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 >40 mostly small CN alterations that have not been detected by conventional CGH (median size <5MB for losses and <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 >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.

Genome-Wide DNA Copy Number Analysis by SNP Arrays of B-Cell Chronic Lymphocytic Leukemia: Correlation with Known Biological and Molecular Prognostic Markers.

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 1061-1061
Author(s):  
Laura Mosca ◽  
Sonia Fabris ◽  
Giovanna Cutrona ◽  
Luca Agnelli ◽  
Serena Matis ◽  
...  
Keyword(s):  
High Resolution ◽  
Copy Number ◽  
Prognostic Markers ◽  
Snp Array ◽  
Lymphocytic Leukemia ◽  
Array Analysis ◽  
Genome Wide ◽  
Trisomy 12 ◽  
Snp Array Analysis ◽  
Cell Chronic Lymphocytic Leukemia

Abstract B-cell chronic lymphocytic leukemia (B-CLL) is a genetically heterogeneous disease with a variable clinical course. Chromosomal changes have been identified by FISH in approximately 80% of patients, and the presence of specific lesions, such as trisomy 12 and 13q14, 11q23, 17p13.1 and 6q23 deletions represent prognostic markers for disease progression and survival. In order to characterize further the complexity of B-CLL genomic lesions, we performed high density, single nucleotide polymorphism (SNP) array analysis in highly purified neoplastic cells (>92%) from a panel of 100 untreated, newly diagnosed patients (57 males and 43 females; age, median 63 years, range 30–87) in Binet stage A. All patients were investigated by FISH for the presence of trisomy 12 (21 cases); 13q14 deletion (44 cases, 34 as the sole abnormality); 11q22.3, 17p13.1 and 6q23 (15, 7 and 2 patients, respectively). In addition, ZAP-70 and CD38 expression resulted positive in 42 and 46 patients, whereas IgVH genes were mutated in 45 patients. Genome-wide DNA profiling data were generated on GeneChip® Human Mapping 250K NspI arrays (Affymetrix); copy number alterations (CNA) were calculated using the DNA copy Bioconductor package, which looks for optimal breakpoints using circular binary segmentation (CBS) (Olshen et al, 2004). A total of 782 CNAs (ranging from 1 to 31 per sample, mean and median values 7.82 and 7, respectively) were detected; DNA losses (365/782=46.67% loss; 194/782=24.81% biallelic deletion) were found to be more frequent than gains (148/782=18.93% gain; 75/782=9.59% amplification). The most recurrent alterations detected by FISH were all confirmed by SNP array analysis, strengthening further the good reliability of such high-resolution technology. We identified 12 minimally altered regions (MARs) larger than 100 kb with a frequency higher than 5%. Among well known alterations, the largest was represented by chromosome 12 trisomy, followed by 6q, 17p and 11q23 deletions (32.87, 19.09 and 10.43 Mb, respectively) and 13q14 deletion (635 kb). Gain of 2p25.3 involves a common region of 4.39 Mb region in 7 patients, although it was extended to the whole short arm of chromosome 2 in 3 cases. Among those alterations previously described in B-CLL, we found losses at 14q32.33 (12 pts) and 22q11.2 (5 pts) involving the IGH and IGLλ loci, respectively. With regard to novel regions, we identified losses at 4q35.2 (5 pts) and 11q25 (6 pts). In addition we found a high frequency of losses/gains at 14q11.2 (42 pts) and 15q11.2 (33 pts), two genomic regions reported to be affected by DNA copy number variations in normal individuals. As regards correlations between CNAs and biological markers, we found that the number of CNAs is significantly higher in cases with unmutated IgVH (9.4; range 2–31) as compared with mutated IgVH (6; range 1–13) (p=0.002), while neither CD38 nor ZAP-70 expression showed significant correlation. In addition, a significant higher number of either CNAs (p=0.001), total MARs (p<0.0001) or even only novel MARs (p=0.009) was significantly associated with cases with 17p deletion or multiple cytogenetic aberrations as evaluated by FISH analysis. Our data indicate that genetic abnormalities involving chromosomal gains and losses are very common in early-stage B-CLL and further support the application of high resolution SNP array platforms in the characterization of genetic changes in the disease. In addition, we detected novel altered chromosomal regions that warrant further investigations to better define their pathogenetic and prognostic role in B-CLL.

