2009 Vienna - European Society of Human Genetics

Genomics, Genomic technology and Epigenetics
Birmingham, United Kingdom, 2 West Midlands Regional Genetics Service,
Birmingham Women’s Hospital, Birmingham, United Kingdom.
Birt-Hogg-Dubé (BHD) syndrome is an autosomal dominantly inherited
familial cancer syndrome characterised most commonly by the
development of facial fibrofolliculomas, pulmonary cysts (predisposing
to spontaneous pneumothorax) and renal tumours. Germline mutations
in FLCN on 17p11.2 have been reported in patients with BHD
and also in patients with isolated primary spontaneous pneumothorax.
The function of the FLCN gene product, folliculin, is not well characterised
but recent studies have suggested that it may be implicated in
the regulation of several key signalling pathways including the AMPKmTOR
route.
We describe the FLCN mutation database which is based on the
Leiden Open (source) Variant Database (LOVD) system. To date the
variants described in the database were extracted from the published
literature and from unpublished mutations detected in Birmingham,
UK. However the database will be expanded to include further mutations
from partners in the European BHD Consortium (http://www.
europeanbhdconsortium.eu/members.aspx). Researchers can also
directly submit new sequence variants (to Derek.Lim@bwhct.nhs.uk
or E.R.Maher@bham.ac.uk). The FLCN mutation database offers a
valuable resource and tool for clinicians involved in the management
of BHD patients, clinical geneticists and researchers.
P11.012
Grid-enabling G2P association studies: a knowledge discovery
scenario
G. Potamias 1 , L. Koumakis 1 , D. Kafetzopoulos 2 , P. Flicek 3 , H. Parkinson 3 ;
1 Institute of Computer Science, Heraklion, Greece, 2 Institute of Molecular Biology
and Biotechnology, Heraklion, Greece, 3 European Bioinformatics Institute,
Hinxton, Cambridge, United Kingdom.
The heterogeneity and scale of the data generated by high throughput
(HTP) genetic association studies calls for the seamless access
to respective distributed data sources. In this context, GEN2PHEN
devotes efforts on the utilisation and harmonisation of Semantic Grid
(SG), Web Services (WS), Scientific Workflows (SWf), and Knowledge
Discovery (KD) technology. The task is realised in a Grid-enabled G2P
SWf (GG2P).
GG2P SWf unfolds into five steps: (i) using EBI’s and custom-made
WSs registered genotype experiments are accessed from public repositories
(e.g., ArrayExpress) - respective XML files are downloaded,
(ii) custom-made WSs are called to parse the XML files and download
the respective raw data, (iii) with custom-made WSs the data are
brought into formats suitable for data-analysis; (iv) data-mining algorithms,
wrapped as WSs, are called to discover indicative SNPs that
discriminate between phenotypic classes, and (v) special WSs are
called to map the discovered most-discriminant SNPs to corresponding
genome regions, and visualise them within the Ensembl genome
browser.
GG2P SWf was applied on a HTP SNP-genotyping experiment that
concerns 36 BRCA and 36 control/normal samples (E-GEOD-3743).
We were able to identify a set of about 100 SNPs, the heterozygosity
profile of which exhibit a clear LOH in the BRCA cases.
GG2P utilises a BPEL-compliant Wf editing and enactment environment.
We plan to devise an integrated Grid reference architecture for
the GEN2PHEN environment able to support GG2P-like scenarios and
SWs.
Acknowledgements: GEN2PHEN is funded by the European Community’s
Seventh Framework Programme (FP7/2007-2013) under grant
agreement 200754.
P11.013
High-density, flexible arrays for genome-wide or targeted
analysis of epigenetic mechanisms of disease
T. Takova 1 , C. Kashuk 1 , H. Rosenbaum 1 , H. Holster 1 , A. Sharp 2 , J. Kitzman 1 , L.
Freeberg 1 , M. Rodesch 1 , B. Godwin 3 , H. Halvensleben 1 , T. Millard 1 , R. Selzer 1 ,
T. Albert 1 , T. Richmond 1 , J. Greally 4 , J. A. Jeddeloh 1 , A. L. Iniguez 1 ;
1 Roche NimbleGen, Madison, WI, United States, 2 University of Geneva, Geneva,
Switzerland, 3 Roche 454 Life Sciences, Branford, CT, United States, 4 Albert
Einstein College of Medicine, New York, NY, United States.
