Pan-Cancer Splicing Web Beacon to be Presented at ACMG Meeting

We’re giving a demonstration and a poster presentation of our new GA4GH-compliant web-based Beacon (https://validsplicemut.cytognomix.com) at the 2019 American College of Medical Genetics and Genomics annual conference this week.
Here are the details:

Pan-Cancer Repository of Validated Natural and Cryptic mRNA Splicing MutationsCategory: “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

An e-poster is available on the CytoGnomix website (direct link to poster). The work has been published in F1000Research (link).

If you’d like to meet with Dr. Rogan, please contact him at info@cytognomix.com

This Beacon resource was created using the MutationForecaster system.

March 20, 2019. Presentation at the 2019 American College of Medical Genetics and Genomics annual conference

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.

 

 

 

 

September 19. Abstract on metaphase epigenetics: platform presentation at American Society of Human Genetics meeting

Non-random, locus-specific differences in DNA accessibility are present in homologous metaphase chromosomes. W. A. Khan1,3, P. K. Rogan2,3,4, J. H. M. Knoll1,3,4 1) Department of Pathology; 2) Departments of Biochemistry and Computer Science; 3) University of Western Ontario, London, Ontario, Canada; 4) Cytognomix, London, Ontario, Canada.
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Condensation differences between heterochromatin and euchromatin along the lengths of homologous, mitotic metaphase chromosomes are well known. This study describes differences in metaphase compaction between homologous euchromatic loci. We report molecular cytogenetic data showing local differences in condensation between homologs that are related to differences in accessibility (DA) of associated DNA probe targets. Reproducible DA was observed at ~10% of 450 distinct genomic regions mapped by single copy fluorescence in situ hybridization (scFISH). Fourteen short (1.5-5kb) sc and low copy (lc) FISH probes (from chromosomes 1, 5, 9, 11, 15, 16, 17, 22) targeting genic and non-genic regions with and without DA were developed and hybridized to cells from 10 individuals with cytogenetically-distinguishable homologs. Differences in hybridization were non-random for 6 genomic regions (RGS7CACNAB1HERC2PMP22:IVS3, ADORA2B:IVS1, ACR) and were significantly-biased towards the same homolog (p< 0.01; n = 355 cells). The imprinted paternal chromosome 15 in a three-generation pedigree also showed non-random bias in DA. DNA probes within CCNB1C9orf66ADORA2B:Ex 1-IVS1, PMP22:IVS4-Ex 5, and a nongenic region within 1p36.3 did not show DA, while OPCML showed unbiased DA. A subset of probes was mapped onto chromosome topography by FISH-correlated atomic force microscopy (AFM). To quantify DA and pinpoint probe locations, we performed 3D-structured illumination super-resolution microscopy (3D-SIM). 3D anaglyph videos showed genomic regions with DA having nearly 5-fold larger differences in volumetric integrated probe intensities between homologs. Additional non-DA probes (NOMO1NOMO3) hybridized to grooves in chromosome topography and exhibited a narrow range of probe depths (average: 0.08 μm) along axial and lateral axes of the 2 homologs. In contrast, probe for targets with DA (HERC2PMP22:IVS3, ACR) significantly differed in probe depth (average: 0.77 μm) and volume (p < 0.05) between each homolog. Interestingly, genomic regions without DA are enriched in epigenetic marks (DHS, H3K27Ac, H3K4me1) of accessible interphase chromatin to a greater extent than regions with DA, suggesting these differences may be correlated with epigenetic marks established during the previous interphase. In summary, we present several lines of evidence that regional differences in condensation between homologs are programmed during metaphase chromosome compaction.

Click here for presentation details:  session, location, time.

April 24, 2012. Mutation interpretation in deep sequencing data

Cytognomix’s new software product, the Shannon pipeline for human splicing mutation analysis of NGS sequencing data was presented at the BioIT World Conference and Expo (Apr 24-26, 2012), Boston.

Dr. Rogan describes our poster:

Large scale interpretation and stratification of non-coding sequence variants in the human genome. Ben Shirley1,Eliseos Mucaki2, & Peter Rogan1,2,3. Depts of Computer Science1 and Biochemistry2, and Cytognomix Inc3, London ON, Canada.