Broad copy neutral-loss of heterozygosity regions and rare recurring copy number abnormalities in normal karyotype-acute myeloid leukemia genomes

2010 ◽  
Vol 49 (11) ◽  
pp. 1014-1023 ◽  
Author(s):  
Vincenza Barresi ◽  
Alessandra Romano ◽  
Nicolò Musso ◽  
Carmela Capizzi ◽  
Carla Consoli ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Loss Of Heterozygosity ◽  
Copy Number ◽  
Myeloid Leukemia ◽  
Neutral Loss ◽  
Normal Karyotype ◽  
Acute Myeloid

scholarly journals A Novel Case of Extreme Thrombocytosis in Acute Myeloid Leukemia Associated With Isochromosome 17q and Copy Neutral Loss of Heterozygosity

2015 ◽  
Vol 35 (3) ◽  
pp. 366-369 ◽  
Author(s):  
Eunkyoung You ◽  
Sun Young Cho ◽  
John Jeongseok Yang ◽  
Hee Joo Lee ◽  
Woo-In Lee ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Loss Of Heterozygosity ◽  
Myeloid Leukemia ◽  
Neutral Loss ◽  
Acute Myeloid

Loss of Heterozygosity Identified in Acute Myeloid Leukemia with Normal Karyotype Using SNP Microarrays.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 760-760
Author(s):  
Christine Steudel ◽  
Sofia Traikov ◽  
Uta Oelschlägel ◽  
Markus Schaich ◽  
Gerhard Ehninger ◽  
...  
Keyword(s):  
T Cells ◽  
Acute Myeloid Leukemia ◽  
Loss Of Heterozygosity ◽  
Myeloid Leukemia ◽  
Normal Karyotype ◽  
Snp Analysis ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Free Material ◽  
Acute Myeloid

Abstract Loss of heterozygosity (LOH) is detectable in many forms of cancer including leukemia and contributes to tumorigenesis through the deletion of tumor suppressor genes. It derives from the loss of one of the two alleles at a given locus caused by deletion or uniparental disomy (UPD). In this study we describe the genome wide analysis of LOH in purified leukemic blasts from acute myeloid leukemia (AML) samples with normal karyotype using a novel technique based on single nucleotide polymorphisms (SNP). In total we selected 50 peripheral blood samples of de novo AML patients with normal karyotype at the time of diagnosis. Patients were treated according to the AML-96 multi-center protocol of the DSIL. Pure leukemic cells and tumor free material (T cells) from each patient were obtained using FACS-Vantage cell-sorting (BD Sciences, Germany). DNA was isolated from sorted cells. Genome wide SNP analysis was carried out according to the standard GeneChip Mapping Assay protocol (Affymetrix, USA) with pre-amplified DNA (Repli-g™ Kit; Molecular Staging Inc. USA) using the Human Mapping 10K Arrays XbaI 131 (Affymetrix). Individual regions of potential LOH identified by the Affymetrix® GeneChip® Chromosome Copy Number Analysis tool were confirmed by microsatellite analysis of short tandem repeat (STR) markers using the matched non-manipulated original DNA samples. Genome wide analysis of SNP in pre amplified DNA of FACS sorted cells from AML samples with normal karyotype detected long stretches of hemizygosity, indicative of LOH in 8/49 evaluable patients (16%). In 6 of these cases STR-analysis of T cells representing the corresponding tumor free material confirmed the regions of partial UPD. UPD affected four different chromosomes (chromosome 2p and 11q, in each case twice; chromosome 8q, and 13q) and covered between 11.5 and 88 Mb. To our surprise in the healthy material of the remaining two cases no heterozygote loci were identified at the affected chromosomal regions (chromosome 3 14.5 Mb; chromosome 20 29.3 Mb) and consequently identified as unusual long stretches of homozygosity present in both the malignant and the healthy cells. These cases might reflect genotypes with high susceptibility to malignant mutations. No differences were observed for any clinical factors, including age, WBC-counts, sex and FAB-subtype. Also, several of the mutations frequently identified in patients with normal karyotype (FLT3-ITD, MLL-PTD, NPM1) had a comparable prevalence in patients with and without UPD. Interestingly, although 5/6 patients with UPD achieved complete remission after induction chemotherapy, 4/5 (80%) relapsed within the first 6 months. In contrast the rate of relapse in patients without UPD was only 54% (15/28). The only patient positive for UPD and alive in remission received an allogeneic stem cell transplantation. In conclusion, the combination of whole genome amplification method and SNP array technology allows the identification and mapping of LOH in AML patients with normal karyotype. Our data also point to the necessity to analyze tumor free material to confirm the somatic origin of the alteration. Although small numbers of patients were investigated, our data might indicate that patients with UPD have a high rate of treatment failure. This should be further investigated in larger cohorts of patients.

A Genome-Wide Map of Acquired Uniparental Disomy in Acute Myeloid Leukemia.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 996-996 ◽  
Author(s):  
Manu Gupta ◽  
Manoj Raghavan ◽  
Rosemary E. Gale ◽  
Claude Chelala ◽  
Christopher Allen ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Copy Number ◽  
Myeloid Leukemia ◽  
Uniparental Disomy ◽  
Normal Karyotype ◽  
Intermediate Risk ◽  
Snp Arrays ◽  
Risk Patients ◽  
Control Set ◽  
Acute Myeloid

Abstract The recent discovery of acquired uniparental disomy (aUPD) in acute myeloid leukemia (AML) has been linked to homozygosity for mutations in certain genes (Raghavan et al, Cancer Res. 2005, Fitzgibbon et al, Cancer Res. 2005). Although this phenomenon, which is undetectable by conventional cytogenetics, has been confirmed in subsequent small-scale studies, its extent and frequency remains uncertain. To determine the frequency and distribution of aUPD, DNA samples from 455 young adult AML patients entered in the UK Medical Research Council AML10 trial were analyzed using Mapping 10K 2.0 single nucleotide polymorphism (SNP) arrays (Affymetrix Inc.). Genomic DNA from blood samples of ten non-leukemic individuals was used as control to estimate the copy number values (control set I). We defined aUPD as 50 consecutive homozygous markers but allowed 2 heterozygous calls to accommodate contaminating normal tissue. Using this criterion a false positive rate of 3.3% was calculated from an available data of 90 independent controls (control set I). Overall, 120 regions of UPD were observed in 79 AML cases (17%), 87% of which involved at least one breakpoint, i.e. resulted from mitotic recombination, and 13% were whole chromosome aUPDs arising from chromosomal non-disjunction. They were the sole aberration, as detected by SNP arrays, in 61 samples (13%), and 84% of these had only a single region of aUPD. There was a non-random distribution across chromosomes; 13q (n=18 cases), 11p (n=8) and 11q (n=9) were the most frequently affected. Other chromosomes with regions of recurrent aUPD were 2p (n=7), 2q (n=6), 1p (n=5), 19q (n=4), 17q12–q21.2 (n=4), 21q (n=4), 9p (n=3), Xq (n=3), 6p (n=2), and 17p (n=2). Acquired UPDs were observed across all cytogenetic risk groups: in 25% of adverse risk patients, 11% of favorable risk, 19% of normal karyotype and 10% of the remaining intermediate risk patients. Samples with aUPD13q (5% of samples) belonged exclusively to the intermediate risk group. Chromosome 13 was the only chromosome to show recurrent whole chromosome aUPD. Fifteen samples with aUPD13q covered the region of the FLT3 gene at 13q12.2; all 15 had a FLT3-internal tandem duplication (ITD) and all cases with a high FLT3-ITD mutant level > 50% of total had 13q aUPD. Gains and losses were observed in 12% and 14% of the samples respectively. As expected, gains on chromosome 8 and losses on chromosomes 5 and 7 were common, confirming the general utility of this approach. No homozygous losses were observed. Comparison of arrays with cytogenetic analysis showed that additional information (aUPDs and/or copy number changes) was obtained in 23% of cases with a normal karyotype and 38% of cases without available cytogenetics. This study highlights the importance of aUPD in the development of AML and pinpoints regions that may contain novel mutational targets.

