2008 Barcelona - European Society of Human Genetics

Cytogenetics
rangements ranged between 12 Kb and 10 Mb . With this technique,
also single gene deletions were detected, which directly pointed to the
causative mutation . Our data show that this novel approach detects
up to 20% genomic abnormalities in a highly selected MCD patient
population, mostly in the group of PMG and PNH .
P02.034
Detection of genomic copy number changes in Estonian patients
with idiopathic mental retardation
O. Zilina 1 , K. Männik 1 , H. Puusepp 1,2 , S. Parkel 1 , P. Palta 1 , K. Õunap 2,3 , A.
Kurg 1 ;
1 Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia, 2 Department
of Pediatrics, University of Tartu, Tartu, Estonia, 3 Medical Genetics
Centre, United Laboratories, Tartu University Hospital, Tartu, Estonia.
Mental retardation (MR) is a highly heterogeneous condition with a
prevalence of ~1-3% . It is caused by genetic, epigenetic or environmental
factors solely or in combination . Despite extensive investigations
the underlying reason remains unknown in about half of the
cases .
We started the first comprehensive study in Estonia in order to find out
causative factors in families with idiopathic MR and help to shed light
on molecular mechanisms underlying MR . To date, we collected more
then 230 DNA samples from MR patients with normal karyotypes and
their unaffected family members .
Infinium-2 genotyping assay with Human370CNV BeadChips (Illumina
Inc) was applied as initial screening tool for detection of DNA copy
number changes and copy-neutral LOH events in the samples . Acquired
data were analyzed using BeadStudio v3 .1 (Illumina Inc) and
QuantiSNP (Colella et al 2007) software . Relevant results were confirmed
by RT-qPCR.
After validation of the study-platform using reference DNAs, first 100
individuals from 22 families were screened . About 35 genomic rearrangements
per individual were detected, most of which are reported
in the Database of Genomic Variants or present recurrently in our
samples .
In three families, possible disease-related imbalances were
found: 1 .6Mb dup(X)(p22 .31), 3 .9Mb del(15)(q13 .1q13 .2), 8 .3Mb
del(7)(q31 .1q32 .1) . The detected rearrangements were not present
in unaffected family members . Cases with similar phenotypes and
aberration(s) in the overlapping regions are also reported in the DECI-
PHER database .
In addition, several other potentially clinically significant aberrations
were found . Involvement of these aberrations in the etiology of MR is
currently under investigation .
P02.035
Application of two different copy-number detection
methodologies - array-cGH and array-mAPH - with identical
amplifiable target sequences.
L. K. Kousoulidou 1 , K. Männik 2 , O. Zilina 2 , S. Parkel 2 , P. Palta 2 , M. Remm 2 , A.
Kurg 2 , P. C. Patsalis 1 ;
1 Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus, 2 Institute of Molecular
and Cell Biology, University of Tartu/Estonian Biocentre, Tartu, Estonia.
Array-CGH has become the method of choice for the detection of
subtle imbalances as cause of genomic disorders . Novel array-CGH
modifications were introduced in order to detect smaller aberrations by
varying the type and density of arrayed target sequences . At the same
time, certain limitations have become obvious, emerging the need for
alternative methodologies. Array-based Multiplex Amplifiable Probe
Hybridization (array-MAPH) is a recent approach, where the analysis
of copy-number data is performed by conventional MAPH, followed by
rehybridization to microarrays containing DNA sequences, identical to
MAPH probes. Thus, targeted amplification and reduction of the complexity
in genomic material is achieved .
The aim of this study was to estimate whether a probe set, initially
developed for array-MAPH, is potentially useful for array-CGH . The
same human chromosome X specific probe set was applied to compare
array-CGH and array-MAPH performance and to further evaluate
the potential of array-MAPH methodology to be used for genome-wide
identification of locus copy-number changes.
Normal male and female DNA samples were studied, as well as three
patients with known chromosome X aberrations: two patients with a
12-Mb deletion and one patient with 1-Mb duplication . Our data has
proven that array-MAPH clones can be also efficiently implemented
in array-CGH .
