Uniparental Disomy May Be Associated with NPM Mutations in AML with a Normal Karyotype.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 2310-2310
Author(s):  
Elena Serrano ◽  
Vanesa Orantes ◽  
Camino Estivill ◽  
Adriana Lasa ◽  
Salut Brunet ◽  
...  
Keyword(s):  
Complete Remission ◽  
Copy Number ◽  
Germ Line ◽  
Snp Array ◽  
Uniparental Disomy ◽  
Normal Karyotype ◽  
Copy Number Analysis ◽  
Complex Germ ◽  
Flt3 Mutations ◽  
Tandem Duplications

Abstract Acute myeloid leukemia (AML) is a heterogeneous group of neoplastic disorders characterized by an abnormal proliferation of the myeloid precursors and a maturation block. A large proportion of AML cases have either a normal karyotype or non-recurrent chromosomal alterations. Underlying genetic lesions of some of these cases have been characterized with the discovery of MLL-internal tandem duplications, activating FLT3 mutations and NPM mutations. Loss of heterozygosity (LOH) derives from the loss of one of the two alleles at a given locus and can be a sign of inactivation of tumor-suppressor genes. We performed a high-resolution genotype analysis on DNA obtained from 19 AML patients with a normal karyotype, both at diagnosis and in samples obtained in complete remission(assessed by multiparametric flow cytometry) using the 10K SNP Array (Affymetrix). Both LOH and copy number analysis, as well as visualization of these analysis were performed by means of the dChip software (M. Lin et al., Bioinformatics (2004), 20:1233–40). A mean call rate of 96.8%. SNP array-based LOH analysis revealed that 4 patients presented large regions of homozygosity at diagnosis which were absent from samples in complete remission. In all four patients copy number analysis indicated no gross chromosomal losses or gains, as was confirmed by conventional cytogenetic analysis. Therefore, it can concluded that the LOH observed in these four patients was due to the presence of uniparental disomy. Simultaneous analysis of FLT-3 internal tandem duplications (FLT-3/ITD), FLT3- D835 mutations, NPM mutations and MLL rearrangements was performed using conventional molecular methods. Two of these patients (UPN2 and UPN12) had FLT-3/ITD in association with NPM mutations. UPN4 had a mutated form of NPM whereas in patient UPN16 FLT-3 and NPM genes were in the germ line configuration. All four cases were negative for MLL rearrangements and FLT-3-D835 mutations. These results suggest that NPM and FLT3 mutations may be associated with acquired somatic recombinations. It remains to be investigated whether there are loci preferentially involved by these events. Uniparental disomy and genetic lesions in normal karyotype AML Patient LOH FLT3 NPM D835 MLL UPN2 13q Mutated Mutated Germ line Germ line UPN4 6pter-p12.212q13.12-qter Germ line Mutated Germ line Germ line UPN12 2p Mutated Mutated Germ line Germ line UPN16 complex Germ line Germ line Germ line Germ line

An Increased Frequency of Abnormalities Including Uniparental Disomy Is Detected by SNP Array Compared with Conventional Karyotype Analysis in Acute Myeloid Leukemia.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 97-97 ◽  
Author(s):  
Manoj Raghavan ◽  
Rosemary E. Gale ◽  
Spyros Skoulakis ◽  
Tracy Chaplin ◽  
Gael Y. Molloy ◽  
...  
Keyword(s):  
Copy Number ◽  
Chromosomal Abnormalities ◽  
Germ Line ◽  
Snp Array ◽  
Uniparental Disomy ◽  
Data Set ◽  
Array Data ◽  
The Mean ◽  
Homozygous Mutations ◽  
Acute Myeloid

