检索结果-南通市图书馆

The Role of Quality Control in Targeted Next-generation Sequencing Library Preparation

在线全文

学校读者我要写书评

暂无评论

Genomics, Proteomics & Bioinformatics 2016年第4期14卷 200-206页

作者： Rouven Nietsch Jan Haas Alan Lai Daniel Oehler Stefan Mester Karen S. Frese Farbod Sedaghat-Hamedani Elham Kayvanpour Andreas Keller benjamin meder Institute for Cardiomyopathies Department of Internal Medicine IIIUniversity of Heidelberg69120 HeidelbergGermany German Centre for Cardiovascular Research(DZHK) Heidelberg/MannheimGermany Chair for Clinical Bioinformatics Medical FacultySaarland University66123 SaarbruckenGermany

Next-generation sequencing （NGS） is getting routinely used in the diagnosis of hereditary diseases, such as human cardiomyopathies. Hence. it is of utter importance to secure high quality sequencing data, enabling the identification of disease-relevant mutations or the conclusion of negative test results. During the process of sample preparation, each protocol for target enrichment library preparation has its own requirements for quality control （QC）; however, there is little evi- dence on the actual impact of these guidelines on resulting data quality. In this study, we analyzed the impact of QC during the diverse library preparation steps of Agilent SureSelect XT target enrichment and lllumina sequencing. We quantified the parameters for a cohort of around 600 samples, which include starting amount of DNA, amount of sheared DNA, smallest and largest fragment size of the starting DNA; amount of DNA after the pre-PCR, and smallest and largest fragment size of the resulting DNA; as well as the amount of the final library, the corresponding smallest and largest fragment size, and the number of detected variants. Intriguingly, there is a high tolerance for variations in all QC steps, meaning that within the boundaries proposed in the current study, a considerable variance at each step of QC can be well tolerated without compromising NGS quality.

关键词： Next-generation sequencing Quality control Library preparation Target enrichment Sequence variants

Whole miRNome-wide Differential Co-expression of MicroRNAs

在线全文

学校读者我要写书评

暂无评论

Genomics, Proteomics & Bioinformatics 2012年第5期10卷 285-294页

作者： Cord F.Stehler Andreas Keller Petra Leidinger Christina Backes Anoop Chandran Jerg Wischhusen benjamin meder Eckart Meese Siemens Healthcare Strategy Department of Human Genetics Saarland University Interdisciplinary Center for Clinical Research University of Wuerzburg Department of Internal Medicine III Heidelberg University

Co-regulation of genes has been extensively analyzed, however, rather limited knowledge is available on co-regulations within the miRNome. We investigated differential co-expression of microRNAs （miRNAs） based on miRNome profiles of whole blood from 540 individuals. These include patients suffering from different cancer and non-cancer diseases, and unaffected controls. Using hierarchi- cal clustering, we found 9 significant clusters of co-expressed miRNAs containing 2-36 individual miRNAs. Through analyzing multiple sequencing alignments in the clusters, we found that co-expression of miRNAs is associated with both sequence similarity and genomic co-localization. We calculated correlations for all 371,953 pairs of miRNAs for all 540 individuals and identified 184 pairs of miRNAs with high correlation values. Out of these 184 pairs of miRNAs, 16 pairs （8.7%） were differentially co-expressed in unaffected controls, cancer patients and patients with non-cancer diseases. By computing correlated and anti-correlated miRNA pairs, we constructed a net- work with 184 putative co-regulations as edges and 100 miRNAs as nodes. Thereby, we detected specific clusters of miRNAs with high and low correlation values. Our approach represents the most comprehensive co-regulation analysis based on whole miRNome-wide expression profiling. Our findings further decrypt the interactions of miRNAs in normal and human pathological processes.

