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Human Genomics

Xiaowei Fan, Lifeng Ma, Zhiying Zhang, Yi Li, Meng Hao, Zhipeng Zhao, Yiduo Zhao, Fang Liu, Lijun Liu, Xingguang Luo, Peng Cai, Yansong Li, Longli Kang
BACKGROUND: High-altitude polycythemia (HAPC) is a chronic high-altitude disease that can lead to an increase in the production of red blood cells in the people who live in the plateau, a hypoxia environment, for a long time. The most frequent symptoms of HAPC include headache, dizziness, breathlessness, sleep disorders, and dilation of veins. Although chronic hypoxia is the main cause of HAPC, the fundamental pathophysiologic process and related molecular mechanisms responsible for its development remain largely unclear yet...
July 27, 2018: Human Genomics
Isabelle Cusin, Daniel Teixeira, Monique Zahn-Zabal, Valentine Rech de Laval, Anne Gleizes, Valeria Viassolo, Pierre O Chappuis, Pierre Hutter, Amos Bairoch, Pascale Gaudet
BACKGROUND: Germline pathogenic variants in the breast cancer type 1 susceptibility gene BRCA1 are associated with a 60% lifetime risk for breast and ovarian cancer. This overall risk estimate is for all BRCA1 variants; obviously, not all variants confer the same risk of developing a disease. In cancer patients, loss of BRCA1 function in tumor tissue has been associated with an increased sensitivity to platinum agents and to poly-(ADP-ribose) polymerase (PARP) inhibitors. For clinical management of both at-risk individuals and cancer patients, it would be important that each identified genetic variant be associated with clinical significance...
July 11, 2018: Human Genomics
Yabin Chen, Li Huang, Xiaodong Jiao, Sheikh Riazuddin, S Amer Riazuddin, J Fielding Hetmancik
BACKGROUND AND PURPOSE: Retinitis pigmentosa is an important cause of severe visual dysfunction. This study reports a novel splicing mutation in the lecithin retinol acyltransferase (LRAT) gene associated with early onset retinitis pigmentosa and characterizes the effects of this mutation on mRNA splicing and structure. METHODS: Genome-wide linkage analysis followed by dideoxy sequencing of the linked candidate gene LRAT was performed in a consanguineous Pakistani family with autosomal recessive retinitis pigmentosa...
July 4, 2018: Human Genomics
Jakub Piotr Fichna, Anna Macias, Marcin Piechota, Michał Korostyński, Anna Potulska-Chromik, Maria Jolanta Redowicz, Cezary Zekanowski
BACKGROUND: Limb girdle muscular dystrophies (LGMD) are a group of heterogeneous hereditary myopathies with similar clinical symptoms. Disease onset and progression are highly variable, with an elusive genetic background, and around 50% cases lacking molecular diagnosis. METHODS: Whole exome sequencing (WES) was performed in 73 patients with clinically diagnosed LGMD. A filtering strategy aimed at identification of variants related to the disease included integrative analysis of WES data and human phenotype ontology (HPO) terms, analysis of genes expressed in muscle, analysis of the disease-associated interactome and copy number variants analysis...
July 3, 2018: Human Genomics
Sankar Subramanian
Previous studies showed that the magnitude of selection pressure in constitutive exons is higher than that in alternatively spliced exons. The intensity of selection was also shown to be depended on the inclusion level of exons: the number of transcripts that include an exon. Here, we examined how the difference in selection pressure influences the patterns of clinical variants in human exons. Our analysis revealed a positive relationship between exon inclusion level and the abundance of pathogenic variants...
June 28, 2018: Human Genomics
Niv Sabath, Anna Vilborg, Joan A Steitz, Reut Shalgi
Naturally occurring stress-induced transcriptional readthrough is a recently discovered phenomenon, in which stress conditions lead to dramatic induction of long transcripts as a result of transcription termination failure. In 2015, we reported the induction of such downstream of gene (DoG) containing transcripts upon osmotic stress in human cells, while others observed similar transcripts in virus-infected and cancer cells. Using the rigorous methodology Cap-Seq, we demonstrated that DoGs result from transcriptional readthrough, not de novo initiation...
June 27, 2018: Human Genomics
Hui He, Zhiping Hu, Han Xiao, Fangfang Zhou, Binbin Yang
Epigenetics defines the persistent modifications of gene expression in a manner that does not involve the corresponding alterations in DNA sequences. It includes modifications of DNA nucleotides, nucleosomal remodeling, and post-translational modifications (PTMs). It is becoming evident that PTMs which act singly or in combination to form "histone codes" orchestrate the chromatin structure and dynamic functions. PTMs of histone tails have been demonstrated to influence numerous biological developments, as well as disease onset and progression...
