Array CGH Identifies Copy Number Changes In 10% Of 520 MDS Patients With Normal Karyotype: Deletions Encompass The Genes TET2, DNMT3A, ETV6, NF1, RUNX1, and STAG2 and Are Associated With Shorter Survival

Abstract Background In MDS, cytogenetic aberrations play an important role for classification and prognostication. The original IPSS and the revised IPSS classifiers have clearly demonstrated the prognostic impact of distinct cytogenetic abnormalities. The vast majority of chromosome aberrations in MDS are gains or losses of chromosomal material while balanced rearrangements are rare. However, more than 50% of MDS and even more in low risk MDS harbor a normal karyotype. Chromosome banding analysis can only detect gains and losses of more than 10 Mb size due to its limited resolution and is dependent on proliferation of the MDS clone in vitro to obtain metaphases. Array CGH has a considerably higher resolution and does not rely on proliferating cells. Aims In this study we addressed the question whether MDS with normal karyotype harbor cytogenetically cryptic gains and losses. Patients and Methods 520 MDS patients with normal karyotype were analyzed by array CGH (Human CGH 12x270K Whole-Genome Tiling Array, Roche NimbleGen, Madison, WI). For all patients cytomorphology and chromosome banding analysis had been performed in our laboratory. The cohort comprised the following MDS subtypes: RA (n=22), RARS (n=43), RARS-T (n=27), RCMD (n=124), RCMD-RS (n=111), RAEB-1 (n=104), and RAEB-2 (n=89). Median age was 72.2 years (range: 8.9-90.1 years). Subsequently, recurrently deleted regions detected by array CGH were validated using interphase-FISH. Results In 52/520 (10.0%) patients copy number changes were identified by array CGH. Only eight cases (1.5%) harbored large copy number alterations >10 Mb in size, as such generally detectable by chromosome banding analysis. These copy number alterations were confirmed by interphase-FISH. They were missed by chromosome banding analysis due to small clone size (n=2), insufficient in vitro proliferation (n=3) or poor chromosome morphology (n=3). In the other 44 patients with submicroscopic copy number alterations 18 gains and 32 losses were detected. The sizes ranged from 193,879 bp to 1,690,880 bp (median: 960,176 bp) in gained regions and 135,309 bp to 3,468,165 bp (median: 850,803 bp) in lost regions. Recurrently deleted regions as confirmed by interphase-FISH encompassed the genes TET2 (4q24; n=9), DNMT3A (2p23; n=3), ETV6 (12p13; n=2), NF1 (17q11; n=2), RUNX1 (21q22; n=2), and STAG2 (Xq25, deleted in 2 female patients). No recurrent submicroscopic gain was detected. In addition, we performed survival analysis and compared the outcome of patients with normal karyotype also proven by array CGH (n=462) to patients with aberrant karyotype as demonstrated by array CGH (n=52). No differences in overall survival were observed. However, overall survival in 35 patients harboring deletions detected solely by array CGH was significantly shorter compared to all others (median OS: 62.1 vs 42.4 months, p=0.023). Conclusions 1. Array CGH detected copy number changes in 10.0% of MDS patients with cytogenetically normal karyotype as investigated by the gold standard method, i.e. chromosome banding analysis. 2. Most of these alterations were submicroscopic deletions encompassing the genes TET2, ETV6, DNMT3A, NF1, RUNX1, and STAG2. 3. Interphase-FISH for these loci can reliably pick up these alterations and is an option to be easily performed in routine diagnostics in MDS with normal karyotype. 4. Patients harboring deletions detected solely by array-CGH showed worse prognosis. Disclosures: Haferlach: MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Zenger:MLL Munich Leukemia Laboratory: Employment. Staller:MLL Munich Leukemia Laboratory: Employment. Roller:MLL Munich Leukemia Laboratory: Employment. Raitner:MLL Munich Leukemia Laboratory: Employment. Holzwarth:MLL Munich Leukemia Laboratory: Employment. Kern:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Schnittger:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Kohlmann:MLL Munich Leukemia Laboratory: Employment. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership.

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In Depth Characterization of CLL with Normal Karyotype By Array CGH and Mutation Screening

Blood ◽

10.1182/blood.v126.23.1707.1707 ◽

2015 ◽

Vol 126 (23) ◽

pp. 1707-1707 ◽

Cited By ~ 2

Author(s):

Claudia Haferlach ◽

Sabine Jeromin ◽

Wolfgang Kern ◽

Susanne Schnittger ◽

Torsten Haferlach

Keyword(s):

