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Genome Medicine

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https://www.readbyqxmd.com/read/28511717/pancreatic-%C3%AE-cell-regeneration-advances-in-understanding-the-genes-and-signaling-pathways-involved
#1
Solomon Afelik, Meritxell Rovira
Recent advances in β-cell regeneration in vivo are providing insights into the mechanisms involved in the conversion of distinct pancreatic cell lineages into β cells. These mechanisms mostly involve reactivation of the gene encoding the pancreatic endocrine cell-specifying transcription factor neurogenin-3.
May 16, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28454591/lost-in-translation-returning-germline-genetic-results-in-genome-scale-cancer-research
#2
Amber L Johns, Skye H McKay, Jeremy L Humphris, Mark Pinese, Lorraine A Chantrill, R Scott Mead, Katherine Tucker, Lesley Andrews, Annabel Goodwin, Conrad Leonard, Hilda A High, Katia Nones, Ann-Marie Patch, Neil D Merrett, Nick Pavlakis, Karin S Kassahn, Jaswinder S Samra, David K Miller, David K Chang, Marina Pajic, John V Pearson, Sean M Grimmond, Nicola Waddell, Nikolajs Zeps, Anthony J Gill, Andrew V Biankin
BACKGROUND: The return of research results (RoR) remains a complex and well-debated issue. Despite the debate, actual data related to the experience of giving individual results back, and the impact these results may have on clinical care and health outcomes, is sorely lacking. Through the work of the Australian Pancreatic Cancer Genome Initiative (APGI) we: (1) delineate the pathway back to the patient where actionable research data were identified; and (2) report the clinical utilisation of individual results returned...
April 28, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28449715/functional-implications-of-microbial-and-viral-gut-metagenome-changes-in-early-stage-l-dopa-na%C3%A3-ve-parkinson-s-disease-patients
#3
J R Bedarf, F Hildebrand, L P Coelho, S Sunagawa, M Bahram, F Goeser, P Bork, U Wüllner
BACKGROUND: Parkinson's disease (PD) presently is conceptualized as a protein aggregation disease in which pathology involves both the enteric and the central nervous system, possibly spreading from one to another via the vagus nerves. As gastrointestinal dysfunction often precedes or parallels motor symptoms, the enteric system with its vast diversity of microorganisms may be involved in PD pathogenesis. Alterations in the enteric microbial taxonomic level of L-DOPA-naïve PD patients might also serve as a biomarker...
April 28, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28446242/activity-of-distinct-growth-factor-receptor-network-components-in-breast-tumors-uncovers-two-biologically-relevant-subtypes
#4
Mumtahena Rahman, Shelley M MacNeil, David F Jenkins, Gajendra Shrestha, Sydney R Wyatt, Jasmine A McQuerry, Stephen R Piccolo, Laura M Heiser, Joe W Gray, W Evan Johnson, Andrea H Bild
BACKGROUND: The growth factor receptor network (GFRN) plays a significant role in driving key oncogenic processes. However, assessment of global GFRN activity is challenging due to complex crosstalk among GFRN components, or pathways, and the inability to study complex signaling networks in patient tumors. Here, pathway-specific genomic signatures were used to interrogate GFRN activity in breast tumors and the consequent phenotypic impact of GRFN activity patterns. METHODS: Novel pathway signatures were generated in human primary mammary epithelial cells by overexpressing key genes from GFRN pathways (HER2, IGF1R, AKT1, EGFR, KRAS (G12V), RAF1, BAD)...