Abstract SNP array technology permits the simultaneous analysis of copy number and allelotype data. This approach has revealed the somatic acquisition of uniparental disomy (UPD) in approximately 20% of acute myeloid leukemias (AMLs) (Raghavan et al. Cancer Res2005;65:375–378). UPD, which mostly appears to be the consequence of mitotic recombination, cannot be detected by conventional analysis. We have conducted a pilot investigation of samples from the UK MRC AML 10 trial in order to confirm these findings in a larger data set from a large clinical trial. The Affymetrix 10K GeneChip Mapping Array was used to type DNA from 100 AML blast samples of which 87 produced arrays with call rates in excess of 90%. Analysis was performed using the genome orientated laboratory file (GOLF) system, an in-house software package designed to interpret SNP array data. Control germline DNA was not available for each AML and GOLF was used to create a control copy number experiment from the mean of 52 array data sets from normal tissue (blood and remission marrow). The copy number ratio was calculated for each SNP for each sample. In 44 samples the karyotype concurred with the SNP array results (excluding balanced translocations which cannot be detected by SNP array). In the other samples, 54 abnormalities were detected that were not seen in the karyotype (6 samples had no karyotype information). Nine were amplifications, 12 were deletions and 31 were UPDs (35%). Of the UPDs, 12 were either whole chromosome or extended to the most telomeric SNP, with the others therefore being interstitial changes. The mean size of an interstitial LOH was 13.3 Mb, with the smallest detected being 3.2 Mb. Recurrent chromosomal abnormalities not detected by giemsa banding are listed in table 1. Twenty samples that were regarded as normal karyotype by gene banding had abnormalities by SNP array. In three examples numerical karyotypic abnormalities were not seen on SNP array analysis (add4q, −8 and a hypodiploid AML). This may be because a minority clone of the AML cells had this karyotype. UPD is known to be associated with homozygous mutations in AML (Fitzgibbon et al. Cancer Res 2005; in press). In this series, two patients had UPD13, both with biallelic FLT3 internal tandem duplication mutations. However, this study has identified several new areas to look for potential homozygous mutations. Given that in this study germ-line comparison has not been made one should not rule out the possibility of some of the smaller abnormalities being copy number polymorphisms (Bailey et al. Science2005;297;1003–1007). However, consanguinity can probably be ruled out given the lack of widespread homozygosity. This study confirms the frequency of UPD and illustrates the potential of SNP arrays for highlighting novel genetic events in AML. Table 1: Recurrent chromosomal abnormalities not detected by gene banding Previously Undetected Abnormality Number UPD1p 2 Amplified 1p 2 UPD2p 2 Del7q 3 UPD8p 2 UPD11p 2 UPD11q 3 Amplified 12 3 Amplified 13 2 UPD16p 4 UPD16q 2 Del20q 2

SNP Karyotyping in Myelodysplastic Syndromes (MDS) Reveals the Presence of Cryptic Karyotypic Abnormalities, Including Uniparental Disomy, and Has Important Prognostic Implications.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 853-853 ◽  
Author(s):  
Lukasz P. Gondek ◽  
Abdo Haddad ◽  
Christine O’Keefe ◽  
Ramon Tiu ◽  
Zachary Nearman ◽  
...  
Keyword(s):  
Copy Number ◽  
Uniparental Disomy ◽  
Normal Karyotype ◽  
Genome Scan ◽  
Whole Genome ◽  
Healthy Controls ◽  
Copy Number Analysis ◽  
Snp Arrays ◽  
Whole Genome Scan ◽  
Prognostic Implications