Chromosome Banding ◽

Array Cgh ◽

Mutation Screening ◽

Normal Karyotype ◽

Employment Equity ◽

Cytogenetic Abnormalities ◽

Interphase Fish ◽

Banding Analysis ◽

Chromosome Banding Analysis ◽

Equity Ownership

Abstract Background: CLL is characterized by a distinct pattern of cytogenetic abnormalities. The most frequent aberrations are deletions of 13q, 11q, 6q and 17p and trisomy 12. However, based on chromosome banding analysis complemented by interphase FISH no abnormalities are identified in approximately 15-20% of cases. In these cases either no cytogenetic aberrations are present or these may be missed by chromosome banding analysis (CBA) due to insufficient cell division in vitro or to too low resolution of chromosome banding analysis (10 MB). On the other hand by FISH a respective abnormality can only be detected if it is covered by the applied probe panel. Aims: 1. Apply array CGH and molecular mutation screening to characterize CLL cases in which CBA and FISH both did not reveal any cytogenetic abnormalities. 2. Determine prognostic factors in this CLL subset. Patients and Methods: Diagnosis of CLL was based on cytomorphology and immunophenotyping. All cases showed at least 15% of CLL cells. The median age was 67 years (range: 40-84, mean 64 years). Overall survival (OS) at 10 years was 81% and median time to treatment (TTT) was 8.9 years. 136 CLL patients were selected based on a normal karyotype in CBA and no abnormalities in interphase FISH with probes for 17p13 (TP53), 13q14 (D13S25, D13S319, DLEU), 11q22 (ATM), the centromeric region of chromosome 12 and t(11;14)(q13;q32) (IGH -CCND1). For all 136 patients the IGHV mutation status was determined and array CGH (SurePrint G3 ISCA CGH+SNP Microarray, Agilent, Waldbronn, Germany) was performed. Further, mutation analysis by DNA sequencing was performed in the following genes: TP53 (n=106), SF3B1 (n=106), MYD88 (n=83), XPO1 (n=83), NOTCH1 (n=83), FBXW7 (n=83), BIRC3 (n=45) and ATM (n=44). Results: In total 55 abnormalities were detected in 26/136 (19%) patients by array CGH. Of these 25 were deletions (size of 17 deletions was <10MB and 8 were >10MB), 23 were gains (17 <10MB; 6 >10MB) and 7 were CN-LOH (2 <10MB; 5 >10MB). The following recurrent abnormalities were identified: deletions of 13q14 (n=3); 1q42.12 (n=4), 4p16.3 (n=2), 7p14 (n=3); gains of Xp22.31 (n=2), 3q26-28 (n=2); and CN-LOH 17q (n=2). A mutated IGHV status was present in 68% of cases. Mutations were observed in SF3B1 (19%), NOTCH1 (7%), ATM (5%), XPO1 (4%), TP53 (3%), MYD88 (2%), FBXW7 (1%) and no mutation in BIRC3. Compared to a cohort of 1,115 CLL with aberrant karyotype by CBA/FISH, in the present CLL cohort with normal karyotype SF3B1 mutations were significantly more frequent (19% vs 8%, p=0.001), while TP53 mutations tended to be less frequent (3% vs 8%, p=0.07). In the 26 patients with normal karyotype by CBA/FISH but aberrant karyotype by array CGH (CGHpos) SF3B1 mutations were even more frequent than in cases with normal karyotype by both CBA/FISH and array CGH (CGHneg) (33% vs 14%, p=0.043). A mutated IGHV status was found in 71% of CGHneg patients compared to 58% of CGHpos cases (n.s.). Only age (relative risk (RR): 1.16 per decade, p=0.006) and percentage of CLL cells as determined by flow cytometry (% CLL cells) (RR: 1.36 per 10% increase) were significantly associated with OS and the impact of both parameters was independent of each other. TTT was significantly influenced by the following parameters: CGHpos (RR: 2.4, p=0.017), unmutated IGHV (RR: 4.7, p<0.0001), SF3B1 mutation (RR: 2.9, p=0.006), % CLL cells (RR: 1.32 per 10% increase, p<0.0001), and leucocyte count (RR: 1.043 per 10,000 increase, p=0.031). Multivariate Cox regression analysis revealed an independent impact on TTT for an unmutated IGHV status (RR: 4.7, p<0.0001), mutated SF3B1 (RR: 2.9, p=0.006), and % CLL cells (RR: 1.32 per 10%, p<0.0001). The median TTT was significantly shorter in patients with unmutated IGHV status and/or SF3B1 mutation (n=55) as compared to those without (n=57) (5.1 years vs not reached, p<0.0001). Conclusions: 1. CLL with normal karyotype as determined by chromosome banding analysis and FISH is characterized by a high frequency of SF3B1 mutations (19%). 2. Array CGH detects abnormalities in 19% of CLL with normal karyotype by CBA/FISH. 3. In CLL with normal karyotype by CBA/FISH a negative effect on TTT was found for the presence of any abnormalities detected by array CGH, SF3B1 mutations, an unmutated IGHV status, and the percentage of CLL cells. Thus, in younger patients the analysis of these parameters should be discussed to better define prognosis. Disclosures Haferlach: MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Jeromin:MLL Munich Leukemia Laboratory: Employment. Kern:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Schnittger:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership.

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Abnormalities Detected By Array CGH and Fluorescence in Situ Hybridization in AML with Normal Karyotype Lacking Mutations in NPM1, CEBPA, RUNX1 and MLL Partial Tandem Duplications Are Associated with Unfavorable Outcome

Blood ◽

10.1182/blood.v126.23.1371.1371 ◽

2015 ◽

Vol 126 (23) ◽

pp. 1371-1371

Author(s):

Claudia Haferlach ◽

Kathleen Zieschang ◽

Susanne Schnittger ◽

Tamara Alpermann ◽

Melanie Zenger ◽

...

Keyword(s):

