2008 Barcelona - European Society of Human Genetics

Genomics, technology, bioinformatics
line generates assays for genomic DNA targets, and includes genome
specificity checks and screens to minimize oligo interactions. TaqMan
Copy Number Assays are run together with a reference assay and
gDNA in a duplex real-time PCR . The TaqMan Copy Number Assay
detects the target gene or genomic sequence of interest and the reference
assay detects a sequence that is known to be present in two
copies in a diploid genome. Relative quantification is achieved using
a data analysis tool which has been developed for copy number determination
. We will discuss progress in development of the assay design
pipeline, and data analysis tool, and assay development including
studies of reference assays, gDNA input titration, and the accuracy
and precision of TaqMan CN assays .
P08.18
in silico search for the cryptic Rss in repetitive elements of
human genome
A. Y. Gubsky1 , V. G. Zinkovsky2 ;
1 2 Odessa National I.I. Mechnikov University, Odessa, Ukraine, University of
Opole, Opole, Poland.
Cryptic recombination signal sequences (cRSS) are targets sites of
RAG1/2 proteins when the V(D)J-recombination system gets out of
control . Early, we showed that in the human genome (outside the Ig
and TCR loci) there are 5649 cRSS which supposedly have high recombination
potential (their heptamers and nonamers corresponded
to CACAGTG and ACAAAAACC sequences or differed from them for
1-2 not functional nucleotides) . Some of them can hypothetically participate
in the formation of intragenic deletions and inversions . At present,
having matched coordinates of such cRSS with coordinates of
9933066 known in the human genome repetitive elements in silico, we
observed that 3500 (61 %), 265 (5 %), 102 (2 %), 51 (1 %) 7 (0,1 %)
cRSS are the structural elements of non-LTR retrotransposons (AluY,
AluSx, L1, MIRb, etc), endogenous retroviruses and LTR retrotransposons
(LTR1B, MLT1C, ERVL-E, etc), DNA transposons (Charlie1,
MER58A, Tigger1, etc), simple repeats ((CA)n, (CAAAA)n, etc) and
other repeats (not identified) respectively. Having researched the localization
of such cRSS, we observed that in 85 % cases the nucleotide
sequences of motives are fully localized inside repeats and in 15
% cases are localized partly . In whole, cRSS were found in structure
of 414 unique types of repeats of 16 families . We consider, that many
types of repetitive elements can participate in spreading of motives
which can theoretically mediate instability in human genome when the
V(D)J-recombination system gets out of control .
P08.19
Development of a taqman® cytochrome P450 Panel Array and
Positive controls
T. Hartshorne, D. Merrill, S. Desai, T. Ceccardi;
Applied Biosystems, Foster City, CA, United States.
The Cytochrome P450 enzymes: CYP2D6, CYP2C9 and CYP2C19
metabolize the majority of currently prescribed drugs . Pharmacogenetic
analysis of polymorphic alleles of their genes has demonstrated
numerous links between functional polymorphisms, having absent or
altered enzyme activity, and cases of non-response or adverse drug
reactions. Genotyping these variants can have a significant role in predictive
drug metabolism and safe, efficacious drug therapy.
Applied Biosystems offers over 2600 TaqMan® Drug Metabolism
(DME) Genotyping Assays that detect polymorphisms in coding and
regulatory regions of over 220 DME genes . To facilitate pharmacogenetic
research, TaqMan® DME Assay panels on TaqMan® Arrays
were developed including a P450 array containing 48 assays to important
CYP2D6, CYP2C9 and CYP2C19 variants . Arrays are 384-well
microfluidic cards that are pre-loaded with assays, greatly reducing
experimental preparation time and eliminating the need for liquid-handling
robots or multi-channel pipettes . Benchmark tests conducted to
compare the performance of assays run on arrays to data from 384well
plates showed that assays on arrays can be genotyped with the
same high success rate as on plates . An interactive data analysis tool,
AutoCaller software, enabled overlaying and viewing cluster plots
from multiple arrays and facilitated genotyping analysis . Synthetic
positive control templates for each assay were run on arrays in pools
to represent all 3 genotypes; controls demonstrated assay functionality
for each probe and aided genotype calling . TaqMan® DME SNP
Arrays and positive control templates (available through Gene Link)
offers an easy to use platform for accurate, reliable genotyping of drug
metabolism and response variation .
