This article has now been accepted for publication and indexing in PubMed:
Lu R and Rogan PK. Transcription factor binding site clusters identify target genes with similar tissue-wide expression and buffer against mutations [version 2; peer review: 2 approved]. F1000Research 2019, 7:1933 (https://doi.org/10.12688/f1000research.17363.2)
The following paper has been accepted for presentation:
“Pan-Cancer Repository of Validated Natural and Cryptic mRNA Splicing Mutations”,
Category: “Laboratory genetics and genomics”, Abstract Poster Number: 754 (link to Abstract)
Where: Exhibit hall, Washington Convention Center, ACMG Clinical Genetics Meeting in Seattle, Washington
When: April 2 – 6, 2019; Poster presentation time: Friday, 4/5 from 10:30am-12:00pm
This work will be available as an ePoster AS WELL AS being presented in printed format on a poster board during the Annual Meeting. Details to access the ePoster will be available soon.
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.
Our paper, “RADIATION DOSE ESTIMATION BY COMPLETELY AUTOMATED INTERPRETATION OF THE DICENTRIC CHROMOSOME ASSAY” is now published in the journal Radiation Protection Dosimetry.
Unfortunately, the journal has not made the article open access. We have made it available on our ADCIWiki website, as permitted by the copyright agreement.
The link to the pdf full text is:
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.
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
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:
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.