Use of SNP-array-based karyotyping for cytogenetic prognostication in unclassified cases of myelodysplasia and associated overlap disorders

7016 Background: Myeloproliferative disorders (MPD) and myelodysplastic syndromes (MDS) often have overlapping features resulting in unclassifiable cases (MDS-U and MDS/MPD-U). Chromosomal abnormalities impact prognosis, but 50% of cases show normal karyotype by metaphase cytogenetics (MC). Single nucleotide polymorphism arrays (SNP-A) are novel karyotyping tools with superior resolution and ability to detect copy neutral loss of heterozygosity, a defect not detected by MC. Methods: MDS-U (N = 17) and MDS/MPD-U (N = 61) patients were selected from an MDS database (N = 720, median age = 76, median follow-up = 42 mos). SNP-A was performed on 67 patients and 751 controls. An algorithm for identification of somatic lesions was designed: 1) Lesions detected by MC and SNP-A required no further analysis; 2) Micro-duplications/ deletions overlapping with copy number variants (CNV) were excluded. Lesions not in CNV databases were confirmed by CD3 lymphocytes; 3) UPD <25 Mb were unlikely somatic and excluded. Telomeric and interstitial (≥ 25 Mb) UPD were considered somatic. International Prognostic Scoring System (IPSS) was used to assess routine risk. Fisher's exact test was used for categorical variables. Overall (OS) and event-free (EFS) survival defined by the MDS working group criteria were analyzed by Kaplan Meier analysis (log-rank or Wilcoxon and 2-sided significance). Results: SNP-A yielded superior detection rate for chromosomal defects compared to MC (71% vs 47%, p = 0.008). UPD was seen in 17 patients and frequently involved chromosomes 1, 3, 6, 8, 11, 17. MDS/MPD-U and MDS-U patients had similar OS and EFS (OS = 42 vs. 45 mos, p = 0.13; EFS = 42 vs. 45 mos p = 0.63). SNP-A revealed a more complex karyotype in patients with advanced MDS. Furthermore, SNP-A karyotyping resulted in prognostic refinement of previously assigned IPSS: Unclassified cases = 6% versus 0%, int-1 = 45% versus 53%, int-2 = 6% versus 19%, high = 5% versus 8%. Overall, patients with new SNP-A lesions had worse OS and EFS (OS = 41 mos vs NR, p = 0.07; EFS = 32 vs 112 mos, p = 0.07). Conclusions: SNP-A karyotyping complements MC in detecting chromosomal defects in MDS-U and MDS/MPD-U. This technology will be helpful in refining diagnosis based on characteristic recurrent chromosomal lesions including UPD. No significant financial relationships to disclose.

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Prevalence of Chromosomal Abnormalities in Infertile Couples in Romania

Balkan Journal of Medical Genetics ◽

10.1515/bjmg-2015-0002 ◽

2015 ◽

Vol 18 (1) ◽

pp. 23-30 ◽

Cited By ~ 5

Author(s):

Dana Mierla ◽

M. Malageanu ◽

R. Tulin ◽

D. Albu

Keyword(s):