Prognostic significance of acquired copy-neutral loss of heterozygosity in acute myeloid leukemia

Cancer ◽  
2015 ◽  
Vol 121 (17) ◽  
pp. 2900-2908 ◽  
Author(s):  
Christine M. Gronseth ◽  
Scott E. McElhone ◽  
Barry E. Storer ◽  
Kathleen A. Kroeger ◽  
Vicky Sandhu ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Loss Of Heterozygosity ◽  
Myeloid Leukemia ◽  
Neutral Loss ◽  
Prognostic Significance ◽  
Acute Myeloid

Genome-Wide Micro-Deletions and Amplifications Acquired at Relapse in Acute Myeloid Leukemia.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 166-166 ◽  
Author(s):  
Manoj Raghavan ◽  
Manu Gupta ◽  
Tracy Chaplin ◽  
Sabah Khalid ◽  
T. Andrew Lister ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Copy Number ◽  
Myeloid Leukemia ◽  
Conflicts Of Interest ◽  
Snp Array ◽  
Uniparental Disomy ◽  
Normal Karyotype ◽  
P Value ◽  
Copy Number Changes ◽  
Acute Myeloid

Abstract Abstract 166 Recurrence of acute myeloid leukemia AML has a poor prognosis with only 20% of adults surviving to 5 years. Therefore it is of importance to identify molecular changes that explain the pathogenesis of relapsed AML. Previous studies had not identified consistently acquired cytogenetic changes at relapse. Recently, acquired uniparental disomy due to mitotic recombination was described in 40% of relapsed AML (Raghavan et al 2008). Most of the events lead to homozygosity for FLT3 mutations. This study aimed to discover if there are further genetic abnormalities acquired at disease recurrence that cannot be identified by conventional cytogenetics, i.e. microdeletions or gains. Twenty-one presentation and relapse paired AML patient blood and marrow samples were stored with consent at St Bartholomew's Hospital, London. Eleven patient samples had a normal karyotype at diagnosis, two had favourable prognosis cytogenetics (inv(16) and t(8;21)) and others had varying numerical cytogenetic abnormalities and rearrangements associated with an intermediate prognosis. DNA from the samples was analysed by array based high-resolution single nucleotide polymorphism (SNP) genotyping (Affymetrix Human SNP array 6.0). Data was analysed using Partek Genome Browser (Partek, MO). In all cases, the leukemia infiltrate of the marrow or blood was greater than 60% and most cases were greater than 90% allowing accurate identification of DNA copy number changes. Abnormalities of a size that would be identified by cytogenetics were disregarded. Using segmentation analysis using a p-value less than 0.001, over 400 microdeletions and gains were detected that were acquired at relapse in the 21 pairs. Each of the copy number changes was less than 2 megabases in size. One AML sample with a normal karyotype at diagnosis and trisomy 8 and add(9)(q34) at relapse had not acquired any microdeletions or gains. In contrast, in other samples as many as 69 microdeletions/gains were detected. There was no correlation between increased complexity of the karyotype of the leukemia and the number of microdeletions/gains. Several of the acquired microdeletions/gains were in regions containing genes known to be involved in AML, including a deletion of 234Kb at 13q12.2 involving FLT3 and CDX2, and an acquired deletion at 21p11.2 of 150Kb involving exons encoding the runt domain of RUNX1. Another copy number gain was detected at the MLL locus, suggestive of partial tandem duplication. Other detected locations are in Table 1.Table 1Location by cytobandCopy number changeSize / KbP valueGene13q12.2Deletion23410−33FLT3, CDX221q22.12Deletion15010−13RUNX111q23.3Gain5.10.0099MLL11p15.4Gain830.00001NUP9817q21.31Deletion8.00.0007BRCA1The results indicate that recurrent AML may be associated with the deletion or gain of several genes involved in leukaemogenesis. Many other locations are involved throughout the genome, suggesting at least some of these are also involved in the clonal evolution of the leukaemia at recurrence. Further studies should identify novel genes from these regions involved in the pathogenesis of AML. Disclosures: No relevant conflicts of interest to declare.