April 26, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28438193/pathos-a-decision-support-system-for-reporting-high-throughput-sequencing-of-cancers-in-clinical-diagnostic-laboratories
#5
Kenneth D Doig, Andrew Fellowes, Anthony H Bell, Andrei Seleznev, David Ma, Jason Ellul, Jason Li, Maria A Doyle, Ella R Thompson, Amit Kumar, Luis Lara, Ravikiran Vedururu, Gareth Reid, Thomas Conway, Anthony T Papenfuss, Stephen B Fox
BACKGROUND: The increasing affordability of DNA sequencing has allowed it to be widely deployed in pathology laboratories. However, this has exposed many issues with the analysis and reporting of variants for clinical diagnostic use. Implementing a high-throughput sequencing (NGS) clinical reporting system requires a diverse combination of capabilities, statistical methods to identify variants, global variant databases, a validated bioinformatics pipeline, an auditable laboratory workflow, reproducible clinical assays and quality control monitoring throughout...
April 24, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28431544/strategies-for-monitoring-and-combating-resistance-to-combination-kinase-inhibitors-for-cancer-therapy
#6
REVIEW
Leanne G Ahronian, Ryan B Corcoran
Targeted therapies such as kinase inhibitors and monoclonal antibodies have dramatically altered cancer care in recent decades. Although these targeted therapies have improved patient outcomes in several cancer types, resistance ultimately develops to these agents. One potential strategy proposed to overcome acquired resistance involves taking repeat tumor biopsies at the time of disease progression, to identify the specific molecular mechanism driving resistance in an individual patient and to select a new agent or combination of agents capable of surmounting that specific resistance mechanism...
April 21, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28420421/analysis-of-100-000-human-cancer-genomes-reveals-the-landscape-of-tumor-mutational-burden
#7
Zachary R Chalmers, Caitlin F Connelly, David Fabrizio, Laurie Gay, Siraj M Ali, Riley Ennis, Alexa Schrock, Brittany Campbell, Adam Shlien, Juliann Chmielecki, Franklin Huang, Yuting He, James Sun, Uri Tabori, Mark Kennedy, Daniel S Lieber, Steven Roels, Jared White, Geoffrey A Otto, Jeffrey S Ross, Levi Garraway, Vincent A Miller, Phillip J Stephens, Garrett M Frampton
BACKGROUND: High tumor mutational burden (TMB) is an emerging biomarker of sensitivity to immune checkpoint inhibitors and has been shown to be more significantly associated with response to PD-1 and PD-L1 blockade immunotherapy than PD-1 or PD-L1 expression, as measured by immunohistochemistry (IHC). The distribution of TMB and the subset of patients with high TMB has not been well characterized in the majority of cancer types. METHODS: In this study, we compare TMB measured by a targeted comprehensive genomic profiling (CGP) assay to TMB measured by exome sequencing and simulate the expected variance in TMB when sequencing less than the whole exome...
April 19, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28420414/integrated-genomic-analysis-of-mitochondrial-rna-processing-in-human-cancers
#8
Youssef Idaghdour, Alan Hodgkinson
BACKGROUND: The mitochondrial genome is transcribed as continuous polycistrons of RNA containing multiple genes. As a consequence, post-transcriptional events are critical for the regulation of gene expression and therefore all aspects of mitochondrial function. One particularly important process is the m(1)A/m(1)G RNA methylation of the ninth position of different mitochondrial tRNAs, which allows efficient processing of mitochondrial mRNAs and protein translation, and de-regulation of genes involved in these processes has been associated with altered mitochondrial function...
April 18, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28420412/intersect-then-combine-approach-improving-the-performance-of-somatic-variant-calling-in-whole-exome-sequencing-data-using-multiple-aligners-and-callers
#9
Maurizio Callari, Stephen-John Sammut, Leticia De Mattos-Arruda, Alejandra Bruna, Oscar M Rueda, Suet-Feung Chin, Carlos Caldas
Bioinformatic analysis of genomic sequencing data to identify somatic mutations in cancer samples is far from achieving the required robustness and standardisation. In this study we generated a whole exome sequencing benchmark dataset using the platinum genome sample NA12878 and developed an intersect-then-combine (ITC) approach to increase the accuracy in calling single nucleotide variants (SNVs) and indels in tumour-normal pairs. We evaluated the effect of alignment, base quality recalibration, mutation caller and filtering on sensitivity and false positive rate...
