Improved detection of chromosomal abnormalities in CLL by G-band analysis David Bohanna West Midlands Regional Genetics Laboratory CLL Most frequent leukaemia in the Western world Characterised by accumulation of long lived B-lymphocytes in the blood Most (~80%) patients diagnosed early without symptoms – Detected as a result of a routine blood test – Require markers that can predict the prognosis in these patients West Midlands Regional Genetics Laboratory Prognostic Markers IGH mutational status – Mutated have superior survival – High expense and expertise CD38 and ZAP70 expression – Increased expression correlates with unmutated IGH (although not perfectly) Cytogenetics – G-band analysis (hampered by low MI) – Prognostic information obtained from interphase FISH studies West Midlands Regional Genetics Laboratory Interphase FISH prognostic markers Byrd et al, 2004 Poor: 17p (TP53) deletion, 11q (ATM) deletion Intermediate: trisomy 12 Good: 13q mono allelic deletion* 13q14.3 13q34 * Prognostic significance of bi allelic deletions of 13q uncertain West Midlands Regional Genetics Laboratory Techniques at the WMRGL Standard – 1. Interphase FISH studies Mainly TP53 and ATM Not a whole genome screen like G-band analysis – 2. Set up B-cell mitogen (TPA) stimulated cultures ~40-50% abnormality rate Experimental – Use of alternative B-cell mitogens West Midlands Regional Genetics Laboratory Alternative B-cell mitogen DNA fractions from Mycobacterium bovis shown to have mitogenic effect for B-cells in mice (Tokunaga et al, 1984) Mycobacterium bovis Synthetic CpG oligonucleotides (ODN) later shown to mimic these effects ODN that contain cytosine nucleotide next to guanine nucleotide in the linear DNA sequence CpG ODN West Midlands Regional Genetics Laboratory DSP30 and CLL DSP30 (CpG ODN) – Used to stimulate B-cells in CLL by Claudia Haferlach’s group – Interleukin-2 (IL-2) required – 72hr ONC (overnight colcemid) culture Haferlach et al (2007) – 415/500 (83%) showed abnormalities visible by G-band analysis. – 392/500 (78%) were abnormal by interphase FISH (with an 8 probe panel). – 38% showed abnormalities by G-banding in addition to those covered by the FISH panel (including complex karyotypes). West Midlands Regional Genetics Laboratory Aims Improve the G-band abnormality rate achieved by WMRGL Compare the G-band abnormality rate of DSP30/IL-2 cultures with TPA cultures Compare G-band abnormality rate of DSP30/IL-2 cultures with interphase FISH West Midlands Regional Genetics Laboratory Methodology 35 patients with confirmed diagnosis of CLL 72hr DSP30/IL-2 (ONC) culture 6 day TPA (1hr colcemid) culture Interphase FISH on unstimulated culture – – – – 13q14.3 ATM (11q22.3) TP53 (17p13.1) CEP 12 West Midlands Regional Genetics Laboratory Methodology G-band analysis of 20 cells from each of the stimulated cultures 100 cells (approx.) scored by interphase FISH West Midlands Regional Genetics Laboratory Results Summary DSP30/IL-2 ONC Cultures TPA Cultures Interphase FISH (ATM,13q,p53,+12) Success Rate 94% (33/35) 66% (23/35) 100% (35/35) Abnormality Rate 67% (22/33) 57% (13/23) 74% (26/35) Abnormality Rate (Including fails) 63% (22/35) 37% (13/35) 74% (26/35) West Midlands Regional Genetics Laboratory Comparison of G-band analysis of DSP30/IL-2 cultures and TPA cultures 22 cases failed/normal in 6DTPA cultures 10/22 abnormal in the DSP30/IL-2 culture 13 cases failed/normal in DSP30/IL-2 cultures 1/13 abnormal in the 6DTPA culture West Midlands Regional Genetics Laboratory Comparison of G-band analysis of DSP30/IL-2 cultures with interphase FISH 13 cases failed/normal in DSP30/IL-2 cultures 7/13 abnormal by interphase FISH 9 cases normal by interphase FISH 4/9 abnormal in DSP30/IL-2 cultures 11/26 cases abnormal by interphase FISH show additional abnormalities in DSP30/IL-2 