Retrospective Study ◽

Chromosomal Abnormalities ◽

Normal Karyotype ◽

Control Group ◽

Chromosomal Anomalies ◽

Exact Test ◽

Infertile Women ◽

Infertile Men ◽

Significant Statistical Association

AbstractThe purpose of this study was to establish a correlation between the presence of chromosomal abnormalities in one of the partners and infertility. This retrospective study was performed at the Department of Reproductive Medicine, Life Memorial Hospital, Bucharest, Romania, between August 2007 to December 2011. Two thousand, one hundred and ninety-five patients with reproductive problems were investigated, and the frequency of chromosomal abnormalities was calculated. The control group consisting of 87 fertile persons who had two or more children, was investigated in this retrospective study. All the patients of this study were investigated by cytogenetic techniques and the results of the two groups were compared by a two-tailed Fisher’s exact test. In this study, 94.99% patients had a normal karyotype and 5.01% had chromosomal abnormalities (numerical and structural chromosomal abnormalities). In the study group, numerical chromosomal abnormalities were detected in 1.14% of infertile men and 0.62% of infertile women, and structural chromosomal abnormalities were detected in 1.38% of infertile men and 1.87% of infertile women, respectively. The correlation between the incidence of chromosomal anomalies in the two sexes in couple with reproductive problems was not statistically significant. Recently, a possible association between infertility and chromosomal abnormalities with a significant statistical association has been reported. Our study shows that there is no association between chromosomal abnormalities and infertility, but this study needs to be confirmed with further investigations and a larger control group to establish the role of chromosomal abnormalities in the etiology of infertility.

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Genomic Changes Associated with Leukemic Transformation of Myeloproliferative Disorders.

Blood ◽

10.1182/blood.v112.11.3371.3371 ◽

2008 ◽

Vol 112 (11) ◽

pp. 3371-3371

Author(s):

Nils Heinrich Thoennissen ◽

Norihiko Kawamata ◽

Terra L Lasho ◽

Tamara Weiss ◽

Daniel Nowak ◽

...

Keyword(s):

Molecular Mechanisms ◽

Chromosomal Abnormalities ◽

Neutral Loss ◽

Uniparental Disomy ◽

Myeloproliferative Disorders ◽

Lymphoid Cells ◽

Leukemic Transformation ◽

Altered Expression ◽

Snp Chip ◽

Genomic Changes

Abstract Myeloproliferative disorders (MPD) are a group of heterogeneous diseases that include polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF). They are characterized by increased hematopoiesis leading to elevated numbers of non-lymphoid cells and/or platelets in the peripheral blood. Beside thrombotic and hemorrhagic complications, MPD may evolve into secondary acute myeloid leukemia (sAML). Recently characterized markers suggest an opportunity to diagnose and identify subpopulations of MPD patients. In particular, altered expression and point mutations of PRV-1, MPL and JAK2 were commonly found in MPD, as well as deletions on chromosome 20q (del20q). Acquired uniparental disomy (UPD) on chromosome 1p (1pUPD) and 9p (9pUPD) leading to copy-neutral loss of heterozygosity (LOH) is a further mechanism found in MPD which often leads to homozygous activated mutations of MPL and JAK2, respectively. However, the molecular mechanisms involved in the transformation process to sAML remains unclear. Using standard metaphase cytogenetics (MC), chromosomal abnormalities are found in only a proportion of patients with MPD. We hypothesized that with new precise methods more genomic lesions can be uncovered that may be associated with leukemic transformation. To address this issue, we used 250K single nucleotide polymorphisms (SNP) Chip arrays to study chromosomal lesions in 40 sAML samples from patients who evolved from MPD; 7 had preexisting PV, 25 PMF, and 8 ET. Moreover, 43 additional samples of MPD (10 PV, 17 ET, and 16 PMF) were included in this study. SNP-chip analysis showed major chromosomal changes in almost all the sAML samples including monosomy 16, deletions of 1q-, 3p-, 6p-, 5q-, 7q-, 9q-, 12p-, 6q-, 3q-, 17p-, 19q-, and 20q- as well as trisomy 2, 3, 8, 9, 12, 15, 19, 21, and 22. We validated these data by MC. However, numerous new genomic alterations which contained potentially interesting genes that might contribute to leukemic transformation were detected by SNP Chip Array in patient samples with normal karyotype. Moreover, UPD was very frequent: 44% (19/43) of MPD and 53 % (21/40) sAML samples. 1pUPD occurred in 5 patients with MPD (1PV, 4 PMF; 12 %) compared to 5 patients with sAML (1 PV, 4 PMF; 13 %). 9pUPD was found in 16 MPD patients (8 PV, 7 PMF, 1 ET; 37%) and 6 sAML patients (3 PV, 2 PMF, 1ET; 15 %). All patients with 9pUPD proved to be positive for the JAK2 V617F mutation seen by allele specific PCR. Interestingly, the MPD samples only had UPD on 1p, 9p, and 12q. In contrast, sAML samples showed additional UPD regions on 7q, 11q, 12q, 16p, 17p, 19q, and 21q. Beside the evaluation of the non-matching groups of patients with MPD and sAML, we also evaluated 4 patients during their PMF and sAML stages by SNP Chip. The sAML samples acquired additional genomic changes including trisomy 8, 10, 14, 19, duplication on 3q and 6p, and heterozygote deletion on 18q. In contrast, 1pUPD, 9pUPD, and 12qUPD were detected in both MPD and sAML matching samples, suggesting that these changes do not play an immediate role in causing transformation. In conclusion, we detected chromosomal regions possessing genes which may be involved in the leukemic transformation of MPD patients.

