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BMC Medical Genomics

Xing-Cheng Zhao, Shao-Hua Yang, Yi-Quan Yan, Xin Zhang, Lin Zhang, Bo Jiao, Shuai Jiang, Zhi-Bin Yu
BACKGROUND: Elevated blood pressure is an important risk factor for cardiovascular disease and is also an important factor in global mortality. Military pilots are at high risk of cardiovascular disease because they undergo persistent noise, high mental tension, high altitude hypoxia, high acceleration and high calorie diet. Hypertension is the leading cause of cardiovascular disease in military pilots. In this study, we want to identify key genes from peripheral blood cells of military pilots with hypertension...
July 11, 2018: BMC Medical Genomics
Rubén Cabanillas, Marta Diñeiro, Guadalupe A Cifuentes, David Castillo, Patricia C Pruneda, Rebeca Álvarez, Noelia Sánchez-Durán, Raquel Capín, Ana Plasencia, Mónica Viejo-Díaz, Noelia García-González, Inés Hernando, José L Llorente, Alfredo Repáraz-Andrade, Cristina Torreira-Banzas, Jordi Rosell, Nancy Govea, Justo Ramón Gómez-Martínez, Faustino Núñez-Batalla, José A Garrote, Ángel Mazón-Gutiérrez, María Costales, María Isidoro-García, Belén García-Berrocal, Gonzalo R Ordóñez, Juan Cadiñanos
BACKGROUND: Sensorineural hearing loss (SNHL) is the most common sensory impairment. Comprehensive next-generation sequencing (NGS) has become the standard for the etiological diagnosis of early-onset SNHL. However, accurate selection of target genomic regions (gene panel/exome/genome), analytical performance and variant interpretation remain relevant difficulties for its clinical implementation. METHODS: We developed a novel NGS panel with 199 genes associated with non-syndromic and/or syndromic SNHL...
July 9, 2018: BMC Medical Genomics
Aditya Rao, Saipradeep Vg, Thomas Joseph, Sujatha Kotte, Naveen Sivadasan, Rajgopal Srinivasan
BACKGROUND: One of the major goals of genomic medicine is the identification of causal genomic variants in a patient and their relation to the observed clinical phenotypes. Prioritizing the genomic variants by considering only the genotype information usually identifies a few hundred potential variants. Narrowing it down further to find the causal disease genes and relating them to the observed clinical phenotypes remains a significant challenge, especially for rare diseases. METHODS: We propose a phenotype-driven gene prioritization approach using heterogeneous networks in the context of rare diseases...
July 6, 2018: BMC Medical Genomics
Ting Yu, Lei Xia, Dan Bi, Yangong Wang, Qing Shang, Dengna Zhu, Juan Song, Yong Wang, Xiaoyang Wang, Changlian Zhu, Qinghe Xing
BACKGROUND: Cerebral palsy (CP) is the leading cause of motor disability in children; however, its pathogenesis is unknown in most cases. Growing evidence suggests that Nitric oxide synthase 1 (NOS1) is involved in neural development and neurologic diseases. The purpose of this study was to determine whether genetic variants of NOS1 contribute to CP susceptibility in a Han Chinese population. METHODS: A case-control study involving 652 CP patients and 636 healthy controls was conducted...
June 25, 2018: BMC Medical Genomics
Ana Caroline C Sá, Amy Webb, Yan Gong, Caitrin W McDonough, Mohamed H Shahin, Somnath Datta, Taimour Y Langaee, Stephen T Turner, Amber L Beitelshees, Arlene B Chapman, Eric Boerwinkle, John G Gums, Steven E Scherer, Rhonda M Cooper-DeHoff, Wolfgang Sadee, Julie A Johnson
BACKGROUND: Recently, 34 genes had been associated with differential expression relative to blood pressure (BP)/ hypertension (HTN). We hypothesize that some of the genes associated with BP/HTN are also associated with BP response to antihypertensive treatment with thiazide diuretics. METHODS: We assessed these 34 genes for association with differential expression to BP response to thiazide diuretics with RNA sequencing in whole blood samples from 150 hypertensive participants from the Pharmacogenomic Evaluation of Antihypertensive Responses (PEAR) and PEAR-2 studies...
June 20, 2018: BMC Medical Genomics
Hyung Jun Woo, Jaques Reifman
BACKGROUND: Common metabolic diseases, including type 2 diabetes, coronary artery disease, and hypertension, arise from disruptions of the body's metabolic homeostasis, with relatively strong contributions from genetic risk factors and substantial comorbidity with obesity. Although genome-wide association studies have revealed many genomic loci robustly associated with these diseases, biological interpretation of such association is challenging because of the difficulty in mapping single-nucleotide polymorphisms (SNPs) onto the underlying causal genes and pathways...
