Routine application of a novel MLPA-based first-line screening test uncovers clinically relevant copy number aberrations in haematological malignancies undetectable by conventional cytogenetics.
OBJECTIVE
The presence of numerical and/or structural chromosomal abnormalities is a frequent finding in clonal hematopoietic malignant disease, typically diagnosed through routine karyotyping and/or fluorescent in situ hybridization (FISH) analysis. Recently, the application of array comparative genomic hybridization (aCGH) has uncovered many new cryptic genomic copy number imbalances, most of which are now recognized as clinically useful markers of haematological malignancies. In view of the limitations of both FISH and aCGH techniques, in terms of their routine application as a first line screening test, we designed a new multiple ligation-dependent probe amplification (MLPA) probemix for use in addition to classic karyotype analysis.


METHODS
A novel MLPA probemix was developed to interrogate copy number changes involving chromosomal regions: 2p23-24 (MYCN, ALK), 5q32-34 (MIR145A, EBF1, MIR146A), 6q21-27, 7p12.2 (IKZF1), 7q21-36, 8q24.21 (MYC), 9p24 (JAK2 V617F point mutation), 9p21.3 (CDKN2A/2B), 9p13.2 (PAX5), 10q23 (PTEN), 11q22.3 (ATM), 12p13.2 (ETV6), 13q14 (RB1, MIR15A, DLEU2, DLEU1), 17p13.1 (TP53), and 21q22.1 (RUNX1/AML1) and was applied to DNA extracted from 313 consecutive bone marrow patient samples, referred for routine karyotype analysis.


RESULTS
More than half of the samples originated from newly investigated patients. We discovered clinically relevant genomic aberrations, involving a total of 24 patients (8%) all with a normal karyotype, which would have remained undiagnosed.


CONCLUSIONS
Our data clearly indicate that routine application of this MLPA screening panel, as an adjunct to karyotype analysis, provides a sensitive, robust, rapid and low-cost approach for uncovering clinically important genomic abnormalities, which would have otherwise remained undetected.
Christopher
C
Konialis
Suvi
S
Savola
Sophia
S
Karapanou
Aggeliki
A
Markaki
Maria
M
Karabela
Sophia
S
Polychronopoulou
Maria
M
Ampatzidou
Michael
M
Voulgarelis
Nora-Athina
NA
Viniou
Eleni
E
Variami
Argyro
A
Koumarianou
Katerina
K
Zoi
Birgitta
B
Hagnefelt
Jan P
JP
Schouten
Constantinos
C
Pangalos
D002869:Chromosome Aberrations; D020732:Cytogenetic Analysis / Q000191:economics / Q000379:methods*; D018628:Gene Dosage; D023281:Genomics / Q000191:economics / Q000379:methods; D019337:Hematologic Neoplasms / Q000235:genetics*; D006801:Humans
Copy number aberrations; Haematological malignancies; Leukaemia; Multiple ligation-dependent probe amplification