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SNP Array Karyotyping Improves Detection Rate of Clonal Chromosomal Abnormalities in Refractory Anemia with Ringed Sideroblasts.

Blood ◽

10.1182/blood.v110.11.4132.4132 ◽

2007 ◽

Vol 110 (11) ◽

pp. 4132-4132

Author(s):

Theodore Ghazal ◽

Lukasz P. Gondek ◽

Abdo S. Haddad ◽

Karl S. Theil ◽

Mikkael A. Sekeres ◽

...

Keyword(s):

Copy Number ◽

Chromosomal Abnormalities ◽

Neutral Loss ◽

Snp Array ◽

Uniparental Disomy ◽

Blood Analysis ◽

Refractory Anemia ◽

Ringed Sideroblasts ◽

Normal Copy Number

Abstract Among WHO low-risk categories of MDS, refractory anemia with ringed sideroblasts (RARS) can be more accurately diagnosed by characteristic pathomorphology. Clonal hematopoiesis and chromosomal abnormalities exemplify a close pathogenetic relationship to other forms of MDS. RARS shows considerable clinical variability even for patients (pts) with identical cytogenetic defects. Due to the low resolution of metaphase cytogenetics (MC) and its dependence on cell growth in vitro, this test is often non-informative in MDS. High-density SNP arrays (SNP-A) allow for a precise identification of unbalanced genomic lesions and copy-neutral loss of heterozygozity. We hypothesize that cryptic chromosomal (chr) aberrations exist in most, if not all, pts with RARS. Their detection may help to improve prognostication, distinguish distinct phenotypes and point towards unifying pathogenic defects. Initially, we analyzed the results of MC in pts with MDS and MDS/MPD (N=455) and in a sub-cohort of RARS, RCMD-RS, RARSt and other MDS subtypes with >15% RS. When we compared pts with/without RS, chr defects were found at comparable frequencies (∼50%). The most commonly occurring defects associated with RS, compared to other forms of MDS, included those of chr 5 (9% vs. 16%, 7 (8% vs. 12%) and 20 (3% vs. 8%). DNA was available for 36 pts with RS and was subjected to 250K SNP-A karyotyping. Pathologic lesions were defined upon exclusion of normal copy number polymorphisms identified in 81 controls (O’Keefe at al ASH 2007), as well as the Database of Genomic Variants (http://projects.tcag.ca/variation). By MC, a defective karyotype was present in 16/36 pts (44%). Deletions involving chr 5, 7 and complex MC were found in 3, 5, and 2pts, respectively. However, when SNP-A was applied as a karyotyping tool (copy number and LOH analysis), all aberrations found by MC were confirmed, but also new lesions were detected so that an abnormal karyotype was established in 62% of pts. Several previously cryptic/recurrent lesions included losses of a portion of chr. 2 (N=2; 2p16.2, 2p16.3), and deletions (N=4; 7p11.1–14.1, 7p21.3, 7q11.23–21.11, 7q21.12-qter) as well as gains (N=1; 7q33) on chr 7. We have also detected segmental uniparental disomy (UPD) in chr 1 (N=2; 1p21.3–22.2, 1p). This type of lesion cannot be detected using MC and provides an additional mechanism leading to LOH. When both bone marrow and blood of 5 RARS patient were tested using SNP-A, blood analysis had 100% accuracy rate as compared to marrow; all defects seen in the marrow were also found in blood. We conclude that chromosomal defects are present in a majority of RARS patients and arrays with higher resolution will identify defects in most, if not all of the patients. Our study also demonstrates testing of peripheral blood by SNP-A can complement marrow MC, especially in cases in which marrow is not available. Detection of clonal marker aberrations in blood of RARS patients suggests that mostly clonal dysplastic progenitor cells contribute to blood production rather than residual “normal” progenitors.

