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BMC Medical Genomics

Tonje G Lien, Ørnulf Borgan, Sjur Reppe, Kaare Gautvik, Ingrid Kristine Glad
BACKGROUND: Using high-dimensional penalized regression we studied genome-wide DNA-methylation in bone biopsies of 80 postmenopausal women in relation to their bone mineral density (BMD). The women showed BMD varying from severely osteoporotic to normal. Global gene expression data from the same individuals was available, and since DNA-methylation often affects gene expression, the overall aim of this paper was to include both of these omics data sets into an integrated analysis. METHODS: The classical penalized regression uses one penalty, but we incorporated individual penalties for each of the DNA-methylation sites...
March 7, 2018: BMC Medical Genomics
Alain Calender, Pierre Antoine Rollat Farnier, Adrien Buisson, Stéphane Pinson, Abderrazzaq Bentaher, Serge Lebecque, Harriet Corvol, Rola Abou Taam, Véronique Houdouin, Claire Bardel, Pascal Roy, Gilles Devouassoux, Vincent Cottin, Pascal Seve, Jean-François Bernaudin, Clarice X Lim, Thomas Weichhart, Dominique Valeyre, Yves Pacheco, Annick Clement, Nadia Nathan
BACKGROUND: Sarcoidosis (OMIM 181000) is a multi-systemic granulomatous disorder of unknown origin. Despite multiple genome-wide association (GWAS) studies, no major pathogenic pathways have been identified to date. To find out relevant sarcoidosis predisposing genes, we searched for de novo and recessive mutations in 3 young probands with sarcoidosis and their healthy parents using a whole-exome sequencing (WES) methodology. METHODS: From the SARCFAM project based on a national network collecting familial cases of sarcoidosis, we selected three families (trios) in which a child, despite healthy parents, develop the disease before age 15 yr...
March 6, 2018: BMC Medical Genomics
Claudia Tamar Silva, Irina V Zorkoltseva, Maartje N Niemeijer, Marten E van den Berg, Najaf Amin, Ayşe Demirkan, Elisa van Leeuwen, Adriana I Iglesias, Laura B Piñeros-Hernández, Carlos M Restrepo, Jan A Kors, Anatoly V Kirichenko, Rob Willemsen, Ben A Oostra, Bruno H Stricker, André G Uitterlinden, Tatiana I Axenovich, Cornelia M van Duijn, Aaron Isaacs
BACKGROUND: Electrocardiographic measures of left ventricular hypertrophy (LVH) are used as predictors of cardiovascular risk. We combined linkage and association analyses to discover novel rare genetic variants involved in three such measures and two principal components derived from them. METHODS: The study was conducted among participants from the Erasmus Rucphen Family Study (ERF), a Dutch family-based sample from the southwestern Netherlands. Variance components linkage analyses were performed using Merlin...
March 5, 2018: BMC Medical Genomics
Jose L Gomez, Maria P Diaz, Gustavo Nino, Clemente J Britto
BACKGROUND: Asthma exacerbations are an important cause of morbidity in asthma. Respiratory infections are often involved in asthma exacerbations in both children and adults. Some individuals with asthma have increased susceptibility to viral infections and as a result increased rates of asthma exacerbations. We sought to identify a transcriptomic signature in the blood associated with asthma exacerbations triggered by respiratory infections (AETRI) and determine its association with increased risk for asthma exacerbations...
February 27, 2018: BMC Medical Genomics
Na Zhang, Yun-Juan Bao, Amy Hin-Yan Tong, Scott Zuyderduyn, Gary D Bader, J S Malik Peiris, Si Lok, Suki Man-Yan Lee
BACKGROUND: Avian influenza A H5N1 virus can cause lethal disease in humans. The virus can trigger severe pneumonia and lead to acute respiratory distress syndrome. Data from clinical, in vitro and in vivo suggest that virus-induced cytokine dysregulation could be a contributory factor to the pathogenesis of human H5N1 disease. However, the precise mechanism of H5N1 infection eliciting the unique host response are still not well understood. METHODS: To obtain a better understanding of the molecular events at the earliest time points, we used RNA-Seq to quantify and compare the host mRNA and miRNA transcriptomes induced by the highly pathogenic influenza A H5N1 (A/Vietnam/3212/04) or low virulent H1N1 (A/Hong Kong/54/98) viruses in human monocyte-derived macrophages at 1-, 3-, and 6-h post infection...
February 23, 2018: BMC Medical Genomics
Ulyana Boyarskikh, Sergey Pintus, Nikita Mandrik, Daria Stelmashenko, Ilya Kiselev, Ivan Evshin, Ruslan Sharipov, Philip Stegmaier, Fedor Kolpakov, Maxim Filipenko, Alexander Kel
BACKGROUND: Small molecule Nutlin-3 reactivates p53 in cancer cells by interacting with the complex between p53 and its repressor Mdm-2 and causing an increase in cancer cell apoptosis. Therefore, Nutlin-3 has potent anticancer properties. Clinical and experimental studies of Nutlin-3 showed that some cancer cells may lose sensitivity to this compound. Here we analyze possible mechanisms for insensitivity of cancer cells to Nutlin-3. METHODS: We applied upstream analysis approach implemented in geneXplain platform ( genexplain...
