March 26, 2013. New article published on chromosome centromere structure and composition.

Posted on March 26, 2013March 29, 2014 by Peter Rogan

Khan W.A., Chisholm R., Tadayyon S., Subasinghe A., Norton P., Samarabandu J., Johnston L.J., Knoll J.H., Rogan P.K. Relating Centromeric Topography in Fixed Human Chromosomes to α-Satellite DNA and CENP-B Distribution. Cytogenetics and Genome Research, 2013 (DOI: 10.1159/000348744).

Abstract

Despite extensive analyses on the centromere and its associated proteins, detailed studies of centromeric DNA structure have provided limited information about its topography in condensed chromatin. We have developed a method with correlative fluorescence light microscopy and atomic force microscopy that investigates the physical and structural organization of α-satellite DNA sequences in the context of its associated protein, CENP-B, on human metaphase chromosome topography. Comparison of centromeric DNA and protein distribution patterns in fixed homologous chromosomes indicates that CENP-B and α-satellite DNA are distributed distinctly from one another and relative to observed centromeric ridge topography. Our approach facilitates correlated studies of multiple chromatin components comprising higher-order structures of human metaphase chromosomes.

March 26, 2013. New US Patent issued.

Posted on March 26, 2013May 20, 2014 by Peter Rogan

US Pat. No.8,407,013 issued: “Ab initio generation of single copy probes”.

This patent covers single copy probes that also contain divergent repetitive sequences, which under certain conditions, hybridize like single copy sequences. This expands the human genomic real estate accessible for single copy genomic analysis techniques. Cytognomix has used this approach to produce FISH probes in regions that could not be accessed by repeat masking, genomic microarrays, and capture arrays for next generation sequencing.

If you are interested in licensing any of these fields of use, please contact us at info@cytognomix.com.

March 15, 2013. Paper describing the Shannon pipeline for human mRNA splicing mutation analysis.

Posted on March 15, 2013March 29, 2014 by Peter Rogan

Interpretation, Stratification and Evidence for Sequence Variants Affecting mRNA Splicing in Complete Human Genome Sequences.

B.C. Shirley, E.J. Mucaki, T. Whitehead, P.I. Costea, P. Akan, P.K. Rogan (2013), Genomics, Proteomics and Bioinformatics.

DOI:10.1016/j.gpb.2013.01.008

(http://www.sciencedirect.com/science/article/pii/S1672022913000296)

March 9, 2013. New Publication on Chromosome Centromere Detection in Metaphase Cell Images

Posted on March 9, 2013March 29, 2014 by Peter Rogan

Intensity Integrated Laplacian Based Thickness Measurement for Detecting Human Metaphase Chromosome Centromere Location.
Arachchige AS, Samarabandu J, Knoll J, Rogan P.
IEEE Trans Biomed Eng. 2013 Feb 20.
PMID: 23434602

Abstract

Accurate detection of the human metaphase chromosome centromere is an important step in many chromosome analysis and medical diagnosis algorithms. The centromere location can be utilized to derive information such as the chromosome type, polarity assignment etc. Methods available in literature yield unreliable results mainly due to high variability of morphology in metaphase chromosomes and boundary noise present in the image. In this article we have proposed a multi-staged algorithm which includes the use of discrete curve evolution (DCE), gradient vector flow (GVF) active contours, functional approximation of curve segments and support vector machine (SVM) classification. The standard Laplacian thickness measurement algorithm was enhanced to incorporate both contour information as well as intensity information to obtain a more accurate centromere location. In addition to segmentation and width profile measurement, the proposed algorithm can also correct for sister chromatid separation in cell images. The proposed method was observed to be more accurate and statistically significant compared to a centerline based method when tested with 226 human metaphase chromosomes.