang, Qingxiao Hong, Yanfei Xin, Mary Qu Yang, Youping Deng, Shiwei Duan
BACKGROUND: Chronic inflammation has been widely considered to be the major risk factor of coronary heart disease (CHD). The goal of our study was to explore the possible association with CHD for inflammation-related single nucleotide polymorphisms (SNPs) involved in cytosine-phosphate-guanine (CpG) dinucleotides. A total of 784 CHD patients and 739 non-CHD controls were recruited from Zhejiang Province, China. Using the Sequenom MassARRAY platform, we measured the genotypes of six inflammation-related CpG-SNPs, including IL1B rs16944, IL1R2 rs2071008, PLA2G7 rs9395208, FAM5C rs12732361, CD40 rs1800686, and CD36 rs2065666)...
2016: Human Genomics
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