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Genome Medicine

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https://www.readbyqxmd.com/read/29132412/prospects-for-using-risk-scores-in-polygenic-medicine
#1
Cathryn M Lewis, Evangelos Vassos
Genome-wide association studies have made strides in identifying common variation associated with disease. The modest effect sizes preclude risk prediction based on single genetic variants, but polygenic risk scores that combine thousands of variants show some predictive ability across a range of complex traits and diseases, including neuropsychiatric disorders. Here, we consider the potential for translation to clinical use.
November 13, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29089060/actionable-gene-based-classification-toward-precision-medicine-in-gastric-cancer
#2
Hiroshi Ichikawa, Masayuki Nagahashi, Yoshifumi Shimada, Takaaki Hanyu, Takashi Ishikawa, Hitoshi Kameyama, Takashi Kobayashi, Jun Sakata, Hiroshi Yabusaki, Satoru Nakagawa, Nobuaki Sato, Yuki Hirata, Yuko Kitagawa, Toshiyuki Tanahashi, Kazuhiro Yoshida, Ryota Nakanishi, Eiji Oki, Dana Vuzman, Stephen Lyle, Kazuaki Takabe, Yiwei Ling, Shujiro Okuda, Kohei Akazawa, Toshifumi Wakai
BACKGROUND: Intertumoral heterogeneity represents a significant hurdle to identifying optimized targeted therapies in gastric cancer (GC). To realize precision medicine for GC patients, an actionable gene alteration-based molecular classification that directly associates GCs with targeted therapies is needed. METHODS: A total of 207 Japanese patients with GC were included in this study. Formalin-fixed, paraffin-embedded (FFPE) tumor tissues were obtained from surgical or biopsy specimens and were subjected to DNA extraction...
October 31, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29089048/the-circadian-clock-system-s-influence-in-health-and-disease
#3
Joseph T Bass
Joseph T. Bass discusses recent developments in circadian clock research and reflects on the future of the field and its potential applications to clinical medicine.
October 31, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29089047/whole-exome-sequencing-in-342-congenital-cardiac-left-sided-lesion-cases-reveals-extensive-genetic-heterogeneity-and-complex-inheritance-patterns
#4
Alexander H Li, Neil A Hanchard, Dieter Furthner, Susan Fernbach, Mahshid Azamian, Annarita Nicosia, Jill Rosenfeld, Donna Muzny, Lisa C A D'Alessandro, Shaine Morris, Shalini Jhangiani, Dhaval R Parekh, Wayne J Franklin, Mark Lewin, Jeffrey A Towbin, Daniel J Penny, Charles D Fraser, James F Martin, Christine Eng, James R Lupski, Richard A Gibbs, Eric Boerwinkle, John W Belmont
BACKGROUND: Left-sided lesions (LSLs) account for an important fraction of severe congenital cardiovascular malformations (CVMs). The genetic contributions to LSLs are complex, and the mutations that cause these malformations span several diverse biological signaling pathways: TGFB, NOTCH, SHH, and more. Here, we use whole exome sequence data generated in 342 LSL cases to identify likely damaging variants in putative candidate CVM genes. METHODS: Using a series of bioinformatics filters, we focused on genes harboring population-rare, putative loss-of-function (LOF), and predicted damaging variants in 1760 CVM candidate genes constructed a priori from the literature and model organism databases...
October 31, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29084588/public-health-surveillance-in-the-uk-revolutionises-our-understanding-of-the-invasive-salmonella-typhimurium-epidemic-in-africa
#5
Philip M Ashton, Siân V Owen, Lukeki Kaindama, Will P M Rowe, Chris R Lane, Lesley Larkin, Satheesh Nair, Claire Jenkins, Elizabeth M de Pinna, Nicholas A Feasey, Jay C D Hinton, Timothy J Dallman
BACKGROUND: The ST313 sequence type of Salmonella Typhimurium causes invasive non-typhoidal salmonellosis and was thought to be confined to sub-Saharan Africa. Two distinct phylogenetic lineages of African ST313 have been identified. METHODS: We analysed the whole genome sequences of S. Typhimurium isolates from UK patients that were generated following the introduction of routine whole-genome sequencing (WGS) of Salmonella enterica by Public Health England in 2014...