April 18, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28381277/unique-dna-methylation-signature-in-hpv-positive-head-and-neck-squamous-cell-carcinomas
#10
Davide Degli Esposti, Athena Sklias, Sheila C Lima, Stéphanie Beghelli-de la Forest Divonne, Vincent Cahais, Nora Fernandez-Jimenez, Marie-Pierre Cros, Szilvia Ecsedi, Cyrille Cuenin, Liacine Bouaoun, Graham Byrnes, Rosita Accardi, Anne Sudaka, Valérie Giordanengo, Hector Hernandez-Vargas, Luis Felipe Ribeiro Pinto, Ellen Van Obberghen-Schilling, Zdenko Herceg
BACKGROUND: Head and neck squamous cell carcinomas (HNSCCs) represent a heterogeneous group of cancers for which human papilloma virus (HPV) infection is an emerging risk factor. Previous studies showed promoter hypermethylation in HPV(+) oropharyngeal cancers, but only few consistent target genes have been so far described, and the evidence of a functional impact on gene expression is still limited. METHODS: We performed global and stratified pooled analyses of epigenome-wide data in HNSCCs based on the Illumina HumanMethylation450 bead-array data in order to identify tissue-specific components and common viral epigenetic targets in HPV-associated tumours...
April 5, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28356157/migration-of-mitochondrial-dna-in-the-nuclear-genome-of-colorectal-adenocarcinoma
#11
Vinodh Srinivasainagendra, Michael W Sandel, Bhupendra Singh, Aishwarya Sundaresan, Ved P Mooga, Prachi Bajpai, Hemant K Tiwari, Keshav K Singh
BACKGROUND: Colorectal adenocarcinomas are characterized by abnormal mitochondrial DNA (mtDNA) copy number and genomic instability, but a molecular interaction between mitochondrial and nuclear genome remains unknown. Here we report the discovery of increased copies of nuclear mtDNA (NUMT) in colorectal adenocarcinomas, which supports link between mtDNA and genomic instability in the nucleus. We name this phenomenon of nuclear occurrence of mitochondrial component as numtogenesis. We provide a description of NUMT abundance and distribution in tumor versus matched blood-derived normal genomes...
March 29, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28356137/ethnic-and-diet-related-differences-in-the-healthy-infant-microbiome
#12
Jennifer C Stearns, Michael A Zulyniak, Russell J de Souza, Natalie C Campbell, Michelle Fontes, Mateen Shaikh, Malcolm R Sears, Allan B Becker, Piushkumar J Mandhane, Padmaja Subbarao, Stuart E Turvey, Milan Gupta, Joseph Beyene, Michael G Surette, Sonia S Anand
BACKGROUND: The infant gut is rapidly colonized by microorganisms soon after birth, and the composition of the microbiota is dynamic in the first year of life. Although a stable microbiome may not be established until 1 to 3 years after birth, the infant gut microbiota appears to be an important predictor of health outcomes in later life. METHODS: We obtained stool at one year of age from 173 white Caucasian and 182 South Asian infants from two Canadian birth cohorts to gain insight into how maternal and early infancy exposures influence the development of the gut microbiota...