Dissection of Submicroscopical Aberrations and Clonal Evolution from Birth To Diagnosis and Relapse in a Childhood AML FLT3-ITD Positive Patient by RQ-PCR and SNP Array Analyses.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 4337-4337
Author(s):  
Giovanni Cazzaniga ◽  
Silvia Bungaro ◽  
Manoj Raghavan ◽  
Chiara Beretta ◽  
Maria G. Dell’Oro ◽  
...  
Keyword(s):  
Disease Progression ◽  
Copy Number ◽  
Clonal Evolution ◽  
Snp Array ◽  
Array Analysis ◽  
Highly Sensitive ◽  
Snp Array Analysis ◽  
Childhood Aml ◽  
Copy Number Changes ◽  
Array Analyses

Abstract We have performed a combined Real Time Quantitative-PCR and single nucleotide polymorphisms array analyses for dissecting the clonal evolution in a childhood AML patient who experienced two relapses and for whom we had the availability of the cord blood (CB) sample. The patient was diagnosed at 6 years of age with an AML-M1 and showed normal karyotype and a FLT3-ITD mutation as a sole abnormality. She underwent autologous-BMT; however, 3.5 months later the patient relapsed, and 4 months after an allogeneic-BMT she suffered from a second relapse and died for disease progression. Highly sensitive (10−4) monitoring of FLT3-ITD was performed by patient-specific RQ-PCR, and showed a progressive decrease of minimal residual disease (MRD) during induction therapy. MRD was below the detection limit before auto-BMT, but the same FLT3-ITD clone re-emerged three months after auto-BMT, and preceded the clinical relapse. Thus, the same FLT3-ITD mutation was detected at the time of relapse, suggesting that the leukemic clone responsible for the first diagnosis was still present and could be potentially used as a marker for backtracking the leukemia into the CB. When tested by highly sensitive RQ-PCR, the DNA from CB resulted negative for the FLT3-ITD mutation. Although the relatively limited sensitivity of the technique might impair the interpretation, the FLT3-ITD negative result in CB is consistent with the hypothesis that FLT3-ITD mutations are secondary events, not sufficient by themselves to induce leukemia transformation in hematopoietic stem cells without a necessary primary event. With the aim to find additional submicroscopical genetic changes associated to the highly aggressive nature of the patient disease, we performed a genome wide SNP array analysis on the patient DNA through the clinical evolution of the disease, from birth to relapse. This new SNP array strategy is emerging as a powerful method to detect loss of heterozygosity (LOH) and/or copy number changes in a DNA sample with high resolution. The Affymetrix GeneChip® Mapping 10K platform has been used, which allows the scanning of more than 10.000 SNPs. SNP array analysis on DNA from the first relapse showed the deletion of the long arm of chromosome 9, a recurring chromosomal aberration in AML, and LOH on the whole chromosome 13 not associated with copy number changes. This latter has been confirmed by FISH, and it is consistent with uniparental isodisomy (UPD) as a responsible mechanism for the somatically acquired homozygosity of FLT3-ITD at 13q14. This mechanism is emerging as a frequent way of disease progression and represents a subsequent event to FLT3-ITD heterozygous mutation. The deletion of the wild type FLT3 allele has been confirmed by PCR. 10K SNP array analysis failed to reveal LOH or copy number changes in the diagnostic and in CB samples. These findings are compatible with a somatic post-natal origin of the FLT3-ITD positive AML subtype. Additional abnormalities can be responsible for the disease progression, via different mechanisms, including UPD. Other methods must be applied to find the primary event(s) giving rise to leukemia in association with FLT3-ITD mutation.