Chromosome Banding ◽

Array Cgh ◽

Normal Karyotype ◽

Employment Equity ◽

In Vitro Proliferation ◽

Banding Analysis ◽

Chromosome Banding Analysis ◽

Impact On Survival ◽

Equity Ownership

Abstract Background: AML is a group of genetically distinct entities which have been defined by the presence of certain recurrent, mutually exclusive genetic abnormalities such as AML-specific fusion genes (e.g. PML-RARA, RUNX1-RUNX1T1) or recurrent molecular mutations (NPM1 mutations and CEBPA double mutations (dm)). In addition partial tandem duplications within the MLL gene (MLL-PTD) and RUNX1 mutations seem to play an important role in certain AML subtypes. A subset of AML with normal karyotype lacking the above-mentioned mutations is still poorly characterized. Array CGH and fluorescence in situ hybridization are able to detect abnormalities which are undetectable by chromosome banding analysis either due to a higher resolution, ability to detect copy neutral loss of heterozygosity (CN-LOH) and independence of in vitro proliferation. Aims: 1. Search for submicroscopic copy number changes and cryptic rearrangements in AML with normal karyotype lacking NPM1 and RUNX1 mutations, CEBPA dm, and MLL-PTD. 2. Determine whether submicroscopic cytogenetic changes impact on survival. Patients and Methods: For 1473 AML cases with normal karyotype complete data on mutation status of NPM1, CEBPA, RUNX1 and MLL -PTD was available. Of these 303 cases (21%) did not carry one of these mutations. Out of these 159 cases with de novo AML (median age: 68 years (range: 19-93)) were selected on the basis of availability of material for array CGH (SurePrint G3 ISCA CGH+SNP Microarray, Agilent, Waldbronn, Germany) and FISH screening with probes for MLL, RUNX1, CBFB, NUP98, MECOM/EVI1, NPM1, ETV6 and DEK-NUP214 (MetaSystems, Altlussheim, Germany; ABBOTT, Wiesbaden Germany). Results: In total in 67 of 159 patients (42%) abnormalities were identified by FISH and/or array CGH. In detail, 12 balanced rearrangements were detected by FISH screening involving NUP98 (n=7, in 6 of these a NUP98-NSD1 rearrangement was identified by PCR), MLL (n=2) and MECOM, RUNX1 and CBFB (one each). In addition, 27 gains, 42 losses and 41 copy neutral losses of heterozygosity (CN-LOH) were observed in 58 (37%) patients. Recurrent gains affected regions 6q23.3q23.3 (135.325.751-135.607.060) (n=2) and 8q24.21q24.21 (130.517.732-130.808.381) (n=2) while recurrent losses were found for the regions 21q22.12q22.12 encompassing the RUNX1 gene (36.228.735-36.303.952) (n=5), 5q31.2q31.2 including i.a. EGR1 and CTNNA1 (137.617.569-138.993.959) (n=3), 2q34q34 including i.a. IKZF2 (213.371.237-214.560.488) (n=2), 7q22.1q22.1 encompassing i.a. CUX1 (100.485.221-101.916.623) (n=2), and Yq11.223q12 (24.980.949-28.804.541) (n=2). Recurrent CN-LOH were observed on chromosomes 11q (n=10), 2p (n=5), 4q (n=4), 21q (n=3), 1p (n=2), 17q (n=2) and 18q (n=2). 20/27 gains and 38/42 losses were < 10 megabases in sizes and thus below the resolution of chromosome banding analysis. Only in 7 (4%) patients abnormalities (n=11) were identified which in principle are detectable by chromosome banding analysis. These were missed by chromosome banding analysis due to insufficient in vitro proliferation of the aberrant clone, small clone size or poor chromosome morphology. Comparing age, white blood cell count and bone marrow blast counts revealed no differences between patients with or without abnormalities detected by FISH and/or array CGH. However, FLT3-ITD and WT1 mutations were more frequent in cases with abnormalities (25% vs 7%, p=0.001; 9% vs 1%, p=0.021). Survival analysis was performed for 90 intensively treated patients. Overall survival (OS), event-free survival (EFS) and OS with censoring at time of allogeneic SCT (OSctx) were significantly shorter in patients with abnormalities detected by FISH and/or array CGH compared to those without (median OS: 19 vs 49 months, p=0.027; Figure 1; median EFS: 9 vs 21 months, p=0.016; median OSctx: 13 vs 26 months, p=0.018). Conclusions: 1. AML with normal karyotype based on chromosome banding analysis lacking a disease defining molecular mutation harbor balanced rearrangements, copy number gains and losses as well as CN-LOH at a high frequency (42%). 2. The presence of these abnormalities has a negative impact on survival demonstrating that FISH and array CGH can add prognostic information in the diagnostic work-up of AML with normal karyotype lacking a disease defining mutation. 3. Further investigations of mutations in genes located in regions of recurrent CN-LOH is necessary. Figure 1. Figure 1. Disclosures Haferlach: MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Zieschang:MLL Munich Leukemia Laboratory: Employment. Schnittger:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Alpermann:MLL Munich Leukemia Laboratory: Employment. Zenger:MLL Munich Leukemia Laboratory: Employment. Perglerová:MLL2 s.r.o.: Employment. Kern:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership.

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Targeted Next-Generation Sequencing Of 2,761 Genes Detects Copy Number States and Molecular Mutations In a Single Approach

Blood ◽

10.1182/blood.v122.21.1371.1371 ◽

2013 ◽

Vol 122 (21) ◽

pp. 1371-1371

Author(s):

Alexander Kohlmann ◽

Andreas Roller ◽

Sandra Weissmann ◽

Sabrina Kuznia ◽

Melanie Zenger ◽

...

Keyword(s):