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SNP-Array Based Karyotyping Complements Routine Cytogenetics in Diagnosis and Risk Stratification Schemes of MDS

Blood ◽

10.1182/blood.v112.11.639.639 ◽

2008 ◽

Vol 112 (11) ◽

pp. 639-639

Author(s):

Ramon V. Tiu ◽

Lukasz P Gondek ◽

Jungwon Huh ◽

Christine O’Keefe ◽

Mikkael A. Sekeres ◽

...

Keyword(s):

Risk Stratification ◽

Chromosomal Abnormalities ◽

Diagnostic Yield ◽

Neutral Loss ◽

Prognostic Significance ◽

Significant Proportion ◽

Snp Array ◽

Uniparental Disomy ◽

Abnormal Karyotype ◽

Novel Technologies

Abstract While current pathomorphologic criteria distinguish MDS, MDS/MPD and MDSderived AML (sAML), these conditions share common unbalanced chromosomal abnormalities highly predictive of prognosis. Reflecting their clinical importance, IPSS is highly influenced by metaphase cytogenetics (MC), the standard for detection of chromosomal abnormalities. Due to its low resolution and need for cell divisions, MC can only detect abnormalities in 50% of patients with MDS, novel technologies have been developed that could improve the diagnostic yield. Among these methods, single nucleotide polymorphism arrays (SNP-A) have been adopted as a cytogenetic platform. SNP-A karyotyping can be performed on interphase cells and allows for detection of smaller lesions as well as for copy-neutral loss of heterozygosity (LOH). As a result, some reference laboratories offer this test for routine cytogenetic diagnostics. However, the clinical relevance of lesions detected by SNP-A remains unclear and, consequently, we designed this comprehensive study to clarify the clinical impact of cytogenetic results generated through a combined application of SNP-A and MC. A cohort of 352 patients (218 MDS, 59 MDS/MPD, 75 sAML) was studied using Affymetrix 250K (N=160), Affymetrix 6.0 (N=190) and both platforms (N=95). Controls included 362 and 118 samples analyzed by 250k and 6.0 arrays, respectively. CNAGv3 or GCv2.1 software was used for analysis. To avoid biological and technical artifacts, known copy number variants as well as areas of LOH<2.5Mba were excluded. All other lesions, if not present on MC, were confirmed in germ line DNA if possible. The median follow-up time was 29 months (95% CI; 21-38 mo) and for many patients serial samples were studied, showing sequential acquisition of chromosomal defects. Overall, the detection rate of chromosomal abnormalities was improved compared to MC (57% vs. 44%; p=.0096), MDS/MPD (66% vs. 39%, p=.0055) and sAML (63% vs. 45%, p=.048). Somatic uniparental disomy (UPD) accounted for a significant proportion of newly detected defects (26% of new lesions). Overall, UPD was detected in 100 patients (78 as the sole and 22 as an additional lesion). Chromosomal lesions were identified in 98/180 with normal MC. In 61% of patients with non-informative MC (N=18), SNP-A demonstrated an abnormal karyotype; those with newly detected lesions showed inferior outcomes in overall survival (OS) [16 vs. 36 mo, p=.03]. Analysis of OS showed that patients with new defects detected by SNP-A and previously normal MC have worse outcomes compared to those in whom normal chromosomes were confirmed (39 vs. 73 mo, p=.03). Moreover, additional lesions also conferred worse prognosis for patients with abnormal karyotype by MC (17 vs. 38 mo, p=.01). This trend was even more pronounced when specific subgroups were analyzed based on OS and event free survival (EFS). For example, detection of new lesions in MDS (OS p=.02), MDS/MPD (OS p=.009, EFS p=.01) or sAML (OS p=.02, EFS p=.008) results in significant worsening of OS and EFS as compared to patients with truly normal cytogenetics. Newly detected lesions allowed for more precise prognostication within established IPSS strata of MDS and MDS/MPD patients. The detection of SNP-A defects negatively impacted OS/EFS in patients with low IPSS (NR vs. 69 mo, p=<.0001; 42 vs. 112 mo, p=<.0001), decreased EFS in Int-1/2 (24 vs. 29 mo; p=<.0001) and decreased OS/ EFS in high IPSS categories (11 vs. 26 mo, p=<.0001; 7 vs. 14 mo, p=<.0001). In sAML, patients with SNP-A lesions, regardless of MC, have worse OS (6 vs. 21 mo, p=.009) and EFS (5 vs. 13 mo, p=.01). In summary, SNP-A karyotyping facilitates detection of lesions which can complement MC and contribute to a better molecular diagnosis. SNPdetected lesions have impact on prognostic parameters which will likely affect future risk stratification schemes and have prognostic significance regardless of MC in sAML. As a result, new molecular subtypes of MDS may be identified and better-defined recurrent lesions will contribute to identification of causative genes.