October 31, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29082853/cancer-gene-profiling-in-non-small-cell-lung-cancers-reveals-activating-mutations-in-jak2-and-jak3-with-therapeutic-implications
#6
Shuyu D Li, Meng Ma, Hui Li, Aneta Waluszko, Tatyana Sidorenko, Eric E Schadt, David Y Zhang, Rong Chen, Fei Ye
BACKGROUND: Next-generation sequencing (NGS) of cancer gene panels are widely applied to enable personalized cancer therapy and to identify novel oncogenic mutations. METHODS: We performed targeted NGS on 932 clinical cases of non-small-cell lung cancers (NSCLCs) using the Ion AmpliSeq™ Cancer Hotspot panel v2 assay. RESULTS: Actionable mutations were identified in 65% of the cases with available targeted therapeutic options, including 26% of the patients with mutations in National Comprehensive Cancer Network (NCCN) guideline genes...
October 30, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29078804/nuclear-wiskott-aldrich-syndrome-protein-co-regulates-t-cell-factor-1-mediated-transcription-in-t-cells
#7
Nikolai V Kuznetsov, Bader Almuzzaini, Joanna S Kritikou, Marisa A P Baptista, Mariana M S Oliveira, Marton Keszei, Scott B Snapper, Piergiorgio Percipalle, Lisa S Westerberg
BACKGROUND: The Wiskott-Aldrich syndrome protein (WASp) family of actin-nucleating factors are present in the cytoplasm and in the nucleus. The role of nuclear WASp for T cell development remains incompletely defined. METHODS: We performed WASp chromatin immunoprecipitation and deep sequencing (ChIP-seq) in thymocytes and spleen CD4(+) T cells. RESULTS: WASp was enriched at genic and intergenic regions and associated with the transcription start sites of protein-coding genes...
October 27, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29070057/next-generation-mapping-a-novel-approach-for-detection-of-pathogenic-structural-variants-with-a-potential-utility-in-clinical-diagnosis
#8
Hayk Barseghyan, Wilson Tang, Richard T Wang, Miguel Almalvez, Eva Segura, Matthew S Bramble, Allen Lipson, Emilie D Douine, Hane Lee, Emmanuèle C Délot, Stanley F Nelson, Eric Vilain
BACKGROUND: Massively parallel DNA sequencing, such as exome sequencing, has become a routine clinical procedure to identify pathogenic variants responsible for a patient's phenotype. Exome sequencing has the capability of reliably identifying inherited and de novo single-nucleotide variants, small insertions, and deletions. However, due to the use of 100-300-bp fragment reads, this platform is not well powered to sensitively identify moderate to large structural variants (SV), such as insertions, deletions, inversions, and translocations...
October 25, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29052536/breathing-new-life-into-an-old-target-pulmonary-disease-drugs-for-parkinson-s-disease-therapy
#9
Hisham Abdelmotilib, Andrew B West
Increases in α-synuclein protein expression are suspected to increase the risk of the development of Parkinson's disease (PD). A recent study has demonstrated that β2-adrenergic receptor (β2AR) agonists decrease histone acetylation in the α-synuclein gene and suppress transcription. Coupled with the anti-inflammatory effects that are associated with β2AR activation, this two-pronged attack holds promise for PD treatment and the development of new therapeutic approaches for this disease.
October 19, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28964259/three-dimensional-genome-architecture-and-emerging-technologies-looping-in-disease
#10
REVIEW
Arpit Mishra, R David Hawkins
Genome compaction is a universal feature of cells and has emerged as a global regulator of gene expression. Compaction is maintained by a multitude of architectural proteins, long non-coding RNAs (lncRNAs), and regulatory DNA. Each component comprises interlinked regulatory circuits that organize the genome in three-dimensional (3D) space to manage gene expression. In this review, we update the current state of 3D genome catalogues and focus on how recent technological advances in 3D genomics are leading to an enhanced understanding of disease mechanisms...
September 30, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28954626/hlaprofiler-utilizes-k-mer-profiles-to-improve-hla-calling-accuracy-for-rare-and-common-alleles-in-rna-seq-data
#11
Martin L Buchkovich, Chad C Brown, Kimberly Robasky, Shengjie Chai, Sharon Westfall, Benjamin G Vincent, Eric T Weimer, Jason G Powers
BACKGROUND: The human leukocyte antigen (HLA) system is a genomic region involved in regulating the human immune system by encoding cell membrane major histocompatibility complex (MHC) proteins that are responsible for self-recognition. Understanding the variation in this region provides important insights into autoimmune disorders, disease susceptibility, oncological immunotherapy, regenerative medicine, transplant rejection, and toxicogenomics. Traditional approaches to HLA typing are low throughput, target only a few genes, are labor intensive and costly, or require specialized protocols...
