1. Discrepant cytogenetic, MLPA and array CGH results on a der(X)(pter->q27.2::p22.31->pter): the advantages of an integrated approach.
M N Collinson, S Huang, JN Macpherson, VK Maloney, AC Skinner, A Karcanias, NA Affara, NS Thomas

2. 30 year old female with premature ovarian failure (POF)
molecular genetic testing
for a FRAXA premutation
cytogenetic analysis
only one allele found
?45,X or 46,XY
46,XX

3. MLPA with the Rett syndrome kit
MRC-Holland kit PO15C

4. LIST OF PROBES USED FOR FISH TO CONFIRM DELETION Centromere
RP1-142F18 Normal (Xq27.2)
RP1-315J21 Deleted (Xq27.3)
RP11-79A21 Deleted (Xq27.3)
RP11-37P24 Deleted (fragile X locus)
RP11-161L9 Deleted (fragile X locus)
RP11-64L19 Deleted (Xq28)
RP11-533H4 Deleted (Xq28)
RP11-76K17 Deleted (Xq28)
RP11-402H20 Deleted (Xq28)
Telomere

5. FISH with a probe for the FRAXA gene
RP11-161L9
X centromere (control)

6. Blind cytogenetic analysis – 3 control slides and 3 slides from POF patient scored by 3 independent analysts
Analyst
Slide 1 2 3 4 5 6 X 

7. Partial karyotype of the X chromosomes
(abnormal X on the right)

8. MLPA with the subtelomere probe kit
MRC-Holland kit PO36B

9. FISH with the Xp and Xq subtelomere probes
CY29 (Xp subtelomere)
c8.1/2 (Xq subtelomere)

10. Array-CGH
Agilent 244K oligoarray

11. FISH with SHOX probe
RP11-946P8
DXZ2 (X centromere control)

12. MLPA with SHOX kit PO18B
Duplication of SHOX
POF case

13. Array CGH with chip specifically designed for
NORMAL CASE
FEMALE CONTROL
MALE CONTROL
Array CGH with chip specifically designed for
sex chromosome abnormalities

14. Array CGH with chip specifically designed for
POF CASE
FEMALE CONTROL
MALE CONTROL
Array CGH with chip specifically designed for
sex chromosome abnormalities

15. L.M. Russell et al, Cytogenet Genome Res 116:181-185 (2007)

16. Original cytogenetic analysis – 1/30 metaphases 45,X
Blind FISH study with X centromere probe (DXZ2)
POF case
Control
Metaphases
1/30 45,X (3.3%)
1/30 45,X (3.3%)
Interphase cells
8/100 45,X (8%)
6/100 45,X (6%)

17. Summary
An integrated approach was required to establish the true nature of the X chromosome abnormality
Highlights the fact that one should be cautious of any shifts from the baseline when analysing array CGH as it may mask significant changes in log ratios
We still do not have a satisfactory explanation of our results other than mosaicism
Deletions of this region of Xq have been reported in association with POF