New article in bioRxiv:
Expression changes confirm predicted single nucleotide variants affecting mRNA splicing. E. J. Mucaki and P.K. Rogan. (https://www.biorxiv.org/content/10.1101/549089v1)

This paper describes high quality qRT-PCR and microarray expression data of predicted splicing variants. The results confirm results of genome-wide TCGA and ICGC RNASeq findings (https://f1000research.com/articles/7-1908/v1). The genome scale results were obtained using CytoGnomix’s MutationForecaster (http://mutationforecaster.com ) system.

CytoGnomix is licensing its Automated Dicentric Chromosome Identifier and Dose Estimator  product  to a Canadian government-owned contractor-operated laboratory through 2020.  This organization’s primary business is in nuclear science and technology.

We have just updated the CytoVA software product. It now contains all PubMed references through Dec 2018 and the most recent version of the human phenotype ontology (HPO). With CytoVA (see below), you can query Shannon pipeline, Veridical or VEP output, the list of predicted deleterious variants, with this software  for HPO clinical phenotypes.  The software  reports the articles, and PubMed index codes that support the relationship between the gene variants and the queried phenotype. It’s a very effective way of filtering exome or complete genome sequencing results to limit the best candidate variants.

Lu R and Rogan PK. Transcription factor binding site clusters identify target genes with similar tissue-wide expression and buffer against mutations [version 1 ]. F1000Research 2018, 7:1933 (DOI: 10.12688/f1000research.17363.1):     https://f1000research.com/articles/7-1933/v1

Shirley BC, Mucaki EJ and Rogan PK. Pan-cancer repository of validated natural and cryptic mRNA splicing mutations [version 1; referees: awaiting peer review].  F1000Research 2018, 7:1908     (https://doi.org/10.12688/f1000research.17204.1

Website to perform database search:   https://validsplicemut.cytognomix.com/

RADIATION DOSE ESTIMATION BY COMPLETELY AUTOMATED INTERPRETATION OF THE

DICENTRIC CHROMOSOME ASSAY

Li, Yanxin; Shirley, Ben; Wilkins, Ruth; Norton, Farrah; Knoll, Joan; Rogan,Peter

Radiation Protection Dosimetry, in press

Figure 2 (from the article): Representative heat maps of chromosome object count distributions for Health Canada calibration (HC ##Gy.csv) and exercise (S##.csv) samples. Show: legend indicates significance of pairwise comparisons of object counts in (bottom panel) unselected vs. (top panel) Model B_C filter (5) selected images from each sample. Values close to 10^0 are not significant, whereas values such as 10^-20 are significant differences between samples. The legend displays probability thresholds of Wilcoxon signed rank tests of chromosome object counts between each pair of samples from the HC laboratory. Similar results were obtained for other chromosomal features.

Mucaki EJ, Zhao J, Lizotte D, Rogan PK. Predicting response to platin chemotherapy agents with biochemically-inspired machine learning. Signal Transduction and Targeted Therapy, in press.

A preprint of this article has been released on the  BioRxiv server:   https://doi.org/10.1101/231712

CytoGnomix and the University of Western Ontario presented several papers about differential accessibility of single copy FISH probes to metaphase chromosomes at the Chromosome Pairing conference, held at Laurentian University, Sudbury, Ontario, Canada. We are grateful to Prof. Thomas Merritt for inviting us to participate in this exciting conference. The following talks were presented:

Seana Hill (Knoll and Rogan labs): Defining differentially accessible domains within human
metaphase homologues.

Jerry Wang (Knoll and Rogan labs): Expanding the catalog of differentially compacted loci
on homologous chromosomes in the human genome.

Peter Rogan (Rogan lab): A proposed mechanism to establish differential allelic
accessibility to homologous metaphase chromosomes.