September 27, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28946923/key-challenges-in-bringing-crispr-mediated-somatic-cell-therapy-into-the-clinic
#12
Dianne Nicol, Lisa Eckstein, Michael Morrison, Jacob S Sherkow, Margaret Otlowski, Tess Whitton, Tania Bubela, Kathryn P Burdon, Don Chalmers, Sarah Chan, Jac Charlesworth, Christine Critchley, Merlin Crossley, Sheryl de Lacey, Joanne L Dickinson, Alex W Hewitt, Joanne Kamens, Kazuto Kato, Erika Kleiderman, Satoshi Kodama, John Liddicoat, David A Mackey, Ainsley J Newson, Jane Nielsen, Jennifer K Wagner, Rebekah E McWhirter
Genome editing using clustered regularly interspersed short palindromic repeats (CRISPR) and CRISPR-associated proteins offers the potential to facilitate safe and effective treatment of genetic diseases refractory to other types of intervention. Here, we identify some of the major challenges for clinicians, regulators, and human research ethics committees in the clinical translation of CRISPR-mediated somatic cell therapy.
September 25, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28938910/creating-a-data-resource-what-will-it-take-to-build-a-medical-information-commons
#13
Patricia A Deverka, Mary A Majumder, Angela G Villanueva, Margaret Anderson, Annette C Bakker, Jessica Bardill, Eric Boerwinkle, Tania Bubela, Barbara J Evans, Nanibaa' A Garrison, Richard A Gibbs, Robert Gentleman, David Glazer, Melissa M Goldstein, Hank Greely, Crane Harris, Bartha M Knoppers, Barbara A Koenig, Isaac S Kohane, Salvatore La Rosa, John Mattison, Christopher J O'Donnell, Arti K Rai, Heidi L Rehm, Laura L Rodriguez, Robert Shelton, Tania Simoncelli, Sharon F Terry, Michael S Watson, John Wilbanks, Robert Cook-Deegan, Amy L McGuire
National and international public-private partnerships, consortia, and government initiatives are underway to collect and share genomic, personal, and healthcare data on a massive scale. Ideally, these efforts will contribute to the creation of a medical information commons (MIC), a comprehensive data resource that is widely available for both research and clinical uses. Stakeholder participation is essential in clarifying goals, deepening understanding of areas of complexity, and addressing long-standing policy concerns such as privacy and security and data ownership...
September 22, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28934986/identification-of-novel-candidate-disease-genes-from-de-novo-exonic-copy-number-variants
#14
Tomasz Gambin, Bo Yuan, Weimin Bi, Pengfei Liu, Jill A Rosenfeld, Zeynep Coban-Akdemir, Amber N Pursley, Sandesh C S Nagamani, Ronit Marom, Sailaja Golla, Lauren Dengle, Heather G Petrie, Reuben Matalon, Lisa Emrick, Monica B Proud, Diane Treadwell-Deering, Hsiao-Tuan Chao, Hannele Koillinen, Chester Brown, Nora Urraca, Roya Mostafavi, Saunder Bernes, Elizabeth R Roeder, Kimberly M Nugent, Patricia I Bader, Gary Bellus, Michael Cummings, Hope Northrup, Myla Ashfaq, Rachel Westman, Robert Wildin, Anita E Beck, LaDonna Immken, Lindsay Elton, Shaun Varghese, Edward Buchanan, Laurence Faivre, Mathilde Lefebvre, Christian P Schaaf, Magdalena Walkiewicz, Yaping Yang, Sung-Hae L Kang, Seema R Lalani, Carlos A Bacino, Arthur L Beaudet, Amy M Breman, Janice L Smith, Sau Wai Cheung, James R Lupski, Ankita Patel, Chad A Shaw, Paweł Stankiewicz
BACKGROUND: Exon-targeted microarrays can detect small (<1000 bp) intragenic copy number variants (CNVs), including those that affect only a single exon. This genome-wide high-sensitivity approach increases the molecular diagnosis for conditions with known disease-associated genes, enables better genotype-phenotype correlations, and facilitates variant allele detection allowing novel disease gene discovery. METHODS: We retrospectively analyzed data from 63,127 patients referred for clinical chromosomal microarray analysis (CMA) at Baylor Genetics laboratories, including 46,755 individuals tested using exon-targeted arrays, from 2007 to 2017...