Large Regions of Uniparental Disomy (UPD) Establish Clonal Hematopoietic Stem Cell Selection in a Subset of Myelodysplastic Syndrome (MDS) Patients with Normal Bone Marrow Cell Karyotypes.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 120-120 ◽  
Author(s):  
Stefan Heinrichs ◽  
Rima V. Kulkarni ◽  
Carlos E. Bueso-Ramos ◽  
Mignon Loh ◽  
Ross Levine ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Stem Cell ◽  
Cytogenetic Analysis ◽  
Copy Number ◽  
Snp Array ◽  
Uniparental Disomy ◽  
Normal Bone Marrow ◽  
Array Analysis ◽  
Normal Bone ◽  
Snp Array Analysis

Abstract Myelodysplastic syndromes (MDS) comprise a large group of hematological diseases sharing clinical features, but the diverse mechanisms underlying their molecular pathogenesis remain largely undefined. In this study, we used high-density 250K SNP arrays to analyze matched constitutional (buccal) and whole bone marrow DNAs from 36 patients with MDS. In 14 cases, we also selected CD34+ stem and progenitor cells for comparison. 23 of the cases were cytogenetically normal. Whereas regions of genomic amplification were rare, we found distinct regions of heterozygous deletion in 9 patients, most frequently targeting chromosomes 5q, 7q, 17p and 20q. In one patient with a large heterozygous 5q deletion, a smaller region in 5q34 was homozygously lost. Based on genotyping we could identify regions of uniparental disomy (UPD) in 4 patients, three of whom had normal bone marrow karyotypes. Two of the regions of UPD targeted chromosome 7q, suggesting that the frequency of 7q deletion is underestimated by conventional cytogenetics, and that a mutation has occurred in these cases within the reduplicated region involved in UPD. Comparison with constitutional DNA was critical for accurate SNP analysis in MDS, allowing us to focus on acquired clonal abnormalities and control for changes due to inherited copy number variation or unusual regions of germline homozygosity. For example, one case had several large blocks of germline homozygosity distributed over various chromosomes, and by comparison with the buccal DNA we were able to discern that these regions did not result from clonal somatic abnormalities associated with MDS. The analysis of CD34+ cellular DNA in 14 cases revealed that all aberrations identified in the stem and progenitor fraction were also identified in whole bone marrow DNA. This finding emphasizes the dominance and stem cell involvement of the abnormal clone in MDS, which makes purification of CD34 cells unnecessary for SNP array analysis in this disease. Most, but not all, clonal deletions evident by cytogenetic analysis were detected as copy number alterations by SNP array, possibly indicating that such abnormalities occurred in subpopulations of the cytogenetically analyzed MDS cells. Thus, SNP array and cytogenetic analysis are complementary methods for the identification of abnormal clones in MDS patients, each detecting overlapping but distinct subsets of patients. Our data indicate that SNP array analysis should be performed in all patients with MDS and normal bone marrow cytogenetics, in order to help discriminate patients with UPD indicating cell autonomous clonal stem cell malignancy from those who might have extrinsically mediated bone marrow failure syndromes.

Validation of Whole Genome SNP Array As the Primary Genetic Test in Myelodysplastic Syndrome, to Replace Chromosome and FISH Copy Number Analysis, in a UK Diagnostic Genetic Laboratory

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 3184-3184
Author(s):  
Sally Jeffries ◽  
Nicola Trim ◽  
Emma Huxley ◽  
Judith Caddick ◽  
Jane Soden ◽  
...  
Keyword(s):  
Myelodysplastic Syndrome ◽  
Validation Study ◽  
Copy Number ◽  
Genetic Test ◽  
Diagnostic Yield ◽  
Snp Array ◽  
Gene Mutations ◽  
Array Analysis ◽  
Snp Array Analysis ◽  
Copy Number Changes