June 20, 2018: BMC Medical Genomics
Aliz R Rao, Stanley F Nelson
BACKGROUND: With the expanding use of next-gen sequencing (NGS) to diagnose the thousands of rare Mendelian genetic diseases, it is critical to be able to interpret individual DNA variation. To calculate the significance of finding a rare protein-altering variant in a given gene, one must know the frequency of seeing a variant in the general population that is at least as damaging as the variant in question. METHODS: We developed a general method to better interpret the likelihood that a rare variant is disease causing if observed in a given gene or genic region mapping to a described protein domain, using genome-wide information from a large control sample...
June 13, 2018: BMC Medical Genomics
Lingyan Wang, Xiaoling Yu, Chao Wu, Teng Zhu, Wenming Wang, Xiaofeng Zheng, Hongzhong Jin
BACKGROUND: Generalized pustular psoriasis (GPP) is a rare, episodic, potentially life-threatening inflammatory disease. However, the pathogenesis of GPP, and universally accepted therapies for treating it, remain undefined. METHODS: To better understand the disease mechanism of GPP, we performed a transcriptome analysis to profile the gene expression of peripheral blood mononuclear cells (PBMCs) from patients enrolled at the time of diagnosis and receiving follow-up treatment for up to 6 months...
June 5, 2018: BMC Medical Genomics
Lili Ding, Dan Li, Michael Wathen, Mekibib Altaye, Tesfaye B Mersha
BACKGROUND: Childhood asthma is a syndrome composed of heterogeneous phenotypes; furthermore, intrinsic biologic variation among racial/ethnic populations suggests possible genetic ancestry variation in childhood asthma. The objective of the study is to identify clinically homogeneous asthma subphenotypes in a diverse sample of asthmatic children and to assess subphenotype-specific genetic ancestry in African-American asthmatic children. METHODS: A total of 1211 asthmatic children including 813 in the Childhood Asthma Management Program and 398 in the Childhood Asthma Research and Education program were studied...
May 31, 2018: BMC Medical Genomics
Elysa Jill Marco, Anne Brandes Aitken, Vishnu Prakas Nair, Gilberto da Gente, Molly Rae Gerdes, Leyla Bologlu, Sean Thomas, Elliott H Sherr
BACKGROUND: In children with sensory processing dysfunction (SPD), who do not meet criteria for autism spectrum disorder (ASD) or intellectual disability, the contribution of de novo pathogenic mutation in neurodevelopmental genes is unknown and in need of investigation. We hypothesize that children with SPD may have pathogenic variants in genes that have been identified as causing other neurodevelopmental disorders including ASD. This genetic information may provide important insight into the etiology of sensory processing dysfunction and guide clinical evaluation and care...
May 25, 2018: BMC Medical Genomics
Yanjie Fan, Yanming Wu, Lili Wang, Yu Wang, Zhuwen Gong, Wenjuan Qiu, Jingmin Wang, Huiwen Zhang, Xing Ji, Jun Ye, Lianshu Han, Xingming Jin, Yongnian Shen, Fei Li, Bing Xiao, Lili Liang, Xia Zhang, Xiaomin Liu, Xuefan Gu, Yongguo Yu
BACKGROUND: Developmental delay (DD) and intellectual disability (ID) are frequently associated with a broad spectrum of additional phenotypes. Chromosomal microarray analysis (CMA) has been recommended as a first-tier test for DD/ID in general, whereas the diagnostic yield differs significantly among DD/ID patients with different comorbid conditions. METHODS: To investigate the genotype-phenotype correlation, we examined the characteristics of identified pathogenic copy number variations (pCNVs) and compared the diagnostic yields among patient subgroups with different co-occurring conditions...
May 24, 2018: BMC Medical Genomics
Kira Groen, Vicki E Maltby, Rodney A Lea, Katherine A Sanders, J Lynn Fink, Rodney J Scott, Lotti Tajouri, Jeannette Lechner-Scott
BACKGROUND: There is a paucity of knowledge concerning erythrocytes in the aetiology of Multiple Sclerosis (MS) despite their potential to contribute to disease through impaired antioxidant capacity and altered haemorheological features. Several studies have identified an abundance of erythrocyte miRNAs and variable profiles associated with disease states, such as sickle cell disease and malaria. The aim of this study was to compare the erythrocyte miRNA profile of relapsing-remitting MS (RRMS) patients to healthy sex- and age-matched controls...
May 21, 2018: BMC Medical Genomics
Jie-Qiong Li, Xiang-Zhen Yuan, Hai-Yan Li, Xi-Peng Cao, Jin-Tai Yu, Lan Tan, Wei-An Chen
BACKGROUND: Plasma neurofilament light (NFL) is a promising biomarker for Alzheimer disease (AD), which increases in the early stage of AD and is associated with the progression of AD. We performed a genome-wide association study (GWAS) of plasma NFL in Alzheimer's Disease Neuroimaging Initiative 1 (ADNI-1) cohort to identify novel variants associated with AD. METHODS: This study included 179 cognitively healthy controls (HC), 176 patients with mild cognitive impairment (MCI), and 172 patients with AD...
