I used the MutationForecaster system to predict the effects of intronic variants in NTRK1, The results are precise. For example, the variant NM_002529.3:c.851-33T>A was predicted to affect lariat formation in mRNA splicing, which has been verified by our laboratory. It was a bit difficult for me to interpret the results, but your company staff provided me with good support. Thank you!

Thanks for keeping me informed on your interesting work. Glad to see you are making progress on this important problem of figuring out which variants in noncoding regions may be important.

The increasing amount of sequencing data that is being generated in many biological systems has represented a real challenge to researchers in terms of trying to link individual changes to a particular biological process. The attempt, described in this work, to use IT approaches to evaluate the potential biological significance can significantly contribute to fill this gap. The laboratory of Peter Rogan has a long standing and internationally prominent role in addressing the possible consequences of sequence variants on the pre-mRNA splicing process especially with regards to its connection with human disease. The ValidSpliceMut developed in this work presents a user friendly interface that allows users to manually search for a variant (by gene name or genome coordinate range) and obtain information with regards to its possible effect on splicing. This will greatly help to better appreciate the functionality of Variants of Unknown Significance that are currently abundant genomic and transcriptomic Atlases.

The analytic tool is being applied to evaluate a variety of variants which can be difficult to interpret in terms of their effects on protein function. Analysis of variants for potential effects on splicing provides a tool to distinguish deleterious mutations from passenger variants and generates hypotheses that can be experimentally evaluated using PCR of reverse-transcribed tumor RNA.

It's a great work you and your colleagues have performed. I was guided to your homepage by a couple of publication of yours.

Cytognomix's Shannon pipeline is resolving significant data interpretation issues in cancer research.

Based on what I saw, it seems reasonably easy to run… Thank you again, this is support right up to the top of the knowledge on the product.

I was happy with the pipeline – it was easy to use and makes it feasible to analyze potential changes in splicing pattern in a large amount of data. I do think that the pipeline is very promising and could be useful for us for the analysis of whole genome/exome data.

It is indeed the first one which can provide high throughput results about the consequences of variants on splicing, and I was very eager to use it. Since we have indeed obtained useful results ... we are now discussing if it will be useful for the entire laboratory to subscribe a license, but I anticipate that we would be more interested in a CLC-free version, since we are rather using perl scripts and linux command lines for genome variant analysis.

Coby Viner presented the Veridical algorithm and software at the 2014 Compute Ontario 1st Annual Research Conference (Waterloo, Ontario, May 7, 2014) and at the 9th Annual Great Lakes Bioinformatics Conference (Cincinnati, Ohio, May 17). He received the Best Oral Presentation and Best Highlights Presentation award, respectively.

... the interpretation of genetic variants is a difficult and key issue in current research. The integration of genomic and transcriptomic data, namely the use of RNA-seq-based transcriptome characterization as a "molecular phenotype" of cells is useful and meaningful.

This outstanding tool appears very useful to screen the wealth of transcriptomic data for effects in splicing due to mutations in disease samples, and I think that it will potentially be of interest for many if not all such RNAseq-based studies. In addition, this could spur further efforts to derive similar tools with improved efficiencies. Use of this method should help establish the importance of aberrant splicing in disease as well as the effects of genomic mutations at the RNA level.

It's a great work you and your colleagues have performed. I was guided to your homepage by a couple of publication of yours.

I haven’t yet had a chance to deep-dive the article, but from my first read it looks like an interesting and novel piece of software. Congrats ...

That is sensational ... looks like a break-through. People really should start using your prediction model.

Very interesting and useful indeed!

The idea is ingenious and novel as applied to mutations affecting splicing … The software is fast and practical, being able to test thousands of variants in hundreds of samples within hours. This is the first software of its kind, and if accurate it will be a very valuable resource for clinical genomics.

The program fulfils an important need in the community, the results appear promising and will be of special interest to groups performing RNA-seq analysis in medical settings.