scholarly journals Phylloid Pattern of Hypomelanosis Closely Related to Chromosomal Abnormalities in the 13q Detected by SNP Array Analysis

Dermatology ◽  
2012 ◽  
Vol 225 (4) ◽  
pp. 294-297 ◽  
Author(s):  
F. Faletra ◽  
I. Berti ◽  
A. Tommasini ◽  
V. Pecile ◽  
L. Cleva ◽  
...  
Keyword(s):  
Chromosomal Abnormalities ◽  
Snp Array ◽  
Array Analysis ◽  
Snp Array Analysis

Use of high-density SNP-array analysis to identify novel chromosomal abnormalities that predict survival in multiple myeloma

2008 ◽  
Vol 26 (15_suppl) ◽  
pp. 8522-8522 ◽  
Author(s):  
H. Avet-Loiseau ◽  
N. Munshi ◽  
C. LI ◽  
F. Magrangeas ◽  
W. Gouraud ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Chromosomal Abnormalities ◽  
Snp Array ◽  
High Density ◽  
Array Analysis ◽  
Snp Array Analysis

A Comprehensive Genetic Analysis of MDS Patients From Peripheral Blood Combining FISH- and SNP-Array-Analysis

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 4926-4926
Author(s):  
Christina Ganster ◽  
Katayoon Shirneshan ◽  
Gabriela Salinas-Riester ◽  
Friederike Braulke ◽  
Julie Schanz ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Genetic Analysis ◽  
Peripheral Blood ◽  
Chromosomal Abnormalities ◽  
Clonal Evolution ◽  
Snp Array ◽  
The Other ◽  
Array Analysis ◽  
Bone Marrow Biopsies ◽  
Snp Array Analysis

Abstract Abstract 4926 Introduction: Chromosomal banding analysis (CBA) of bone marrow metaphases is the gold standard to identify chromosomal abnormalities in myelodysplastic syndromes (MDS). We aim to comprehensively detect and follow chromosomal abnormalities during the course of the disease without the need of repeated bone marrow biopsies. In ongoing studies we attempt to achieve this goal by performing serial fluorescence in situ hybridization (FISH) analysis on CD34+ peripheral blood cells (PBC). The aim of this pilot study was to establish SNP-array-analysis (SNP-A) on CD34+ PBC to complement genetic analysis on peripheral blood by identifying chromosomal abnormalities not detectable by FISH and/or CBA. Methods: We immunomagnetically enriched CD34+ PBC of 20 patients (pts) with MDS (16 pts), suspected MDS (1 pts) and secondary acute myeloid leukemia (sAML, 3 pts). SNP-A was performed with arrays from Affymetrix (3x SNP 6. 0, 4x Cyto 2. 7, 13x CytoScanHD). Fresh or frozen CD34+ PBC of 10 pts and in methanol/acetic acid fixed CD34+ PBC of 9 patients were successfully processed. One whole genome amplified sample was included. CBA and FISH-A was done for all patients. Results: By CBA, 3 pts had no chromosomal abnormalities, 8 pts had one abnormality, 6 pts had 2–4 abnormalities and 3 pts had more than 6 abnormalities. By SNP-A on CD34+ PBC, additional abnormalities could be revealed in 13/20 pts. In two pts they were also confirmed by FISH-A. Most of them were micro-deletions not detectable by CBA. In addition, SNP-A revealed uniparental disomies (UPD) in 5/20 pts. Of the 3 pts with no detectable abnormalities in CBA, one had a micro-deletion in 4q24 (TET2). The other two had an insufficient number of metaphases. One of them showed a highly complex karyotype by FISH-A and SNP-A on CD34+ PBC. The other one had suspected MDS and did not show any abnormalities by SNP-A. The 17 pts with ≤ 6 abnormalities in CBA showed 55 abnormalities by CBA, FISH-A and SNP-A altogether. 34/55 (62%) abnormalities could be detected by SNP-A and/or FISH-A, but not by CBA. 24/55 (44%) abnormalities could only be detected by SNP-A. 4/55 (7%) of abnormalities were structural abnormalities or small clones and were only detected by CBA. Serial analysis indicated clonal evolution: A patient with 16 abnormalities detectable by CBA and additional three by FISH and SNP-A developed two further micro-deletions (del(2)(q31q32), del(4)(q24q26)) within four months. When a MDS patient with a known 20q-deletion (isolated by CBA and FISH) progressed to AML 25 months after first diagnosis we detected 3 micro-deletions by SNP-A of peripheral blood (0. 98 Mb on 4q, 1. 31 Mb on 12q, 2. 55 Mb on 12q) thus resulting in 4 cytogenetic alterations fulfilling the criteria of complex and prognostically unfavorable abnormalities. Conclusions: Recently it was shown that abnormalities detectable by SNP-A, but not by CBA, could worsen prognosis of MDS patients. We succeeded in detecting these additional abnormalities without the need of bone marrow biopsies out of peripheral blood. Nevertheless, by parallel FISH and SNP-A of CD34+ PBC, most abnormalities detectable by CBA of bone marrow metaphases could be detected. Comprehensive genetic analysis at close intervals thus is possible without the need of bone marrow biopsies to study clonal evolution. The information gained could be used for therapy decisions, to improve prognostication and to unravel genetic evolutionary steps towards acute leukemia. Disclosures: No relevant conflicts of interest to declare.