Abstract Metaphase cytogenetic (MC) analysis in patients with myelodysplastic syndrome (MDS) remains the only essential recommended genetic test in Europe(Malcovati et al, Blood 2013). The chromosome abnormalities identified provide evidence of clonality and information regarding disease characterisation, risk stratification, treatment strategies and disease monitoring. With the exception of the 3q/MECOM gene rearrangement, observed in 1% MDS, the common, recurrent chromosome abnormalities and all specified abnormalities in the revised International Prognostic Scoring System (IPSS-R) for MDS are copy number changes (deletion, duplication, amplification) (Greenberg et al, Blood 2012). However, the identification of gene mutations is increasingly becoming important to confirm a diagnosis of MDS in problematic cases, refine risk (particularly in those with lower risk IPSS-R scores) and improve patient management (Bejar et al, JCO 2011;Haferlach et al, Leukemia 2014). Currently there is insufficient prognostic evidence to use gene mutation analysis as the sole genetic test, but SNP array technology may be seen as a stepping stone towards providing some gene mutation information as it detects copy number variation (CNV) at single gene, and sometimes intragenic, resolution and copy neutral loss of heterozygosity (CN-LOH), regions which are known to harbor bi-allelic gene mutations. CN-LOH is common in hematological neoplasia, including MDS. We undertook a prospective validation study using the Affymetrix Cytoscan® HD SNP array, with more than 2.6 million copy number markers, to compare SNP array with MC in patient samples at presentation with confirmed or highly suspected MDS. Subsequent monitoring by SNP array was performed in those patients where samples were received routinely for MC. Expectations were that SNP array analysis would be at least comparable to MC, by detecting all copy number changes detected by chromosome analysis; increase the diagnostic yield of MDS, due to the detection of both sub microscopic CNV and chromosome cryptic CN-LOH; and increase the number of prognostically relevant genetic abnormalities identified. Samples from 358 patients at disease presentation were received for MC at the West Midlands Regional Genetics Laboratory, UK and were used in this study. Of the 358 patients, 207 had a diagnosis of MDS confirmed and 29 had a diagnosis of MDS/MPN confirmed. The remaining 122 cases were classified as follows: 26 other hematological neoplasia (including MPN, AML, CLL and MM), 51 reactive, 32 non-neoplastic disorders and 13 non-diagnostic. In the 236 confirmed MDS or MDS/MPN cases, marrow was available in 219 and peripheral blood (PB) only in 17. PB samples were abnormal by SNP array in 11/17 (65%). Of the 219 marrows, 146/219 (67%) had comparable SNP array and MC results. A normal karyotype or failed MC result was observed in 130 samples, of these 35 (27%) had an abnormal SNP array. Cases were abnormal by both SNP array and MC in 84 (38%) samples, of these additional abnormalities were detected by SNP array in 30 (36%), including gene mutations with prognostic significance, such as KMT2A-itd, TP53 deletion and RUNX1 deletion. A normal SNP array was observed in 5 (2%) samples with abnormal MC due to balanced rearrangements (SNP array will not detect balanced rearrangements) and low level (1-3%) abnormal clones. In marrow samples, the diagnostic yield by MC alone was 91/219 (42%) and by SNP array analysis alone 119/219 (54%). Therefore, SNP array increased the diagnostic yield of MDS and MDS/MPN by 12% and identified further abnormalities in an additional 30/219 (14%) samples. In conclusion, this validation study demonstrates that SNP array may be offered as an alternative test to MC in patients with a confirmed or highly suspected diagnosis of MDS. Patients with features suggesting 3q/MECOM involvement should have FISH for MECOM rearrangements. Disclosures Griffiths: Affymetrix: Research Funding.

High Density SNP Array Analysis of Tyrosine Kinase Inhibitor (TKI) Resistant Chronic Myeloid Leukemia (CML) Shows Secondary Genomic Alterations

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 3182-3182
Author(s):  
Daniel Nowak ◽  
Norihiko Kawamata ◽  
Tadayuki Akagi ◽  
Ryoko Okamoto ◽  
Nils Thoennissen ◽  
...  
Keyword(s):  
Chronic Myeloid Leukemia ◽  
Tyrosine Kinase ◽  
Copy Number ◽  
Myeloid Leukemia ◽  
Snp Array ◽  
High Density ◽  
Array Analysis ◽  
Snp Arrays ◽  
Tki Resistance ◽  
Snp Array Analysis