May 10, 2018: BMC Medical Genomics
Ji Hyae Lim, You Jung Han, Hyun Jin Kim, Moon Young Kim, So Yeon Park, Youl-Hee Cho, Hyun Mee Ryu
BACKGROUND: The most frequent chromosomal aneuploidy is trisomy 21 (T21) that is caused by an extra copy of chromosome 21. The imbalance of whole genome including genes and microRNAs contributes to the various phenotypes of T21. However, the integrative association between genes and microRNAs in the T21 placenta has yet to be determined. METHODS: We analyzed the expressions of genes and microRNAs in the whole genomes of chorionic villi cells from normal and T21 human fetal placentas based on our prior studies...
May 9, 2018: BMC Medical Genomics
Julia Wynn, Katie Lewis, Laura M Amendola, Barbara A Bernhardt, Sawona Biswas, Manasi Joshi, Carmit McMullen, Sarah Scollon
BACKGROUND: Current medical practice includes the application of genomic sequencing (GS) in clinical and research settings. Despite expanded use of this technology, the process of disclosure of genomic results to patients and research participants has not been thoroughly examined and there are no established best practices. METHODS: We conducted semi-structured interviews with 21 genetic and non-genetic clinicians returning results of GS as part of the NIH funded Clinical Sequencing Exploratory Research (CSER) Consortium projects...
May 8, 2018: BMC Medical Genomics
Jiaxuan Liu, Wei Zhao, Erin B Ware, Stephen T Turner, Thomas H Mosley, Jennifer A Smith
BACKGROUND: Genetic variations in apolipoprotein E (APOE) and proximal genes (PVRL2, TOMM40, and APOC1) are associated with cognitive function and dementia, particularly Alzheimer's disease. Epigenetic mechanisms such as DNA methylation play a central role in the regulation of gene expression. Recent studies have found evidence that DNA methylation may contribute to the pathogenesis of dementia, but its association with cognitive function in populations without dementia remains unclear...
May 8, 2018: BMC Medical Genomics
C S Paththinige, N D Sirisena, U G I U Kariyawasam, R C Ediriweera, P Kruszka, M Muenke, V H W Dissanayake
BACKGROUND: Parental balanced reciprocal translocations can result in partial aneuploidies in the offspring due to unbalanced meiotic segregation during gametogenesis. Herein, we report the phenotypic and molecular cytogenetic characterization of a 2 years and 4 months old female child with partial trisomy 7q22 → qter. This is the first such reported case resulting from a parental balanced translocation involving the long arms of chromosomes 7 and 14. The phenotype of the proband was compared with that of previously reported cases of trisomy 7q21 → qter or 7q22 → qter resulting from parental balanced translocations...
May 8, 2018: BMC Medical Genomics
Mitsuko Furuya, Hironori Kobayashi, Masaya Baba, Takaaki Ito, Reiko Tanaka, Yukio Nakatani
BACKGROUND: Birt-Hogg-Dubé syndrome (BHD) is an autosomal dominant disorder caused by germline mutations in the folliculin gene (FLCN). Nearly 150 pathogenic mutations have been identified in FLCN. The most frequent pattern is a frameshift mutation within a coding exon. In addition, splice-site mutations have been reported, and previous studies have confirmed exon skipping in several cases. However, it is poorly understood whether there are any splice-site mutations that cause translation of intron regions in FLCN...
May 2, 2018: BMC Medical Genomics
Ute Scheller, Kathrin Pfisterer, Steffen Uebe, Arif B Ekici, André Reis, Rami Jamra, Fulvia Ferrazzi
BACKGROUND: Decapping of mRNA is an important step in the regulation of mRNA turnover and therefore of gene expression, which is a key process controlling development and homeostasis of all organisms. It has been shown that EDC3 plays a role in mRNA decapping, however its function is not well understood. Previously, we have associated a homozygous variant in EDC3 with autosomal recessive intellectual disability. Here, we investigate the functional role of EDC3. METHODS: We performed transcriptome analyses in patients' samples...
April 23, 2018: BMC Medical Genomics
Jing Guo, Hao Chen, Peng Yang, Yew Ti Lee, Min Wu, Teresa M Przytycka, Chee Keong Kwoh, Jie Zheng
BACKGROUND: Meiotic recombination happens during the process of meiosis when chromosomes inherited from two parents exchange genetic materials to generate chromosomes in the gamete cells. The recombination events tend to occur in narrow genomic regions called recombination hotspots. Its dysregulation could lead to serious human diseases such as birth defects. Although the regulatory mechanism of recombination events is still unclear, DNA sequence polymorphisms have been found to play crucial roles in the regulation of recombination hotspots...
April 20, 2018: BMC Medical Genomics
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