关键词： Co-expression Microarray MicroRNA Network analysis

Personalized Computer Simulation of Diastolic Function in Heart Failure

在线全文

学校读者我要写书评

暂无评论

Genomics, Proteomics & Bioinformatics 2016年第4期14卷 244-252页

作者： Ali Amr Elham Kayvanpour Farbod Sedaghat-Hamedani Tiziano Passerini Viorel Mihalef Alan Lai Dominik Neumann Bogdan Georgescu Sebastian Buss Derliz Mercies Edgar Zitron Andreas E. Posch Maximilian Wurstle Tommaso Mansi Hugo A. Katus benjamin meder Institute for Cardiomyopathies Department of Medicine IIIUniversity of Heidelberg69120 Heidelberg.Germany German Centre for Cardiovascular Research(DZHK) Heidelberg/MannlleimGermany Siemens Healthcare Medical Imaging TechnologiesPrincetonNJ 08540USA Siemens Healthcare Strategy and Innovation91052 ErlangenGermany

The search for a parameter representing left ventricular relaxation from non-invasive and invasive diagnostic tools has been extensive, since heart failure （HF） with preserved ejection fraction （HF-pEF） is a global health problem. We explore here the feasibility using patient-specific cardiac computer modeling to capture diastolic parameters in patients suffering from different degrees of systolic HF. Fifty eight patients with idiopathic dilated cardiomyopathy have undergone thorough clinical evaluation, including cardiac magnetic resonance imaging （MRI）, heart catheterization, echocardiography, and cardiac biomarker assessment. A previously-introduced framework for creating multi-scale patient-specific cardiac models has been applied on all these patients. Novel parameters, such as global stiffness factor and maximum left ventricular active stress, representing cardiac active and passive tissue properties have been computed for all patients. Invasive pressure measurements from heart catheterization were then used to evaluate ventricular relaxation using the time constant of isovolumic relaxation Tau （τ）. Parameters from heart catheterization and the multi-scale model have been evaluated and compared to patient clinical presentation. The model parameter global stiffness factor, representing diastolic passive tissue properties, is correlated significantly across the patient population with τ. This study shows that multi-modal cardiac models can successfully capture diastolic （dys） function, a prerequisite for future clinical trials on HF-pEF.

关键词： Dilated cardiomyopathy Tau Myocardial stiffness Computer-based 3D modelPersonalized medicine Diastolic function

SLM2 Is A Novel Cardiac Splicing Factor Involved in Heart Failure due to Dilated Cardiomyopathy

在线全文

学校读者我要写书评

暂无评论

Genomics, Proteomics & Bioinformatics 2022年第1期20卷 129-146页

作者： Jes-Niels Boeckel Maximilian Mobius-Winkler Marion Muller Sabine Rebs Nicole Eger Laura Schoppe Rewati Tappu Karoline E.Kokot Jasmin M.Kneuer Susanne Gaul Diana M.Bordalo Alan Lai Jan Haas Mahsa Ghanbari Philipp Drewe-Boss Martin Liss Hugo A.Katus Uwe Ohler Michael Gotthardt Ulrich Laufs Katrin Streckfuss-Bomeke benjamin meder Department of Cardiology Angiology and PneumologyUniversity Hospital HeidelbergD-69120 HeidelbergGermany Klinik und Poliklinik fur Kardiologie Universitatskrankenhaus LeipzigD-04103 LeipzigGermany German Center for Cardiovascular Research(DZHK) Partner site HeidelbergD-69120 HeidelbergGermany Clinic for General and Interventional Cardiology/Angiology Herz-und Diabeteszentrum NRWRuhr-Universitat BochumD-32545 Bad OeynhausenGermany Department of Cardiology and Pneumology University HospitalGeorg-August University GoettingenD-37075 GoettingenGermany German Center for Cardiovascular Research(DZHK) Partner site GoettingenD-37075 GoettingenGermany Berlin Institute for Medical Systems Biology Max Delbruck Center for Molecular Medicine in the Helmholtz AssociationD-10115 BerlinGermany Institute of Biology Humboldt Universitat zu BerlinD-10099 BerlinGermany Neuromuscular and Cardiovascular Cell Biology Max Delbruck Center for Molecular Medicine in the Helmholtz AssociationD-13092 BerlinGermany German Center for Cardiovascular Research(DZHK) Partner site BerlinD-10117 BerlinGermany Stanford Genome Technology Center Department of GeneticsStanford Medical SchoolPalo AltoCA 94304USA

