2008 Barcelona - European Society of Human Genetics

Cytogenetics
lona, Spain.
Cytogenetically balanced chromosome rearrangements constitute
chromosome abnormalities that may be associated with mental retardation
and dysmorphic features, suggesting possible cryptic imbalances
in the breakpoint . Due to the limited resolution of conventional
cytogenetics, new molecular techniques are required for their detection,
such as array-CGH .
We present two patients with phenotypic abnormalities and de novo
cytogenetically balanced rearrangements . After analysing them by 1
Mb array-CGH, imbalances were observed in both cases (just one
case involving the breakpoints) .
In patient 1, who presented deafness, hidrocephaly and coloboma,
the karyotype was 46,XX,t(6;13)(q23;q31)dn . Array-CGH detected a
13q32 .2 deletion, 13q33 .1 duplication, 1q44 duplication and 16q21-22
deletion. The last one is the only confirmed abnormality by FISH for
the time being (BACs RP11-89O14 and RP11-468F3), but it has been
described as a polymorphism .
Patient 2, with a Silver-Russell-like phenotype, showed the karyotype
46,XX,inv(7)(q21 .12q34)dn . Array-CGH did not show any deletion in
the breakpoints, but highlighted a de novo microdeletion of 5Mb at
3p12.3-3p13, confirmed by FISH (BACs RP11-781E19 and RP11-
59O5) .
In relation to patient 2, the only confirmed case for now, a review of
similar reported cases has been performed . Although none of them
has an identical microdeletion, common features have been observed,
ranging from minor anomalies to growth and mental retardation, and
brain, heart and lung malformations . Many genes of 3p12 .3-3p13 region
remain still unknown, making it difficult to establish a good genotype-phenotype
correlation .
These results underline the importance of the use of molecular cytogenetics
in patients with apparently cytogenetically balanced chromosome
rearrangements associated with phenotypic abnormalities .
P02.022
Oligonucleotide array-cGH in postnatal cytogenetics
H. Tönnies 1 , A. Caliebe 1 , I. Martin-Subero 1 , S. Gesk 1 , N. Husemeyer 1 , I.
Stefanova 2 , G. Gillessen-Kaesbach 2 , K. Bruhn 3 , U. Stephani 3 , G. Krüger 4 , M.
Kautza 5 , J. Weimer 6 , R. Siebert 1 ;
1 Institut für Humangenetik, Kiel, Germany, 2 Institut für Humangenetik, Lübeck,
Germany, 3 Klinik für Neuropädiatrie, Kiel, Germany, 4 Abteilung für Medizinische
Genetik, Rostock, Germany, 5 Praxis für Humangenetik, Kiel, Germany, 6 Onkologisches
Labor der Klinik für Gynäkologie und Geburtshilfe, Kiel, Germany.
High-resolution array-CGH (aCGH) allows the detection of small, submicroscopic
imbalances in euchromatic chromosomal segments . We
have performed aCGH for the detection of constitutional imbalances
in 129 patients with normal karyotype and developmental delay and/
or various malformations, dysmorphisms, or complicated epilepsy of
unknown etiology using 44K, 105K, and 244K oligonucleotide arrays
(Agilent) . In 22 of 129 patients euchromatic imbalances have been detected
(~17%) by aCGH and verified by FISH analyses. In seven out of
18 cases where parental samples were available for verification analyses,
it could be shown that the euchromatic imbalance (3 deletions: 0 .4
Mb-1 .9 Mb; 4 duplications: 1 .3 Mb-5 .3 Mb) has been transmitted from
a phenotypically normal parent . Overall, in 14 of 129 patients (~11%)
a de novo aberration has been detected; some of thosw representing
well known, others recently established microdeletion and microduplication
syndromes . In addition to the 129 patients, 19 patient samples
were analyzed to further characterize a chromosomal aberration detected
initially by conventional cytogenetics . In eleven of these cases
(~58%) including complex translocations and ring chromosomes, the
imbalance(s) could be characterized successfully in more detail using
aCGH . Hybridization of microdissected chromosome material of a supernumerary
ring chromosome 19 onto a 105 K array allowed the high
resolution mapping of the nonlinear euchromatic content . However,
in eight preselected cytogenetic samples no euchromatic imbalance
could be detected by aCGH using whole genomic DNA . In summary,
aCGH and array-hybridization of microdissected chromosomes are
highly informative methods for the detection and characterization of
chromosomal imbalances in postnatal cytogenetics .