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Prevalence and prognostic impact of allelic imbalances associated with leukemic transformation of Philadelphia chromosome–negative myeloproliferative neoplasms

Blood ◽

10.1182/blood-2009-07-235119 ◽

2010 ◽

Vol 115 (14) ◽

pp. 2882-2890 ◽

Cited By ~ 81

Author(s):

Nils H. Thoennissen ◽

Utz O. Krug ◽

Dhong Hyun Tony Lee ◽

Norihiko Kawamata ◽

Gabriela B. Iwanski ◽

...

Keyword(s):

Target Genes ◽

Chromosomal Abnormalities ◽

Myeloproliferative Neoplasms ◽

Neutral Loss ◽

Philadelphia Chromosome ◽

Snp Array ◽

Chronic Phase ◽

Prognostic Impact ◽

Leukemic Transformation ◽

Blast Phase

Abstract Philadelphia chromosome–negative myeloproliferative neoplasms (MPNs) including polycythemia vera, essential thrombocythemia, and primary myelofibrosis show an inherent tendency for transformation into leukemia (MPN-blast phase), which is hypothesized to be accompanied by acquisition of additional genomic lesions. We, therefore, examined chromosomal abnormalities by high-resolution single nucleotide polymorphism (SNP) array in 88 MPN patients, as well as 71 cases with MPN-blast phase, and correlated these findings with their clinical parameters. Frequent genomic alterations were found in MPN after leukemic transformation with up to 3-fold more genomic changes per sample compared with samples in chronic phase (P < .001). We identified commonly altered regions involved in disease progression including not only established targets (ETV6, TP53, and RUNX1) but also new candidate genes on 7q, 16q, 19p, and 21q. Moreover, trisomy 8 or amplification of 8q24 (MYC) was almost exclusively detected in JAK2V617F− cases with MPN-blast phase. Remarkably, copy number–neutral loss of heterozygosity (CNN-LOH) on either 7q or 9p including homozygous JAK2V617F was related to decreased survival after leukemic transformation (P = .01 and P = .016, respectively). Our high-density SNP-array analysis of MPN genomes in the chronic compared with leukemic stage identified novel target genes and provided prognostic insights associated with the evolution to leukemia.