March 29, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28351419/new-var-reconstruction-algorithm-exposes-high-var-sequence-diversity-in-a-single-geographic-location-in-mali
#13
Antoine Dara, Elliott F Drábek, Mark A Travassos, Kara A Moser, Arthur L Delcher, Qi Su, Timothy Hostelley, Drissa Coulibaly, Modibo Daou, Ahmadou Dembele, Issa Diarra, Abdoulaye K Kone, Bourema Kouriba, Matthew B Laurens, Amadou Niangaly, Karim Traore, Youssouf Tolo, Claire M Fraser, Mahamadou A Thera, Abdoulaye A Djimde, Ogobara K Doumbo, Christopher V Plowe, Joana C Silva
BACKGROUND: Encoded by the var gene family, highly variable Plasmodium falciparum erythrocyte membrane protein-1 (PfEMP1) proteins mediate tissue-specific cytoadherence of infected erythrocytes, resulting in immune evasion and severe malaria disease. Sequencing and assembling the 40-60 var gene complement for individual infections has been notoriously difficult, impeding molecular epidemiological studies and the assessment of particular var elements as subunit vaccine candidates. METHODS: We developed and validated a novel algorithm, Exon-Targeted Hybrid Assembly (ETHA), to perform targeted assembly of var gene sequences, based on a combination of Pacific Biosciences and Illumina data...
March 28, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28347358/genetic-pleiotropy-between-age-related-macular-degeneration-and-16-complex-diseases-and-traits
#14
Felix Grassmann, Christina Kiel, Martina E Zimmermann, Mathias Gorski, Veronika Grassmann, Klaus Stark, Iris M Heid, Bernhard H F Weber
BACKGROUND: Age-related macular degeneration (AMD) is a common condition of vision loss with disease development strongly influenced by environmental and genetic factors. Recently, 34 loci were associated with AMD at genome-wide significance. So far, little is known about a genetic overlap between AMD and other complex diseases or disease-relevant traits. METHODS: For each of 60 complex diseases/traits with publicly available genome-wide significant association data, the lead genetic variant per independent locus was extracted and a genetic score was calculated for each disease/trait as the weighted sum of risk alleles...
March 27, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28340599/dna-methylation-changes-at-infertility-genes-in-newborn-twins-conceived-by-in-vitro-fertilisation
#15
Juan E Castillo-Fernandez, Yuk Jing Loke, Sebastian Bass-Stringer, Fei Gao, Yudong Xia, Honglong Wu, Hanlin Lu, Yuan Liu, Jun Wang, Tim D Spector, Richard Saffery, Jeffrey M Craig, Jordana T Bell
BACKGROUND: The association of in vitro fertilisation (IVF) and DNA methylation has been studied predominantly at regulatory regions of imprinted genes and at just thousands of the ~28 million CpG sites in the human genome. METHODS: We investigated the links between IVF and DNA methylation patterns in whole cord blood cells (n = 98) and cord blood mononuclear cells (n = 82) from newborn twins using genome-wide methylated DNA immunoprecipitation coupled with deep sequencing...
March 24, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28330499/a-novel-multi-network-approach-reveals-tissue-specific-cellular-modulators-of-fibrosis-in-systemic-sclerosis
#16
Jaclyn N Taroni, Casey S Greene, Viktor Martyanov, Tammara A Wood, Romy B Christmann, Harrison W Farber, Robert A Lafyatis, Christopher P Denton, Monique E Hinchcliff, Patricia A Pioli, J Matthew Mahoney, Michael L Whitfield
BACKGROUND: Systemic sclerosis (SSc) is a multi-organ autoimmune disease characterized by skin fibrosis. Internal organ involvement is heterogeneous. It is unknown whether disease mechanisms are common across all involved affected tissues or if each manifestation has a distinct underlying pathology. METHODS: We used consensus clustering to compare gene expression profiles of biopsies from four SSc-affected tissues (skin, lung, esophagus, and peripheral blood) from patients with SSc, and the related conditions pulmonary fibrosis (PF) and pulmonary arterial hypertension, and derived a consensus disease-associate signature across all tissues...
