Go Back   SEQanswers > Events / Conferences

Similar Threads
Thread Thread Starter Forum Replies Last Post
RNase III digestion time for Ion Total RNA-seq kwalton Sample Prep / Library Generation 0 03-06-2014 10:40 AM
CASIM: RNA-Seq Power Analysis casim UK - Cambridge 1 06-27-2013 10:58 AM
Power in RNA Seq studies aoifemc RNA Sequencing 0 02-22-2013 08:00 AM
Publicly available strand-specific RNA-Seq data for MAQC samples? tmy1018 Bioinformatics 4 06-11-2012 09:18 PM

Thread Tools
Old 07-02-2014, 03:45 AM   #1
Location: Vienna

Join Date: Oct 2010
Posts: 86
Exclamation Power and Limitations of RNA-Seq: findings from the SEQC (MAQC-III) consortium

Dear All,

It is a pleasure to announce that during the Highlight Track of the ISMB 2014 conference we will give a talk where we will present the key findings of the SEQC/MAQC-III Consortium.

The main manuscript of the SEQC Consortium:
A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequence Quality Control consortium
is already at the copy-editing stage in the Nature Biotechnology and should be available shortly.

We therefore invite you to take part in the talk (HT-PP27 more details below) and following discussion as well as visit our posters adversing selected key results of the study: F45, F46, F47, F48, and N56

PP27 (HT)
Power and Limitations of RNA-Seq: findings from the SEQC (MAQC-III) consortium
Date: Monday, July 14, 11:00 am - 11:25 am
Room: 304

We present an extensive multi-centre multi-platform study of the US-FDA MAQC/SEQC-consortium, introducing a landmark RNA-Seq reference dataset comprising 30 billion reads. Several next-generation-sequencing, microarray, and qPCR platforms were examined. The study design features known mixtures, wide-dynamic range ERCC spikes, and a nested replication structure -- together allowing a large variety of complementary benchmarks and metrics. We find that none of the examined technologies can provide a ‘gold standard,’ making the built-in truths of this reference set a critical device for the development and validation of novel or improved algorithms and data processing pipelines. In contrast to absolute expression-levels, for relative expression measures, good inter-site reproducibility and agreement of across platforms could be achieved with additional filtering steps. Comparisons with microarrays identified complementary strengths, with RNA-Seq at sufficient read-depth detecting differential expression more sensitively, and microarrays achieving higher rank-reproducibility. At the gene level, comparable performance was reached at widely varying read-depths, depending on the application scenario. On the other hand, RNA-Seq has heralded a gold-rush for the study of alternative gene-transcripts. Even at read-depths beyond 100 million, we find thousands of novel junctions, with good agreement between platforms. Remarkably, junctions supported by only ~10 reads achieved qPCR validation-rates >80-100%, illustrating the unique discovery power of RNA-Seq. Finally, the modelling approaches for inferring alternative transcripts expression-levels from read counts along a gene can similarly be applied to probes along a gene in high-density next-generation microarrays. We show that this has advantages in quantitative transcript-resolved expression profiling. There is still much to do!
Pawel Labaj
plabaj is offline   Reply With Quote

ismb, maqc, rna-seq, seqc

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 08:10 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO