Clinical utility of DNA microarrays in acute
lymphoblastic leukaemia
Meg Wall, Adrian Zordan, Ruth N. MacKinnon, Lynda J. Campbell
Victorian Cancer Cytogenetics Service
Acute Lymphoblastic Leukaemia
• An aggressive haemopoietic
malignancy of immature
lymphoid precursors.
• The most common cancer of
childhood comprising 25% of all
cases.
• Cure rates in paediatric ALL are
approaching 90%.
• Adult ALL is less common and
has a worse prognosis. Long
term survival rates are <40%.
Cytogenetics has a prognostic role in ALL
Relapse free survival in UK MRC ALL97/99
Moorman et al, Lancet Oncol 2010; 11: 429-38
HeH
t(12;21)
t(9;22)
t(v;11q23)
iAMP21
Cytogenetics has a prognostic role in ALL
However, characterising the neoplastic clone can be challenging due to:
• the low mitotic index of ALL cells in culture,
• low resolution due to the poor chromosome morphology.
DNA microarray techniques:
• are not dependent on the presence of dividing cells in culture,
• can identify copy number aberrations with higher resolution than
metaphase cytogenetics.
Non-random, recurrent copy number aberrations detected by
microarrays have been linked with tumour cell biology and clinical
outcomes.
Methods 1. Phase 1 - aCGH (31/08/2009-09/02/2010), n=3:
gDNA shipped to Signature Genomic Laboratories (Spokane, WA)
for aCGH on a 133K whole genome custom designed
oligonucleotide microarray (Signature OncoChip by Roche
Nimblegen) and analysed using Oncoglyphix software.
2. Phase 2 - SNP-A (19/07/2010-14/12/2010), n=8:
gDNA hybridised to 300K HumanCytoSNP-12 BeadChip (Illumina,
San Diego, CA) at VCCS or AGRF and analysed using
KaryoStudio software.
3. Phase 3 – SNP-A (10/01/2012-26/03/2012), n=2
gDNA hybridised to CytoScan 750K array (Affymetrix, Santa Clara,
CA) at Mater Medical Research Institute and analysed using
Chromosome Analysis Suite software.
ALL4 - SNP-A
G-banded karyotype:
29,<n>,X,+X,+8,+10,+14,
+18,+21[9]/58,idemx2[8]/
46,XX[3]
1 2 3 4 5
6 7 8 9 10
… etc.
ALL10: G banded karyotype: 45,XY,del(1)(p12p?21),-
13[3]/46,XY,add(1)(q21),add(3)(q?13),-
12,del(13)(q12q14),+mar1[3]/46,XY[24]
ALL10 - chromothripsis 1p
Chromosome 1 39 y.o. man with T-ALL. CALM-AF10 fusion in a complex karyotype.
Case B/T Age (y) Karyotype summary Microarray summary
ALL1 B 1 45,XY,dic(9;20)(p13.2;q11.2) CDKN2A deletion
ALL2 B 6 46,XY,r(9)(p?13q?33) CDKN2A deletion, PAX5 amplification,
BTG1 deletion
ALL3 B 18 47,XY,complex CDKN2A deletion, PAX5 amplification,
BTG1 deletion
ALL4 B 4 Near-haploid IKZF3 deletion
ALL5 B 5 HeH CDKN2A deletion
ALL6 B 6 46,XX,iAMP21 IKZF1 deletion
ALL7 B 10 Low hypodiploid Low hypodiploid
ALL8 B 18 46,XX,del(9)(p?21),del(12)
(p12)
CDKN2A, PAX5 & BTG1 deletions
ALL9 B 28 Normal CDKN2A deletion, large 9q deletion
ALL10 T 5 NUP214-ABL1 fusion CDKN2A deletion, NUP214-ABL1 fusion
ALL9 T 9 46,XY,t(5;14)(q3?1;q?32) 9p & 11p upd
ALL10 T 39 CALM-AF10 in complex
karyotype
Chromothripsis 1p
ALL11 T 66 Normal 2p upd
Acknowledgements: VCCS Cris Batzios Rebecca Bowen Lynda Campbell Melissa Curtis Pina D’Achille Caroline Dobrzelak Lee Harrison Nicole Hatzopoulos Veronica Hoctor Kinjal Joshi Ruth MacKinnon Bruce Mercer Azrene Malik Trish Michael Megan Nolan Srilakshmi Nutalapati Fran O’Malley Kathleen Rayeroux Anne Robertson Dora Stamatonikolos Louise Sweeney Lan Ta Meg Wall Joanne White Adrian Zordan
Illumina Derek Campbell Vanessa Tyrell
Signature Genomic Laboratories Lisa Shaffer Marilyn Slovak
AGRF Melinda Ziino Jonathon Spanos
Millennium Science Michelle Garred