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Inherited unbalanced translocation (4p16.3p15.32 duplication/8p23.3p23.2deletion) in the four generation pedigree with intellectual disability/developmental delay

Molecular Cytogenetics ◽

10.1186/s13039-021-00552-3 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Dongmei Hao ◽

Yajuan Li ◽

Lisha Chen ◽

Xiliang Wang ◽

Mengxing Wang ◽

...

Keyword(s):

Mental Retardation ◽

Intellectual Disability ◽

Developmental Delay ◽

Copy Number Variants ◽

Snp Array ◽

Normal Karyotype ◽

Clinical Syndrome ◽

Chromosome 8 ◽

Fish Analysis ◽

Balanced Translocation

AbstractChromosomal copy number variants (CNVs) are an important cause of congenital malformations and mental retardation. This study reported a large Chinese pedigree (4-generation, 76 members) with mental retardation caused by chromosome microduplication/microdeletion. There were 10 affected individuals with intellectual disability (ID), developmental delay (DD), and language delay phenotypes. SNP array analysis was performed in the proband and eight patients and found all of them had a microduplication of chromosome 4p16.3p15.2 and a microdeletion of chromosome 8p23.3p23.2. The high-resolution karyotyping analysis of the proband had unbalanced karyotype [46, XY, der(8)t(4;8)(p15.2;p23.1)mat], his mother had balanced karyotype [46, XX, t(4;8) (p15.2;p23.1)], whereas his father had normal karyotype [46,XY]. Fluorescence in situ hybridization (FISH) analysis further confirmed that the proband’s mother had a balanced translocation between the short arm terminal segment of chromosome 4 and the short arm end segment of chromosome 8, ish t(4;8)(8p + ,4q + ;4p + ,8q +). In conclusion, all the patients inherited chromosomes 8 with 4p16.3p15.2 duplication and 8p23.3p23.2 deletion from their parental balanced translocation, which might be the cause of the prevalence of intellectual disability. Meanwhile, 8p23.3p23.2 deletion, rather than 4p16.3p15.2 duplication might cause a more severe clinical syndrome.

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

Blood ◽

10.1182/blood.v110.11.108.108 ◽

2007 ◽

Vol 110 (11) ◽

pp. 108-108 ◽

Cited By ~ 2

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.

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SNP-a Karyotyping Provides a Clonal Molecular Marker and Is Associated with a High Incidence of Segmental Uniparental Disomy in Patients with CMML

Blood ◽

10.1182/blood.v112.11.3657.3657 ◽

2008 ◽

Vol 112 (11) ◽

pp. 3657-3657

Author(s):

Michael McDevitt ◽

Andrew Jeffrey Dunbar ◽

Christine O’Keefe ◽

Hideki Makishima ◽

Ramon V. Tiu ◽

...

Keyword(s):

Poor Prognosis ◽

Chromosomal Abnormalities ◽

Uniparental Disomy ◽

Normal Karyotype ◽

Myeloproliferative Disorders ◽

Size Exclusion ◽

Response Monitoring ◽

Monosomy 7 ◽

Entire Cohort ◽

Diagnosis And Prognosis

Abstract Chronic myelomonocytic leukemia (CMML) patients display poor prognosis with median survival of 20 months (range 10–60). The WHO classification recognizes CMML as an overlap syndrome with mixed clinical and histomorphological features of both myelodysplastic syndrome (MDS) and myeloproliferative disorders (MPD). The underlying molecular basis for the poor prognosis and clinical and pathological features including the dysplasia and monocytosis are currently unknown. A lack of clonal markers in the majority of patients impedes diagnosis and prognosis assignment, as well as treatment response monitoring. Individual cases are associated with rare (5;12) translocations, RAS mutations, and unbalanced chromosomal changes. Since chromosomal defects have a major impact on the diagnosis and prognosis of myeloid malignancies, it is likely that cytogenetic methods with higher resolution and an ability to detect uniparental disomy (UPD) could explain clinical heterogeneity and point to potential therapeutic targets in CMML. Our study included 101 cases including 70 cases of both CMML1 and 2 and CMML-derived AML. We also studied 31 M4/M5/monocytic subtype AML cases (8 FLT3+) to allow interpretation of the 17 CMML cases that were analyzed at the time of AML transformation. Both 250K and a more sensitive 6.0 SNP-A array were utilized. Copy number variants (CNV) were identified and excluded from analysis by comparison with simultaneous arrays with CD3+ normal T cells from the test individual, or when not available, by comparison of results with published and our extensive internal CNV databases, and experimentally determined size exclusion parameters from over 500 MDS and AML cases run on the same platform. In total, 67/70 patients had samples sent for metaphase cytogenetics (MC) and 45% of these cases had an abnormal karyotype. Expected lesions commonly associated with MDS/CMML, such as +8 (N=4) and −7/del(7q) (N=5) were observed. When SNP-A was applied to the entire cohort, defects found by MC were confirmed. Also, new chromosomal abnormalities were identified for a total detection rate of 55/70 (79%). When patients with CMML-1, CMML-2 vs CMML-derived AML were analyzed for gains, losses and UPD, several results are apparent. First, subcytogenetic loci on the chromosomes affected by large gains (e.g., 8 and 21) and losses (e.g., del7 or del5) were identified in additional patients. Second, cytogenetic amplification (amp) and deletion (del) regions seen by MC were confirmed by SNP-A. Examples of recurrent amplifications and deletions included amp21q21 (N=8), amp8p23.2–q24.3 (N=5), amp13q31.1(N=4), amp20p(N=3), del7q21.1(N=4), del12p12.2(N=4), del7q34(N=3), and del5q(N=3). We found a high prevalence of segmental UPD, not otherwise detectable by MC, occurring in 54 % of primary CMML/CMML-derived AML. Recurrent lesions were identified on chrs. 1(N=3), 2(N=3), 4(N=5), 6(N=3), 7(N=5), 11(N=7), 13(N=3), 14(N=3), and 21(N=4). Fifteen of seventy (21%) had UPD as a sole or isolated abnormality. In 6/7 of the UPD11 cases, this was present as a sole abnormality. In a separate abstract we present 12 UPD11q cases with MDS/MPD-U and sAML; in 7 of these cases inactivating c-Cbl mutations were found. All were associated with CMML cases associated with AML transformation. Overall survival was compared for patients with CMML (WHO 1 and 2), CMML into AML, and M4/M5 with either normal karyotype and normal SNP-A results (no amplifications, deletions, UPD), relative to those with detectable genomic lesions. Outcome was poor for all CMML groups however. In summary, SNP-A-based karyotyping complements MC and allows for precise definition of chromosomal aberrations in patients with CMML, including copy-neutral LOH/UPD. UPD is common in CMML and overlapping regions may point to potential causative genes. The identification of c-Cbl demonstrates the utility of this approach, identifying pathways to explore for therapeutic intervention. Overall, SNP-A reveals evidence for significant cytogenetic and subcytogenetic genomic instability in CMML, perhaps not surprisingly with the known adverse prognosis of this disorder. UPD 7 and UPD 21 abnormalities are particularly interesting based on the frequency of these lesions, and the known association of monosomy 7 with CMML. They may provide markers for diagnosis and response monitoring, as more novel therapeutics are being developed for this poor prognosis disorder.

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Prognostic impact of SNP array karyotyping in myelodysplastic syndromes and related myeloid malignancies

Blood ◽

10.1182/blood-2010-07-295857 ◽

2011 ◽

Vol 117 (17) ◽

pp. 4552-4560 ◽

Cited By ~ 147

Author(s):

Ramon V. Tiu ◽

Lukasz P. Gondek ◽

Christine L. O'Keefe ◽

Paul Elson ◽

Jungwon Huh ◽

...