Abstract Using metaphase cytogenetics (MC), chromosomal abnormalities can be found in approximately 50% of patients with MDS (in our cohort (N=356), 46% of patients had normal karyotype by MC), in whom they have important prognostic implications. However, patients with identical lesions, including normal karyotype may show variable clinical behavior. We hypothesized that if a more precise method is used, previously cryptic karyotypic lesions can be found in patients with known aberrations as well as in those with normal MC. High-density SNP arrays (SNP-A) can be used for precise LOH and gene copy number analysis. We have applied this new platform (Affymetrix 250K SNP arrays) to study chromosomal lesions in bone marrow samples from 112 MDS patients, 6 hematologic and 36 healthy controls. Our MDS cohort included patients with RA/RCMD (N=30), RARS/RCMD-RS (N=18), RAEB1/2 and sAML (N=45), and CMML1/2 (N=19); by traditional MC, aberrations of chromosomes 5, 8, 7, and complex karyotypes were present in 13%, 9%, 6% and 8% of patients, respectively. A normal MC exam was obtained in 44% of this sample; in 4% of cases the results were non-informative due to lack of growth. We first applied whole genome scan by SNP-A to establish parameters for minimal pathogenic lesions in healthy controls in whom copy number polymorphisms were easily detectable, but only a limited number of small random defects was found (O’Keefe, ASH 2006). Hematologic controls all showed a normal whole genome scan. However, when this method was applied to MDS patients, chromosomal aberrations were detected in 79% (vs. 52% by MC, p<0.001). Previously unrecognized lesions were detected in both patients with a normal MC test, as well as in those with known lesions. Consequently, a higher proportion of patients showed >1 genomic lesion (e.g. for MC vs. SNP-A, 2 defects in 10/112 vs. 27/112, and ≥3 in 9/112 vs. 31/112, respectively). Newly identified lesions were confirmed by microsatellite and TaqMan PCR copy number analysis in clonal and wt hematopoietic cells. Most significantly, in a proportion of patients, we have identified segmental uniparental disomy (UPD), a lesion resulting in LOH that cannot be detected by MC; it was found in 24% of patients. Most often, UPD involved chromosomes/regions that are frequently affected by loss of genetic material, including chromosome 7q (N=5), 11q (N=5) and 6p (N=3), but also in chromosomes 1 (N=5) and 17 (N=3). As a result, shared areas of LOH were identified in a higher proportion of patients. For example, in addition to known 7/7q deletions (N=7), we have detected 2 new losses involving 7q34 (N=3) and 7q22.1 (N=2) as well as UPD in 7q (N=5), increasing the proportion of patients with aberrant chromosome 7 from 6% by MC to 15% by SNP-A (p<0.03). Clinical analysis of the impact of previously cryptic lesions analogous to those with established adverse prognostic impact (new del7/upd7 or complex) suggests that that SNP-A karyotyping will have clinical utility above and beyond the value of MC. In sum, SNP-A-based karyotyping allows for precise detection of chromosomal lesions in MDS. Previously cryptic defects, including UPD may have clinical and prognostic relevance and help identify genes responsible for the phenotype of the dysplastic clone.

Enhancement of Cytogenetic Diagnosis of Myeloid Disorders through Application of SNP-Array-Based Karyotyping.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 108-108 ◽  
Author(s):  
Lukasz P. Gondek ◽  
Ramon Tiu ◽  
Marcin Wlodarski ◽  
Christine O’Keefe ◽  
Michael McDevitt ◽  
...  
Keyword(s):  
Clinical Relevance ◽  
Germ Line ◽  
Copy Number Variants ◽  
Snp Array ◽  
Uniparental Disomy ◽  
Disease Process ◽  
Normal Karyotype ◽  
Diagnostic Value ◽  
Differential Analysis ◽  
The Impact