February 13, 2018: BMC Medical Genomics
Vladimir V Galatenko, Diana V Maltseva, Alexey V Galatenko, Sergey Rodin, Alexander G Tonevitsky
BACKGROUND: Laminins are a major family of extracellular matrix proteins and the main component of basement membranes. Laminins are involved in many if not all stages of cancer progression, and expression of laminin genes has prognostic value in various types of cancer, including colorectal. Only single laminin genes or components of a single laminin trimer with significant differential expression have been regarded as potential biomarkers to date. RESULTS: Here we compared prognostic power of classifiers constructed from sets of laminin genes with that of any single laminin gene...
February 13, 2018: BMC Medical Genomics
Olga V Saik, Pavel S Demenkov, Timofey V Ivanisenko, Elena Yu Bragina, Maxim B Freidin, Irina A Goncharova, Victor E Dosenko, Olga I Zolotareva, Ralf Hofestaedt, Inna N Lavrik, Evgeny I Rogaev, Vladimir A Ivanisenko
BACKGROUND: Hypertension and bronchial asthma are a major issue for people's health. As of 2014, approximately one billion adults, or ~ 22% of the world population, have had hypertension. As of 2011, 235-330 million people globally have been affected by asthma and approximately 250,000-345,000 people have died each year from the disease. The development of the effective treatment therapies against these diseases is complicated by their comorbidity features. This is often a major problem in diagnosis and their treatment...
February 13, 2018: BMC Medical Genomics
Maxim Ivanov, Alina Matsvay, Olga Glazova, Stanislav Krasovskiy, Mariya Usacheva, Elena Amelina, Aleksandr Chernyak, Mikhail Ivanov, Sergey Musienko, Timofey Prodanov, Sergey Kovalenko, Ancha Baranova, Kamil Khafizov
BACKGROUND: Cystic fibrosis (CF) is one of the most common life-threatening genetic disorders. Around 2000 variants in the CFTR gene have been identified, with some proportion known to be pathogenic and 300 disease-causing mutations have been characterized in detail by CFTR2 database, which complicates its analysis with conventional methods. METHODS: We conducted next-generation sequencing (NGS) in a cohort of 89 adult patients negative for p.Phe508del homozygosity...
February 13, 2018: BMC Medical Genomics
Abeer Fadda, Mohammed El Anbari, Andrey Ptitsyn
BACKGROUND: Oscillations of different origin, period and amplitude play an important role in the regulation of cellular processes. Most widely studied is the circadian or approximately daily variation in gene expression activity. Timing of gene expression is controlled by internal molecular clock keeping steady periodic expression. In this study, we shift attention towards a broad range of periodically expressed genes involved in multiple cellular functions which may or may not be under direct control of the intrinsic circadian clock...
February 13, 2018: BMC Medical Genomics
Yu-Feng Huang, Yen-Ju Chen, Tan-Chi Fan, Nai-Chuan Chang, Yi-Jie Chen, Mohit K Midha, Tzu-Han Chen, Hsiao-Hsiang Yang, Yu-Tai Wang, Alice L Yu, Kuo-Ping Chiu
BACKGROUND: Cell-free circulating DNA (cfDNA) is becoming a useful biopsy for noninvasive diagnosis of diseases. Microbial sequences in plasma cfDNA may provide important information to improve prognosis and treatment. We have developed a stringent method to identify microbial species via microbial cfDNA in the blood plasma of early-onset breast cancer (EOBC) patients and healthy females. Empirically, microbe-originated sequence reads were identified by mapping non-human PE reads in cfDNA libraries to microbial databases...
February 13, 2018: BMC Medical Genomics
Anastasiya V Snezhkina, Elena N Lukyanova, Dmitry V Kalinin, Anatoly V Pokrovsky, Alexey A Dmitriev, Nadezhda V Koroban, Elena A Pudova, Maria S Fedorova, Nadezhda N Volchenko, Oleg A Stepanov, Ekaterina A Zhevelyuk, Sergey L Kharitonov, Anastasiya V Lipatova, Ivan S Abramov, Alexander V Golovyuk, Yegor E Yegorov, Khava S Vishnyakova, Alexey A Moskalev, George S Krasnov, Nataliya V Melnikova, Dmitry S Shcherbo, Marina V Kiseleva, Andrey D Kaprin, Boris Y Alekseev, Andrew R Zaretsky, Anna V Kudryavtseva
BACKGROUND: Carotid body tumor (CBT) is a form of head and neck paragangliomas (HNPGLs) arising at the bifurcation of carotid arteries. Paragangliomas are commonly associated with germline and somatic mutations involving at least one of more than thirty causative genes. However, the specific functionality of a number of these genes involved in the formation of paragangliomas has not yet been fully investigated. METHODS: Exome library preparation was carried out using Nextera® Rapid Capture Exome Kit (Illumina, USA)...