Abstract Despite the success story of tyrosine kinase inhibitors (TKIs) for the treatment of Chronic Myeloid Leukemia (CML), patients can develop resistances against the drugs. The main known causes for resistance are mutations or over-expression of the BCR/ABL fusion protein, reduced bioavailability of the drugs and activation of compensatory molecular pathways. It is hypothesized that during disease progression, genomic instability of CML cells increases, which may lead to new genomic lesions harboring additional mechanisms of resistance. In this context, we studied genomic DNA profiles of 32 Imatinib resistant CML patients with high density 250K SNP arrays (Affymetrix). Molecular allelokaryotyping for allele specific copy number and loss of heterozygosity analysis was performed with the CNAG software. Single DNA samples from 27 patients were extracted after they had acquired resistance to Imatinib or alternative TKIs such as Nilotinib or Dasatinib. DNA from 12 patients could be analyzed in sequential samples from the initial diagnosis timepoint and a second timepoint upon the emergence of TKI resistance. All patients were positive for BCR/ABL by PCR and FISH. 10 relapse patient samples had known BCR/ABL mutations of which two were T315I mutations. High density allelokaryotyping confirmed pre-existent data on unbalanced translocations, amplifications and deletions from routine cytogenetics: 5 samples displayed a genomic duplication of the BCR/ABL fusion gene, 4 samples had trisomy 8, 1 sample showed deletion of chromosome 17p, 1 sample had heterozygous deletion of chromosome 9. Apart from this, SNP array analysis revealed numerous new submicroscopic genomic lesions. After exclusion of genomic copy number polymorphisms (CNPs) by comparison to recorded CNPs in the UCSC Genome Browser (http://genome.ucsc.edu/) the following results were obtained: Two patients displayed common heterozygous microdeletions of the reciprocal ABL/BCR fusion product. Furthermore, single samples displayed heterozygous micro-deletions on chromosomes 1, 2, 10, 12, 15, 17, and 22 or microduplications on chromosomes 2,3,6, 8, 9, 11, 12, 14, 15, 22. The affected regions contained potentially interesting genes in respect to resistance to therapy such as tumor suppressor candidate MBP-1, apoptosis related protein RERE, metastasis associated gene MTA3, nuclear body associated gene SP100, alpha-T-catenin (CTNNA3), Cbl-interacting protein Sts-1 and the DNA repair associated gene RAD51. As a new genomic alteration in CML, we detected acquired uniparental disomy (UPD) in 5 samples with a common site of UPD on chromosome 19q in 2 patients. In conclusion, in 14 out of 39 TKI resistant cases, high density SNP arrays enabled us to identify submicroscopic copy number lesions and regions of UPD containing promising candidate genes, which merit further research as sites conferring TKI resistance.

High Density SNP Array Analysis of Acute Promyelocytic Leukemia (APL) Detects New Common Genomic Copy Number Alterations as Possible Cooperating Lesions

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 2721-2721
Author(s):  
Daniel Nowak ◽  
Marion Klaumuenzer ◽  
Benjamin Hanfstein ◽  
Maximilian Mossner ◽  
Florian Nolte ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Acute Promyelocytic Leukemia ◽  
Copy Number ◽  
Genomic Dna ◽  
Snp Array ◽  
Promyelocytic Leukemia ◽  
High Density ◽  
Copy Number Alterations ◽  
Array Analysis ◽  
Snp Array Analysis