Abstract Cytogenetic testing improves diagnosis in myeloid disorders; chromosomal (chr) aberrations have important clinical implications. SNP arrays (SNP-A) can be applied for karyotyping with a superb resolution of unbalanced defects and detection of uniparental disomy (UPD). We stipulated that SNP-A will enhance diagnostic value of metaphase cytogenetics (MC) and uncover new random/recurrent lesions. We applied 250K SNP-A to analysis of 76 controls and 318 patients, including 95 MDS, 64 AA, 20 PNH, 48 MDS/MPD, and AML both as primary (N=32) and secondary (N=59). Multiple samples were obtained in 13 patients. Minimal clonal size detectable by SNP-A was 25–50% by dilution studies. Repetitive testing resulted in congruent results; analysis of chr X in males showed >99% fidelity. To obtain reference, deletions and duplications seen in controls were analyzed. These abnormalities correspond to germ line encoded copy number variants (CNV). In patients such CNV were not deemed pathogenic. SNP-A confirmed 82% of unbalanced chr lesions detected by MC; discordant cases included defects involving smaller clones (<8/20 metaphases) and aberrations of Y. SNP-A allowed for detection of defects in 63% vs. 37% by MC, including 77% vs. 58% in MDS, 75% vs. 37% in MDS/MPD, 33% vs. 0% in AA, 30% vs. 0% in PNH, 59% vs. 31% in AML and 76% vs. 53% in sAML. New lesions were confirmed by paired SNP-A and microsatellite analysis. Concurrent analysis of blood and marrow showed concordant results suggesting utility of SNP-A performed on blood. Serially followed patients N=6, showed occurrence of new lesions (del(4)(q) and del(7)(q)) and earlier detection of the chr aberrations. In sAML, differential analysis of blasts and granulatocytes revealed occurrence of new lesions e.g., UPD6 or 7. In both MDS and AML, UPD of various chrs was present in 20% of patients and found in up to 35% of MDS/MPD (in addition to 9p involving also chrs 6,7,11 & 14). Other newly detected lesions included isolated/recurrent microdeletions and duplications involving genes such as AML1 or Ftl3 among others. Clinical utility of SNP-A depends on whether SNP-A karyotypig will have impact on disease parameters. In all groups tested the newly detected lesions showed impact on overall survival. While the detailed results will be a subject of our presentation, survival analysis in AML can illustrate our point; cases with a normal karyotype showed superior OS to those with newly detected defects (21 vs. 6 mo, p=.05). Similarly, new additional lesions worsen the survival as compared to those with confirmed MC (3 vs. 10 mo, p=.004). The impact on OS was also established for some of the new recurrent lesions such as UPD7q (3 vs. 39 mo, p=.002). Clinical relevance of SNP-A karyotyping is also demonstrated in AA; it may help to distinguish AA from hypocellular MDS (clonal chr. defects, including UPD, occur in 33% of AA patients), AA with normal SNP-A testing showed superior response to immunosuppression as compared to patients with a totally normal karyotype. Aside of the clinical relevance, new overlapping/recurrent lesions point towards genes involved in the disease process. We conclude that SNP-A karyotyping may enhance MC in diagnosis of chr. defects and allow for a better clinical correlations of the defects with the phnenotypic and clinical features.

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.

Constitutional Segmental Uniparental Disomy in a Twin Pair with t(12;21) Positive Acute Lymphoblastic Leukemia Characterized by the Same Prenatal Clone and Divergent Clonal Evolution.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 4549-4549
Author(s):  
Giovanni Cazzaniga ◽  
Julie Irving ◽  
Marco Citterio ◽  
Silvia Bungaro ◽  
Roxane Tussiwand ◽  
...  
Keyword(s):  
Germ Line ◽  
Twin Pair ◽  
Rapid Determination ◽  
Lymphoblastic Leukemia ◽  
Clonal Evolution ◽  
Snp Array ◽  
Uniparental Disomy ◽  
Monozygotic Twin ◽  
Nucleotide Polymorphisms ◽  
Overt Leukemia

