2008 Barcelona - European Society of Human Genetics

Genomics, technology, bioinformatics
has been implicated in neurodegenerative disorders and proposed
as a candidate gene for mental retardation . The remarkable size of
CDK5R1 3’UTR, which is highly conserved in mammals and contains
AREs and miRNA target sites, suggests a role in post-transcriptional
regulation of its expression . The insertion of CDK5R1 3’UTR into luciferase
gene causes a decreased luciferase activity in four transfected
cell lines . A 3’UTR region (named C2) leads to a very strong luciferase
mRNA reduction, owing to a significantly lower half-life, indicating accelerated
mRNA degradation . This fragment was dissected into smaller
regions and a 65 bp sequence (C2 .11), in which no known regulatory
elements were predicted, has been identified to be responsible
of the decreased gene expression . A stable structural motif (forming
a hairpin) of C2.11 fragment was predicted by RnaProfile and SFold
programs, both starting from the isolated fragment and considering it
within the whole 3’UTR . Lowering of luciferase levels for the construct
with an intact hairpin structure in contrast with unchanged levels for
four mutated/deleted structures suggests that this putative element
might really have a regulatory role . Since complementary mutations
restoring the hairpin did not affect luciferase activity, we suggest that
both the sequence and the structure are essential for the ability of
C2 .11 fragment to reduce transcript stability . Further mutagenesis experiments,
binding assays and RNAse protection assays will disclose
the function of this novel CDK5R1 3’UTR regulatory element .
P08.14
computational analysis of structural and non-structural proteins
of chikungunya virus - mosquito borne disease as potential
target for vaccine
K. R. Rupesh1 , K. Mahdieh2 ;
1 2 IFREMER, Plouzane, France, Special Medical Center, Tehran, Islamic Republic
of Iran.
Chikungunya virus (CHIK), an alphavirus borne by Aedes mosquitoes
that produces dengue-like illness in humans, characterized by
fever, rash, painful arthralgia, and sometimes arthritis throughout sub-
Saharan Africa, Southeast Asia, India, and Western Pacific. Recent
widespread geographic distribution, recurrent epidemics, and infection
of military personnel, travelers and laboratory staff working with
CHIK have indicated need for more understanding and to have safe
and efficacious vaccine. In our present study we have analyzed the
characteristics of structural and non-structural proteins synthesized by
CHIK using computational tools and predicted the potential vaccine
candidates . CHIK contains two proteins - non-structural and structural .
Computational analysis of non-structural protein revealed that it is
275 .65 kDa hydrophilic protein, pI 6 .841, while that of the structural
protein revealed a 138 .88 kDa hydrophilic protein of pI 8 .88 . Antigenic
prediction sites on non-structural and structural proteins predicted
were examined for their use as vaccine candidates for effective control
of the disease . Positions of alpha helix and b-sheets in the secondary
structure of the proteins were predicted which laid the path for 3D
structural characterization of the target proteins . On analyzing hydropathy
plot, structural protein and non-structural protein were found to be
hydrophilic . Using nucleotide sequences of the proteins, degenerate
primers were designed for its use in PCR based diagnostic identification
of the CHIK. Primers designed could find its use as a diagnostic
tool for identifying CHIK infected patients specifically. The predicted
antigenic sites could be used as potential vaccine candidates .
P08.15
cHDWiki: a comprehensive tool to gather and manage
cardiogenetic data
J. Breckpot1 , R. Barriot2 , B. Thienpont1 , S. Van Vooren2 , L. Tranchevent2 , B.
Coessens2 , M. Gewillig3 , Y. Moreau2 , K. Devriendt1 ;
1 2 Center for Human Genetics, Leuven, Leuven, Belgium, Department of Electrical
Engineering (ESAT), Catholic University of Leuven, Leuven, Belgium,
3Paediatric Cardiology Unit, Catholic University of Leuven, Belgium, Leuven,
Belgium.
We present a Wiki based information system designed for the collaborative
annotation of genes involved in congenital heart defects (CHD) .
In this context, a Wiki has many appealing features such as collaborative
user-friendly publication . However, a major obstacle for its use is
that, unlike databases, it lacks structure and semantics, which prevents
the use of further computational knowledge discovery approaches.
