2008 Barcelona - European Society of Human Genetics

Genomics, technology, bioinformatics
probes while retaining or improving the predictive power . Validation
of the model was performed using 10-fold cross-validation regime to
avoid overfitting and assure statistical validity of results. The predictive
model was evaluated on the basis of three performance measures:
sensitivity, specificity, and the area under the receiver operating characteristics
curve (Table 1). Proposed model confirm the known and
indicate some novel patterns which may contribute to a better understanding
of SMA .
Table 1 . Performance measures .
Model
Full Stepwise
SMA I SMA II SMA III SMA I SMA II SMA III
Sensitivity 0 .471 0 .679 0 .700 0 .571 0 .719 0 .737
Specificity 0 .896 0 .676 0 .844 0 .902 0 .758 0 .848
AUC 0 .772 0 .676 0 .707 0 .748 0 .746 0 .771
P08.73
smRt arrays as a high resolution technique for detection of DNA
microvariations
P. Armero, C. Maqueda, A. Hernández, S. Esteban, P. Madero;
Centro de Análisis Genéticos, Zaragoza, Spain.
Introduction: Nowadays, array CGH is one of the highest resolution
techniques for genome-wide detection of chromosomal alterations .
Genome screening using array CGH has great potential in the characterization
of numerous unexplained chromosomal aberrations . The
whole genome Sub-Megabase Resolution Tiling Array (SMRT array)
is capable of identifying microamplifications and microdeletions at a
resolution of 100 Kb .
The aim of this study was to show the utility of this SMRT arrays to
provide precise information about the size and breakpoints of DNA
copy number gains and losses .
Methods: We present a patient with microcephaly, epilepsy and mental
retardation, with a female normal karyotipe 46, XX . A SMRT array,
(from Wan Lam Laboratory at the BC Cancer Research Centre) analysis
was performed . Moreover, two MLPA kits (SALSA P096 and SAL-
SA, from MRC-Holland) and fluorescent in situ hybridization (FISH)
technique were carried out .
Results: The SMRT array analysis showed a 4p subtelomeric deletion
of 1.25 Mb. MLPA study of the specific 4p16.3 subtelomeric region
confirmed this microdeletion. Five of the sixteen specific probes of
MLPA kit, located in the new defined WHSCR-2, were deleted. FISH
assays showed a deleted pattern with the 4p subtelomeric probe but
normal results were obtained when hybridization was performed with
specific WHS probe.
Conclusions: The SMRT array study confirms the small deletion WH-
SCR-2 previously detected by MLPA and not detected by WHS FISH .
SMRT array arises as an effective technique to detect DNA microvariations
and provides more information about their size and precise
breakpoints .
P08.74
Flexible and 640-multiplex array detection of nucleic acid
variations
K. Krjutskov 1 , R. Andreson 1 , R. Mägi 1 , A. Khrunin 2 , A. Metspalu 1 ;
1 IMCB, Tartu, Estonia, 2 IMG RAS, Moscow, Russian Federation.
DNA sequence variation detection is important in various biomedical
applications such as gene identification of common diseases, disease
diagnosis and -treatment, drug discovery and forensic analysis . Here,
we describe an arrayed primer extension-based genotyping method
(APEX-2) that allows multiplex DNA amplification (640-plex) and
detection of single nucleotide polymorphism (SNP) or mutations on
microarray through four-color single-base extension . The principle of
multiplex PCR needs two oligonucleotides per SNP/mutation generating
amplicons that contain the unknown base pair (studied position) .
The same oligonucleotides are used in the following step as attached
single-base extension primers on a microarray . The call rate of 640plex
APEX-2 was 99 .87%, the reproducibility was 99 .92% and the coincidence
between Illumina HumanCNV370-Duo v1.0 BeadChips and
APEX-2 genotyping was 98 .6% . The method described here may be
very useful for a custom number of SNP- or mutation detection analysis,
molecular diagnostics and in forensic analysis . APEX-2 has also
the potential to fill the gap (up to 1500 positions) between expensive
high-density platforms and low-multiplex level detection systems .