Abstract We previously reported (Tussiwand R. et al., ASH 2002) the case of a monozygotic twin pair with concordant ALL aged 3.0 years at diagnosis, with only 13 days difference in latency. Twin 1 was classified as pre-B ALL and twin 2 as common-ALL, based on standard immunophenotyping criteria. A large screening for TcR and Ig gene rearrangements was performed, resulting in only one common VKII-Kde rearrangement, the others being not related to each others. Highly sensitive RQ-PCR was performed for all markers in both twins. The result of the crossed analysis was consistent with the hypothesis that after a prenatal event resulting in a preleukemic clone, at least a second independent event must have occurred before overt leukemia. To further identify markers of the clonal evolution, high-resolution single nucleotide polymorphisms (SNP) genotype analysis was performed on the DNA using the 10K SNP array (Affymetrix). Remission bone marrow was taken as a germ line samples. Array-based analysis of SNPs allows the rapid determination of genome-wide allelic information at high density, including the identification of submicroscopical copy number changes and/or loss of heterozygosity (LOH). SNP array analysis have been so far successfully applied to demonstrate allelic imbalance in ALL and AML blasts. A 12p12-13 deletion was observed on twin 2. The deletion of the TEL allele not involved in the t(12;21) was confirmed in twin 2 by FISH and microsatellite analyses. The twin 1 did not show any 12p deletion. Similar observations have been made in late-relapses occurring in ALL carrying the t(12;21) translocation: the predominant clone did not correspond to the same clone observed at diagnosis, but represented a second, independent transformation event within the fetal pre-leukemic clone, even when in the presence of the same genetic background. More interestingly, we found by SNP array a 13Mb area of LOH in remission and presentation samples of both twins involving the 2q13-14.3 region. As further confirmed by FISH with 2q probes, LOH was not associated with chromosomal loss, implying a recombination event resulting in Uniparental Isodisomy (UPD). The UPD area includes 57 known genes, several of them implicated in oncogenesis; they include translin, a gene involved in the control of chromosomal translocation and implicated in lymphoid malignancy. UPD of this region has not been reported in other tumors or in remission samples of leukemia; in genetic diseases few cases have been reported with maternal or paternal UPD 2, never associated with haematological disorders. By contrast, it has been shown that a transmitted deletion of 2q13 to 2q14.1 causes no phenotypic abnormalities. This is the first report on constitutional UPD in leukemia patients. Further analyses are necessary to understand the clinical meaning of this chromosomal abnormality; one hypothesis could be that the twins were born with a genetic predisposition to develop leukaemia. In this context, t(12;21) and additional events (i.e. TEL deletion) may be responsible for the overt leukemia.

SNP Array Analysis Reveals Copy Number Alterations and Uniparental Disomy in Mantle Cell Lymphomas at High Resolution.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 1585-1585
Author(s):  
Elena M. Hartmann ◽  
Itziar Salaverria ◽  
Silvia Bea ◽  
Andreas Zettl ◽  
Pedro Jares ◽  
...  
Keyword(s):  
High Resolution ◽  
Cell Lines ◽  
Copy Number ◽  
Snp Array ◽  
Uniparental Disomy ◽  
Genetic Alterations ◽  
Array Analysis ◽  
Snp Array Analysis ◽  
Copy Number Changes ◽  
500K Array

Abstract Mantle Cell Lymphoma (MCL) is an aggressive B-Cell Non Hodgkin Lymphoma which is genetically characterized by the translocation t(11;14). This translocation leads to juxtaposition of the Cyclin D1 gene and the IgH locus, resulting in constitutive overexpression of Cyclin D1 and consecutive cell cycle dysregulation. Apart from this typical structural genetic alteration, several studies using conventional or array-based comparative genomic hybridization (CGH) reported a high number of secondary numerical genetic alterations contributing to MCL lymphomagenesis and influencing the clinical behavior. Increasingly, there is evidence that loss of heterozygosity (LOH) without copy number changes (e.g. caused by mitotic recombination between the chromosomal homologues, also referred to as acquired (partial) uniparental disomy (a(p)UPD), is an important alternative mechanism for tumor suppressor gene inactivation. However, this phenomenon is undetectable by CGH techniques. Single Nucleotide Polymorphism (SNP) based arrays allow - in addition to high resolution copy number (CN) analyses and SNP genotyping - in the same experiment the analysis of loss of heterozygosity (LOH) events and hereby enable the detection of copy neutral LOH. We analyzed the 3 t(11;14)-positive MCL cell lines Granta 519, HBL-2 and JVM-2 and 5 primary tumor specimens from untreated MCL patients with both the Affymetrix GeneChip®Human Mapping 100K and 500K array sets. In the 3 cell lines, we found an excellent agreement between the copy number changes obtained by SNP array analysis and previously published array CGH results. Extending published results (Nielaender et al., Leukemia 2006), we found regions of pUPD in all 3 MCL cell lines, which often affected regions reported as commonly deleted in MCL. Intriguingly, HBL-2 that is characterized by relatively few chromosomal losses, carries an increased number of large regions showing copy neutral LOH. Furthermore, we compared the results obtained by the 100K and 500K mapping array sets from 5 primary MCL tumor specimens with previously published conventional CGH data. All cases showed genetic alterations in both conventional CGH and SNP array analysis. The total number of copy number alterations detected by conventional CGH was 35, including 23 losses, 10 gains and 2 amplifications. The total number of CN alterations detected by the mapping 100K and 500K array sets was 81 (50 losses, 26 gains and 5 amplifications) and 82 (50 losses, 27 gains and 5 amplifications), respectively. We found an excellent agreement in the large CN alterations detected by conventional CGH and both SNP array platforms. Furthermore, we identified &gt;40 mostly small CN alterations that have not been detected by conventional CGH (median size &lt;5MB for losses and &lt;3Mb for gains). The CN alterations detected by the 100k and the 500K array sets were highly identical. Importantly, we discovered regions of partial UPD in 4 of the 5 MCL cases (size range from around 2Mb up to a single region &gt;40Mb). In conclusion, the results demonstrate the capability of SNP array analysis for identifying CN alterations and partial UPD at high resolution in MCL cell lines as well as in primary tumor samples.

