2008 Barcelona - European Society of Human Genetics

Genomics, technology, bioinformatics 0
of the pipeline to design TaqMan assays for quantitation of siRNAs as
well as the potential for designing assays for other small RNA genes .
P08.54
Human mitochondrial DNA data integration with the semantic
web
J. S. Moilanen1,2 ;
1Institute of Medical Technology, University of Tampere, Tampere, Finland,
2Department of Clinical Genetics, University of Oulu, Oulu, Finland.
Human mitochondrial DNA (mtDNA) is a 16 .5 kb circular genome in
which numerous polymorphisms have been detected in thousands
of sequenced genomes from various populations and patient groups
worldwide . Evolutionary data and the lack of introns in mtDNA suggest
that many of these polymorphisms have functional significance, and
there are many reports suggesting that some polymorphisms or continent-specific
mtDNA lineages (haplogroups) are associated with an
increased risk of certain complex diseases or traits . Association data,
haplogroup definitions, sequences, polymorphisms and structural and
functional features of mtDNA-encoded genes form an immense body
of knowledge which is currently scattered around different databases
and resources . Current mtDNA databases have been designed principally
to be viewed by human researchers and do not provide uniform
access to all data and are therefore not optimal for data mining or
other purposes where hypotheses are tested against huge amounts of
heterogeneous data .
The semantic web is an emerging technology which allows integration
of almost any kind of data in a framework which also makes it possible
for computers to perform inference tasks in an unified and standardized
manner . Mitochondrial Information Integration Initiative (MitoI3)
aims at developing an open resource that will collect data on available
human mtDNA sequences, polymorphisms, haplogroup definitions and
other aspects of mitochondrial genomics . The data are stored as RDF
(Resource Description Framework) statements in a RDF triple store
which can be accessed with semantic web browsers and which also
provides a SPARQL interface for performing complex queries over the
data .
P08.55
the effects of the MTHFR gene variations for drug response in
rheumatoid arthritis and psoriatic arthritis patients treated with
methotrexate
N. Horelli-Kuitunen1 , M. Kaistamaa2 , P. Onkamo2 , A. Nenonen3 , L. Ahola1 , J.
Ihalainen1 , K. Laiho3 , M. Kauppi3 , M. Nyström2 ;
1 2 Medix Laboratories Ltd, Espoo, Finland, University of Helsinki, Helsinki, Finland,
3Rheumatism Foundation Hospital Heinola, Heinola, Finland.
Methotrexate (MTX) is a folic acid antagonist widely used to treat immunosuppressive
disorders such as rheumatoid arthritis (RA) . The enzyme
5,10-methylenetetrahydrofolate reductase (MTHFR) is involved
in maintaining folate and homocysteine homeostasis and common
genetic variations, c .677C>T and c .1298A>C, in the MTHFR gene are
associated with decreased enzyme activity and altered folate levels,
which may predispose to increased susceptibility to the anti-folate effects
of MTX therapy . Here, we studied the effects of these variations
for MTX response in a total of 298 Finnish patients who had either
rheumatoid (218) or psoriatic arthritis (80) . Together with genotyping
we also analyzed folate, homocysteine, ALAT, and B12 vitamin levels
as well as clinical patient data concerning toxicity and efficiency of the
MTX treatments . Finally, statistical analyses were done to evaluate
possible associations between the MTHFR gene variations and MTX
toxicity and efficiency. Our results show that the patients with two normal
alleles (677TT/1298AA) are less likely to experience side effects
during MTX therapy although, no statistically significant association
between variations and methotrexate toxicity was found . Remarkably,
MTHFR 677TT was recognised to be a risk genotype for elevated
ALAT as well as a serious risk factor for low folate and accordingly
elevated homocysteine levels both during and after MTX treatment . In
addition, the state of the disease stayed remarkably more often active
in patients having 677TT genotype and low folate levels suggesting
that MTHFR c .677C>T is critical genotype and should be taken into
account in patient treatment strategy .
P08.56
Denaturing electrophoresis on Lab-on-chip Agilent BioAnalyzer
platform: A novel approach for rapid screening of DNA
mutations
M. Minarik1 , R. Chudoba2 , B. Belsanova1 , B. Gas2 , L. Benesova1 ;
1 2 Genomac International, Prague, Czech Republic, Charles University, Prague,
Czech Republic.
Recent expansion in genome research brought a number of new
analytical technologies for detection of DNA mutations and polymorphisms.
Although many exciting approaches are presented in scientific
environment, only a relatively small fraction subsequently finds its way
to practical application in routine diagnostic testing . Among the most
widely used methods are either enzymatic methods such as RFLP,
OLA, TaqMAN, etc . or methods based on separation due to secondary
DNA structure effects such as DGGE, TGGE, SSCP, dHPLC and
others .
Over the past several years, many of the electrophoresis-based techniques
have been adapted to capillary electrophoresis DNA sequencers
utilizing separation under partial denaturing conditions at either
constant-temperature or in temperature gradients settings .
In the current work we introduce a DNA melting separation on an electrophoresis
chip platform . We adapt Agilent 2100 Bioanalyzer for detection
of common point mutations in Factor V Leiden and Factor II
Prothrombin genes . The technique employs denaturing temperature
gradients on the chip to reliably separate homo- and hetero-duplex
forms .
This work was supported by the Czech Ministry of Industry grant FI-
IM3/215 .
P08.57
Web-based collection of gene-specific sequence variants and
their phenotypic consequences
I. F. A. C. Fokkema, G. B. van Ommen, J. T. den Dunnen, P. E. M. Taschner;
Human and Clinical Gentics, Leiden, The Netherlands.
Soon it will be possible to sequence a human genome for a reasonable
price, making medical and clinical application of human genome
sequencing a realistic option . However, as highlighted by the Human
Variome Project meeting in Melbourne (2006), when we want to understand
the consequences of all the variation we will see, we need
to improve significantly in reporting and cataloguing the variants and
their consequences we identify at the moment . To facilitate the collection
of sequence variants and their phenotypic consequences we
have developed the Leiden Open-source Variation Database (LOVD)
software (www .LOVD .nl) . LOVD provides a free, open-source, platform-independent
and fully web-based tool to build, curate and share
Locus-Specific mutation DataBases (LSDBs). In addition, to facilitate
error-free reporting of variants we have developed the Mutalyzer nomenclature
checker (www .LOVD .nl/mutalyzer) and coupled it to LOVD .
Mutalyzer names sequence variants following the HGVS mutation nomenclature
recommendations, using a GenBank accession number,
a HGCN gene symbol and the variant as input . Currently, our Leiden
server hosts over 70 gene variation databases, with data collected for
more then 20,000 patients contributed by 150 submitters world-wide,
the largest series covering gene variants in relation to neuromuscular
disorders .
P08.58
Next Generation sequencing
K. A. Stangier;
GATC Biotech AG, Konstanz, Germany.
The next generation sequencing technologies, embodied by the Roche
Diagnostics/454, Illumina/Solexa and Applied Biosystems sequencing
machines, provide the opportunity to generate huge amounts of sequence
information for de novo and resequencing of genomes . GATC
uses all three leading high throughput sequencing machines in house:
the GS FLX from Roche Diagnostics, the Illumina Genome Analyzer
and the SOLiD system of Applied Biosystems, providing the flexibility
to tailor sequencing projects to meet customer requirements . The
bioinformatic analysis of the huge amount of data is still a challenge,
especially for the human genome (3 GB) . In addition, many questions
regarding cancer research or disease related topics, can be addressed
by sequencing just the area of interest of the human genome . Often
these areas are too big to be amplified out of the whole genome. GATC