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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
N Nazaripanah, F Adelirad, A Delbari, R Sahaf, T Abbasi-Asl, M Ohadi
BACKGROUND: While there is an ongoing trend to identify single nucleotide substitutions (SNSs) that are linked to inter/intra-species differences and disease phenotypes, short tandem repeats (STRs)/microsatellites may be of equal (if not more) importance in the above processes. Genes that contain STRs in their promoters have higher expression divergence compared to genes with fixed or no STRs in the gene promoters. In line with the above, recent reports indicate a role of repetitive sequences in the rise of young transcription start sites (TSSs) in human evolution...
April 5, 2018: Human Genomics
Brenda C Minatel, Victor D Martinez, Kevin W Ng, Adam P Sage, Tomas Tokar, Erin A Marshall, Christine Anderson, Katey S S Enfield, Greg L Stewart, Patricia P Reis, Igor Jurisica, Wan L Lam
MicroRNAs (miRNAs) are crucial regulators of gene expression in normal development and cellular homeostasis. While miRNA repositories contain thousands of unique sequences, they primarily contain molecules that are conserved across several tissues, largely excluding lineage and tissue-specific miRNAs. By analyzing small non-coding RNA sequencing data for abundance and secondary RNA structure, we discovered 103 miRNA candidates previously undescribed in liver tissue. While expression of some of these unannotated sequences is restricted to non-malignant tissue, downregulation of most of the sequences was detected in liver tumors, indicating their importance in the maintenance of liver homeostasis...
March 27, 2018: Human Genomics
Ming-Yu Huang, Ji-Long Liu
Previous studies demonstrated that massive induction of transcriptional readthrough generates downstream of gene-containing transcripts (DoGs) in cells under stress condition. Here, we analyzed TSS-seq (transcription start site sequencing) data from the DBTSS database. We investigated TSS tags at the end of gene for all pan-stress and untreated-cell DoGs, in comparison with expression-matched non-DoGs. We observed significantly more TSS tags at the end of pan-stress and untreated-cell DoG genes than non-DoG genes, even though their TSS tags in the promoter is the same...
March 16, 2018: Human Genomics
U Plöckinger, V Prasad, A Ziagaki, N Tiling, A Poellinger
BACKGROUND: Pompe disease (PD) is an autosomal recessive, lysosomal storage disease due to a mutation of the acid α-glucosidase (GAA) gene. In adult patients, PD is characterized by slowly progressive limb-girdle and trunk myopathy and restrictive respiratory insufficiency. Enzyme replacement therapy (ERT) is available, improving or stabilizing muscle-function in some and slowing deterioration in other patients. Unfortunately, there is no biomarker available to indicate therapeutic efficacy and/or disease activity...
March 9, 2018: Human Genomics
Jane Kaye, Sharon F Terry, Eric Juengst, Sarah Coy, Jennifer R Harris, Don Chalmers, Edward S Dove, Isabelle Budin-Ljøsne, Clement Adebamowo, Emilomo Ogbe, Louise Bezuidenhout, Michael Morrison, Joel T Minion, Madeleine J Murtagh, Jusaku Minari, Harriet Teare, Rosario Isasi, Kazuto Kato, Emmanuelle Rial-Sebbag, Patricia Marshall, Barbara Koenig, Anne Cambon-Thomsen
BACKGROUND: Governments, funding bodies, institutions, and publishers have developed a number of strategies to encourage researchers to facilitate access to datasets. The rationale behind this approach is that this will bring a number of benefits and enable advances in healthcare and medicine by allowing the maximum returns from the investment in research, as well as reducing waste and promoting transparency. As this approach gains momentum, these data-sharing practices have implications for many kinds of research as they become standard practice across the world...
March 7, 2018: Human Genomics
Anna Sundby, Merete Watt Boolsen, Kristoffer Sølvsten Burgdorf, Henrik Ullum, Thomas Folkmann Hansen, Ole Mors
BACKGROUND: Genomic sequencing of children in research raises complex ethical issues. This study aims to gain more knowledge on the attitudes towards the inclusion of children as research subjects in genomic research and towards the disclosure of pertinent and incidental findings to the parents and the child. METHODS: Qualitative data were collected from interviews with a wide range of informants: experts engaged in genomic research, clinical geneticists, persons with mental disorders, relatives, and blood donors...
March 5, 2018: Human Genomics
Georgios Kellaris, Kamal Khan, Shahid M Baig, I-Chun Tsai, Francisca Millan Zamora, Paul Ruggieri, Marvin R Natowicz, Nicholas Katsanis
BACKGROUND: Intellectual disability (ID) is a common condition with a population prevalence frequency of 1-3% and an enrichment for males, driven in part by the contribution of mutant alleles on the X-chromosome. Among the more than 500 genes associated with ID, DDX3X represents an outlier in sex specificity. Nearly all reported pathogenic variants of DDX3X are de novo, affect mostly females, and appear to be loss of function variants, consistent with the hypothesis that haploinsufficiency at this locus on the X-chromosome is likely to be lethal in males...
March 1, 2018: Human Genomics
Georgia Charkoftaki, Nicholas J W Rattray, Per E Andrén, Richard M Caprioli, Steve Castellino, Mark W Duncan, Richard J A Goodwin, Kevin L Schey, Sheerin K Shahidi-Latham, Kirill A Veselkov, Caroline H Johnson, Vasilis Vasiliou
No abstract text is available yet for this article.
February 27, 2018: Human Genomics
Shuvra Shekhar Roy, Ananda Kishore Mukherjee, Shantanu Chowdhury
Over the last 15 years, development of chromosome conformation capture (3C) and its subsequent high-throughput variants in conjunction with the fast development of sequencing technology has allowed investigators to generate large volumes of data giving insights into the spatial three-dimensional (3D) architecture of the genome. This huge data has been analyzed and validated using various statistical, mathematical, genomics, and biophysical tools in order to examine the chromosomal interaction patterns, understand the organization of the chromosome, and find out functional implications of the interactions...
February 20, 2018: Human Genomics
Adrian Thorogood, Jason Bobe, Barbara Prainsack, Anna Middleton, Erick Scott, Sarah Nelson, Manuel Corpas, Natasha Bonhomme, Laura Lyman Rodriguez, Madeleine Murtagh, Erika Kleiderman
BACKGROUND: There is a growing support for the stance that patients and research participants should have better and easier access to their raw (uninterpreted) genomic sequence data in both clinical and research contexts. MAIN BODY: We review legal frameworks and literature on the benefits, risks, and practical barriers of providing individuals access to their data. We also survey genomic sequencing initiatives that provide or plan to provide individual access. Many patients and research participants expect to be able to access their health and genomic data...
February 17, 2018: Human Genomics
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