September 21, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28923095/genetic-and-epigenetic-studies-of-adiposity-and-cardiometabolic-disease
#15
REVIEW
Michael V Holmes, Sara L Pulit, Cecilia M Lindgren
Over 300 million adults are obese, but little is known about the impact of obesity on cardiovascular health. We discuss recent genetic and epigenetic studies of adiposity that indicate a causal role for general and central adiposity in cardiometabolic disease, and highlight potential mechanisms including insulin resistance and gene expression.
September 18, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28877757/whole-genome-sequencing-of-esbl-producing-escherichia-coli-isolated-from-patients-farm-waste-and-canals-in-thailand
#16
Chakkaphan Runcharoen, Kathy E Raven, Sandra Reuter, Teemu Kallonen, Suporn Paksanont, Jeeranan Thammachote, Suthatip Anun, Beth Blane, Julian Parkhill, Sharon J Peacock, Narisara Chantratita
BACKGROUND: Tackling multidrug-resistant Escherichia coli requires evidence from One Health studies that capture numerous potential reservoirs in circumscribed geographic areas. METHODS: We conducted a survey of extended β-lactamase (ESBL)-producing E. coli isolated from patients, canals and livestock wastewater in eastern Thailand between 2014 and 2015, and analyzed isolates using whole genome sequencing. RESULTS: The bacterial collection of 149 isolates consisted of 84 isolates from a single hospital and 65 from the hospital sewer, canals and farm wastewater within a 20 km radius...
September 6, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28854978/the-neoepitope-landscape-in-pediatric-cancers
#17
Ti-Cheng Chang, Robert A Carter, Yongjin Li, Yuxin Li, Hong Wang, Michael N Edmonson, Xiang Chen, Paula Arnold, Terrence L Geiger, Gang Wu, Junmin Peng, Michael Dyer, James R Downing, Douglas R Green, Paul G Thomas, Jinghui Zhang
BACKGROUND: Neoepitopes derived from tumor-specific somatic mutations are promising targets for immunotherapy in childhood cancers. However, the potential for such therapies in targeting these epitopes remains uncertain due to a lack of knowledge of the neoepitope landscape in childhood cancer. Studies to date have focused primarily on missense mutations without exploring gene fusions, which are a major class of oncogenic drivers in pediatric cancer. METHODS: We developed an analytical workflow for identification of putative neoepitopes based on somatic missense mutations and gene fusions using whole-genome sequencing data...
August 31, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28854952/clinical-implications-of-neoepitope-landscapes-for-adult-and-pediatric-cancers
#18
REVIEW
Yang-Yang Feng, Obi L Griffith, Malachi Griffith
Many immunotherapies rely on the presence of neoepitopes derived from somatic mutations that lead to altered peptide sequences. Several studies have now analyzed the neoepitope landscape of different cancer subtypes, predominantly for adult samples, which tend to feature significantly higher mutational burden. However, a new report publishing the first comprehensive analysis of the pediatric neoepitope landscape suggests that immunotherapies could also hold promise for pediatric cancers.See related research article 10...
August 31, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28854983/identification-of-cis-regulatory-mutations-generating-de-novo-edges-in-personalized-cancer-gene-regulatory-networks
#19
Zeynep Kalender Atak, Hana Imrichova, Dmitry Svetlichnyy, Gert Hulselmans, Valerie Christiaens, Joke Reumers, Hugo Ceulemans, Stein Aerts
The identification of functional non-coding mutations is a key challenge in the field of genomics. Here we introduce μ-cisTarget to filter, annotate and prioritize cis-regulatory mutations based on their putative effect on the underlying "personal" gene regulatory network. We validated μ-cisTarget by re-analyzing the TAL1 and LMO1 enhancer mutations in T-ALL, and the TERT promoter mutation in melanoma. Next, we re-sequenced the full genomes of ten cancer cell lines and used matched transcriptome data and motif discovery to identify master regulators with de novo binding sites that result in the up-regulation of nearby oncogenic drivers...
August 30, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28851441/parkinson-s-disease-is-associated-with-dna-methylation-levels-in-human-blood-and-saliva
#20
Yu-Hsuan Chuang, Kimberly C Paul, Jeff M Bronstein, Yvette Bordelon, Steve Horvath, Beate Ritz
BACKGROUND: Several articles suggest that DNA methylation levels in blood relate to Parkinson's disease (PD) but there is a need for a large-scale study that involves suitable population based controls. The purposes of the study were: (1) to study whether PD status is associated with DNA methylation levels in blood/saliva; (2) to study whether observed associations relate to blood cell types; and (3) to characterize genome-wide significant markers ("CpGs") and clusters of CpGs (co-methylation modules) in terms of biological pathways...
August 30, 2017: Genome Medicine
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