Biodosimetry: Automated Dicentric Chromosome Identifier

Dicentric chromosomes detected with Cytognomix’s proprietary method. Centromeres are labeled with yellow and blue dots.

Ionizing radiation produces characteristic chromosome changes. The altered chromosomes contain two central constrictions, termed centromeres, instead of one (known as dicentric chromosomes [DCs]). Chromosome biodosimetry is approved by the IAEA for occupational radiation exposure, radiation emergencies, or monitoring long term exposures. In emergency responses to a range of doses, labs need efficient methods that identify DCs.

Cytognomix has developed a novel approach to find DCs that is independent of chromosome length, shape and structure from different laboratories (paper: TBME). The Automated Dicentric Chromosome Identifier and Dose Estimator (ADCI) software examines images produced by any of the existing automated metaphase capture systems found in most cytogenetic laboratories.

ADCI is now available for for trial or purchase (link)

Or contact us for details (pricing)

ADCI uses machine learning based algorithms with high sensitivity and specificity that distinguish monocentric and dicentric chromosomes (Try the Dicentric Chromosome Identifier web app). With novel image segmentation, ADCI has become a fully functional cytogenetic biodosimetry system. ADCI takes images from all types of commercial metaphase scanning systems, selects high quality cells for analysis, identifies dicentric chromosomes (removing false positives), builds biodosimetry calibration curves, and estimates exposures. ADCI fulfills the criteria established by the IAEA for accurate triage biodosimetry of a sample in less than an hour. The accuracy is comparable to an experienced cytogeneticist. Check out our online user manual: wiki.

Early development of ADCI was supported by the US Public Health Service 5U01AI091173-02. Product testing is currently supported by the Build-in-Canada Innovation Progam. Working with IBM Canada and Western University, we have developed a high performance computing version, ADCI-BG/Q has demonstrated adequate throughput to handle the workload from a simulated mass casualty event (1000 samples in 1.4 hr; Li et al. IEEE Intnl Conf on Automation for Sustainability, 2012. Pp. 30 – 35 DOI 10.1109/ICIAFS.2012.6420039 (paper: ICIAFS); and paper: Rogan et al. Radiat Prot Dosimetry, 2014).

Some presentations and articles about ADCI:

Yanxin Li, Joan H. Knoll, Ruth Wilkins, Farrah Flegal, and Peter K. Rogan. Automated Discrimination of Dicentric and Monocentric Chromosomes by Machine Learning-based Image Processing. EPR Biodosimetry International conference. Dartmouth College Oct 4-8, 2015. Now published in Microscopy Research and Technique (link). Manuscript (pdf): Li et al 2016. Companion on-line software, the Dicentric Chromosome Analyzer is at: cytobiodose.cytognomix.com

Peter K Rogan, Yanxin Li, Ruth Wilkins, Farrah Flegal, Joan H. Knoll. Radiation dose estimation by automated chromosome biodosimetry. EPR Biodosimetry International conference. Dartmouth College Oct 4-8, 2015. Now published in Radiation Protection Dosimetry (link). Manuscript (pdf): Rogan et al. 2016.

*ADCI is covered by US Patent 8,605,981, German Patent 11 2011103687, and others pending.

Software for validation of predicted mRNA splicing mutations

We have released Veridical, which uses transcriptomic data to assess evidence for all predicted splicing mutations in a genome, exome or gene panels. This software has been integrated into our new MutationFore cas te r webservice. To validate splicing mutations predicted by the Shannon pipeline, a set of gene variants and RNASeq data from the same individual are uploaded. The online version features built-in controls, automated analyses, and directly returns results to users.

Commercial, long term, multi-seat licenses and installation support for the standalone version are also available. Contact Cytognomix.

Previous trial users of Veridical may register with MutationForecaster. After logging in, subscriptions to use Veridical and all other products can be activated through the Account menu on the system.

Read our peer-reviewed paper: Validation of predicted mRNA splicing mutations using high-throughput transcriptome data. C. Viner, S.N. Dorman, B.C. Shirley, P.K. Rogan. F1000Research 2014, 3:8.

Read Testimonials for Veridical

Watch C. Viner’s award winning presentation at 2014 Compute Ontario Research Day:

Presentation: Handouts

Abbreviated User Guide: VeridicalUserDoc

Program Documentation: Veridical program Documentation

Veridical is patent pending.

Automated Splice Site and Exon Definition Server (ASSEDA)

ASSEDA has been incorporated into Cytognomix’s MutationForecaster system. Current paid subscribers will have access to splice.uwo.ca until their subscription ends. Previous trial users of ASSEDA may register with MutationForecaster. After logging in, subscriptions to use ASSEDA and all other products can be activated through the Account menu on the system.

