Samstag, 18. Juni 2016

Toward reliable biomarker signatures in the age of liquid biopsies

Toward reliable biomarker signatures in the age of liquid biopsies - how to standardize the small RNA-Seq workflow
Dominik Buschmann, Anna Haberberger, Benedikt Kirchner, Melanie Spornraft, Irmgard Riedmaier, Gustav Schelling and Michael W. Pfaffl
Nucleic Acids Research, June 17, 2016 doi:10.1093/nar/gkw545

Small RNA-Seq has emerged as a powerful tool in transcriptomics, gene expression profiling and biomarker discovery. Sequencing cell-free nucleic acids, particularly microRNA (miRNA), from liquid biopsies additionally provides exciting possibilities for molecular diagnostics, and might help establish disease-specific biomarker signatures. The complexity of the small RNA-Seq workflow, however, bears challenges and biases that researchers need to be aware of in order to generate high-quality data. Rigorous standardization and extensive validation are required to guarantee reliability, reproducibility and comparability of research findings. Hypotheses based on flawed experimental conditions can be inconsistent and even misleading. Comparable to the well-established MIQE guidelines for qPCR experiments, this work aims at establishing guidelines for experimental design and pre-analytical sample processing, standardization of library preparation and sequencing reactions, as well as facilitating data analysis. We highlight bottlenecks in small RNA-Seq experiments, point out the importance of stringent quality control and validation, and provide a primer for differential expression analysis and biomarker discovery. Following our recommendations will encourage better sequencing practice, increase experimental transparency and lead to more reproducible small RNA-Seq results. This will ultimately enhance the validity of biomarker signatures, and allow reliable and robust clinical predictions.

Montag, 25. April 2016

qPCR NEWS April 2016 -- Powerful tools -- MIQE press review -- BDQ in PMC



Dear researcher,

Our newsletter informs about the latest news in gene expression profiling using qPCR and related methods, which are compiled and summarised on www.Gene-Quantification.info
The focus of this qPCR NEWS issue is:
  • Powerful tools --  mRNA.gene-quantification.info
    • The inclusion of transcriptome anaylsis datasets to the Human Protein Atlas database makes it even more comprehensive.
    • MTD -- A mammalian transcriptomic database to explore gene expression and regulation.
  • MIQE Press Review - Find a summary of MIQE Press Review and related publications - MIQE-press.gene-quantification.info
  • Now listed in PMC -- Biomolecular Detection and Quantification -- www.ncbi.nlm.nih.gov/pmc/journals/2977/      
  • Call for Papers -- Biomolecular Detection and Quantification -- BDQ.Gene-Quantification.info
    • Recent Advances in MicroGenomics "Molecular Analysis at the Tissue-specific and Single Cell Level"
  • GenEx 6.1 -- The most powerful tool for complex qPCR data analysis  => download a free trial version -- GenEx.Gene-Quantification.info
Join the updated eConferences streaming webportal
www.eConferences.de -- Amplify your knowledge in  qPCR, dPCR and NGS!
This streaming portal is dedicated to scientists from the community of qPCR, digital PCR, Next Generation Sequencing (NGS), MicroGenomics (MG) and Molecular Diagnostics (MDx). You’ll find here all the records of 280 presentations held at qPCR & NGS and MG Events in the past years – qPCR 2010 in Vienna  to qPCR & NGS 2015 in Freising-Weihenstephan.
We provide the presentations via movie streaming technology in high quality – high resolution and perfect sound quality in high speed – on any internet browser or mobile device.

Montag, 21. März 2016

Join our next symposium -- MicroGenomics 2016


MicroGenomics 2016
The 2nd edition of this unique event will be held once again in Paris, France
2-3 June 2016,  Symposium Venue -- French National Library (La Bibliothèque National de France François Mitterand)

Aims and Topics:  Today, one of the biggest challenges for biologists is the ability to understand and analyze the genome expressed in a given cell type in the tissue environment, which means you can specifically isolate these cells and work on very small quantities of biological material. The aim of the congress is to bring together internationally renowned experts in the field and offer an overview of the present knowledge for obtaining high quality molecules and future developments in "omic" tools (DNA, RNA and protein) for genome analysis and its expression at the cell level. The latest advances in technology in the field will be introduced (flow cytometry, laser capture microdissection, NGS, digital PCR, WGA, LC-MS/MS, RPLA, etc).

The symposium will be divided into four sessions introduced by keynote lecturers, experts in their field:

  1- Sampling methods (flow cytometry, laser capture microdissection, DEP array)
  2- Microgrenomics and DNA
  3- Microgenomics and RNA and small RNA
  4- Microgrenomics and Proteins

https://www6.inra.fr/microgenomics-2016/

Donnerstag, 17. März 2016

Biomolecular Detection and Quantification Volume 7 , March 2016

Biomolecular Detection and Quantification Biomolecular Detection and Quantification
Volume 7
March 2016

 Improving the reliability of peer-reviewed publications: We are all in it together   
 Pages A1-A5
 Stephen A. Bustin, Tania Nolan

Real-time PCR probe optimization using design of experiments approach   
Original Research Article
Pages 1-8
S. Wadle, M. Lehnert, S. Rubenwolf, R. Zengerle, F. von Stetten

Optimization of digital droplet polymerase chain reaction for quantification of genetically modified organisms   
Original Research Article
Pages 9-20
Lars Gerdes, Azuka Iwobi, Ulrich Busch, Sven Pecoraro 
qPCR based mRNA quality score show intact mRNA after heat stabilization
Original Research Article
Pages 21-26
Oskar Karlsson, Lova Segerström, Robert Sjöback, Ingrid Nylander, Mats Borén



Evaluation of microbial qPCR workflows using engineered Saccharomyces cerevisiae 
Original Research Article
Pages 27-33
S.M. Da Silva, L.K. Vang, N.D. Olson, S.P. Lund, A.S. Downey, Z. Kelman, M.L. Salit, N.J. Lin, J.B. Morrow 

Sonntag, 6. März 2016

GenEx 6.1 offers advanced methods to analyze real-time qPCR data with simple clicks of the mouse

TATAA Biocenter, Europe´s leading provider of genomic services using quantitative real-time PCR (qPCR), and MultiD Analyses, Europe’s prime software developer for the analysis of multivariate data, offers an advanced GenEx version 6.1 for accurate analysis of qPCR data compliant with current MIQE guidelines and Clinical Laboratory Standards Institute (CLSI) guidelines.

The GenEx version 6.1 include:
Estimating PCR efficiency, testing for outliers, testing linear model, estimating dynamic range, estimating random error, estimating limit of detection, estimating limit of quantification, estimating concentrations of unknowns, evaluation of precision, and verification of precision. For all estimates confidence intervals are calculated. Additional new features include: transcript distribution for single cell analysis, Survival Analysis, Receiver Operator Characteristics (ROC), Wizard for ProSeek protein analysis, and reader for 3DGene microRNA analysis.

“We have been using GenEx for many years at Technical University of Munich. With every new released version we are impressed by the many clever functionalities introduced for RT-qPCR analysis, especially the data normalisation and visualisation tools like PCA or HCA”, says Michael W. Pfaffl. “The new CLSI compliant analyses are most interesting to us and a natural extension of the MIQE guidelines”.




Attached is the full press release, please contact us if you have any questions!