1. “Mechanisms and assays
for rare
genomic disorders”
Cristina Skrypnyk
University of Oradea,
Faculty of Medicine and Pharmacy,
Genetics Department

2. Wolf Hirschhorn OMIM 194190 1/5 0000 del (4p)(16.3)
Williams-Beuren OMIM 194050 1/20 000 del (7)(q 11.23)
Langer-Giedion del (8)(q 24.11-q 24.13)
WAGRO OMIM 194072 1/60 000 del (11)(p 13)
Prader-Willi OMIM 76270 1/20 000 del (15)(q11.2-q 13)pat
Angelman OMIM 105830 1/20 000 del (15)(q11.2-q 13)mat
Rubinstein-Taybi OMIM 180849 1/125 000 del (16)(p 13.3)
Smith-Magenis OMIM 182290 1/25 000 del (17)(p 11.2)
Miller-Dieker del (17)(p 13.3)
Alagille OMIM 118450 1/70 000 del (20)(p12.1-p11.23)
Displasia
Di George OMIM 188400 1/ 4000 del (22)(q11.21-q 11.23)
Velo-cardio-facial del (10)(p13)
Kallmann del(X)(p 22.3)

3. Charcot-Marie-Tooth type 1A
Pelizaeus-Merzbacher
Parkinson
Alzheimer
Autism
Beckwith Wiedemann
Cat eye
Russel Silver
Neurofibromatosis type 1
and many other....

4. Genomic Disorders
 genetic diseases that
result from DNA
rearrangements
(deletion, duplication,
inversion, insertion)
from kb to Mb,
covering clusters of
different genes
-CNVs-
(Lupski et al.1998, Stankiewicz et al. 2002, Lupski et al. 2003, Waltz et al. 2004).

5. Genomic Disorders
 Mechanisms mediated by genomic architecture
- non-allelic homologous recombination(NAHR)
- non-homologous end-joining (NHEJ)
- Fork Stalling and Template Switching models
(FoSTeS)

6. Genomic Disorders
 non-allelic homologous
recombination(NAHR)
- produced between two low-copy repeats
(LCRs, also called segmental duplications, SD)
- LCRs are region-specific DNA blocks of 10 to 300(kb) in
size and of > 95% to 97% similarity to each other

7. Genomic Disorders
 Due to their high degree of sequence identity, can
sometimes be aligned in meiosis or mitosis, the
'misalignment' and the subsequent crossover
between them can result in genomic
rearrangements in progeny cells
 The non-allelic copies act as the substrates of the
homologous recombination and they are responsible
for the observed breakpoint clustering.

8. Genomic Disorders
 When the two LCRs are
located on the same
chromosome and in
direct orientation, NAHR
between them causes
duplication and/or
deletion.

9. Genomic Disorders
 When they are on the
same chromosome but in
opposite orientation, NAHR
results in inversion of the
fragment flanked by them.

10. Genomic Disorders
 Interchromosomal and interchromatid NAHR
between LCRs in direct orientation result in
reciprocal duplication and deletion, whereas
intrachromatid NAHR only creates deletion.

11. Syndrome OMIM Rearrangement Size Genes LCRs
(Mb) I II III IV
Wolf Hirschhorn del(4)(p
Williams Beuren 194050 del (7)(q11.23q11.23) 1,6 ELN, 330 1,6 98 C
IMK1
CYLN2
WAGR 194072 del(11)(p12p14) PAX6,
WTI
Prader Willi 176270 del(15)(q11.2q13) pat 4 SNRNP, 500 3,5 C
NDN, P
Angelmann 105830 del(15)(q11.2q13)mat 4 UBE3A, 500 3,5 C
P
Rubinstein Taybi 180849 del(16)(p13.3p13.3) CBP
Smith-Magenis 182290 del(17)(p11.2p11.2) 5 RAII 250 5 98 C
Alagille 118450 del(20)(p12.2p12.2) JAGI
Di George/ VCFS 188400 del(22)(q11.2q11.2) 3 TBXI 225 3 97 C
400 98
HNPP 162500 del(17)(p12p12) 1,5 PMP22 24 1,5 C
Ichtyosis X 308100 del(X)(p22.3p22.3) 1,9 STS 1,9
LCRs- I-size kb; II-distance Mb; III -homology %; IV- orientation type: C-complex
( Lupski et al. 1998, Emanuel et al. 2001, Shaffer et al. 2000, Stankiewicz et. al. 2002, Waltz et al. 2004)

13. (Stankiewicz and Lupski, 2002)

14. LCRs 22q11.21
(Shaikh TH. 2000).

15. Genomic Disorders
Diagnostic methods for the detection and
characterization of DNA rearrangements
 fluorescence in situ hybridization (FISH)
 pulsed-field gel electrophoresis (PFGE)
 in silico analyses
 multiplex ligation-dependent probe amplification
(MLPA)
 array comparative genomic hybridization (aCGH)

17. FL1 gene in Smith-Magenis critical region in 17p11.2 - FITC (green), LIS1 in 17p13.3 - Texas Red.
Both 17s are identified by the red LIS1signal. Deletion of the green FLI signal is seen in one 17.

18. N 5
S q
D 3
1 5
Sotos critical region - NSD1 (reed), in 5q35. Both 17s are identified by the centromere
green signal. Deletion of the reedNSDN1 signal is seen in one 5q.

20. Blake C et all
Discovery of a previously unrecognized microdeletion syndrome of 16p11.2–p12.2
Nature Genetics 39, 1071 - 1073 (2007)

21. THANK YOU!
 The clinical implementation of such advanced
techniques is revolutionizing clinical
cytogenetics, improving the understanding of
genomic disorders and helping the doctors to
offer a better genetics approach for the
patients and their families.

22. THANK YOU!