The software is described in “Prediction of mutant mRNA splice isoforms by information theory-based exon definition,” by Eliseos Mucaki, Ben Shirley and Peter Rogan, published in Human Mutation in 2013. The paper (link) was highlighted by the journal editors and is open access.

Since this publication, information models for 10 splicing regulatory binding factors have been added to ASSEDA and incorporated in the computation of exon definition. The next release of the software will filter results to relevant mutations, by limiting results to expressed factors and target genes based on tissue of origin.

Paid subscribers, including renewals, include laboratories at:

North York General Hospital (Ontario, Canada)
Trillium Health Care (Ontario, Canada)
INSERM (Paris, France)
Beijing Tongren Hospital (Beijing, PRC)
Tulane University (New Orleans, USA)
Johns Hopkins Medical Institutions (Baltimore, USA)
Università di Milano-Bicocca (Monza, Italy)
The University of Hong Kong (Special Administrative Region, PRC)
University of Washington Health Sciences Center (Seattle, WA)
GSTS Pathology (London, England)
University of Padua (Padova, Italy)
University of Western Ontario (Ontario, Canada)
Università di Modena e Reggio Emilia (Modena, Italy)

Resources: Video Tutorial on the use of the ASSEDA server on You Tube.

ASSEDA is is covered by US Patent 5867402 and patents pending.

Interpretation of mutations in next generation sequencing data: Shannon pipeline

Shannon Pipeline for Human mRNA splicing and transcription factor binding site mutation analysis

This software is used to predict functionally-significant, non-coding variants in complete genome or exome sequences. Access fast, comprehensive genome-scale analysis for inactivating, leaky or cryptic splicing mutations using the reliable information theory-based methods employed in the Automated Splice Site and Exon Definition Analysis server. The latest release supports multiple input formats and processes all variants in a complete genome is <15 minutes. Available versions include:

A Web-based online version of the pipeline – now embedded within our MutationForecaster system. Contact us to submit a purchase order or for long term access.

The standalone product can be custom integrated into your existing NGS software analysis pipeline . It produces the same results as our own web-based service. Please contact Cytognomix if you are interested in this capability.
It is also distributed as an Application in the Illumina’s BaseSpace system. Download the Shannon_Pipeline Documentation or view a video presentation of results that can be obtained.

Previous trial users of the Shannon pipeline webservice may register with MutationForecaster. After logging in, subscriptions to use the Shannon pipeline and all other products can be activated through the Account menu on the system.

Read testimonials for the Shannon pipeline … Also, US National Cancer Institute renews license to the Shannon human mRNA splicing mutation pipeline.

Tutorials on the Web-based product (for assistance: Contact us):

How to interpret the results: Play video.
Basic functionality and how to submit your data: Play video.

New features in Version 2.0:

now handles insertions and deletions, (in addition to SNP snd DNPs),
integrated with the ASSEDA software
exports results to the Cytognomix User Variation Database
downstream analysis of genes containing mutations with phenotypes and literature evidence with Cytognomix Visual Analytics
performs gene set, ie. pathway, analysis on the genes found to contain mutations
has been updated to Ensembl v. 71 annotations
results can be optionally limited to Refseq genes,
and contains preset mutation filters to simplify analyses.

Try it now!

Press release: US National Cancer Institute acquires Shannon Human Splicing Pipeline

Download: Product Description and Specifications

Peer-reviewed publications: B.C. Shirley, E.J. Mucaki, T. Whitehead, P.I. Costea, P. Akan, P.K. Rogan, Interpretation,Stratification and Evidence for Sequence Variants Affecting mRNA Splicing in Complete Human Genome Sequences, Genomics Proteomics Bioinformatics (2013), 11:77-85.

CaminskyNG, MucakiEJ, PerriAM, LuR, Knoll JHM and Rogan PK. Prioritizing variants in complete Hereditary Breast and Ovarian Cancer (HBOC) genes in patients lacking known BRCA mutations. Human Mutation, 37:640-52, 2016

Mucaki, E*, Caminsky N*, Perri A, Lu R, Laederach A, Halvorsen, M, Knoll, JHM, Rogan PK. A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer, BMC Medical Genomics, 9:19, 2016.

Lu R, Mucaki E and Rogan PK. Discovery and Validation of Information Theory-Based Transcription Factor and Cofactor Binding Site Motifs, Nucleic Acids Research 2016. DOI: 10.1093/nar/gkw1036

The Ontario Genomics Institute (OGI) and Cytognomix Inc. hosted a 30 minute Webinar about the Shannon Human Splicing Pipeline – software for genome-scale splicing mutation analysis. The webinar powerpoint slides are available (ShannonPipeline-OGI-Webinar-Presentation).

How it’s used…

Mutations in BRCA1 were analyzed for changes in splice site information content and depicted in this custom genome browser track

Continue reading→

Targeted array CGH

Genomic hybridization with ab initio vs competitor probes

Wouldn’t you want the most reliable data on the market for your clinical studies?