We suggest that efforts for upgrading genomic copy-number screening
should not only focus on new CGH microarray probes, but also on
introducing new platforms, such as array-MAPH, as a reliable, flexible
and cost-effective alternative to array-CGH and high-density genotyping
chips .
P02.036
Array comparative genomic hybridization and computational
genome annotation in constitutional cytogenetics: suggesting
candidate genes for novel submicroscopic chromosomal
imbalance syndromes.
B. Coessens1 , S. Van Vooren1 , B. De Moor1 , Y. Moreau1 , J. Vermeesch2 ;
1 2 K.U.Leuven, ESAT / SCD (SISTA), Leuven, Belgium, K.U.Leuven, Center for
Human Genetics, Leuven, Belgium.
Genome-wide array comparative genomic hybridization screening is
uncovering pathogenic submicroscopic chromosomal imbalances in
patients with developmental disorders . In those patients, imbalances
appear now to be scattered across the whole genome, and most patients
carry different chromosomal anomalies . Screening patients with
developmental disorders can be considered a forward functional genome
screen . The imbalances pinpoint the location of genes that are
involved in human development . Because most imbalances encompass
regions harboring multiple genes, the challenge is to (1) identify
those genes responsible for the specific phenotype and (2) disentangle
the role of the different genes located in an imbalanced region . We
discuss our work on novel tools and databases that we recently developed
to aid this gene discovery process. Identification of the functional
relevance of genes will not only deepen our understanding of human
development but will, in addition, aid in the data interpretation and improve
genetic counseling .
P02.037
cryptic chromosomal imbalances in patients with idiopathic
mental retardation and multiple congenital anomalies
C. Orellana, S. Monfort, M. Rosello, I. Ferrer, S. Oltra, F. Martinez;
Fundacion Para La Investigacion, Valencia, Spain.
Background: Chromosomal abnormalities are a major cause of mental
retardation and multiple congenital anomalies . Array CGH studies
have shown an incidence of 10-15% of formerly undetected imbalances
among these patients .
Objective: To report array CGH screening of a series of 160 patients
with idiopathic mental retardation and congenital abnormalities .
Material and methods: 160 patients with normal karyotype and normal
subtelomeric results by MLPA were evaluated for cryptic chromosomal
rearrangements by array-CGH using a high-definition microarray consisting
of 44 .000 probes (Agilent technologies) .
Results: A total of 46 (29%) probably pathological rearrangements
were detected . Of these, 11 alterations have been proved to be pathological,
while the remaining are under study . Deletions and duplications
are equally represented . Duplication sizes ranged from to 20 to
3,859 kb (mean 1,250 kb, SD 2,276) . Deletion sizes ranged from to 0 .4
to 10,314 kb (mean 1,369 kb, SD 2,319) .
It is worth to note the occurrence of two de novo alterations in one
patient: a 10,3 Mb deletion at 6q16 and a 360 kb duplication at 16p11 .
As the phenotype is comparable to other cases with 6q16 deletion, the
duplication can be considered as a de novo polymorphism .
Conclusions: Array CGH should be considered an essential tool for
the genetic analysis of patients with mental retardation and congenital
anomalies . However, caution must be taken when interpreting the
results in order to distinguish pathological from polymorphic imbalances
.
P02.038
Identification of disease-related copy number variation (CNV) in
patients with mental retardation by high-dense sNP genotyping
microarrays
N. Rivera Brugués 1 , J. Wagenstaller 1 , M. Hempel 1 , S. Spranger 2 , B. Kazmierczak
2 , C. Daumer-Haas 3 , K. Hörtnagel 3 , T. Meitinger 1 , T. M. Strom 1 ;
1 Institute of Human Genetics, Technical University Munich and Helmholtz Center
Munich, German Research Center for Environmental Health, Neuherberg-
Munich, Germany, 2 Praxis für Humangenetik, Bremen, Germany, 3 Pränatal-