Abstract Abstract 2721 Introduction: Acute Promyelocytic Leukemia (APL) is characterized by the typical chromosomal translocation t(15;17)(q22;q21) leading to the fusion product PML-RARA, which blocks granulocytic differentiation in the promyelocyte stage. Several experimental in vitro and in vivo studies have demonstrated that PML-RARA is necessary but not sufficient for the generation of APL. This circumstance has motivated the search for additional leukemogenic and cooperating molecular lesions. Patients and Methods: We have analyzed 101 APL patient bone marrow samples with high density Genome-Wide Human SNP 6.0 arrays, which interrogate >900.000 SNPs and >900.000 non-polymorphic copy number markers throughout the genome (Affymetrix, Santa Clara, CA, USA) in search for copy number alterations (CNAs) potentially relevant in the pathogenesis of APL. Genomic DNA from samples at initial diagnosis of 94 patients was analyzed. Furthermore, DNA from 11 samples at relapse was available, whereby 4 of these relapse samples also had paired DNA from initial diagnosis. Data analysis was carried out with the CNAG 3.3 software using anonymous references. For exclusion of copy number polymorphisms, all detected CNAs were compared with the databases of known copy number polymorphisms in the UCSC genome browser. For data validation, putatively acquired CNAs and regions of copy number neutral loss of heterozygosity (CNLOH) were confirmed by hybridization of DNA from paired normal samples when the patients were in remission, by quantitative real time PCR of genomic DNA and by direct sequencing of informative SNPs. Results: The high density SNP array analysis detected a total of 120 heterozygous deletions, 97 duplications or amplifications and 7 regions of telomeric CNLOH leading to an average of 2.3 CNAs per sample (range 0–30). The most common numerical and large structural aberrations were found on chromosome (chr.) 8 with either trisomy 8 (n=11) or duplication of regions on chr. 8q (n=10) followed by heterozygous deletions of chr. 7q (n=5) and chr. 16q (n=5). Furthermore, unbalanced translocations of chr. 15 and 17 involving PML and RARalpha were detected in five cases leading to duplication of the PML-RARA fusion or deletion of genomic regions flanking either PML or RARalpha. Recurrent microlesions (<1Mbp) were found in several regions as heterozygous deletions on chr. 1q31.3 containing the micro RNAs MIR181B1 and MIR181A1 (n=5), on chr. 2q32.3 containing serine/threonine kinase 17b (STK17B) (n=5) or chr. 3p24.3 containing ankyrin repeat domain 28 (ANKRD28) (n=5). One recurrent region of telomeric CNLOH was found on chr. 19q in two samples. Of note, besides the few regions of telomeric CNLOH a large number of intrachromosomal CNLOH regions (n=265) was identified, with recurrent regions on chr. 6p21.1 (n=10) or chr. 5q23.3-5q31.1 (n=6) containing genes relevant in hematopoiesis such as IL3, CSF2 or DNA damage repair such as RAD50. Although these CNLOH regions were not somatically acquired they may possibly harbor genetic predispositions for disease. Conclusions: We describe a detailed high density SNP array genomic profiling of bone marrow DNA from patients with APL, which has led to the identification of several new cryptic recurrent genomic lesions. These genomic alterations point to candidate genes, which could be cooperating factors in addition to PML-RARA. Therefore, our data helps to provide a better understanding of the molecular mechanisms underlying the development of APL. Disclosures: Kohlmann: MLL Munich Leukemia Laboratory: Employment. Lengfelder:Cephalon: Research Funding.

scholarly journals Erratum to: high-resolution SNP array analysis of patients with developmental disorder and normal array CGH result

2014 ◽  
Vol 15 (1) ◽  
Author(s):  
Linda Siggberg ◽  
Sirpa Ala-Mello ◽  
Tarja Linnankivi ◽  
Kristiina Avela ◽  
Ilari Scheinin ◽  
...  
Keyword(s):  
High Resolution ◽  
Developmental Disorder ◽  
Array Cgh ◽  
Snp Array ◽  
Array Analysis ◽  
Snp Array Analysis

scholarly journals Evaluating Translocation Gene Fusions by SNP Array Data

2011 ◽  
Vol 11 ◽  
pp. CIN.S8026 ◽  
Author(s):  
Hong Liu ◽  
Asher Zilberstein ◽  
Pascal Pannier ◽  
Frederic Fleche ◽  
Christopher Arendt ◽  
...  
Keyword(s):  
Cell Lines ◽  
Cancer Cell ◽  
Copy Number ◽  
Target Genes ◽  
Snp Array ◽  
Tumor Development ◽  
Cancer Cell Lines ◽  
Genetic Alterations ◽  
Genetic Aberrations ◽  
Array Data

Somatic cell genetic alterations are a hallmark of tumor development and progression. Although various technologies have been developed and utilized to identify genetic aberrations, identifying genetic translocations at the chromosomal level is still a challenging task. High density SNP microarrays are useful to measure DNA copy number variation (CNV) across the genome. Utilizing SNP array data of cancer cell lines and patient samples, we evaluated the CNV and copy number breakpoints for several known fusion genes implicated in tumorigenesis. This analysis demonstrated the potential utility of SNP array data for the prediction of genetic aberrations via translocations based on identifying copy number breakpoints within the target genes. Genome-wide analysis was also performed to identify genes harboring copy number breakpoints across 820 cancer cell lines. Candidate oncogenes were identified that are linked to potential translocations in specific cancer cell lines.