Exome Sequencing ◽

Copy Number ◽

Chromosome Banding ◽

Array Cgh ◽

Copy Number Alterations ◽

Employment Equity ◽

Targeted Exome Sequencing ◽

Banding Analysis ◽

Chromosome Banding Analysis ◽

Equity Ownership

Abstract Introduction In acute myeloid leukemia (AML), the karyotype and molecular mutation profile are the strongest determinants for prognosis and biological subclassification. Yet, diagnostic analyses rely on chromosome banding technique and sequencing of a constantly growing number of genes. Aims In an era of novel high-throughput sequencing assays becoming viable options for diagnostic implementation we aimed to evaluate whether the application of targeted exome sequencing can reliably identify copy number states and molecular mutations in a single-step procedure. Patients and Methods The pilot cohort included four AML cases with a complex karyotype with known chromosomal alterations as detected by chromosome banding analysis, 24-color FISH and array CGH (12x270K microarrays, NimbleGen, Madison, WI). The size of the aberrant clone was determined by suitable probes using interphase-FISH on bone marrow smears. For sequencing analysis genomic DNA was extracted from mononuclear cells and 50 ng were processed using the TruSight Rapid Capture kit (Illumina, San Diego, CA). Sequencing was performed on a MiSeq instrument using the 2x150 bp paired-end read chemistry targeting a subset of the human exome (2,761 genes; 37,366 exons). This exome enrichment library contained >50,000 probes (7.75 Mb) focusing on disease-causing variants in specific inherited conditions (Illumina). Data analysis was performed applying default settings of the on-board MiSeq Reporter Software version 2.2.29 using the Burrows-Wheeler Aligner to align the reads against the hg19 reference genome. Further processing to delineate copy number states was performed using the ExomeCNV package. Results Each patient was analyzed in a single MiSeq run and in median 22,022,240 (range 19,233,134 - 23,507,016) reads were generated. The median coverage per target region was in the range of 74-186 reads. Coverage uniformity was assessed according to the manufacturer's recommendations. Over 98% of bases were covered at 0.12X mean coverage for each sample. Next, two data analysis pipelines were triggered, i.e. copy number states and mutation analysis. With respect to copy number alterations (CNA), in total 65 CNA were detected by chromosome banding analysis/array CGH. Of these, 21 were gains, 44 were losses. The size of the deletions ranged between 378,377 and 141,048,720 bp (median 10,731,680 bp), the size of the gains ranged between 281,608 and 46,404,876 bp (median 4,947,125 bp), respectively. In total, 63/65 (96.9%) copy number alterations were correctly identified by targeted exome sequencing. The NGS assay was able to detect copy number alterations that were present in only 23% of cells as determined by interphase-FISH. In detail, one of the deletions was homozygous with a larger deletion on the long arm of chromosome 17 (size: 1,070,162 bp) and a small intragenic deletion within the NF1 gene. This homozygous deletion was detected by array-CGH and by exome sequencing. Interestingly, the higher resolution of the exome sequencing assay in this area enabled the exact localization (exons 37 to 58) and size determination (78,415 bp) of the deletion. Overall, only 2 gains escaped detection. These were two small gained regions on a highly rearranged chr. 19. Secondly, with respect to mutation analysis, the same assay detected 19, 20, 21 and 28 mutations in the four analyzed patients. This pipeline took only putative variants into account that were not present in the control sample, were having a coverage ≥30 reads with a mutation load ≥10%, and had a confirmed COSMIC mutation entry (v66). 12/2,761 (0.4%) genes harbored mutations in at least 2/4 patients. This included genes known to be involved in leukemogenesis. TP53 mutations were detected in all four cases and all were confirmed by Sanger sequencing. Conclusions A targeted exome sequencing assay allowed to robustly assess copy number states in AML at diagnosis at a resolution greater than current conventional array CGH analyses. Moreover, exome sequencing read data also can be used to delineate mutation profiles. Thus, this workflow enabled to call gene mutations and copy number states in a single assay and is a promising option for a routine diagnostics assay in the future. The gene panel has to be further optimized by adding genes known to be mutated in hematological malignancies. More data is necessary to precisely determine the detection limit and to optimize software tools for a routine use. Disclosures: Kohlmann: MLL Munich Leukemia Laboratory: Employment. Roller:MLL Munich Leukemia Laboratory: Employment. Weissmann:MLL Munich Leukemia Laboratory: Employment. Kuznia:MLL Munich Leukemia Laboratory: Employment. Zenger:MLL Munich Leukemia Laboratory: Employment. Kern:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Schnittger:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership.

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Characterization of CMML with Normal Karyotype in Comparison to CMML with Aberrant Karyotype

Blood ◽

10.1182/blood.v126.23.1674.1674 ◽

2015 ◽

Vol 126 (23) ◽

pp. 1674-1674

Author(s):

Claudia Haferlach ◽

Manja Meggendorfer ◽

Wolfgang Kern ◽

Susanne Schnittger ◽

Torsten Haferlach

Keyword(s):