P08.75
Transplantation of amniotic fluid-derived stem cells in a rodent
model of stroke
I. Antonucci 1,2 , M. Maki 3,4 , S. Yu 3,4 , T. Masuda 3,4 , M. M. Ali 3,4 , D. C. Hess 3,4 , G.
Palka 1 , L. Stuppia 1,2 , C. V. Borlongan 3,4 ;
1 G. D’Annunzio University Foundation, Chieti, Italy, 2 Aging Research Center,
CESI, Chieti, Italy, 3 Department of Neurology, Medical College of Georgia,
Augusta, GA, United States, 4 Research and Affiliations Service Line, Augusta
Veterans Affairs Medical Center, Augusta, GA, United States.
The discovery of amniotic fluid (AF) -derived stem cells initiated a new
and very promising field in stem cell research. These cells possess
immune-privileged characteristics suitable for a successful transplantation
. The purpose of this study was to reveal stemness of rat AF-derived
cells and to test the effectiveness of transplantation of fresh as
compared to cultured AF cells in a rodent model of stroke . Cells were
characterized at day 25 of culture by immunohistochemical analysis to
highlight the presence of embryonic stem cell markers . This analysis
showed that cultured, i .e ., adherent AFcells resembled a mesenchymal-like
morphology and were positive for OCT4 and SSEA, typical
embryonic stem cell markers . A parallel in vivo study subjected rats
to middle cerebral artery (MCA) occlusion for 60 minutes and subsequently
assigned to one of the following intravenous transplantation:
i) freshly isolated AF cells; ii) cultured rat AF mesenchymal-like stem
cells; iii) vehicle . Behavioral tests were performed prior to stroke surgery
and repeated at day 2 post-stroke/post-transplantation to evaluate
the functional consequences of the MCA occlusion and to quantify
improvements in motor and cognitive function after transplantation .
Transplantation of cultured, but not freshly isolated AF mesenchymallike
stem cells promoted significant recovery from stroke-induced motor
and neurologic deficits compared to vehicle-infused stroke animals.
The present study shows that cultured rat AF-derived cells are more
therapeutically active than freshly isolated cells . The observed behavioral
benefits demonstrate that AF stand as a highly potent alternative
source of stem cells for therapeutic strategies in stroke and related
neurological disorders .
P08.76
e-infrastructure for thalassaemia research network (ithanet)
M. Kleanthous;
The Institute of Neurology and Genetics, Nicosia, Cyprus.
The main objective of Ithanet (http://www.ithanet.eu) is to enhance the
scientific potential of the haemoglobinopathies’ research community
using infrastructures and tools of European research networks . Ithanet
aims to harmonise and develop these resources for the coordination of
existing research activities as a base for future collaborative projects .
The consortium comprises of all major European research institutions
active in the field and a number of collaborating partner institutions
from non-EU Mediterranean and Black-Sea countries . In total Ithanet
associates 26 partners from 16 countries . In order to set-up and maintain
interaction between the partners involved as well as to coordinate
training and project management activities, Ithanet utilizes teleconferencing
technology . Additionally Ithanet introduced media broadcasting
and streaming technologies for conferences and teaching courses on
haemoglobinopathies, contributing to the exchange and dissemination
of good practices in the field of e-learning.Aiming to encourage a high
level of interaction among members of the haemoglobinopathy community,
a dedicated portal has been created (http://portal/ithanet.eu) .
Visitors to the Ithanet portal can quickly exchange information, share
ideas, enhance the global awareness of pertinent issues, and help define
critical areas of haemoglobinopathy treatment and research. The
portal offers the latest news, techniques and information on haemoglobinopathies
and also serves as a platform for the easy exchange of information
and dialogues between interested groups, both patients and
researchers . The portal is also used as a database of standard scientific
protocols, methodologies, and repositories. It contains information
on almost all Thalassaemia-related institutions and medical centres as
well as patient and scientific societies.