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Objective Activating mutations of the fms-like tyrosine kinase 3 gene (FLT3) by internal tandem duplications (ITDs) in the juxtamembrane domain (JMD) have been reported in ~30% of adult acute myeloid leukemia (AML) patients with cytogenetically normal karyotype (CN). However, FLT3/ITD mutations are frequently accompanied with leukocytosis, high percentage of blasts in bone marrow (BM), and increased the risk of treatment failure in AML patients. FLT3-ITD mutated AML patients mainly with normal karyotype have higher relapse probability and shorter duration of complete remission (CR) after chemotherapy, so FLT3-ITD mutation is considered as an independent poor prognostic factor in AML. Methods FLT3-ITD and FLT3-KTD were studied by polymerase chain reaction (PCR) and restriction fragment length polymorphism- PCR (RFLP-PCR) in 44 adults AML patients with cytogenetically normal karyotype (AML-CN) at diagnosis to characterize FLT3 status. The results were correlated with the prognostic factors. Results In this study, FLT3-ITD mutations were identified in 7 (15.9%) of the 44 AML-CN patients. Among the 7 patients with FLT3/ITD mutations, 6 patients revealed a typical ITDs mutation (fragment size was 329 bp) and one patient showed untypical ITD mutation (fragment size was ~400 bp). Whereas 37 patients (61.7%) were FLT3-ITD. None of all AML-CN patients examined showed FLT3-KTD mutations. Conclusions Our results support that FLT3-ITD are independent adverse prognostic factors for elderly AML-CN patients and are associated with low overall survival (OS), low rate of CR, high relapse rate (RR), and high percentage of BM blast at diagnosis. We concluded, FLT3 mutation analysis should be performed as a routine test in AML-CN patients.

Objective Somatic mutations in exon 12 of the NPM1 gene is one of the most common genetic abnormalities in adult acute myeloid leukemia (AML), which is observed in 25-35% of AML patients and in 50-60% of patients with cytogenetically normal AML (CN-AML). Methods We performed Sanger sequencing of exon 12 of the NPM1 gene, on 44 CN-AML patients to characterize NPM1 status. Results In this study, NPM1 mutations were identified in 10 (22.7%) of the 44 CN-AML patients. Among the 10 patients with NPM1 mutations, type A NPM1 mutations were identified in 8 (80%) patients, whereas non-A type NPM1 mutations were observed in 2 (20%) patients. Two non-A type NPM1 mutations were not previously reported: c.867-868InsCGGA and c.861-862InsTGCA. These two novel mutant proteins display a nuclear export signal (NES) motif (L-xxx-L-xx-V-x-L) less frequently and L-x-Lx-V-xx-V-x-L it has been never seen before, yet. However, both novel mutations show a tryptophan loss at codon 288 and 290 at the mutant C-terminus which are crucial for aberrant nuclear export of NPM into the cytoplasm. Conclusions This study suggests previously unreported NPM1 mutations may be non-rare and thus additional sequence analysis is needed along with conventional targeted mutational analysis to detect non type-A NPM1 mutations.

Background B cell precursor acute lymphoblastic leukemia (B-ALL) is the most common malignancy of childhood, with, after corresponding treatment, an overall complete remission rate of 90%. Approximately 75% of B-ALL cases harbor recurrent abnormalities, including so-called complex karyotypes (CK). Tumor lysis syndrome (TLS) is a metabolic abnormality which may arise during cancer therapy and also, extremely rarely, as spontaneous TLS before initiation of chemotherapy in patients with ALL. Case presentation Here we report a 9-year-old male, diagnosed with a de novo pre-B-ALL according to the WHO classification. Cytogenetic, molecular cytogenetic approaches and array comparative genomic hybridization analyses revealed a unique CK involving five chromosomes. It included four yet unreported chromosomal aberrations: a der(11)t(7;11)(p22.1;q24.2), a der(18)t(7;18)(q21.3;p11.22), del(11)(q24.2q25) and dup(18)(q11.1q23). Unfortunately, the patient died 3 months after the initial diagnosis. Conclusions To the best of our knowledge, a comparable childhood ALL case was not previously reported. Thus, the combination of the here seen chromosomal aberrations in childhood primary ALL seems to indicate for an extremely adverse prognosis.