Keyword(s):

Myelodysplastic Syndromes ◽

Diagnostic Yield ◽

Neutral Loss ◽

Snp Array ◽

Hematologic Malignancies ◽

Prognostic Impact ◽

Myeloid Malignancies ◽

Genomic Aberrations ◽

Chromosomal Defects

Abstract Single nucleotide polymorphism arrays (SNP-As) have emerged as an important tool in the identification of chromosomal defects undetected by metaphase cytogenetics (MC) in hematologic cancers, offering superior resolution of unbalanced chromosomal defects and acquired copy-neutral loss of heterozygosity. Myelodysplastic syndromes (MDSs) and related cancers share recurrent chromosomal defects and molecular lesions that predict outcomes. We hypothesized that combining SNP-A and MC could improve diagnosis/prognosis and further the molecular characterization of myeloid malignancies. We analyzed MC/SNP-A results from 430 patients (MDS = 250, MDS/myeloproliferative overlap neoplasm = 95, acute myeloid leukemia from MDS = 85). The frequency and clinical significance of genomic aberrations was compared between MC and MC plus SNP-A. Combined MC/SNP-A karyotyping lead to higher diagnostic yield of chromosomal defects (74% vs 44%, P < .0001), compared with MC alone, often through detection of novel lesions in patients with normal/noninformative (54%) and abnormal (62%) MC results. Newly detected SNP-A defects contributed to poorer prognosis for patients stratified by current morphologic and clinical risk schemes. The presence and number of new SNP-A detected lesions are independent predictors of overall and event-free survival. The significant diagnostic and prognostic contributions of SNP-A–detected defects in MDS and related diseases underscore the utility of SNP-A when combined with MC in hematologic malignancies.

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Renal Infarction and Pulmonary Embolism in Patient with Myelodysplastic

Health Sciences ◽

10.15342/hs.1.182 ◽

2020 ◽

Vol 1 (1) ◽

Author(s):

Mounia Bendari ◽

Nouama Bouanani ◽

Mohamed Amine Khalfaoui ◽

Maryam Ahnach ◽

Aziza Laaraj ◽

...

Keyword(s):

Pulmonary Embolism ◽

Myeloproliferative Neoplasms ◽

Bone Biopsy ◽

Bone Marrow Aspiration ◽

Myeloproliferative Disorders ◽

Acute Onset ◽

International Prognostic Scoring System ◽

Renal Infarction ◽

The Right ◽

Enhanced Computed Tomography

The myelodysplastic syndrome-myeloproliferative neoplasms (MDS/MPNs) are defined by a group of heterogeneous hematological malignancies resulting from stem cell−driven clonal growth of pathological hematopoietic progenitors and ineffective hematopoiesis, they are characterized concomitant myelodysplastic and myeloproliferative signs. Myelodysplastic/myeloproliferative disorders have been considered to have a higher risk of thrombus formation.We report a rare case about a 64 years old Moroccan woman, experienced renal infarction (RI) associated with pulmonary embolism as a complication of a myelodysplastic/myeloproliferative disorder.The patient complained of acute-onset severe left flank pain, a contrast-enhanced computed tomography (CT) of the chest and abdomen revealed RI by a large wedge-shaped defect in the right kidney with pulmonary embolism.Biological exam showed deep anemia, the bone marrow aspiration found myelodysplasia.the bone biopsy showed signs of myeloproliferatif disease. The karyotype was normal, BCR-ABL, JAK2, CALR mutations were absents, and MPL mutation was positive. The International Prognostic Scoring System (IPSS-R) was 0, and the patient was included to the low risk group.Anticoagulation therapy was initiated with heparin to treat RI and pulmonary embolism. Three months later, pulmonary embolism had resolved without the appearance of additional peripheral infarction.This case emphasizes the need to consider myelodysplastic/myeloproliferative disorders as a cause of infraction renal and pulmonary embolism.

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