Chromosome Banding ◽

Array Cgh ◽

Negative Impact ◽

Normal Karyotype ◽

Employment Equity ◽

Monosomy 7 ◽

Cytogenetic Abnormalities ◽

Banding Analysis ◽

Chromosome Banding Analysis ◽

Equity Ownership

Abstract Background: CMML is a myelodysplastic/myeloproliferative neoplasm with distinct morphological and genetic features. Based on differences in blast count CMML is divided into CMML-1 (<1% blasts in the peripheral blood (pB) and <10% in the bone marrow (BM)) and CMML-2 (5-19% blasts in pB, 10-19% in BM or presence of Auer rods). Clonal cytogenetic abnormalities are detected in only 20-40% of patients by chromosome banding analysis (CBA) while >90% of patients harbor at least one molecular mutation. The most frequent cytogenetic abnormalities include abnormalities of chromosome 7, trisomy 8 and complex karyotype. The genes most frequently mutated in CMML are TET2, ASXL1 and SRSF2. Aims: 1. Evaluate the frequency of submicroscopic gains and losses of chromosomal material as well as copy neutral loss of heterozygosity (CN-LOH) in CMML with normal karyotype in chromosome banding analysis (CBA). 2. Analyze the association of these lesions with molecular mutations and impact on survival. Patients and Methods: 69 patients with CMML-1 and 31 with CMML-2 and normal karyotype by CBA were evaluated by array CGH (SurePrint G3 ISCA CGH+SNP, Agilent, Waldbronn, Germany). 32 patients were female, 68 male, median age was 75 years (range: 50-89 years). These were compared to 41 cases with aberrant karyotype by CBA. Patients were screened for mutations (mut) in ASXL1, CBL, DNMT3A, EZH2, JAK2 V617F, KITD 816, KRAS, NRAS, RUNX1, SETBP1, SF3B1, SRSF2, TET2, and U2AF1. Results: In 35 cases (35%) with normal karyotype by CBA 46 abnormalities were detected by array CGH (CGHpos). These were 6 gains, 17 losses and 23 CN-LOH. No recurrent gain was observed, while recurrent losses of 4q24 (n=2, including TET2) and of 13q14 (n=2) were identified. CN-LOH was recurrently observed on 4q (n=6, including TET2), 11q (n=5, including CBL), 17q (n=4) and 7q (n=2). Mutations were identified at the following frequencies: TET2: 77% (74/96), SRSF2: 56% (54/97), ASXL1: 48% (46/96), RUNX1: 20% (20/98), CBL: 15% (15/97), KRAS: 12% (12/97), JAK2 V617F: 10% (10/98). The following genes were mutated in <10%: NRAS, SETBP1, EZH2, U2AF1, KIT D816, SF3B1, DNMT3A. 85 patients were analysed for all mutations. In median 3 mutations were identified per patient (range 0-6), while only in 1 patient no mutation was detected. 4/5 (80%) cases with 11q CN-LOH harbored a CBL mut and 7/8 (88%) cases with CN-LOH 4q or 4q24 deletion harbored a TET2 mut, indicating that these two gene mutations might contribute in homozygous manner to pathogenesis. NRAS mut were significantly less frequent in CMML CGHpos compared to CGHneg (0% vs 14.3%, p=0.024). Mutations in ASXL1 and RUNX1 frequently occurred together: 35% of ASXL1 mut cases also carried a RUNX1 mut as compared to 8% of ASXL1 wild-type cases (p=0.002). All 7 SETBP1 mut cases also carried an ASXL1 mut (p=0.04) Patients with CGHneg (n=65) and CGHpos (n=35) were compared to 41 cases with aberrant karyotype by CBA. While TET2 mut were detected at comparable frequencies in CGHneg and CGHpos patients (80% and 71%) they were significantly less frequent in CMML with aberrant karyotype (54%, p=0.021). On the other hand SETBP1 mut were more frequent in CMML with aberrant karyotype as compared to CGHpos and CGHneg (21%, 7%, 9%, p=0.08). A distinct mutation profile was identified in 9 patients with monosomy 7 who showed ASXL1 mut in 78%, SETBP1 mut in 75%, CBL mut in 33% and TET2 mut in only 22%. In CMML-2 RUNX1 mut were more frequent than in CMML-1 (33% vs 12%. p=0.008). No differences in overall survival (OS) were observed between patients with CGHneg, CGHpos and aberrant karyotype. However, Cox regression analyses revealed a negative impact on OS for ASXL1 mut (relative risk (RR): 2.4, p=0.027), RUNX 1mut (RR: 2.5, p=0.025) and CMML-2 (RR: 2.2, p=0.02). Conclusions: 1. 35% of CMML cases with normal karyotype based on chromosome banding analysis harbor abnormalities detectable by array CGH. 2. Prognosis in CMML is determined by the molecular mutation profile, cytogenetic abnormalities play a minor role. 3. Mutations in ASXL1 and RUNX1 are associated with a negative impact on survival. 4. The poor prognosis described for monosomy 7 seems to be due to a high frequency of ASXL1 und SETBP1 mutations. 5. Inferior outcome in CMML-2 might be due to a higher frequency of RUNX1 mutations. 6. In CMML a molecular work up including screening for mutations in ASXL1 and RUNX1 provides more relevant prognostic information than chromosome banding analysis and/or array CGH. Disclosures Haferlach: MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Meggendorfer:MLL Munich Leukemia Laboratory: Employment. Kern:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Schnittger:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership.

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Multiplex ligation-dependent probe amplification identifies copy number changes in normal and undetectable karyotype MDS patients

10.21203/rs.3.rs-32982/v2 ◽

2020 ◽

Author(s):

Jing Ma ◽

xiaofei Ai ◽

Jinhuan Wang ◽

Limin Xing ◽

Chen Tian ◽

...

Keyword(s):

Copy Number ◽

Chromosome Banding ◽

Chromosomal Abnormalities ◽

Normal Karyotype ◽

Prognostic Information ◽

Significant Difference ◽

Banding Analysis ◽

Chromosome Banding Analysis ◽

Copy Number Changes ◽

Dependent Probe

Abstract Background Chromosomal abnormalities play an important role in classification and prognostication of myelodysplastic syndromes (MDS) patients. However, more than 50% low risk MDS patients harbor a normal karyotype. Recently, multiplex ligation-dependent probe amplification (MLPA) has emerged as an effective and robust method for the detection of cytogenetic aberrations in MDS patients. Methods To characterize the subset of MDS with normal karyotype or failed chromosome banding analysis, we analyzed 144 patient samples with normal karyotype or undetectable through regular chromosome banding, which were subjected to parallel comparison via fluorescence in situ hybridization (FISH) and MLPA. Results MLPA identifies copy number changes in 16.7% of 144 MDS patients and we observed a significant difference in overall survival (OS) (median OS: undefined vs 27 months, p=0.0071) in patients with normal karyotype proved by MLPA, versus aberrant karyotype cohort as determined by MLPA. Interestingly, patients with undetectable karyotype via regular chromosome banding indicated inferior outcome. Conclusion Collectively, MDS patients with normal or undetectable karyotype via chromosome banding analysis can be further clarified by MLPA, providing more prognostic information that benefit for individualized therapy.

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Multiplex ligation-dependent probe amplification identifies copy number changes in normal and undetectable karyotype MDS patients

Annals of Hematology ◽

10.1007/s00277-021-04550-8 ◽

2021 ◽

Author(s):

Jing Ma ◽

Xiaofei Ai ◽

Jinhuan Wang ◽

Limin Xing ◽

Chen Tian ◽

...

Keyword(s):

Copy Number ◽

Chromosome Banding ◽

Chromosomal Abnormalities ◽

Normal Karyotype ◽

Prognostic Information ◽

Significant Difference ◽

Banding Analysis ◽

Chromosome Banding Analysis ◽

Copy Number Changes ◽

Dependent Probe

AbstractChromosomal abnormalities play an important role in classification and prognostication of myelodysplastic syndrome (MDS) patients. However, more than 50% of low-risk MDS patients harbor a normal karyotype. Recently, multiplex ligation-dependent probe amplification (MLPA) has emerged as an effective and robust method for the detection of cytogenetic aberrations in MDS patients. To characterize the subset of MDS with normal karyotype or failed chromosome banding analysis, we analyzed 144 patient samples with normal karyotype or undetectable through regular chromosome banding analysis, which were subjected to parallel comparison via fluorescence in situ hybridization (FISH) and MLPA. MLPA identifies copy number changes in 16.7% of 144 MDS patients, and we observed a significant difference in overall survival (OS) (median OS: undefined vs 27 months, p=0.0071) in patients with normal karyotype proved by MLPA versus aberrant karyotype cohort as determined by MLPA. Interestingly, patients with undetectable karyotype via regular chromosome banding indicated inferior outcome. Collectively, MDS patients with normal or undetectable karyotype via chromosome banding analysis can be further clarified by MLPA, providing more prognostic information that benefit for individualized therapy.