June 22, 2018: Human Genomics
Kobi Perl, Ron Shamir, Karen B Avraham
BACKGROUND: Hearing loss is a major cause of disability worldwide, impairing communication, health, and quality of life. Emerging methods of gene therapy aim to address this morbidity, which can be employed to fix a genetic problem causing hair cell dysfunction and to promote the proliferation of supporting cells in the cochlea and their transdifferentiation into hair cells. In order to extend the applicability of gene therapy, the scientific community is focusing on discovery of additional deafness genes, identifying new genetic variants associated with hearing loss, and revealing new factors that can be manipulated in a coordinated manner to improve hair cell regeneration...
June 22, 2018: Human Genomics
Minjoo Kim, Minkyung Kim, Hye Jin Yoo, Jayoung Shon, Jong Ho Lee
BACKGROUND: Oxidative stress is associated with the increased risk of hypertension (HTN). This cross-sectional study is aimed to identify the association between the peroxisome proliferator-activated receptor-δ (PPARD) polymorphism and plasma malondialdehyde (MDA), an oxidative stress marker which is related to HTN development, and to determine whether PPARD gene is a candidate gene for HTN. RESULTS: One thousand seven hundred ninety-three individuals with normal blood pressure (BP) and HTN were included in this cross-sectional study...
June 18, 2018: Human Genomics
Sang-Nee Tan, Sai-Peng Sim, Alan Soo-Beng Khoo
BACKGROUND: The mechanism underlying chromosome rearrangement in nasopharyngeal carcinoma (NPC) remains elusive. It is known that most of the aetiological factors of NPC trigger oxidative stress. Oxidative stress is a potent apoptotic inducer. During apoptosis, chromatin cleavage and DNA fragmentation occur. However, cells may undergo DNA repair and survive apoptosis. Non-homologous end joining (NHEJ) pathway has been known as the primary DNA repair system in human cells. The NHEJ process may repair DNA ends without any homology, although region of microhomology (a few nucleotides) is usually utilised by this DNA repair system...
June 18, 2018: Human Genomics
Magnus Ingelman-Sundberg, Souren Mkrtchian, Yitian Zhou, Volker M Lauschke
BACKGROUND: Variability in genes implicated in drug pharmacokinetics or drug response can modulate treatment efficacy or predispose to adverse drug reactions. Besides common genetic polymorphisms, recent sequencing projects revealed a plethora of rare genetic variants in genes encoding proteins involved in drug metabolism, transport, and response. RESULTS: To understand the global importance of rare pharmacogenetic gene variants, we mapped the variability in 208 pharmacogenes by analyzing exome sequencing data from 60,706 unrelated individuals and estimated the importance of rare and common genetic variants using a computational prediction framework optimized for pharmacogenetic assessments...
May 25, 2018: Human Genomics
Tamilselvi Elango, Jingying Sun, Caihong Zhu, Fusheng Zhou, Yaohua Zhang, Liangdan Sun, Sen Yang, Xuejun Zhang
BACKGROUND: Mutations in keratin proteins have been vastly associated with a wide array of genodermatoses; however, mutations of keratins in psoriasis have not been fully investigated. The main aim of the current research was to identify the mutation in K14, K10, K16, and K17 genes in two stages of psoriasis patients. METHODS: Ninety-six psoriatic skin biopsies were collected. mRNA transcript of K14, K10, K16, and K17 was prepared, amplified, and sequenced. Sanger sequences of all keratins were further validated for mutational analysis using Mutation Surveyor and Alamut Visual...
May 21, 2018: Human Genomics
Luluah Alhusain, Alaaeldin M Hafez
The analysis of population structure has many applications in medical and population genetic research. Such analysis is used to provide clear insight into the underlying genetic population substructure and is a crucial prerequisite for any analysis of genetic data. The analysis involves grouping individuals into subpopulations based on shared genetic variations. The most widely used markers to study the variation of DNA sequences between populations are single nucleotide polymorphisms. Data preprocessing is a necessary step to assess the quality of the data and to determine which markers or individuals can reasonably be included in the analysis...