Mlecular Monitoring of Acute Myeloid Leukemia Patients Carrying Nucleophosmin (NPM1) Mutations Undergoing An Autologous Peripheral Blood Stem Cell Transplantation

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 4864-4864
Author(s):  
Valentina Gianfelici ◽  
Daniela Diverio ◽  
Saveria Capria ◽  
Silvia maria Trisolini ◽  
Sonia Buffolino ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Stem Cell ◽  
Stem Cell Transplantation ◽  
Peripheral Blood ◽  
Copy Number ◽  
Myeloid Leukemia ◽  
Peripheral Blood Stem Cell ◽  
Normal Karyotype ◽  
Blood Stem Cell Transplantation ◽  
Acute Myeloid

Abstract Nucleophosmin (NPM1) gene mutations represent the most common genetic alterations in adult acute myeloid leukemia (AML), accounting for about 30% of cases and 50–60% of AML with normal karyotype. In addition to their recognized prognostic value (when combined with analysis of the FLT3 gene), NPM1 mutations represent an ideal marker for monitoring of minimal residual disease (MRD) since they are very stable during the course of the disease. PCR quantitative monitoring of NPM1 mutant copies has been mainly restricted to patients treated with conventional chemotherapy. In our study, we retrospectively analyzed, by RQ-PCR, MRD in 12 consecutive NPM1-mutated AML patients who underwent an autologous peripheral blood stem cell transplantation (PBSCT) between September 2000 and March 2008 at the Division of Hematology, “Sapienza” University of Rome. By sequencing of the region encompassing NPM1 exon 12, we demonstrated the presence of a type A mutation in 10/12 patients and of a type B in the remaining 2. Moreover, at diagnosis molecular analysis of the FLT3 gene revealed an internal tandem duplication (ITD) in 7/12 patients. Cytogenetic analysis showed a normal karyotype in 11/12, whereas 1 patient presented a minor karyotype aberration (trisomy 4). RQ-PCR was retrospectively performed on bone marrow samples in all patients at diagnosis, in 11/12 patients before the transplant and in 9/12 after the graft. Six of the 12 patients are at present in continuous complete remission (CCR) with a median follow-up of 54 months (range 4–89), 1 patient has died in CCR 55 months after PBSCT due to a pancreatic carcinoma and 5/12 have relapsed. Four of the latter 5 patients relapsed shortly after the transplant (range 3–10 months); 2 of them died of disease progression and 2 of salvage chemotherapy toxicity. One patient, who relapsed 92 months from PBSCT, is alive in second hematological remission following re-induction and consolidation chemotherapy. No significant differences in median levels of transcript at diagnosis were found between relapsing and non-relapsing patients (93,000 and 68,000; range: 86,000–103,000 and 37,000–116,000, respectively). Nine patients were analyzed after PBSCT: 3 persistently positive relapsed and the copy number of the transcript was always higher than at diagnosis. In the other 6 patients, the transcript was undetectable (3 of them were already in molecular remission pre-transplant): 5 are still in CCR while 1 patient relapsed 92 months after the graft. Regarding the FLT3-ITD status at diagnosis, 3/7 patients are in CCR whereas 4 have relapsed. The retention of NPM1 mutations even at relapse further confirms that NPM1 alterations are highly stable, pointing to this event as critical for leukemia growth and survival. Moreover, in our study long-term survival was always associated with a copy number of NPM1 mutant transcripts below the detectable level of the method, suggesting that disappearance of the transcript should be the primary clinical endpoint. Prospective studies and larger case series are necessary in an attempt to identify a cut-off level during treatment which could be predictive of the clinical outcome of AML patients harboring NPM1 mutations and help in therapeutic choices.

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