scholarly journals OC28.03: Whole-genome SNP array analysis in routine prenatal diagnosis of chromosomal abnormalities - a one-year experience

2011 ◽  
Vol 38 (S1) ◽  
pp. 50-50
Author(s):  
M. Hynek ◽  
M. Trkova ◽  
V. Becvarova ◽  
J. Horacek ◽  
M. Putzova ◽  
...  
Keyword(s):  
Prenatal Diagnosis ◽  
Chromosomal Abnormalities ◽  
Snp Array ◽  
Whole Genome ◽  
Array Analysis ◽  
Snp Array Analysis ◽  
One Year

scholarly journals CBFA2T3-GLIS2 Fusion Gene Cause Dismal Clinical Course in Acute Megakaryocytic Leukemia of Down Syndrome

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 5184-5184
Author(s):  
Nao Takasugi ◽  
Kenichi Amano ◽  
Yasuo Kubota ◽  
Shota Kato ◽  
Yuichi Mitani ◽  
...  
Keyword(s):  
Down Syndrome ◽  
Mutational Analysis ◽  
Clinical Course ◽  
Fusion Gene ◽  
Snp Array ◽  
Genomic Analysis ◽  
Array Analysis ◽  
Snp Array Analysis ◽  
Acute Megakaryocytic Leukemia ◽  
Gata1 Mutation