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Array Based Comparative Genomic Hybridization Detects Copy Number Alterations in 80.3% of Adult Acute Lymphoblastic Leukemia (ALL) with Normal Karyotype or Failed Chromosome Banding Analysis and Identifies a Subset with Only Submicroscopic Alterations Associated with Favorable Outcome

Blood ◽

10.1182/blood.v124.21.2409.2409 ◽

2014 ◽

Vol 124 (21) ◽

pp. 2409-2409

Author(s):

Claudia Haferlach ◽

Melanie Zenger ◽

Torsten Haferlach ◽

Wolfgang Kern ◽

Susanne Schnittger

Keyword(s):

Copy Number ◽

Chromosome Banding ◽

Normal Karyotype ◽

Chromosome Abnormalities ◽

Comparative Genomic ◽

Copy Number Alterations ◽

Employment Equity ◽

Chromosome Banding Analysis ◽

Equity Ownership

Abstract Background: Based on chromosome banding analyses (CBA) more than 70% of ALL harbor chromosome abnormalities. These include balanced translocations and a large spectrum of deletions and gains. In up to 10% of ALL CBA fails. In approximately 20% of cases no chromosome abnormalities are detected. This might be due to the fact that ALL blasts failed to proliferate in vitro, to the submicroscopic size of alterations or to a truly normal karyotype. Aim: To characterize the subset of ALL with normal karyotype or failed CBA using array based comparative genomic hybridization (aCGH) and to evaluate whether this technique can provide relevant information in the diagnostic work-up and prognostication of ALL. Patients and Methods: Out of a total of 757 adult ALL patients (age 18.0-91.4 yrs, median 52.5 yrs) analyzed at diagnosis between 2005 and 2014 we selected a subset of 190 cases with normal karyotype (n=144; 75.8%) or failure of CBA (less than 11 analyzable metaphases without clonal chromosome abnormalities, n=46; 24.2%). All cases were analyzed by aCGH (12 x 270 K microarray slides, Roche Nimblegen, Madison, WI). In addition, data on FISH or PCR for BCR-ABL1 and MLL rearrangements was available in 170/190 pts. Results: 92 cases were classified as B-lineage ALL, 46 as T-lineage ALL and 14 showed a Burkitt phenotype. For 38 pts no data on ALL immunophenotype was available. Out of 170 pts investigated by FISH or PCR 21 (12.4%) pts were positive for BCR-ABL1 and 3 (1.8%) pts showed an MLL rearrangement. All 14 pts with a Burkitt phenotype showed a MYC-rearrangement by FISH. In 12 cases (6.3%) aCGH analyses failed due to poor DNA quality. By aCGH 143/178 (80.3%) pts harbored an aberrant karyotype while only 35 showed no copy number alteration (19.7%). 785 copy number alterations were observed in 143 pts (mean 5.5 per case; range: 1-47). 292 were whole chromosome gains (n=164) or losses (n=128) while 493 were alterations affecting certain chromosome regions. Losses of chromosomal regions were more common than gains (333 vs 160). 253 gains and 222 losses, i.e. 60.5% of all affected chromosomes/chromosomal regions, were larger than 10 Mbp. This size is above the resolution of CBA and thus we concluded that these aberrations were missed by CBA due to lack of proliferation of ALL blasts in vitro. 239 losses and 71 gains were smaller than 10 Mbp and thus are not detectable by CBA. In 40 pts (22.5%) only submicroscopic alterations were detected. Most frequent alterations observed by aCGH were: Losses of 9p21 (CDKN2A) (n=58; 32.6%), 6q (n=21; 11.8%), 13q14 (RB1) (n=21; 11.8%), 7q34 (TCRB) (n=21; 11.8%), 12p13 (ETV6) (n=14; 7.9%), 7p12 (IKZF1) (n=13; 7.3%), 14q32 (IGH) (n=8; 4.5%), 5q33 (EBF1) (n=7; 3.9%), 10q23 (GRID1, PTEN) (n=6; 3.4%), 3p (n=6; 3.4%) as well as gains of 1q (n=14; 7.9%). Deletions of 5q33, 6q, 7p12, 7q34, 9p21, 10q23, 12p13 and 13q14 were observed in both B- and T-cell precursor ALL, respectively. In contrast, losses and gains of whole chromosomes, gains of 1q and 14q32 deletions were only detected in pts with B-cell precursor ALL. In the subset of 40 pts harboring only submicroscopic abnormalities the most frequently affected regions were loss of 9p21 (CDKN2A) (40.0%), 14q32 (IGH) (10.0%), 7q34 (TRBV) (10.%), 13q14 (RB1; RCBTB2) (7.5%), 21q22 (KCNJ15) (7.5%). No recurrent gain was identified. Clinical follow-up data was available for 95 pts. Based on aCGH 12 cases with a typical pattern of chromosome losses characteristic for the ALL subset with a low hypodiploid karyotype were detected. As has been described previously for this group they showed a dismal outcome with a median OS of only 5.3 months. The relative risk for death compared to all others amounted to 4.5 (p=0.047). There was a tendency for better OS in patients showing only submicroscopic abnormalities by aCGH, OS at 3 years was 83.6% compared to 60.5% in all others (p=0.09). Conclusions: 80.3% of ALL with normal karyotype in chromosome banding analysis or failed cytogenetics habor copy number alterations detectable by array CGH. The pattern of lost and gained chromosomal regions is comparable to the alterations most frequently occurring in ALL. 12 patients (6.7%) with a characteristic low hypodiploid karyotype were detected, who showed the known poor outcome. A novel subset of 22.5% of pts was identified showing submicroscopic copy number changes only and a favorable outcome. Thus, nearly a third of the target population can be further classified by aCGH for better prognostication. Disclosures Haferlach: MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Zenger:MLL Munich Leukemia Laboratory: Employment. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Kern:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Schnittger:MLL Munich Leukemia Laboratory: Employment, Equity Ownership.