Background Approximately 30% of adult acute myeloid leukemia (AML) acquire within fms-like tyrosine kinase 3 gene (FLT3) internal tandem duplications (FLT3/ITDs) in their juxtamembrane domain (JMD). FLT3/ITDs range in size from three to hundreds of nucleotides, and confer an adverse prognosis. Studies on a possible relationship between of FLT3/ITDs length and clinical outcomes in those AML patients were inconclusive, yet. Case presentation Here we report a 54-year-old Arab male diagnosed with AML who had two FLT3-ITD mutations in addition to NPM1 mutation. Cytogenetic approaches (banding cytogenetics) and fluorescence in situ hybridization (FISH) using specific probes to detect translocations t(8;21), t(15;17), t(16;16), t(12;21), and deletion del(13q)) were applied to exclude chromosomal abnormalities. Molecular genetic approaches (polymerase chain reaction (PCR) and the Sanger sequencing) identified a yet unreported combination of two new mutations in FLT3-ITDs. The first mutation induced a frameshift in JMD, and the second led to a homozygous substitution of c.1836T>A (p.F612L) also in JMD. Additionally a NPM1 type A mutation was detected. The first chemotherapeutic treatment was successful, but 1 month after the initial diagnosis, the patient experienced a relapse and unfortunately died. Conclusions To the best of our knowledge, a combination of two FLT3-ITD mutations in JMD together with an NPM1 type A mutation were not previously reported in adult AML. Further studies are necessary to prove or rule out whether the size of these FLT3-ITDs mutations and potential other double mutations in FLT3-ITD are correlated with the observed adverse outcome.

Background About 25 years ago, the acquired chromosome abnormality dicentric dic(9;20)(p11 ~ 13;q11) was seen described as a non-random aberration in B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Yet, about 200 cases were reported. However, dicentric dic(9;20) is a subtle abnormality which easily may be mixed up with monosomy 20 and/or del(9p). The dicentric dic(9;20) can be found as a sole chromosomal abnormality or can be masked within complex rearrangements; also, a dicentric dic(9;20) is often associated with mono- or biallelic loss of CDKN2A gene. Case presentation Here we report a case of 16-year-old male diagnosed with a de novo pre-B-ALL. Molecular approaches (array-based multicolor banding (aMCB) and array comparative genomic hybridization (aCGH)) were applied, and a unique complex karyotype involving six chromosomes was identified. It included three previously unreported chromosomal aberrations: dicentric dic(9;20;X), deletion del(7)(p22.2p15.2) and dicentric dic(7;13). The dicentric dic(9;20;X) also led to monoallelic loss of tumor suppressor gene CDKN2A. After successful chemotherapeutic treatment the patient experienced a relapse with a secondary ALL without complex karyotype but a deletion del(19)(p13). Unfortunately, the patient died after 17 months of the initial diagnosis. Conclusions To the best of our knowledge, a comparable childhood ALL associated with such complex karyotype and deletion del(19)(p13) in secondary ALL was not previously reported. Thus, the complex karyotype with dicentrc dic(9;20;X) seems to indicate for a poor prognosis.

Additional file 1: Table 1. Clinical history of the patient together with diagnostic results and treatment.