P02.023
Array cGH detection of genomic imbalances in 370 patients with
unresolved retardation syndrome
U. Koehler, E. Holinski-Feder, E. Holinski-Feder;
Medizinisch Genetisches Zentrum, Munich, Germany.
Genomic imbalances are a major cause of mental retardation and developmental
delay in patients with congenital and developmental abnormalities
. With the advent of whole genome array-CGH analysis,
the number especially of interstitial genomic imbalances increased
dramatically . Here we present our results of array-CGH investigations
in 370 cases of patients with retardation syndromes and dysmorphic
features using the Cytochip v2 BAC array (BlueGnome, Cambridge) .
Among these cases we found 55 genomic imbalances (15%) . Seven
(2,1%) of the genomic imbalances were telomeric (3 deletions, 4 duplications)
and 48 interstitial (12,9%, 28 deletions, 12 duplications) .
Of these interstitial imbalances 28 were >1 Mb in size (average 3,5)
whereas 20 were smaller or equal to 1 Mb in size . Four aberrations included
terminal deletion/duplication events (three de novo, one inherited
from a balanced father) . 8 cases (2,4%) were patients with known
microdeletion or microduplication syndromes (two microdeletions
22q11 .2, two microdeletions 17p11 .2, two microdeletions 15q11 .2q13,
two microduplications 17p11 .2) . FISH has not been performed prior
to the array CGH, as no obvious indication of the referrals existed .
All of the detected gains and losses have been confirmed by either
FISH or MLPA . A small 0,8 Mb deletion in the long arm of chromosome
2 (2q22.3) lead to the molecular genetically confirmed diagnosis of
Mowat-Wilson syndrome . To summarize, array CGH is a very powerful
tool to detect genomic imbalances in at up to 15% of previously
unresolved cases .
P02.024
Genome-wide analysis of DNA copy-number changes in subjects
with mental retardation
R. Ciccone, A. Vetro, O. Zuffardi;
University of Pavia, Pavia, Italy.
During the last three years we analyzed more than 1000 individuals
affected by mental retardation and/or congenital anomalies by oligobased
array-CGH . About 300 of these subjects had a known imbalance
already defined by conventional cytogenetics and the genomewide
analysis helped us to better characterize these rearrangements .
A group of 703 individuals with normal karyotype was investigated by
using two different microarrays (Agilent 44K and 244K) which have
an average resolution of about 100Kb and 20Kb respectively . Among
those investigated by the 44K chip (557), 126 (22,6%) subjects were
unbalanced and 82 (14,7%) had imbalances causative of their phenotype
. 146 patients were investigated through the 244K chip; 46 (31,5%)
were unbalanced and 22 (15%) such imbalances were pathogenic . We
are not able to establish whether the remaining 66 imbalances were
causative or not . In fact most of them were inherited from a normal
parent whereas in few cases we could not investigate the parents . Interestingly,
our study highlighted some peculiar rearrangements such
as de novo triplications or two independent genomic disorders in the
same patient . On the other hand, our study demonstrate that increasing
the resolutions may improve the detection rate, although the percentage
of potentially causative imbalances detected using these two
platforms is not significantly different.
P02.025
Validation of BAc-array cGH using a different array cGH
platform
U. Heinrich1 , L. Melanie1 , H. Tanja1 , S. Kai1 , A. Polten2 , R. Imma1 ;
1Centre for Human Genetics and Laboratory Medicine, Martinsried, Germany,
2Agilent, Waldbronn, Germany.
Array CGH utilizing spotted BAC/PAC clone microarrays has recently
been introduced as a valuable diagnostic tool for the detection of chromosomal
imbalances in patients with mental retardation and developmental
delay . Since diagnostics generally requires a binding medical
opinion, results from array CGH analyses need to be validated to avoid
false positive results . The currently most widely used validation method
is FISH of metaphase spreads using the same BAC/PAC clone that
has been identified as conspicuous on the chip array. Whereas FISH
is the method of choice for the validation of deletions, duplications are
generally difficult to interpret. We therefore used a second, oligonucle-