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Multiplex ligation-dependent probe amplification identifies copy number changes in normal and undetectable karyotype MDS patients

10.21203/rs.3.rs-32982/v1 ◽

2020 ◽

Author(s):

Jing Ma ◽

xiaofei Ai ◽

Jinhuan Wang ◽

Limin Xing ◽

Chen Tian ◽

...

Keyword(s):

Copy Number ◽

Chromosome Banding ◽

Normal Karyotype ◽

Prognostic Information ◽

Cytogenetic Aberrations ◽

Significant Difference ◽

Banding Analysis ◽

Chromosome Banding Analysis ◽

Copy Number Changes ◽

Dependent Probe

Abstract Background In myelodysplastic syndromes (MDS), cytogenetic aberrations play an important role for classification and prognostication. However, more than 50% low risk MDS patients harbor a normal karyotype. Recently, multiplex ligation-dependent probe amplification (MLPA) has emerged as an effective and robust method for the detection of cytogenetic aberrations in MDS patients.Methods To characterize the subset of MDS with normal karyotype or failed chromosome banding analysis, we analyzed 144 patient samples with normal karyotype or undetectable through regular chromosome banding, which were subjected to parallel comparison via fluorescence in situ hybridization (FISH) and MLPA.Results MLPA identifies copy number changes in 16.7% of 144 MDS patients and we observed a significant difference in overall survival (OS) (median OS: undefined vs 27 months, p=0.0071) in patients with normal karyotype proved by MLPA, versus aberrant karyotype cohort as determined by MLPA. Interestingly, patients with undetectable karyotype via regular chromosome banding indicated inferior outcome. Conclusion Collectively, MDS patients with normal or undetectable karyotype via chromosome banding analysis can be further clarified by MLPA, providing more prognostic information that benefit for individualized therapy.

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The Prognostic Impact of High EVI1 expression In AML Is Due to Its Close Correlation to Rearrangements Involving EVI1 or MLL, which Are Cytogenetically Cryptic In a Subset of Patients: a Study on 332 Cases.

Blood ◽

10.1182/blood.v116.21.1676.1676 ◽

2010 ◽

Vol 116 (21) ◽

pp. 1676-1676

Author(s):

Claudia Haferlach ◽

Vera Grossmann ◽

Melanie Zenger ◽

Tamara Alpermann ◽

Alexander Kohlmann ◽

...

Keyword(s):

Chromosome Banding ◽

Normal Karyotype ◽

Fish Analysis ◽

Prognostic Impact ◽

Employment Equity ◽

Npm1 Mutation ◽

Banding Analysis ◽

Chromosome Banding Analysis ◽

Equity Ownership ◽

The Impact

Abstract Abstract 1676 Introduction: High EVI1 expression has been proposed as a negative prognostic factor in AML. An association between high EVI1 expression and distinct cytogenetic subgroups, such as 3q26-rearrangements, MLL-rearrangements and -7/7q- have been reported. Both 3q26- and MLL-rearrangements can be difficult to detect by chromosome banding analyses or may even be cytogenetically cryptic in a subset of patients due to limited resolution. Therefore, only studies using FISH for the detection of cryptic EVI1- or MLL-rearrangements can clarify their frequencies in AML with elevated EVI1 expression. Methods/Patients:: The study cohort was composed of 332 AML cases with a) normal karyotype (NK) (n=211), b) -7/7q- (n=77), and for comparison c) 3q26-rearrangements (n=38), and d) MLL-rearrangement (n=6). In all cases EVI1 expression was investigated using quantitative PCR calculating a % EVI1/ABL1 expression. In all cases FISH for EVI1 rearrangement was performed in addition to chromosome banding analysis. Cases with high EVI1 expression were also analyzed for MLL rearrangements by FISH. Results: In the total cohort, EVI1 expression varied between 0 and 1614 (median: 21.1). The highest EVI1 expression was measured in cases with cytogenetically identified 3q26-rearrangements (range: 6.1–566.4; median: 81.9) and in AML with MLL-rearrangements (range: 46.7–831; median: 239). The EVI1 expression was significantly lower in AML with NK (range: 0–1614; median: 0.5, p<0.001) and AML with -7/7q- (range: 0.03–199; mean: 34.5; median: 10.7, p<0.001). In the subgroup of cases with NK 4 MLL-rearrangements (1.9%) were detected by FISH and subsequently verified by fusion gene specific PCR. In addition, 4 cases with cryptic EVI1-rearrangements (1.9%) were identified by FISH analysis. Further genetic analysis revealed that these were due to t(3;8)(q26;q24) (n=2) and t(3;21)(q26;q11) (n=1). In one case, the EVI1-rearrangement could not be further analyzed due to lack of material. In the -7/7q- cohort 14/77 cases (18.2%) with cytogenetically cryptic EVI1 rearrangement including 3 novel recurrent abnormalities were detected: t(3;21)(q26;q11) (n=3), inv(3)(p24q26) (n=4) and t(3;8)(q26;q24) (n=2). In 5 cases FISH analysis revealed that the 7q- was not caused by an interstitial deletion but due to an unbalanced rearrangement between chromosomes 7 and 3: der(7)t(3;7)(q26;q21). In these 5 cases high-resolution SNP microarray were performed and revealed breakpoints in the CDK6 gene and centromeric of the EVI1 gene. Further mutation screening revealed that none of the cases with EVI1- or MLL-rearrangement harboured mutations in NPM1 or CEPBA. In 254 cases clinical follow-up data was available. Different cut-off levels of EVI1 expression were tested, and a cut-off at 30% EVI1/ABL1 expression was the lowest level that had a significant impact on outcome. Separating the cohort at this cut-off into high EVI1 (n=67) and low EVI1 expressors (n=187) showed a shorter EFS in patients with high EVI1-expression (p=0.001; relative risk (RR)=1.87, median EFS 6.2 vs 15.0 months (mo)), while no impact on OS was observed. When the same analyses were performed with respect to EVI1-rearrangements we observed both a significantly shorter EFS in cases with EVI1-rearrangement (n=39) vs all others (n=215) (p=0.001; RR=2.03, median EFS 4.6 vs 15.0 mo) and a significantly shorter OS (p=0.026; RR=1.73, median OS 10.1 vs 26.3 mo). Analyzing the impact of high EVI1 expression separately in the cohort without EVI1 rearrangement revealed no impact of EVI1 expression on EFS. Conclusions: The negative prognostic impact of high EVI1 expression is strongly associated with EVI1- or MLL-rearrangements and is absent in AML without EVI1- and MLL-rearrangement. Applying FISH in addition to chromosome banding analysis we identified cryptic rearrangements in 3.8% of AML with normal karyotype and in 18.2% of AML with -7/7q-, including 3 novel recurrent cytogenetically cryptic EVI1-rearrangements. This data supports the routine performance of FISH screening for EVI1- and MLL-rearrangements in patients with normal karyotype or 7q-/-7 and without NPM1 mutation and CEPBA mutation to assign patients to the correct biologic entity. The postulated independent prognostic impact of EVI1 expression should be tested further including this laboratory workflow as these parameters may have important impact on prognosis and future treatment strategies. Disclosures: Haferlach: MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Grossmann:MLL Munich Leukemia Laboratory: Employment. Zenger:MLL Munich Leukemia Laboratory: Employment. Kohlmann:MLL Munich Leukemia Laboratory: Employment. Kern:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Schnittger:MLL Munich Leukemia Laboratory: Employment, Equity Ownership.