To benefit from both the Wiki flexibility and the databasing advan-
tages, we extended the MediaWiki platform to allow the inclusion and
the interaction with external data and programs . The current online
project contains: (i) genes and gene mutations associated to CHDs
(local curated database), (ii) links from CHD genes to related patient
case reports (local cytogenetic database), (iii) links from CHD genes to
publicly available descriptions of copy number variants, (iv) an interactive
view of this information on chromosomes . Moreover, CHD candidate
genes can be prioritized (Endeavour 1 ) based on easily selectable
training genes associated to CHD types . CHDWiki promises to be the
central resource/reference for CHD genetics . It can be viewed as a dynamic
review of all the knowledge published in this field. Additionally,
the Wiki goes further by managing information on promising candidate
genes . The CHDWiki will be the most comprehensive resource available
on genes associated to CHDs with 48 genes, 40 CHDs and 135
manually curated associations . While initially dedicated to this concrete
project, the system is generic and allows the rapid development
of Wikis augmented by structured data and analysis results .
1 Aerts et al., Nat Biotech, 2006;24:537
P08.16
copy number variants and gene expression in the mouse
E. A. C. Chaignat 1 , C. N. Henrichsen 1 , N. Vinckenbosch 1 , S. Pradervand 1 , M.
Ruedi 2 , S. Zoellner 3 , H. Kaessmann 1 , A. Reymond 1 ;
1 Center for Integrative Genomics, Lausanne, Switzerland, 2 Department of Mammalogy
and Ornithology, Natural History Museum, Geneva, Switzerland, 3 Department
of Biostatistics, University of Michigan, Ann Arbor, MI, United States.
Copy number variants (CNVs), defined as large stretches of DNA that
vary in number of copies among phenotypically normal individuals, are
a source of phenotypic variation . To achieve a more complete mapping
of mouse CNVs, we used whole-genome oligonucleotide array comparative
genome hybridization to identify CNVs in 13 inbred strains
and in 21 wild mice . Using a hidden Markov model, we predicted some
3800 CNV candidate regions, which we subsequently validated using
a custom-made array . Thus multiplying by more than three the number
of copy-number variable regions previously reported in the mouse
genome .
To address whether CNVs affect gene expression, we assessed the
expression levels of 45’037 transcription units in liver, kidney, brain,
heart, lung and testis of of six inbred mouse strains . We found that the
variance of the expression levels for each of the recorded tissues is
significantly larger for genes mapping inside than for genes mapping
outside of CNVs, suggesting that copy number variation affects the
variability of gene expression and must be taken into account when
considering phenotypic differences between strains . Similarly, the
genes mapping on the flanks of the CNVs, despite their not varying in
copy numbers, display a modification of their relative expression levels
. This phenomenon is effective over several hundreds of kilobases
away from a breakpoint . It is present in all assessed tissues and persistent
throughout mouse development . Thus our results demonstrate
that changes in genome structure influence not only gene dosage but
also the expression of neighboring genes .
P08.17
Development of taqman® copy Number Assays for copy
Number Analysis
K. Li, A. Broomer, Y. Wang, C. Xiao, F. Wang, I. Casuga, M. Xia, X. You, M.
Bozzini, T. Hartshorne, G. Janaway, J. Tan, P. White, A. Toeppel, E. Spier, C.
Chen;
Applied Biosystems, Foster City, CA, United States.
Copy number variation is an important polymorphism in the human
genome that can be associated with genomic disorders or various
diseases . Accurate detection of copy number differences is critical for
understanding how copy number variation may play roles in diseases
such as cancer, immune diseases, and neurological disorders, and
also drug response . Although array-based technologies are powerful
for genome-wide CNV discoveries and micro-deletion/micro-duplication
syndrome studies, more quantitative technologies with high accuracy,
specificity, and sample throughput are necessary to validate
identified copy number changes and to detect deletions and duplications
for large sample sizes in candidate regions or genes .
Here we report our progress on the development of TaqMan Copy
Number Assays . High quality targets for assay design are selected
across the whole human genome . A proprietary assay design pipe-