Epigenetic mechanisms, such as DNA methylation and histone modification,
play critical roles in the development of many human diseases
including cancer, pediatric syndromes and genetics disorders. Under-
standing the role epigenetics plays in the development of disease will
ultimately lead to the development of diagnostics and hopefully preventative
and therapeutic options. Roche NimbleGen’s highly flexible,
high density HD2 microarray platform, with 2.1 million (2.1M) long-oligonucleotides
probes per array, affords researchers the opportunity to
examine epigenetic events using ChIP-chip and MeDIP-chip assays
at unprecedented scale and resolution. We will demonstrate (1) the
comprehensive, sensitive, reproducible DNA methylation analysis possible
using MeDIP and the 2.1M DNA Methylation arrays, (2) the utility
of the positive, negative and non-CG controls regions present on
these arrays in analyzing MeDIP experimental performance, and (3)
the power of combining MeDIP, sequence capture, and bisulphite sequencing
to analyze DNA methylation at single-base resolution across
the genome.
P11.014
Amplification of intermethylated sites, Bioinformatics and
capillary electrophoresis: the ABc of the cancer methylomes
A. S. Tanas1 , V. V. Shkarupo1,2 , E. B. Kuznetsova1,2 , D. V. Zaletaev1,2 , V. V.
Strelnikov1,2 ;
1 2 Research Centre for Medical Genetics, Moscow, Russian Federation, Moscow
Medical Academy, Moscow, Russian Federation.
Amplification of intermethylated sites (AIMS) is the method that best
fits the requirements to make it a universal unbiased differential methylation
screening approach. Still it is not frequently elaborated because
it possesses drawbacks in fragments resolution and mapping of the
identified differentially methylated loci. AIMS generates significant
numbers of PCR products, thus the mode of DNA fragments detection
has to be optimized to achieve appropriate resolution and easy mapping
to the genome. We have achieved single-nucleotide resolution by
capillary electrophoresis (CE). At the same time CE does not generally
provide preparative option, thus sequencing the bands in order to identify
the genomic locations of the fragments has to be substituted by
another approach. Knowledge of exact nucleotide length of a predicted
or practically obtained AIMS product allows its in silico identification
in genomic context. In order to utilize this option we have designed
specific software, AIMS in silico, which predicts all possible outcomes
of AIMS and labels the fragments of certain lengths with unique sequence
descriptors allowing their genomic positioning. Elaboration of
this AIMS-bioinformatics-CE approach allows rapid characterization of
normal and cancer methylomes, assessment of tissue-specific methylation,
identification of novel genes prone to abnormal methylation
in cancer, and rough evaluation of the cancer methylome landscapes
for different types of disease. We present the results obtained on
paired (tumor/control) breast tissue samples, control peripheral blood
samples and extraembryonic tissues in order to demonstrate the validity
and potentials of our approach, and describe novel cancer related
genes identified in breast cancer.
P11.015
Expression of centa2 and suz12 during mammalian heart
development
M. Venturin 1 , S. Brunelli 2,3 , G. Gaudenzi 4 , M. Stroppi 1 , F. Cotelli 4 , P. Riva 1 ;
1 Department of Biology and Genetics for Medical Sciences, University of Milan,
Milan, Italy, 2 Stem Cell Research Institute, H. San Raffaele Scientific Institute,
Milan, Italy, 3 Department of Experimental Medicine, University of Milano-Bicocca,
Milan, Italy, 4 Department of Biology, University of Milan, Milan, Italy.
Cardiovascular malformations (CVMs) have a higher incidence in patients
with NF1 microdeletion syndrome, compared to classical NF1
patients, presumably owing to haploinsufficiency of the genes lying in
the deletion interval. Searching for CMVs candidate genes inside the
deletion, we focused our attention on three genes, CENTA2, SUZ12
AND UTP6. Whole mount in situ hybridization (WISH) on mouse embryos
showed high expression of Centa2 in heart at 9-10 dpc, and
of Suz12 in the atrium around 10 dpc, suggesting their involvement
in heart development and CVMs onset. RT-PCR analysis on zebrafish
embryos showed Centa2 and Suz12 expression in oocytes and
throughout all the analyzed stages (8 cells-120 hpf). Centa2, but not
Suz12 was also present in adult heart. We thus carried out WISH experiments
on zebrafish embryos to characterize Canta2/Suz12 spatiotemporal
expression profiles. At 24 hpf we observed a diffuse Centa2
specific hybridization signal in the cephalic and medial portion of the
embryo, which becomes stronger starting from 48 hpf. At 48-72 hpf