SNP-A Based Karyotyping Facilitates Improved Mapping of Deletions and Uniparental Disomy within the Long Arm of Chromosome 5 in Myeloid Disorders.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 2435-2435 ◽  
Author(s):  
Lukasz P. Gondek ◽  
Andrew Dunbar ◽  
Christine O’Keefe ◽  
Michael A. McDevitt ◽  
Denise Batista ◽  
...  
Keyword(s):  
Copy Number ◽  
Chromosomal Rearrangement ◽  
Snp Array ◽  
Uniparental Disomy ◽  
Chromosome 5 ◽  
Chromosome 5Q ◽  
Complex Chromosomal Rearrangement ◽  
Pathogenic Genes ◽  
Definition Of ◽  
Copy Number Changes

Abstract In MDS, cytogenetics has a major prognostic influence on the phenotype of the malignant clone and specific defects may point towards potential therapeutic targets. However, traditional metaphase cytogenetics (MC) has limited resolution and does not allow for detection of uniparental disomy (UPD). Defects on chromosome 5q have been studied using various methods to identify a minimal commonly deleted region (CDR). SNP-array karyoptyping (SNP-A) allows for precise detection of copy number changes as well as UPD. We hypothesized that SNP-A may reveal new lesions on chromosome 5 and allow for better definition of CDRs and pathogenic genes. Of 512 patients, 15% showed a 5q abnormality as a sole or associated aberration by MC. DNA was available in 189 patients and was subjected to 250K SNP-A. In 7 patients with normal/non-informative MC, a deletion on 5q was clearly detectable by SNP-A; in total, SNP-A identified 5q abnormalities in 14% patients in this group (vs. 11% by MC). UPD 5q was found in one patient with CMML. By SNP-A, 6/27 patients showed an isolated 5q deletion. SNP-A can also be used to construct precise cytogenetic maps. The commonly deleted region (CDR1,5q31.2, 137,472,900–139,451,900) was present in 24/27 patients. Significant overlap occurs with the CDR previously defined by Fairman, Zhao, Horrigan et al. This region includes important genes such as Cdc25C and EGR1. Of 24 patients with a deletion in CDR1, 21 had multilineage dysplasia predominantly in the megakaryocytic line (92%). While elevated platelet counts occurred in 3 patients, increased levels of megakaryocytes were common (83%). Previous studies by Bouldwood/Jaju suggested that the minimal CDR among patients with 5q- syndrome (CDR2, 5q33.1-33.2) differs slightly from that associated with secondary AML/MDS (CDR1). However, when patients (5/27) with classical 5q- syndrome were analyzed, all displayed single deletions spanning both CDR1 and CDR2. Other areas of partial overlaps were also identified (5q12.1; 5q13.3) more centromeric to CDR1 and present in 7/27 patients. 2 cases were particularly interesting: 1 with segmental UPD involving the CDR, the other showing a small deletion defining the CDR itself. In the latter patient, marked thrombocytosis was present and SNP-A demonstrated a complex chromosomal rearrangement. While MC revealed a segmental deletion of 5q and a concomitant duplication of this abnormal homolog, SNP-A showed that while the p arm portion had been duplicated, the q arm, with the exception of two small deletions (1.35 and 1.98Mb in length, confirmed by FISH), had a normal diploid set. SKY clarified that chr. 5 material had indeed been displaced to both chr. 3 and 7 with a reciprocal translocation of chr. 3 material occurring on the abnormal chr. 5. In sum, our studies demonstrate the utility of SNP-A as a karyotyping tool that can detect previously cryptic areas of LOH on chr. 5 and facilitate definition of shared 5q defects. We also show that our patients with 5q- syndrome had lesions spanning both 5q33 and the more proximal 5q31.2 area, making pathogenic distinction based on cytogenetics difficult.

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