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Interphase FISH and Comparative Genomic Hybridization Performed in Addition to Chromosome Banding Analysis in AML with Normal Karyotype Detect Prognostically Relevant Chromosome Abnormalities.

Blood ◽

10.1182/blood.v104.11.2016.2016 ◽

2004 ◽

Vol 104 (11) ◽

pp. 2016-2016 ◽

Cited By ~ 1

Author(s):

Claudia Schoch ◽

Mirjam Klaus ◽

Susanne Schnittger ◽

Wolfgang Hiddemann ◽

Wolfgang Kern ◽

...

Keyword(s):

Comparative Genomic Hybridization ◽

Chromosome Banding ◽

Normal Karyotype ◽

Trisomy 13 ◽

Comparative Genomic ◽

Genomic Hybridization ◽

Interphase Fish ◽

Banding Analysis ◽

Chromosome Banding Analysis

Abstract In AML karyotype abnormalities are not detected in 40 to 45% of cases using classical chromosome banding analysis. For several reasons false negative results might occur in chromosome banding analysis: 1. no proliferation of the aberrant clone in vitro, 2. low resolution due to technical problems or limitations of the method itself, 3. real cryptic rearrangements. In order to determine the proportion of “false negative” karyotypes by chromosome banding analysis we conducted a study using interphase-FISH and comparative genomic hybridization in addition to chromosome banding analysis. In total, chromosome banding analysis have been performed in 3849 AML at diagnosis. Of these 1748 showed a normal karyotype (45.4%). Out of these in 3 cases cytomorphology revealed an APL and in 2 cases an AML M4eo. Using interphase FISH with a PML-RARA or CBFB probe we detected cryptic PML-RARA or CBFB-rearrangements, respectively, in all 5 cases, which were cytogenetically invisible due to submicroscopic insertions. 480 cases of AML with normal karyotype were analyzed for MLL gene rearrangements using FISH with an MLL-probe. 11 cases with a cryptic MLL-rearrangement were detected (FAB-subtypes: M5a: 7, M2: 2, M0: 2). In 273 patients interphase-FISH screening with probes for ETO, ABL, ETV6, RB, P53, AML1 and BCR was performed. In 6 out of 273 (2.2%) pts an abnormality was detectable. In two cases the aberrant clone did not proliferate in vitro: 1 case each with monosomy and trisomy 13. Due to limitations of resolution in chromosome banding analysis translocations or deletions of very small chromosome fragments were only detected with FISH in n=4 cases (ETV6 rearrangements: t(11;12)(q24;p13), t(12;22)(p13;q12), ETV6 deletions: del(12)(p13), n=2). Like interphase-FISH comparative genomic hybridization (CGH) does not rely on proliferating tumor cells but in contrast to interphase-FISH allows the detection of all genomic imbalances and not only of selected genomic regions. Therefore, we selected 48 cases with normal karyotype and low in vitro proliferation (less than 15 analyzable metaphases in chromosome banding analysis). In 8 of 48 cases (16.7%) an aberrant CGH-pattern was identified which was verified using interphase-FISH with suitable probes. In 3 cases a typical pattern of chromosomal gains and losses observed in complex aberrant karyotypes was detected. In one case each a trisomy 4 and 13 was observed, respectively. In one case trisomy 13 was accompanied by gain of material of the long arm of chromosome 11 (11q11 to 11q23). One case each showed loss of chromosome 19 and gain of the long arm of chromosome 10, respectively. In conclusion, CGH in combination with interphase-FISH using probes for the detection of balanced rearrangements is a powerful technique for identifying prognostically relevant karyotype abnormalities in AML assigned to normal karyotype by chromosome banding analysis. Especially this is true in cases with a low yield of metaphases and in AML with a high probability of carrying a specific, cytogenetically cryptic fusion-gene. Thus, in these cases interphase-FISH and CGH should be performed in a diagnostic setting to classify and stratify patients best.

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