Applications of genomic arrays in research and diagnostics
Arkadiusz Piotrowski
Rudbeck Laboratory, Uppsala University
Alterations in DNA copy number, indicating failures in the mechanisms that
maintain the integrity of the genome, contribute to tumorigenesis and may
also act as a phenotype modifier in other genetic syndromes. These failures
may lead to the aberrant function of certain genes. Discovery and
functional assessment of Copy Number Polymorphism (CNP) and chromosomal
aberrations are essential for understanding the biology of both normal and
diseased phenotypes.
Genomic microarrays can be used in combination with comparative genomic
hybridization (array-CGH) to assess DNA copy number imbalances in the
genomes of many different genetic disorders. In a typical array-CGH
measurement total genomic DNA is extracted from test and reference cell
populations, differently labeled with fluorescent dyes, and hybridized to
genomic microarrays. The development of whole genome, high resolution
arrays makes it possible to acquire a complete picture of genetic
abnormalities and CNP.
In this talk we will introduce the principles and our solutions for
constructing and using high resolution genomic arrays. We will present our
preliminary results from the investigation of CNP in normal population
using whole genome 32K BAC-array (average resolution 100kb). Furthermore,
we describe our studies of genetically determined disorder
neurofibromatosis type 1 on a PCR-based specialized, high resolution array
(below 10kb). We also show the potential of genomic arrays in the study of
CpG methylation in breast cancer and comparative methylation studies in
normal tissues.
We note that high resolution genomic arrays create formidable data
management and analysis problems.
Copy Number profiling from array-CGH data
Robin Andersson
The Linnaeus Centre for Bioinformatics
Uppsala University
The large amount of data generated from genomic arrays experiments requires
automatic procedures for the management and classification of copy number
profiles of tumor DNA. We will present our bioinformatics solutions to
these issues. In particular, we will discuss a new, statistically motivated
method for CNP profiling.
This research is jointly directed by Professors Jan Dumaqski, Rudbeck
Laboratory and Jan Komorowski, The Linnaeus Centre for Bioinformatics.
Seminarium odbędzie się w dniu 6 marca 2006 o godz. 12:30
w sali 3099 w siedzibie ICM na Wydziale Geologii,
ul. Żwirki i Wigury 91.
2 marca 2006