Alternative mRNA splicing is a fundamental process to increase the versatility of the *** humans,cardiac mRNA splicing is involved in the pathophysiology of heart *** in the splicing factor RNA binding motif protein 20(RBM20) cause severe forms of *** identify novel cardiomyopathy-associated splicing factors,RNA-seq and tissue-enrichment analyses were performed,which identified up-regulated expression of Sam68-Like mammalian protein 2(SLM2) in the left ventricle of dilated cardiomyopathy(DCM) *** the human heart,SLM2 binds to important transcripts of sarcomere constituents,such as those encoding myosin light chain2(MYL2),troponin 13(TNNI3),troponin T2(TNNT2),tropomyosin 1/2(TPM1/2),and titin(TTN).Mechanistically,SLM2 mediates intron retention,prevents exon exclusion,and thereby mediates alternative splicing of the mRNA regions encoding the variable proline-,glutamate-,valine-,and lysine-rich(PEVK) domain and another part of the I-band region of *** summary,SLM2 is a novel cardiac splicing regulator with essential functions for maintaining cardiomyocyte integrity by binding to and processing the mRNAs of essential cardiac constituents such as titin.

关键词： Splicing Titin Dilated cardiomyopathy KHDRBS3 SLM2

Long noncoding RNA MALAT1-derived mascRNA is involved in cardiovascular innate immunity

在线全文

学校读者我要写书评

暂无评论

Journal of Molecular Cell Biology 2016年第2期8卷 178-181页

作者： Martina Gast Blanche Schroen Antje Voigt Jan Haas Uwe Kuehl Dirk Lassner Carsten Skurk Felicitas Escher Xiaomin Wang Adelheid Kratzer Katharina Michalik Anna Papageorgiou Tim Peters Madlen Loebel Sabrina Wilk Nadine Althof Kannanganattu VPrasanth Hugo Katus benjamin meder Shinichi Nakagawa Carmen Scheibenbogen Heinz-Peter Schultheiss Ulf Landmesser Stefanie Dimmeler Stephane Heymans Wolfgang Poller Department of Cardiology and Pneumology Campus Benjamin FranklinCharite–Universitatsmedizin BerlinBerlinGermany Center for Heart Failure Research Cardiovascular Research Institute Maastricht(CARIM)Maastricht UniversityMaastrichtNetherlands Institute of Biochemistry Campus Charite MitteCharite–Universitatsmedizin BerlinBerlinGermany Otto-Meyerhof-Centrum University of HeidelbergHeidelbergGermany Medizinische Klinik University of HeidelbergHeidelbergGermany Institute for Cardiac Diagnostics and Therapy(IKDT) BerlinGermany Institute for Cardiovascular Regeneration Goethe University FrankfurtFrankfurtGermany Institute for Medical Immunology Campus Virchow KlinikumCharite–Universitatsmedizin BerlinBerlinGermany Berlin Center forRegenerative Therapies(BCRT) Charite–Universitatsmedizin BerlinBerlinGermany Department of CellandDevelopmental Biology University of Illinois at Urbana-ChampaignUrbanaIL 61801USA RNA Biology Laboratory RIKEN Advanced Research InstituteWakoSaitama 351-0198Japan German Center for Cardiovascular Research(DZHK) Site BerlinGermany DZHK Site Rhein-MainGermany

Dear Editor,Next-generation sequencing revealed that the majority of the human genome is transcribed but has no coding *** is estimated that.30000 long noncoding RNAs(lncRNAs)are expressed in humans,but their functions are largely unknown(Suckau et al.,2009;Rinn and Chang,2012;Poller et al.,2013).Consideration of noncoding genomic elements in pathogenetic studies is warranted and enabled by technological advances allowing comprehensive transcriptome mapping of protein-coding genes as well as small and long ncRNAs.

关键词： MALAT1 immunity