Paper describing automated  validation of splicing mutations using RNASeq data has been indexed in PubMed:

Validation of predicted mRNA splicing mutations using high-throughput transcriptome data.

Stephanie Dorman presented our paper, “Non-coding mutation analysis reveals previously unrecognized pathways in lymph node-invasive breast cancer,” (Abstract)  at the Annual AACR meeting.  The poster presentation was very well attended with more than 30 visitors, including representatives from several personalized medicine and genomics companies.  Many of the attendees expressed interest in the Shannon human mRNA splicing mutation and Veridical platforms, which were used to generate the results given in this paper.

Why do we sequence gene panels, exomes and complete genomes? To find mutations in genes, of course. This is the currency that allows bioinformaticists and clinicians to determine which metabolic pathways are dysregulated in patients with gene-based disease.

What has surprised me most about NGS since the development of this wonderful technology for finding variation has been the under-investment and significant ignorance (deliberate or incidental) about what constitutes a disease-related mutation. There are a number sources of false positive and negative mutations, which will invariably impact which abnormal pathways are inferred from mutation data. This has significant implications for personalizing diagnosis and therapy.

So much emphasis has placed on coding mutations that alter amino acids and create nonsense codons, in part, because of the false sense of security conferred by apparent understanding of changes in protein coding. All of the tools available for inferring pathogenicity from missense changes are to some extent inaccurate and generally produce results inconsistent with one another.  Even when they are consistent, it is not a guarantee of accuracy*. Leading researchers, recognizing this, have typically shunned incorporation of these results landmark NGS papers. 

Nonsense codons and intronic dinucleotides at exon boundaries recognized in splicing are thought to be the most rigorous evidence for pathogenicity.   Many nonsense codons induce exon skipping, and  these events frequently preserve reading frame, which should dampen confidence about pathogenicity of such mutations, a potential source of false positives. The analyses of dinucleotides in splice sites are known to comprise only a small fraction of known splicing mutations.  We and others have demonstrated that splicing mutations can occur widely throughout genes (in exons and introns), either inactivating splice site and exon recognition, reducing splicing efficiency, or creating novel cryptic splice isoforms.  These account for a substantial fraction of unrecognized, highly deleterious mutations in NGS data. Our company, Cytognomix, has released peer-reviewed software which predicting such mutations in genomic sequences (shannonpipeline.cytognomix.com), and companion software (veridical.org) using RNASeq data for validating these predictions.

Our ongoing analysis of complete gene sequences in breast cancer has revealed breathtaking levels of sequence variation in introns, promoter and downstream regions that dwarf that seen in exons alone. Variants in promoter regions have been proven to explain expression levels in normal individuals. It seems likely that these gene regions will harbor disease causing variants in many patients. Using information theory-based methods we are prioritizing the most likely regulatory mutation candidates. Our aim is to produce a full catalogue of likely disease-causing variants in each patient, to improve our understanding of dyregulated pathways in each individual.

The blog entry has also been posted on the NGSLeaders Discussion Board on Data Analysis and Informatics at www.ngsleaders.org

*The fact that an opinion has been widely held is no evidence whatever that it is not utterly absurd.”
— Bertrand Russell

The article has been published for 7 weeks and has been downloaded or viewed 562 times. Three peer reviews have been submitted to date: one approved and two approved with reservations. We are addressing these comments now and modifying the manuscript accordingly.

Viner C, Dorman SN, Shirley BC and Rogan PK (2014) Validation of predicted mRNA splicing mutations using high-throughput transcriptome data [v1; ref status: indexed, http://f1000r.es/2no] F1000Research 2014, 3:8 (doi: 10.12688/f1000research.3-8.v1)

The paper has also been highlighted on the RNA-Seq Blog.

Our abstract, “Identification, Prediction and Prioritization of Non-Coding Variants of Uncertain Significance in Heritable Breast/Ovarian Cancer,” has been accepted for oral presentation at the BRCA: Twenty Years of Advances – The Fifth International Symposium on Hereditary Breast and Ovarian Cancer Conference in Montreal, Quebec (Apr 23-25).

The authors are:

E.J. Mucaki(1), N. Caminsky(1), A. Stuart(1), C. Viner(1), B. Shirley(2), J.H. Knoll(1,2), P. Ainsworth(1), P.K. Rogan(1,2)

1) University of Western Ontario, 2) Cytognomix Inc., London,  Canada

The Shannon mutation pipeline is now available by online subscription.

See our announcement !