In a collaboration with the ENIGMA Consortium members, we have used bioinformatic and functional genomic analysis to identify gene variants that affect the expression of the BRCA1 and BRCA2 genes. The article is:

Burke LJ, Sevcik J, Gambino G1, Tudini E, Mucaki EJ, Shirley BC, Whiley P, Parsons M, DeLeeneer K, Gutiérrez-Enríquez S, Pena MS, Caputo S, Santana dos Santos E, Soukupova J, Janatova M,  Zemankova P, Lhotova K, Stolarova L, Borecka M, ENIGMA consortium, Edwards S, Blok R, Hansen TvO, Diez O, Vega A, Claes K, Rouleau E, , Radice P, Peterlongo P, Rogan PK, Caligo M, Spurdle AB and Brown MA. BRCA1 and BRCA2 5’ non-coding region variants identified in breast cancer patients alter promoter activity and protein binding, Human Mutation.

Link to full text of accepted paper:   http://www.cytognomix.com/?attachment_id=4541

Permanent link:  https://doi.org/10.1002/humu.23652

A large international consortium based at Harvard University has demonstrated parental homolog-specific differences in chromatin accessibility on human chromosome 19:

Nir et al. BioRxiv  doi: 10.1101/374058 (Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling)

This work reproduces previous reports previously published  by CytoGnomix scientists using our patented scFISH™ probes:

Khan et al. Molecular Cytogenetics 2014 7:70  (Localized, non-random differences in chromatin accessibility between homologous metaphase chromosomes)

Khan et al.  Molecular Cytogenetics 2015 8:65 (Reversing chromatin accessibility differences that distinguish homologous mitotic metaphase chromosomes)

The 2018 Impact report from the  Southern Ontario Smart Computing for Innovation Platform (SOSCIP), which supports the development of a supercomputer version of the Automated Dicentric Chromosome and Dose Estimation (ADCI) system in IBM Blue Gene/Q, contains an article about our project:

https://www.soscip.org/wp-content/uploads/2017/08/soscip_impactreport2018_pages.pdf

Population scale biodosimetry with the Automated Dicentric Chromosome Identifier and Dose Estimator (ADCI) software system. (Platform) Rogan PK, Ali, S, Li Y, Shirley B, Wilkins R, Flegal F, Cooke R, Peerlaproulx T, Waller E, Knoll JHM. EPR Biodose 2018, June 11-15, Munich Germany

Optimization of image selection in Automated Dicentric Chromosome Analysis. Li Y, Shirley B, Wilkins R, Flegal, F, Knoll JHM, Rogan PK. EPR Biodose 2018, June 11-15, Munich Germany.

Predicting exposure to ionizing radiation by biochemically-inspired genomic machine learning. Rogan PK, Zhao JZL, and Mucaki EJ. EPR Biodose 2018, June 11-15, Munich Germany.

Comprehensive prediction of responses to chemotherapies by biochemically-inspired machine learning. (Best Poster session) Rogan PK, Zhao JZL, Mucaki EJ.  European Society of Human Genetics 2018, June 16-19, Milan Italy.

https://f1000research.com/articles/7-233/v1

As of today, we have transitioned the website cytognomix.org to:

http://academic.cytognomix.com

The site contains our published articles, lectures and presentations about human genetics and molecular biology. All of the legacy content at this site (1980-2007) will be  preserved on the new site.

Please update your browser bookmarks to reflect this change.

CytoGnomix’s Mutation Forecaster: Key to discovery of mutations in novel ALS gene. Nicolas et al. Genome-wide Analyses Identify KIF5A as a Novel ALS Gene. Neuron 97:1268-1283.e6, 2018
http://www.cell.com/neuron/fulltext/S0896-6273(18)30148-X

From our subscriber, Dr. John Landers (U. Mass. School of Medicine):

“We used the application ASSEDA (Automated Splice Site and Exon Definition Analyses) to predict any mutant mRNA splice isoforms resulting from these variants (Mucaki et al. 2013). This algorithm was chosen as it is known to have high performance in splice prediction (Caminsky et al., 2014). ASSEDA predicted a complete skipping of exon 27 for all variants, yielding a transcript with a frameshift at coding amino acid 998, the deletion of the normal C-terminal 34 amino acids of the cargo-binding domain, and the extension of an aberrant 39 amino acids to the C terminus (Table 3; Figures 4B and 4C). The presence of transcripts with skipped exon 27 was demonstrated by performing…”

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