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


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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. 30 year old female with premature ovarian failure (POF).

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M N Collinson, S Huang, JN Macpherson, VK Maloney, AC Skinner, A Karcanias, NA Affara, NS Thomas

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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


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


MLPA with the Rett syndrome kit

MRC-Holland kit PO15C


LIST OF PROBES USED FOR FISH TO CONFIRM DELETION

Centromere

RP1-142F18Normal (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


FISH with a probe for the FRAXA gene

RP11-161L9

X centromere (control)


Blind cytogenetic analysis – 3 control slides and 3 slides from POF patient scored by 3 independent analysts


Partial karyotype of the X chromosomes

(abnormal X on the right)


MLPA with the subtelomere probe kit

MRC-Holland kit PO36B


FISH with the Xp and Xq subtelomere probes

CY29 (Xp subtelomere)

c8.1/2 (Xq subtelomere)


Array-CGH

Agilent 244K oligoarray


FISH with SHOX probe

RP11-946P8

DXZ2 (X centromere control)


MLPA with SHOX kit PO18B

Duplication of SHOX

POF case


NORMAL CASE

FEMALE CONTROL

MALE CONTROL

Array CGH with chip specifically designed for

sex chromosome abnormalities


POF CASE

FEMALE CONTROL

MALE CONTROL

Array CGH with chip specifically designed for

sex chromosome abnormalities


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


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%)


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


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