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]

CN gain at 9q34

ALL10 - SNP-A

Amplification of ABL1 (~15-20 signals per cell) in 20% cells

ALL10 – FISH

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

Where to from here?

• Refine or replace?

• Mosaicism in cancer.

• QC and standardization.

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