The paper that we presented at the 2013 EPR BioDose meeting is now in press in the journal:  Radiation Protection Biodosimetry:

Automating dicentric chromosome detection from cytogenetic biodosimetry data

Peter K. Rogan*¹, Yanxin Li¹, Asanka Wickramasinghe¹, Akila Subasinghe¹, Natasha Caminsky¹, Wahab Khan¹, Jagath Samarabandu¹, Joan H. Knoll¹, Ruth Wilkins²,  and Farrah Flegal³

¹University of Western Ontario, 1151 Richmond Street, London, ON, Canada, N6A 3K7, ²Health Canada, 775 Brookfield Road, PL 6303B, Ottawa, ON, Canada K1A 1C1, ³Atomic Energy of Canada Ltd., STN 51, Bldg 513, Chalk River, ON, Canada K0J 1J0

 

 

Stephanie Dorman’s presentation of our analysis of Cancer Genome Atlas genomic and clinical data of somatic breast cancer on January 10, 2014  has been highlighted in the Breast Cancer Society of Canada blog:

http://www.bcsc.ca/blog/2014/01/29/london-citywide-breast-cancer-retreat-2014/

We have just published a  paper describing method and companion software for experimental validation of mutations with NGS (RNASeq) data:

Validation of predicted mRNA splicing mutations using high-throughput transcriptome data. Coby Viner, Stephanie N. Dorman, Ben C. Shirley, Peter K. Rogan. published in F1000Research ( http://f1000research.com/articles/3-8/v1 )

This approach fills a critical unmet need in genome-scale mutation analysis. Contact us if you want to trial the software.

Our abstract, “Identification, Prediction and Prioritization of Non-Coding Variants of Uncertain Significance in Heritable Breast/Ovarian Cancer,” has been accepted for presentation at the BRCA: Twenty Years of Advances – The Fifth International Symposium on Hereditary Breast and Ovarian Cancer Conference in Montreal, Quebec (Apr 23-25).

The authors are:

E.J. Mucaki(1), N. Caminsky(1), A. Stuart(1), C. Viner(1), B. Shirley(2), J.H. Knoll(1,2), P. Ainsworth(1), P.K. Rogan(1,2)

1) University of Western Ontario, 2) Cytognomix Inc., London,  Canada

Cytognomix has agreed to provide hybridization enrichment products to the Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine at the Istituto Nazionale dei Tumori (INT), Fondazione IRCCS-Milan for sequencing of genes associated inherited neoplastic disease. The company’s scProbe design technology was selected by the INT because it provides the highest depth and breadth of sequence coverage for sequencing of complete cancer genes on the market today.

US Patent 8,605,981, titled “Centromere detector and method for determining radiation exposure from chromosome abnormalities,” has been issued to Peter K.  Rogan, Joan H. Knoll, Jagath Samarabandu, and Akila Subasinghe. The patent is assigned to Cytognomix. The inventors have developed Automated Dicentric Chromosome Identifier (ADCI) software based on this technology. The present version of ADCI runs threaded on a multi-CPU desktop PC, and has been parallelized for high throughput processing on a number of multi-core systems, including IBM’s BlueGene/Q.  We have achieved high throughput of automated chromosome-based biodosimetry analysis, completing processing of images from 1000 samples in an hour with this hardware platform.

The Canadian Breast Cancer Foundation has recognized our progress in developing novel next generation DNA sequencing and companion bioinformatic analysis technologies for early detection of breast cancer.

See their profile at:  Canadian Breast Cancer Foundation article on Dr. Peter Rogan.

Update January 20, 2013. CBCF has published a new  full profile of our project.

Stephanie Dorman published a method that improves the accuracy of a test commonly used in the genetic analysis of many types of cancers (Dorman et. al. Expanding probe repertoire and improving reproducibility in human genomic hybridization, Nucleic Acids Research, 41:e81, 2013). This technology was developed, supported and patented by Cytognomix.

See:    The Breast Cancer Society of Canada profiles Cytognomix supported research

Dr. Peter Rogan is presenting at the European Institute of Oncology (IEO) Education Masterclass on 28 Nov in Milan, Italy. His talk is titled “Overview of bioinformatics tools for identification of new determinants of cancer risk.”

Brochure describing: Course at IEO 28_29 nov 2013 on inherited breast cancer

On Monday, November 11 at 2 PM, Dr. Rogan will be presenting a seminar in the DIPARTIMENTO DI BIOTECNOLOGIE MEDICHE E MEDICINA TRASLAZIONALE (Medical Biotechnology and Translational Medicine) at the Universita degli Studi di Milano, titled:

“Deciphering non-coding variants of uncertain significance in inherited and somatic breast cancer”

Location: Room D, ground floor, Palazzo LITA, Via Fratelli Cervi 93, 20090 Segrate, Lombardia Italy

Host : Cristina Battaglia  (cristina.battaglia@unimi.it)

On October 30, Dr. Peter Rogan will be presenting;

“New genetic variants in inherited and somatic breast cancer: clinical implications”

at 12 PM IEO-Istituto Europeo di Oncologia, via Ripamonti 435, 20141 Milano.

He will describe use of the Shannon pipeline and other tools to analyze mutations in inherited and somatic breast cancer.

Contact: Cristina Bonvicini, IEOEducation (ieoedu.seminars@ieo.it), +39 02 57489.814

Since our presentation yesterday at the 2013 American Society of Human Genetics meeting, we have received several requests for information about our ab initio single copy FISH probes.  These FISH probes are only available from Cytognomix and  are the only products that can be used to detect differential accessibility in metaphase chromosomes.  No other company makes these or equivalent FISH products.

Contact:

info@cytognomix.com or

info@scprobe.info