High-Resolution SNP-Array Profiling of Chronic Lymphocytic Leukemia

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 50-50 ◽  
Author(s):  
Jennifer Edelmann ◽  
Karlheinz Holzmann ◽  
W.M. Michael Kühn ◽  
Lars Bullinger ◽  
Ina Radtke ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Copy Number ◽  
Research Funding ◽  
Snp Array ◽  
Normal Karyotype ◽  
Lymphocytic Leukemia ◽  
Fish Analysis ◽  
Paired Data ◽  
New Genes ◽  
Genomic Aberrations

Abstract Abstract 50 Genomic aberrations are important prognostic factors in chronic lymphocytic leukemia (CLL) [Döhner et al., 2000]. However, known genomic aberrations fail to fully explain the biologic and clinical heterogeneity of the disease. We sought to precisely map copy number alterations (CNA) and copy number neutral losses of heterozygocity (LOH) to better characterize known recurrent aberrations and to identify new genetic lesions. We used Affymetrix 6.0 single nucleotide polymorphism (SNP) array analyses on CD19 sorted CLL cells. Data were analyzed using dChipSNP, a modified array normalization algorithm guided by cytogenetic abnormalities and a circular binary segmentation. We studied samples from 346 patients enrolled on the CLL8 trial of the German CLL Study Group. Data of 145 samples were analyzed against intraindividual reference DNA (paired), data of 201 samples against a pool of reference DNA (unpaired). FISH data were available for all samples, the distribution of genomic aberrations was as follows: del(13q14) in 59.8%, del(11q23) in 26.3%, trisomy 12 in 11.6%, and del(17p13) in 8.4%. IGHV was mutated in 32.9%, unmutated in 63.3%, and unknown in 3.8%. In total, 261 tumor-specific CNA could be discovered among the 145 paired samples. Genomic aberrations were found in 85.5% of these cases. The average number of aberrations per case was 1.8; according to the hierarchical model of genomic aberrations, it was 3.5 in del(17p), 2.4 in del(11q23), 1.7 in del(13q14) single, and 0.5 in normal karyotype CLL. The minimally deleted region (MDR) on 13q14 was 277.25 kb in size and contained mir15a and mir16, DLEU1 and DLEU2; RFP2 was not part of the MDR. Deletions on 13q were highly heterogeneous in size, ranging from 294 kb to 68 Mb. On 11q23 the MDR only contained ATM, the smallest lesion of 78.5 kb being intragenic; in two of theses cases, the deletion size was too small to be detected by FISH analysis. TP53 was affected in all del(17p13) cases except two; one tumor-specific deletion of 635.7 kb was detected in cytoband 17p13.2 harboring 30 genes and a second deletion of 780 kb in 17p13.3 containing – among 15 other genes – MNT, a tumor suppressor acting as an antagonist of MYC. A partial trisomy on chromosome 12 was not detected. Of the 261 CNA, 95 were located in genomic regions that are not evaluated by our routine FISH probe panel; 17 regions were affected recurrently: del(1p35.3) [2/145], del(1q23.3) [2/145], del(1q42.12) [2/145], +2p [5/145], del(3p21.31) [2/145], del(6p25.3) [3/145], +(6p25.3) [2/145], del(6q) [11/145], del(7q23.1) [2/145], +(8q24.21) [3/145], del(9q13-q21.13) [2/145], del(10q24) [2/145], del(14q24.3) [2/145], del(14q12.3) [2/145], del(15q15.1) [2/145], +18 [3/145] and +19 [7/145]. The frequency of these CNA was subsequently evaluated within the cohort of 201 (unpaired) samples. Five of 17 regions were affected in more than 2% in the whole cohort: +2p, del(6q), +8q24.21, del(15q15.1), and +19. Gain of 2p was found in 6.9% of cases, the minimally amplified region was 1.9 Mb in size and contained e.g. BCL11A and REL. Del(6q) was detected in 6,4%, the deletions were heterogeneous, an MDR could not be identified. 16 cases had 8q24.21 gains, the minimally amplified region was delineated by three intragenic gains in MYC. 14 cases had loss in 15q15.1 focussing on MGA, a potential suppressor of transcriptional activation by MYC. 8 cases had total or partial gains of chromosome 19, among those two overlapping partial gains with a minimally amplified region of 2.17 Mb in 19p13.2. Tumor-specific LOH were identified in 6.0% (9/145) located on 13q in three cases and in one case each on 17p, 12q, 11p, 1p, 3 and 22q. The LOH on chromosomes one and three overlapped with recurrent losses in 1p35.3 and 3p21.31. Essential members of the ATR-pathway were located in these regions: ATRIP and RPA2. However, mutational analyses of the two candidate genes in 48 cases revealed no mutations. SNP array analysis is a reliable tool to identify and further characterize genomic aberrations in CLL. MDR on 13q14 was delineated to a 277.25 kb segment affecting mir15a, mir16, DLEU1 and DLEU2 but not RFP2; the MDR on 11q23 to a segment only containing ATM. Cases with del(11q23) and del(17p) showed a higher genomic complexity than those with normal karyotype or del(13q14) as single abnormality. Relatively few novel genetic lesions were identified. Although occurring at low frequency, they may lead to the discovery of new genes involved in CLL pathogenesis. Disclosures: Stilgenbauer: Amgen: Research Funding; Bayer: Consultancy, Honoraria, Research Funding; Boehringer-Ingelheim: Consultancy, Honoraria, Research Funding; Celgene: Consultancy, Honoraria, Research Funding; Genzyme: Consultancy, Honoraria, Research Funding; GSK: Consultancy, Honoraria, Research Funding; Mundipharma: Consultancy, Honoraria, Research Funding; Roche: Consultancy, Honoraria, Research Funding; Sanofi Aventis: Research Funding.

scholarly journals Prenatal Diagnosis of Complete Paternal Uniparental Isodisomy for Chromosome 3: A Case Report

2021 ◽  
Author(s):  
xiufen bu ◽  
Xu Li ◽  
Shihao Zhou ◽  
Liangcheng Shi ◽  
Xuanyu Jiang ◽  
...  
Keyword(s):  
Genetic Counseling ◽  
Prenatal Diagnosis ◽  
Snp Array ◽  
Uniparental Disomy ◽  
Rare Condition ◽  
Normal Karyotype ◽  
Chromosome 3 ◽  
Uniparental Isodisomy ◽  
Normal Ultrasound ◽  
Physical Findings