Cytognomix can offer novel array CGH designs with expanded probe sequence repertoire and significantly improved reproducibility than other available platforms. This technology enables higher density arrays to be produced which provide higher granularity and more consistent copy number calls. Arrays can be targeted for specific genomic regions to refine results from lower resolution genome-wide studies or developed for genome-wide applications.

A subscription to our MutationForecaster system provides genome browser access to our genome-wide custom probe designs through the cytogenetic Visual Analytics Decision Support Tool. This tool displays the locations of oligonucleotide products used in microarray design.

Please contact us regarding these designs and protocols.

We have published a paper describing how ab initio sc technology improves microarray reproducibility: Expanding probe repertoire and improving reproducibility in human genomic hybridization. Stephanie N. Dorman; Ben C. Shirley; Joan H. M. Knoll; Peter K. Rogan. Nucleic Acids Research 2013; doi: 10.1093/nar/gkt048

Targeted aCGH arrays are based on our patented ab initio technology (US Patents 7,734,424, 8,209,129, and 8,407,013).

Solution capture pools for targeted deep sequencing

Cytognomix has designed and developed a unique type of reagents for targeted hybridization capture of breast cancer genes. These capture reagent have maximal coverage of complete unique gene sequences, covering exons, but also promoter, intronic, and downstream flanking genomic regions. This extensive coverage of regulatory regions is intended to produce companion data for our patented methods for interpreting non-coding variants of unknown significance. Besides single copy sequences, divergent interspersed repetitive element probes extend the genomic coverage in these genes. This targeting results in the most comprehensive coverage available (Dorman et al. Nucleic Acids Res., 2013).

Our hybridization capture array products can be used for mutation detection in hereditary cancer and pharmacogenetic applications and are ready-to-ship:

A. Inherited breast and ovarian cancer complete gene and flanking regions (Caminsky et al. submitted; Mucaki et al. submitted):

Version 1: BRCA1, BRCA2, ATM, CDH1, CHEK2, PALB2, and TP53.

Version 2: ATM, BARD1, BRCA1, BRCA2, CDH1, CHEK2, EPCAM, MLH1, MRE11A, MSH2, MSH6, MUTYH, NBN, PALB2, PMS2, PTEN, RAD51B, STK11, TP53, and XRCC2

B. Chemotherapy resistance (combined paclitaxel + gemcitabine mutation targets; Dorman et al. 2015):

Paclitaxel response: ABCB1, ABCB11, ABCC1, ABCC10, BAD, BBC3, BCAP29, BCL2, BCL2L1, BIRC5, BMF, CNGA3, CSAG2, CYP2C8, CYP3A4, FGF2, FN1, GBP1, MAP2, MAP4, MAPT, NFKB2, NR1I2, OPRK1, SLCO1B3, TLR6, TMEM243, TUBB1, TUBB4A, TUBB4B, TWIST1

Gemcitabine response: ABCB1, ABCC10, AK1, CDA, CMPK1, CTPS1, DCK, DCTD, NME1, NT5C, RRM1, RRM2, RRM2B, SLC28A1, SLC28A3, SLC29A1, SLC29A2, TYMS

C. A subscription to our MutationForecaster system provides genome browser access to our genome-wide custom probe designs through the cytogenetic Visual Analytics Decision Support Tool. This tool displays the locations of oligonucleotide products used in hybridization enrichment for Next generation sequencing.

References:

1) Dorman et al. Expanding probe repertoire and improving reproducibility in human genomic hybridization Nucleic Acids Research 2013; doi: 10.1093/nar/gkt048 This paper has been cited:

“Microarray-based comparative genomic hybridization (aCGH) is widely used in biomedical applications and life sciences research to detect and analyze structural variation in genomes, and novel applications are constantly developed (Dorman et al. 2013)…. Jonker et al. Nucl. Acids Res. (2014)“

2) Dorman et al. Genomic signatures for paclitaxel and gemcitabine resistance in breast cancer derived by machine learning. Mol. Onc. 2015. http://dx.doi.org/10.1016/j.molonc.2015.07.006

3) Mucaki et al. A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer. Preprint at BioRxiv. http://dx.doi.org/10.1101/031419 (submitted for publication)

4) Caminsky et al. Prioritizing variants in complete Hereditary Breast and Ovarian Cancer (HBOC) genes in patients lacking known BRCA mutations. Preprint at BioRxiv. http://dx.doi.org/10.1101/039206 (submitted for publication).

Contact: info@scprobe.info, 519-661-4255

Capture reagents are based on our patented ab initio technology (US Patents 7,734,424, 8,209,129, and 8,407,013)

Map

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22/ DiGeorge Sx E3

Gene:

HIRA

Interval:

IVS 13-IVS 15

Cytogenetic nomenclature: ish del(22)(q11.2)(HIRA-)

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