February 13, 2018: BMC Medical Genomics
Yuriy L Orlov, Julio R Fernandez-Masso, Ming Chen, Ancha V Baranova
No abstract text is available yet for this article.
February 13, 2018: BMC Medical Genomics
Andrey V Marakhonov, Fedor A Konovalov, Amin Kh Makaov, Tatyana A Vasilyeva, Vitaly V Kadyshev, Varvara A Galkina, Elena L Dadali, Sergey I Kutsev, Rena A Zinchenko
BACKGROUND: Primary microcephaly represents an example of clinically and genetically heterogeneous condition. Here we describe a case of primary microcephaly from the Karachay-Cherkess Republic, which was initially diagnosed with Seckel syndrome. CASE PRESENTATION: Clinical exome sequencing of the proband revealed a novel homozygous single nucleotide deletion in ASPM gene, c.1386delC, resulting in preterm termination codon. Population screening reveals allele frequency to be less than 0...
February 13, 2018: BMC Medical Genomics
Aida Catic, Lejla Gurbeta, Amina Kurtovic-Kozaric, Senad Mehmedbasic, Almir Badnjevic
BACKGROUND: The usage of Artificial Neural Networks (ANNs) for genome-enabled classifications and establishing genome-phenotype correlations have been investigated more extensively over the past few years. The reason for this is that ANNs are good approximates of complex functions, so classification can be performed without the need for explicitly defined input-output model. This engineering tool can be applied for optimization of existing methods for disease/syndrome classification. Cytogenetic and molecular analyses are the most frequent tests used in prenatal diagnostic for the early detection of Turner, Klinefelter, Patau, Edwards and Down syndrome...
February 13, 2018: BMC Medical Genomics
Vu T Dung Ha, Julie Frizzo-Barker, Peter Chow-White
BACKGROUND: This article investigates the genomic knowledge of oncology care physicians in the adoption of clinical genomics. We apply Rogers' knowledge framework from his diffusion of innovation theory to identify three types of knowledge in the process of translation and adoption: awareness, how-to, and principles knowledge. The objectives of this systematic review are to: (1) examine the level of knowledge among physicians in clinical cancer genomics, and (2) identify potential interventions or strategies for development of genomic education for oncology practice...
February 13, 2018: BMC Medical Genomics
Cuong C Dang, Antonio Peón, Pedro J Ballester
BACKGROUND: Oncology drugs are only effective in a small proportion of cancer patients. Our current ability to identify these responsive patients before treatment is still poor in most cases. Thus, there is a pressing need to discover response markers for marketed and research oncology drugs. Screening these drugs against a large panel of cancer cell lines has led to the discovery of new genomic markers of in vitro drug response. However, while the identification of such markers among thousands of candidate drug-gene associations in the data is error-prone, an appraisal of the effectiveness of such detection task is currently lacking...
February 6, 2018: BMC Medical Genomics
Qian Zeng, Xiaoping Chen, Chaoxue Ning, Qiao Zhu, Yao Yao, Yali Zhao, Fuxin Luan
BACKGROUND: Human aging is a hot topic in biology, and it has been associated with DNA methylation changes at specific genomic sites. We aimed to study the changes of DNA methylation at a single-CpG-site resolution using peripheral blood samples from centenarians. METHODS: Using Illumina 450 K Methylation BeadChip microarray assays, we carried out a pool-based, epigenome-wide investigation of DNA methylation of blood samples from 12 centenarians and 12 healthy controls...
February 2, 2018: BMC Medical Genomics
John Hoon Rim, Se Hee Kim, In Sik Hwang, Soon Sung Kwon, Jieun Kim, Hyun Woo Kim, Min Jung Cho, Ara Ko, Song Ee Youn, Jihun Kim, Young Mock Lee, Hee Jung Chung, Joon Soo Lee, Heung Dong Kim, Jong Rak Choi, Seung-Tae Lee, Hoon-Chul Kang
BACKGROUND: We intended to evaluate diagnostic utility of a targeted gene sequencing by using next generation sequencing (NGS) panel in patients with intractable early-onset epilepsy (EOE) and find the efficient analytical step for increasing the diagnosis rate. METHODS: We assessed 74 patients with EOE whose seizures started before 3 years of age using a customized NGS panel that included 172 genes. Single nucleotide variants (SNVs) and exonic and chromosomal copy number variations (CNVs) were intensively examined with our customized pipeline and crosschecked with commercial or pre-built software...
February 1, 2018: BMC Medical Genomics
Michael D Linderman, Saskia C Sanderson, Ali Bashir, George A Diaz, Andrew Kasarskis, Randi Zinberg, Milind Mahajan, Sabrina A Suckiel, Micol Zweig, Eric E Schadt
BACKGROUND: To address the need for more effective genomics training, beginning in 2012 the Icahn School of Medicine at Mount Sinai has offered a unique laboratory-style graduate genomics course, "Practical Analysis of Your Personal Genome" (PAPG), in which students optionally sequence and analyze their own whole genome. We hypothesized that incorporating personal genome sequencing (PGS) into the course pedagogy could improve educational outcomes by increasing student motivation and engagement...
January 30, 2018: BMC Medical Genomics
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