March 23, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28327206/lessons-learned-from-additional-research-analyses-of-unsolved-clinical-exome-cases
#17
Mohammad K Eldomery, Zeynep Coban-Akdemir, Tamar Harel, Jill A Rosenfeld, Tomasz Gambin, Asbjørg Stray-Pedersen, Sébastien Küry, Sandra Mercier, Davor Lessel, Jonas Denecke, Wojciech Wiszniewski, Samantha Penney, Pengfei Liu, Weimin Bi, Seema R Lalani, Christian P Schaaf, Michael F Wangler, Carlos A Bacino, Richard Alan Lewis, Lorraine Potocki, Brett H Graham, John W Belmont, Fernando Scaglia, Jordan S Orange, Shalini N Jhangiani, Theodore Chiang, Harsha Doddapaneni, Jianhong Hu, Donna M Muzny, Fan Xia, Arthur L Beaudet, Eric Boerwinkle, Christine M Eng, Sharon E Plon, V Reid Sutton, Richard A Gibbs, Jennifer E Posey, Yaping Yang, James R Lupski
BACKGROUND: Given the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene discovery. METHODS: We designed and implemented protocols for the study of cases for which a plausible molecular diagnosis was not achieved in a clinical genomics diagnostic laboratory (i.e. unsolved clinical exomes). Such cases were recruited to a research laboratory for further analyses, in order to potentially: (1) accelerate novel disease gene discovery; (2) increase the molecular diagnostic yield of whole exome sequencing (WES); and (3) gain insight into the genetic mechanisms of disease...
March 21, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28327175/schizophrenia-and-substance-use-comorbidity-a-genome-wide-perspective
#18
Renato Polimanti, Arpana Agrawal, Joel Gelernter
Dual diagnosis with substance use disorders (SUDs) consistently contributes to the premature mortality and increased disability observed in schizophrenia. Large genome-wide association studies are providing the information needed to investigate the genetic architecture of psychiatric disorders. Here, we discuss recent genetic investigations of dual diagnosis (i.e., schizophrenia plus a SUD) and how these findings can inform public health messages.
March 21, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28279190/imiquimod-has-strain-dependent-effects-in-mice-and-does-not-uniquely-model-human-psoriasis
#19
William R Swindell, Kellie A Michaels, Andrew J Sutter, Doina Diaconu, Yi Fritz, Xianying Xing, Mrinal K Sarkar, Yun Liang, Alex Tsoi, Johann E Gudjonsson, Nicole L Ward
BACKGROUND: Imiquimod (IMQ) produces a cutaneous phenotype in mice frequently studied as an acute model of human psoriasis. Whether this phenotype depends on strain or sex has never been systematically investigated on a large scale. Such effects, however, could lead to conflicts among studies, while further impacting study outcomes and efforts to translate research findings. METHODS: RNA-seq was used to evaluate the psoriasiform phenotype elicited by 6 days of Aldara (5% IMQ) treatment in both sexes of seven mouse strains (C57BL/6 J (B6), BALB/cJ, CD1, DBA/1 J, FVB/NJ, 129X1/SvJ, and MOLF/EiJ)...
March 9, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28270201/exploration-of-haplotype-research-consortium-imputation-for-genome-wide-association-studies-in-20-032-generation-scotland-participants
#20
Reka Nagy, Thibaud S Boutin, Jonathan Marten, Jennifer E Huffman, Shona M Kerr, Archie Campbell, Louise Evenden, Jude Gibson, Carmen Amador, David M Howard, Pau Navarro, Andrew Morris, Ian J Deary, Lynne J Hocking, Sandosh Padmanabhan, Blair H Smith, Peter Joshi, James F Wilson, Nicholas D Hastie, Alan F Wright, Andrew M McIntosh, David J Porteous, Chris S Haley, Veronique Vitart, Caroline Hayward
BACKGROUND: The Generation Scotland: Scottish Family Health Study (GS:SFHS) is a family-based population cohort with DNA, biological samples, socio-demographic, psychological and clinical data from approximately 24,000 adult volunteers across Scotland. Although data collection was cross-sectional, GS:SFHS became a prospective cohort due to of the ability to link to routine Electronic Health Record (EHR) data. Over 20,000 participants were selected for genotyping using a large genome-wide array...
March 7, 2017: Genome Medicine
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