May 9, 2018: Human Genomics
Madeleine J Murtagh, Mwenza T Blell, Olly W Butters, Lorraine Cowley, Edward S Dove, Alissa Goodman, Rebecca L Griggs, Alison Hall, Nina Hallowell, Meena Kumari, Massimo Mangino, Barbara Maughan, Melinda C Mills, Joel T Minion, Tom Murphy, Gillian Prior, Matthew Suderman, Susan M Ring, Nina T Rogers, Stephanie J Roberts, Catherine Van der Straeten, Will Viney, Deborah Wiltshire, Andrew Wong, Neil Walker, Paul R Burton
BACKGROUND: Genomic and biosocial research data about individuals is rapidly proliferating, bringing the potential for novel opportunities for data integration and use. The scale, pace and novelty of these applications raise a number of urgent sociotechnical, ethical and legal questions, including optimal methods of data storage, management and access. Although the open science movement advocates unfettered access to research data, many of the UK's longitudinal cohort studies operate systems of managed data access, in which access is governed by legal and ethical agreements between stewards of research datasets and researchers wishing to make use of them...
April 26, 2018: Human Genomics
Cameron J McDonald, Gautam Rishi, Eriza S Secondes, Lesa Ostini, Daniel F Wallace, Darrell H G Crawford, Hanlon Sia, Paul Clark, V Nathan Subramaniam
BACKGROUND: Atypical iron overload without variation in the five clinically associated hereditary hemochromatosis genes is now recognized; however, their etiology remains unknown. Since the identification of iron overload in the bone morphogenetic protein 6 (Bmp6) knockout mouse, the search has been on for clinically pathogenic variants in the BMP6 gene. A recent report proposes that variants in the pro-peptide region of BMP6 are the underlying cause of several cases of iron overload...
April 25, 2018: Human Genomics
Jusaku Minari, Kyle B Brothers, Michael Morrison
Precision medicine promises to use genomics and other data-intensive approaches to improve diagnosis and develop new treatments for major diseases, but also raises a range of ethical and governance challenges. Implementation of precision medicine in "real world" healthcare systems blurs the boundary between research and care. This has implications for the meaning and validity of consent, and increased potential for discrimination, among other challenges. Increased sharing of personal information raises concerns about privacy, commercialization, and public trust...
April 17, 2018: Human Genomics
Taketoshi Okita, Noriko Ohashi, Daijiro Kabata, Ayumi Shintani, Kazuto Kato
BACKGROUND: Recent innovations in gene analysis technology have allowed for rapid and inexpensive sequencing of entire genomes. Thus, both conducting a study using whole genome sequencing (WGS) in a large population and the clinical application of research findings from such studies are currently feasible. However, to promote WGS studies, understanding and voluntary participation by the general public is needed. Therefore, it is essential to investigate the general public's attitude toward and understanding of WGS studies...
April 13, 2018: Human Genomics
Suleyman Vural, Richard Simon, Julia Krushkal
BACKGROUND: The APOBEC gene family of cytidine deaminases plays important roles in DNA repair and mRNA editing. In many cancers, APOBEC3B increases the mutation load, generating clusters of closely spaced, single-strand-specific DNA substitutions with a characteristic hypermutation signature. Some studies also suggested a possible involvement of APOBEC3A, REV1, UNG, and FHIT in molecular processes affecting APOBEC mutagenesis. It is important to understand how mutagenic processes linked to the activity of these genes may affect sensitivity of cancer cells to treatment...
April 11, 2018: Human Genomics
Fida K Dankar, Andrey Ptitsyn, Samar K Dankar
Contemporary biomedical databases include a wide range of information types from various observational and instrumental sources. Among the most important features that unite biomedical databases across the field are high volume of information and high potential to cause damage through data corruption, loss of performance, and loss of patient privacy. Thus, issues of data governance and privacy protection are essential for the construction of data depositories for biomedical research and healthcare. In this paper, we discuss various challenges of data governance in the context of population genome projects...
April 10, 2018: Human Genomics
Nasser A Elhawary, Essam H Jiffri, Samira Jambi, Ahmad H Mufti, Anas Dannoun, Hassan Kordi, Asim Khogeer, Osama H Jiffri, Abdelrahman N Elhawary, Mohammed T Tayeb
BACKGROUND: In individuals with Duchenne muscular dystrophy (DMD), exon skipping treatment to restore a wild-type phenotype or correct the frame shift of the mRNA transcript of the dystrophin (DMD) gene are mutation-specific. To explore the molecular characterization of DMD rearrangements and predict the reading frame, we simultaneously screened all 79 DMD gene exons of 45 unrelated male DMD patients using a multiplex ligation-dependent probe amplification (MLPA) assay for deletion/duplication patterns...
April 10, 2018: Human Genomics
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