[Introduction] Acute megakaryocytic leukemia of Down syndrome (DS-AMKL) is characterized by excellent outcome with chemotherapy in contrast to non-Down syndrome-related AMKL (non-DS-AMKL). DS-AMKL and non-DS-AMKL have distinct genetic features which may underlie their different clinical characteristics. DS-AMKL is initiated by a GATA1 mutation in the transient abnormal myelopoiesis (TAM) phase and developed with further mutations of other regulators, while non-DS-AMKL is a heterogeneous group which occasionally carry chimeric oncogenes. CBFA2T3-GLIS2 fusion gene is identified in about 30% of children with non-DS-AMKL, and reported as a strong poor prognostic factor in pediatric AMKL. However, CBFA2T3-GLIS2 has never been reported in DS-AMKL and adult AMKL patients. We performed genomic analysis of DS-AMKL including atypical case with difficult clinical course. This is the first report of DS-AMKL harboring the CBFA2T3-GLIS2 fusion gene. [Case] The patient is a 1-year-old female of DS-AMKL with no prior episode of TAM. G-banding analysis revealed the karyotype both of the leukemic cells and normal tissue sample; 47, XX, +21. Chimeric genes of AML1-MTG8, CBFB-MYH, DEK-CAN, MLL-LTG4, MLL-LTG9, MLL-ENL and abnormalities of KIT and FLT3 were not detected. The chemotherapy according to the Japanese Pediatric Leukemia / Lymphoma Study Group AML-D05 protocol, gemtuzumab ozogamicin, IDA-FLAG regimen (idarubicin, fludarabine, cytarabine, filgrastim) and clofarabine-based regimen were tried, but all of them failed to achieve complete remission (CR). She underwent umbilical cord blood transplantation and relapsed on day 35 after transplantation. Once she showed a response to azacitidine, but finally she died on day 293 after transplantation. [Materials and Methods] We performed whole transcriptome sequencing (RNAseq), SNP array analysis, mutational analysis of GATA1 in 6 DS-AMKL samples, which included this refractory sample and five DS-AMKL samples with GATA1 mutations. To analyze gene expression profiling, we applied the hierarchical clustering method and principal component analysis. [Results] RNA sequencing analysis identified a fusion gene involving exon 10 of CBFA2T3 and exon 2 of GLIS2 gene in this refractory sample. This fusion gene was a result of a cryptic inversion on chromosome 16 and the in-frame fusion of both genes. The fusion transcript was validated by reverse transcription-polymerase chain reaction (RT-PCR) followed by Sanger sequencing. Though SNP array analysis confirmed 21 trisomy, it did not identify other copy number aberrations. PCR analysis did not detect GATA1 mutation in this refractory sample, which can be identified in other DS-AMKL samples. Expression analysis elucidated DS-AMKL with CBFA2T3-GLIS2 fusion had distinct expression profile from DS-AMKL with GATA1 mutations. [Discussion] CBFA2T3-GLIS2 fusion is the most common chimeric oncogene identified in non-DS-AMKL children, but has never been detected in DS-AMKL patients. Patients with non-DS-AMKL, especially holding CBFA2T3-GLIS2 fusion gene, have poorer outcomes than DS-AMKL. DS-AMKL patients generally have GATA1 mutations, show high sensitivity to chemotherapy, and can be treated with less intensive chemotherapy. However, our case had no GATA1 mutation and could not achieve CR despite intensive chemotherapy and transplantation. Thus, it is suggested this fusion gene caused the resistance to chemotherapies including hematopoietic stem cell transplantation in our case. Therefore, our case suggests patients with DS-AMKL should be surveyed genomic investigations including RNAseq and mutational analysis of GATA1 to identify their molecular biological subtypes before treatments are initiated. In case that fusion genes are detected in DS-AMKL patients, they must undergo highly intense chemotherapies, looking ahead to transplantation from the beginning of the treatment. Moreover, in case of harboring CBFA2T3-GLIS2 fusion gene, some potential therapies have been proposed, so that efficacy of such new therapies should be validated in a cell line-derived xenograft or patient-derived xenograft model. [Conclusion] DS-AMKL is generally known to show superior outcome, but DS-AMKL without GATA1 mutation and with CBFA2T3-GLIS2 fusion gene shows resistance to chemotherapies. For DS-AMKL patients, it is desirable to perform genomic analysis including RNAseq before chemotherapy. Disclosures No relevant conflicts of interest to declare.

scholarly journals SNP Array Analysis Reveals Novel Genomic Abnormalities Including Copy Neutral Loss of Heterozygosity in Anaplastic Oligodendrogliomas

PLoS ONE ◽  
2012 ◽  
Vol 7 (10) ◽  
pp. e45950 ◽  
Author(s):  
Ahmed Idbaih ◽  
François Ducray ◽  
Caroline Dehais ◽  
Célia Courdy ◽  
Catherine Carpentier ◽  
...  
Keyword(s):  
Loss Of Heterozygosity ◽  
Neutral Loss ◽  
Snp Array ◽  
Array Analysis ◽  
Snp Array Analysis

scholarly journals A novel phenotype of 13q12.3 microdeletion characterized by epilepsy in an Asian child: a case report

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Mina Wang ◽  
Bin Li ◽  
Zehuan Liao ◽  
Yu Jia ◽  
Yuanbo Fu
Keyword(s):  
De Novo ◽  
Snp Array ◽  
Epileptic Seizures ◽  
Slow Waves ◽  
Recessive Mutation ◽  
Array Analysis ◽  
Single Nucleotide ◽  
Case Presentation ◽  
Snp Array Analysis ◽  
Cytogenetic Band

Abstract Background The microdeletion of chromosome 13 has been rarely reported. Here, we report a 14-year old Asian female with a de novo microdeletion on 13q12.3. Case presentation The child suffered mainly from two types of epileptic seizures: partial onset seizures and myoclonic seizures, accompanied with intellectual disability, developmental delay and minor dysmorphic features. The electroencephalogram disclosed slow waves in bilateral temporal, together with generalized spike-and-slow waves, multiple-spike-and-slow waves and slow waves in bilateral occipitotemporal regions. The exome sequencing showed no pathogenic genetic variation in the patient’s DNA sample. While the single nucleotide polymorphism (SNP) array analysis revealed a de novo microdeletion spanning 2.324 Mb, within the cytogenetic band 13q12.3. Conclusions The epilepsy may be associated with the mutation of KATNAL1 gene or the deletion unmasking a recessive mutation on the other allele, and our findings could provide a phenotypic expansion.

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.

Sign in / Sign up

Export Citation Format

Share Document