Abstract Background Paternal uniparental disomy (UPD) of chromosome 3 is a very rare condition. At present, only 5 cases of paternal UPD(3) has been reported. This was the second ascertained paternal UPD(3) with no apparent disease phenotype.Case presentation We hereby reported a case of a fetus with normal karyotype and normal ultrasound features at the whole gestation. A copy neutral regions of homozygosity on chromosome 3 was indentified by Single Nucleotide Polymophism array (SNP array). Subsequent SNP array data of parent–child trios showed the fetus has carried complete paternal uniparental isodisomy (isoUPD) of chromosome 3. The parents decided to continue the pregnancy after genetic counseling. The neonate had normal physical findings at birth and develops normally after 1.5 years. Conclusions The findings could provide further evidence to confirm that there was no important imprinted genes causing serious diseases on paternal chromosome 3 and provided a reference for the prenatal diagnosis and genetic counseling of UPD(3) in the future.

Analysis of Loss of Heterozygosity in Adult Patients with De Novo Acute Myeloid Leukemia and Normal Karyotype.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 806-806 ◽  
Author(s):  
Christian Schon ◽  
Lars Bullinger ◽  
Frank G. Rucker ◽  
Konstanze Dohner ◽  
Hartmut Dohner
Keyword(s):  
Acute Myeloid Leukemia ◽  
Signal Intensity ◽  
Myeloid Leukemia ◽  
De Novo ◽  
Snp Array ◽  
Uniparental Disomy ◽  
Normal Karyotype ◽  
Intensity Data ◽  
Chromosome 13 ◽  
Acute Myeloid

Abstract A large proportion of acute myeloid leukemia (AML) exhibits a normal karyotype in which the underlying pathomechanisms still have to be determined. Novel techniques like arrayCGH or single nucleotide polymorphism (SNP) chip analysis allow the identification and characterization of molecular rearrangements at the sub-megabase level. Recently, the application of genome-wide SNP array technology revealed frequent uniparental disomy (UPD) in approximately 20% of AML suggesting that UPD represents a nonrandom event in leukemogenesis. Uniparental disomy is acquired by somatic recombination and therefore not accessible by conventional cytogenetic methods or arrayCGH. In this study we analyzed DNA from AML patients with normal karyotype for the presence of LOH. SNP analysis was performed on the Mapping 100k GeneChip (Affymetrix, Santa Clara, CA). DNA was extracted from paired samples of 56 de novo AML patients with normal karyotype at diagnosis and in complete remission, respectively. Signal intensity data were analyzed by the GCOS GeneChip analysis software and statistical analysis of SNP call data was performed by the dChipSNP software. In addition, standard mutation screening of the genes encoding NPM1, FLT3, CEBPA, MLL and NRAS was performed in all cases. Using the 100k SNP array, a mean SNP call rate of 98.2% was reached, resulting in &gt; 110,000 SNP genotype calls per sample. Signal intensity data analysis revealed submicroscopic chromosomal deletions resulting in hemizygosity in three patients. Patient 1 had a single 2 Mb deletion in chromosomal band 3p14.1, patient 2 had two small deletions affecting chromosome 12q23 and 12p13, the latter encompassing the ETV6 locus, and patient 3 had two small deletions within the long arm of chromosome 8. Besides these small chromosomal regions of copy number alterations, we found 4 large stretches of somatically acquired homozygosity without numeric alterations, affecting chromosome 6 (6p21 to 6 pter and 6q26 to 6 qter), chromosome 11 (11p12 to 11pter) and chromosome 13 (13q11 to 13qter). Noteworthy, in the case with uniparental disomy of chromosome 13, we could detect a homozygous FLT3-ITD mutation, supporting the findings that acquired isodisomy for chromosome 13 is common in AML, and associated with FLT3-ITD mutations (Griffiths et al., Leukemia, 2005). In summary, high resolution SNP assay technology in AML patients with normal karyotype allowed the identification of distinct chromosomal regions affected by UPD, supporting the postulated nonrandom mechanism of acquired mitotic recombination events in AML. Besides known chromosomal regions known to be affected by genomic aberrations in AML, we found additional submicroscopic chromosomal aberrations in cases with normal karyotype. Analysis of larger patient series will allow the identification of novel regions of interest harboring genes that might be involved in the pathogenesis of AML.

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