cultures West Midlands Regional Genetics Laboratory Abnormalities detected by FISH and G-band analysis 18 No. of cases 16 14 12 FISH 10 8 DSP30/IL-2 TPA 6 4 2 0 del (13q) trisomy 12 del (11q) del (17p) Abnormality • 8/16 13q deletions detected in DSP30/IL-2 cultures • 8/9 +12 clones detected in DSP30/IL-2 cultures • 4/4 11q (ATM) and 17p (TP53) deletions detected in DSP30/IL-2 cultures West Midlands Regional Genetics Laboratory Deletions of 13q 10 mono allelic deletions detected by FISH del(13)(q12q14) 4/10 were visible on G-banding in DSP30/IL-2 cultures – 3/4 had one additional abnormality (undetected by interphase FISH) ? Different prognosis 6/10 had an apparently normal karyotype – are the deletions sub-microscopic or under-represented in metaphases? * 0/10 cases were associated with loss of 11q (ATM) or 17p (TP53) * Metaphase FISH of DSP30/IL-2 cultures showed abnormal population to be significantly under represented or not present in the metaphases. West Midlands Regional Genetics Laboratory Deletions of 13q 6 bi allelic deletions detected by FISH del(13)(q12q14) 4/6 visible as mono allelic deletions in DSP30/IL-2 cultures – 3/4 had additional abnormalities (2 ‘complex’) 2/6 had an apparently normal karyotype – are the deletions sub-microscopic or under-represented in metaphases?* 3/6 were associated with either loss of 11q (ATM) or 17p (TP53) *Metaphase FISH of DSP30/IL-2 cultures showed abnormal population to be significantly under represented or not present in the metaphases. Trisomy 12 8/9 trisomy 12 clones were detected by Gband analysis of DSP30/IL-2 cultures 4/9 trisomy 12 clones had a similar del/add(14q) Del/add (14q) not detected in any other abnormal karyotypes Potential sub group of +12 patients with different prognosis? Case 1 Case 4 Case 10 Case 29 West Midlands Regional Genetics Laboratory 11q and 17p deletions 2/2 cases had loss of 11q (ATM) by G-band analysis of DSP30/IL-2 cultures. del(11)(q14q23) 2/2 cases had loss of 17p (TP53) by G-band analysis of DSP30/IL-2 cultures. add (17)(p1) In 4/4 cases with a poor cytogenetic marker, the abnormality was visible on G-band analysis of DSP30/IL-2 cultures. West Midlands Regional Genetics Laboratory Is a ‘complex’ karyotype in CLL associated with a poor prognosis? Haferlach et al defined a ‘complex’ karyotype as ≥3 chromosome abnormalities – Correlation with unmutated IGH Poor prognosis 3/35 cases in our study had a ‘complex’ karyotype of ≥3 abnormalities – 2 cases had an 11q (ATM) or 17p (TP53) deletion Poor prognosis using interphase FISH data – 1 case had +12 Intermediate prognosis using interphase FISH data; now poor prognosis? West Midlands Regional Genetics Laboratory Conclusions For the 35 cases studied, the overall abnormality rate in DSP30/IL-2 stimulated cultures (63%) is higher than in TPA stimulated cultures (37%). Standard practice at WMRGL has been changed to include a DSP30/IL-2 stimulated culture for all CLL referrals. The abnormality rate for interphase FISH studies was 74%, which was higher than that obtained using DSP30/IL-2. West Midlands Regional Genetics Laboratory Conclusions Additional abnormalities were seen using Gbanding compared to interphase FISH. These included: – del/add(14q) within trisomy 12 clones – additional abnormalities with del(13q) – ‘complex’ karyotypes “Prospective clinical trials should evaluate the prognostic impact of newly available data from G-band analysis of CLL cases”. Haferlach et al, 2007 West Midlands Regional Genetics Laboratory Acknowledgements Susan Rose Project Supervisor Mike Griffiths Head of WMRGL Oncology Section Mary Strachan WMRGL Oncology Section WMRGL Oncology section WMRGL FISH section Professor Paul Moss University Hospital Birmingham West Midlands Regional Genetics Laboratory
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