2008 Barcelona - European Society of Human Genetics

Concurrent Symposia 0
use of positional information . By linking differentiation programs to
cell positions on a coordinate system, an assembly of cells can be
programmed to develop into well-defined spatial patterns that are not
easily perturbed by the removal or addition of cells . In contrast to embryonic
development, the higher-order patterns of cellular specialization
in adult animals and mechanisms of their maintenance are less
well understood . Here I discuss progress in using genomic expression
programs to understand the organization and mechanisms of pattern
formation and maintenance in mammalian epithelia .
The major themes are the encoding positional identity in one class of
cells and the transfer of this information by epithelial-mesenchymal
interaction; the role of chromatin modifications in the fidelity of transcriptional
memory, and the discovery of a class of long non-coding
RNAs that regulate chromosomal domains of chromatin modification
to enable position-specific gene expression.
s07.2
Rapid high-resolution identification of balanced genomic
rearrangements by 4c technology
M. Simonis 1 , P. Klous 1 , R. Galjaard 2 , E. Rijkers 3 , F. Grosveld 1 , J. Meijerink 4 , W.
deLaat 1 ;
1 Department of Cell Biology, Erasmus MC, Rotterdam, Netherlands, 2 Department
of Clinical Genetics, Erasmus MC, Rotterdam, Netherlands, 3 Department
of Biochemistry, Erasmus MC, Rotterdam, Netherlands, 4 Department of Pediatric
Oncology, Erasmus MC, Rotterdam, Netherlands.
The architecture of DNA in the cell nucleus is an emerging key contributor
to genome function . To better understand how DNA is folded
inside the cell nucleus, we recently developed 4C technology . 4C
technology is a high-throughput technique that combines 3C (chromosome
conformation capture) technology with tailored micro-arrays to
uniquely allow for an unbiased genome-wide search for DNA loci that
interact in the nuclear space (Simonis et al ., Nature Genetics 2006) .
It is based on formaldehyde cross-linking and capturing of in vivo interacting
DNA elements, which are subsequently ligated to each other
and PCR amplified.
Here, we will show that 4C technology is also a powerful technique
for the accurate identification of balanced and unbalanced genomic
rearrangements . Balanced chromosomal rearrangements (inversions,
translocations) frequently occur in the human population and
can cause disease, but techniques for their rapid and accurate identification
are missing. 4C technology accurately reconstructs at least
5-10 megabases of the one-dimensional chromosome sequence map
around the selected genomic viewpoint . Changes in this physical map
as a result of genomic rearrangements are therefore identified by 4C
technology . We demonstrate that 4C detects balanced inversions and
translocations, but also unbalanced rearrangements like deletions, at
a resolution (~7kb) that allows immediate sequencing of the breakpoints.
Breakpoints are identified even when they are 4 megabases
away from the genomic viewpoint . We have applied 4C to samples
from patients with congenital malformations and with T cell acute lymphoblastic
leukemia (T-ALL). Using 4C, we have identified novel rearrangements
underlying T-ALL . We will show that balanced rearrangements
are identified also if they occur in a small subpopulation of cells.
4C technology therefore offers a novel high-resolution genomic approach
that can efficiently identify balanced genomic rearrangements.
s07.3
Integrative genomic approaches for the identification of
regulatory variation underlying disease risk
J. Blangero;
Dept. of Genetics, Southwest Foundation for Biomedical Research, San Antonio,
TX.
s08.1
Deciphering Developmental Disorders
N. Carter;
Wellcome Trust Sanger Institute, Genome Campus, Cambridge, United Kingdom.
Genetically determined disorders of development result in malformations
(e .g . congenital heart defects), a dysmorphic appearance (i .e .
unusual craniofacial appearance) and/or neurodevelopmental disability
. They have a profound effect on the life and health of the individual
and of their family . Many developmental disorders are caused by gene
mutations or larger chromosome rearrangements affecting gene copy
number or regulation . However, in spite of expert clinical assessment
and conventional chromosome analysis, most children with developmental
disorders remain undiagnosed and indeed are undiagnosable
using this methodology .
Recently it has become possible to screen patients for submicroscopic
chromosome imbalance (microdeletions and microduplications) and to
identify mutations in genes on a genome-wide scale . The application
of comparative genomic hybridisation to DNA microarrays (array-CGH)
has revolutionised our ability to identify small chromosome imbalances
down to a few Kb not only in patients but also as normal copy number
variation in unaffected individuals . A number of clinical laboratory
centres worldwide are now applying genomic microarray technology
to investigate a small proportion of patients with developmental delay,
learning disability and congenital malformation . However the sporadic
nature and rarity of the majority of these cases limits the ability of the
individual clinician, working in isolation, to interpret the molecular findings
from genome-wide array analysis . There is a great need for international
collaboration to report and catalogue genotype-phenotype
correlations such that clusters of individuals sharing similar genomic
rearrangements and phenotypes can be identified. To facilitate such
international collaboration, we have developed the DECIPHER database
with the general aim of providing a clinical and research tool to:
a . Aid in the interpretation of data from genomic microarray analysis
e .g . the differentiation between pathogenic and polymorphic copy
number changes
b . Utilise the human genome map via the Ensembl genome browser
to define genes involved in a specific microdeletion, microduplication,
translocation or inversion
c . Facilitate collaboration between clinical geneticists and molecular
cytogeneticists using the world-wide-web to accelerate progress in the
delineation of new syndromes and of gene function
s08.2
Processes of allelic and ectopic recombination in the human
genome
A. J. Jeffreys, I. L. Berg, M. C. Ergoren, K. G. Lam, V. E. Lawson, C. A. May,
R. Neumann, L. Odenthal-Hesse, S. Sarbajna, A. Webb;
Department of Genetics, University of Leicester, Leicester, United Kingdom.
Single molecule typing of sperm DNA allows very high resolution analysis
of meiotic recombination events in human DNA and has revealed
narrow crossover hotspots dominating the allelic recombination landscape,
at locations that in general correlate well with regions of breakdown
of linkage disequilibrium . All 36 hotspots characterised to date
by sperm typing show a very similar morphology but vary hugely in
recombination activity . Polymorphism between men in activity at specific
hotspots is common, consistent with rapid evolutionary turnover
of hotspots, but curiously appears to be restricted to less active hotspots,
at least half of which show either quantitative variation or complete
on/off polymorphism . These polymorphisms help identify local
DNA sequence determinants and other factors that appear to influence
hotspot activity . Single DNA molecule methods have also been developed
to explore ectopic recombination between locally repeated DNA
sequences. Analysis of the α-globin gene cluster has revealed recombinational
exchanges between the duplicated α-γλοβιν γενεs leading
to apparently reciprocal duplications and deletions, though with some
evidence for an additional minor pathway of intramolecular deletion .
These exchanges are surprisingly common, contrasting sharply with
the rarity of rearranged chromosomes in most human populations and
implying significant selection pressure against these rearrangements,
despite the lack of obvious phenotypic effect in individuals carrying
these copy number variants . Unlike recombination at allelic crossover
hotspots, exchanges between α-globin genes are not restricted to meiosis
but also arise mitotically to give various classes of rearrangement
whose frequencies can be erratically inflated by mutational mosaicism,
even in the germline . Similar analysis of Lepore-type deletions in the
β-globin gene cluster has provided further support for distinct allelic
and ectopic recombination pathways, with evidence that a very active
allelic recombination hotspot within the cluster is not responsible for
driving ectopic exchanges .