P08.20
GEN2PHEN: An international effort towards the universal
databasing of gene-disease relationships
A. J. Brookes1 , D. Atlan2 , C. Beroud3 , E. Birney4 , S. Brahmachari5 , A. Cambon-
Thomsen6 , R. Dalgleish1 , J. den Dunnen7 , A. Devereau8 , C. Diaz9 , H. Gudbjartsson10
, I. Gut11 , T. Kanninen12 , H. Lehvaslaiho13 , J. Litton14 , J. Muilu15 , J. Oliveira16
, H. Parkinson4 , G. P. Patrinos17 , G. Potamias18 , E. Wingender19 , Y. L. Yip20 ;
1 2 University of Leicester, Leicester, United Kingdom, PhenoSystems SA, Lillois,
Belgium, 3INSERM, Montpellier, France, 4EBI, EMBL, Hinxton, United Kingdom,
5 6 Council of Scientific and Industrial Research, Delhi, India, INSERM, Toulouse,
France, 7Leiden University Medical Center, Leiden, The Netherlands, 8Univer sity of Manchester, Manchester, United Kingdom, 9Fundació IMIM, Barcelona,
Spain, 10deCODE Genetics, Reykjavik, Iceland, 11Commissariat à l’Energie
Atomique, Paris, France, 12Biocomputing Platforms Ltd, Espoo, Finland,
13 14 University of Western Cape, Cape Town, South Africa, Karolinska Institute,
Stockholm, Sweden, 15University of Helsinki, Helsinki, Finland, 16University of Aveiro, Aveiro, Portugal, 17Erasmus University Medical Center, Rotterdam,
The Netherlands, 18Foundation for Research and Technology, Crete, Greece,
19 20 BioBase GmbH, Wolfenbuettel, Germany, Swiss Institute of Bioinformatics,
Geneva, Switzerland.
With disease studies and genomics research producing ever larger datasets,
there is an urgent need for advanced informatics solutions that
can handle such extensive information . Launched in January 2008,
the GEN2PHEN project (Genotype-To-Phenotype Databases: A Holistic
Solution) aims to help address this need .
The GEN2PHEN consortium (http://www .gen2phen .org/) involves 19
research and company partners; including 17 from Europe, one from
India, and one from South Africa . Funding of 12 Million Euro from the
European Commission (7th Framework Programme) is bolstered by
additional funds provided by the partner institutions . Being a key European
program, GEN2PHEN is intimately connected with other major
infrastructure projects such as BBMRI and ELEXIR .
The main objective of GEN2PHEN is to establish the technological
building-blocks needed to evolve today’s diverse databases into a
seamless genotype-to-phenotype (G2P) biomedical knowledge environment,
tied into genome browsers like Ensembl .
The project’s specific objectives include:
1) Analysis of the current G2P informatics
2) Analysis of ethical aspects that need to be addressed
3) Development of key standards
4) Creation of generic database components and integration solutions
5) Creation of search modalities and data presentation solutions
6) Facilitation of data flows into G2P databases
7) Creation of a ‘G2P Knowledge Centre’ providing information exchange
solutions, search/analysis tools, and support for primary data
and comment deposition
8) Deployment of GEN2PHEN solutions to the community
9) Addressing questions of system durability and long-term financing
The research leading to these results has received funding from the
European Community’s Seventh Framework Programme (FP7/2007-
2013) under grant agreement n° 200754 .
P08.21
two-Dimensional Electrophoresis of Nucleic Acids to Assess
Quality of Samples and Efficiency of Molecular Methods
J. J. Jonsson1,2 , H. G. Thormar1,3 , G. H. Gunnarsson1,3 , F. S. Eiriksdottir3 , B.
Gudmundsson3 , S. Sigurdardottir1,2 , P. Estibeiro3 ;
1 2 Univ. of Iceland, Reykjavik, Iceland, Genetics and Molecular Medicine, Landspitali,
Reykjavik, Iceland, 3BioCule Inc., Reykjavik, Iceland.
Two-dimensional (2D) electrophoresis allows separation of molecules
based on different characteristics . Although widely used in proteome
studies, 2D electrophoresis of nucleic acids has so far only had limited
applications mostly in studies on DNA metabolism . We have invented
several new techniques of 2D electrophoresis of nucleic acids .
These techniques can be used to simultaneously assess length distribution
and strandness i .e . amount of single-stranded DNA, doublestranded
DNA (both A and B forms) and RNA-DNA hybrids in various
samples . DNA lesions detected with our technology include nicks,
double-stranded breaks, base modifications and drop outs leading to