Methylenetetrahydrofolate reductase (MTHFR) gene is essential in folate metabolism. Genetic variations in this gene like 677 C>T and 1298 A>C affect its activity; the latter could act efficiently the DNA methylation and may give susceptibility to different malignancies. Not surprisingly, different studies have described a relationship between the presence of 677 C>T and 1298 A>C MTHFR polymorphisms and the leukemia risk development. However, only few studies have reported this issue in CML. For this work, 118 CML patients and 217 controls were studied. The MTHFR 677 C>T and 1298 A>C polymorphisms were investigated by polymerase chain reaction followed by restriction fragment length polymorphism (PCR-RFLP) technique. The frequency of CT and TT genotypes of the MTHFR gene (677 C>T) polymorphism in CML patients was significantly higher compared to controls. Moreover, for the AC and CC genotypes of the MTHFR 1298 A>C polymorphism, a statistically highly significant frequency of 1298 CC genotype was also detected in CML patients when compared to control group (OR = 1.9, 95%, CI = 1.15–3.16, p = 0.01, and OR = 106.92, 95% CI = 14.17–806.64, p = 1.7 × 10−16, respectively). In addition, CML patients with compound 677CT/1298AC, 677TT/1298AA, 677 CC/1298 AC and 677 CC/1298 CC genotypes were related to a high risk of CML (OR = 5.71, 95% CI: 2.751–11.864, p = 0.000001; OR = 59.5, 95% CI: 12.565–282.071, p = 9.8 × 10−12, OR = 1.9, 95% CI: 0.8678–4.549, p = 0.07; OR = 206.8, 95% CI: 26.284–1627.034, p = 1.15 × 10−19 respectively). The frequency of MTHFR 677 C > T and 1298 A > C genotypes was no significantly increased in patients with others phases of CML (accelerated or blastic transformation phases) when compared to the patients in the chronic phase of the disease. We found that both MTHFR 677TT and 1298CC genotypes have been in a high risk to develop a CML in Syrian patients.

Background Children with constitutional trisomy 21, i.e. Down syndrome (DS, OMIM #190685) have a 10 to 20-fold increased risk for a hematopoietic malignancy. They may suffer from acute lymphoblastic leukemia or acute myeloid leukemia (AML). AML referred to as myeloid leukemia of Down syndrome (ML-DS) is observed especially after birth at an early gestational age and characterized by enhanced white blood cell count, failure of spontaneous remission, liver fibrosis or liver dysfunction, and is significantly associated with early death. There are only few studies yet focusing on the clonal cytogenetic changes during evolution of ML-DS. Case presentation In a 1.4-year-old boy with DS an immunophenotype consistent with AML-M1 according to French-American-British (FAB) classification was diagnoses. Cytogenetic and molecular cytogenetic analyses revealed, besides constitutional free trisomy 21, an unbalanced translocation as der(16)t(1;16)(q25.3;q24), plus a balanced translocation t(3;20)(q25;q13.1). A poor clinical outcome was observed here. Conclusions To the best of our knowledge, an ML-DS case associated with identical acquired chromosomal abnormalities was not previously reported. Our findings suggest that especially partial trisomy 1q25 to 1q44 may be indicative for a poor prognosis in ML-DS.

Introduction B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is a clinically and biologically heterogeneous disease resulting from the accumulation of genetic alterations in B lymphoid precursor cells, and represents the most common malignant hematopoietic disease in childhood. Approximately 75% of BCP-ALL cases harbor a recurrent chromosomal alteration detectable by banding cytogenetic approaches. Some of these recurrent abnormalities define ALL subgroups and are used for risk stratification. However, coexistence of two normally independent, primary genetic aberrations within the same clone is rare in ALL. Case presentation Here we report an 8-year-old Syrian boy with B-ALL. He presented at diagnosis with two cytogenetic events, yet unreported to appear in common, i.e. a reciprocal translocation t(8;14) leading to cMYC / IGH gene fusion, and monoallelic loss of tumor suppressor gene TP53 . This patient received treatment with prednisolone according to ALL Intercontinental Berlin-Frankfurt-Munster (IC-BFM) 2002 chemotherapy protocol but he relapsed early. Bone marrow and central nervous system were finally involved and he died within 6 months after initial diagnosis due to intracranial hemorrhage. Conclusion The reported combination of aberrations in a childhood case of BCP-ALL here seems to indicate an adverse prognosis, and shows that otherwise independent predictive chromosomal aberrations may arise also together.

Background Splenic marginal zone lymphoma (SMZL) is an extremely rare low-grade malignancy of the B-cells, comprising The pathogenesis of SMZL still remains unclear. Approximately 70–80% of cases have been reported to exhibit detectable cytogenetic and/or molecular genetic abnormalities. The most frequent cytogenetic abnormalities are deletions in 7q22–q32, followed by gain of chromosomes 3/3q, 5q, 9q, 12q and 20q, and deletion in 17p. Complex karyotypes are common: the most frequently involved chromosomes are 1, 3, 7, 8, and 14. However, the incidence of specific recurrent clonal cytogenetic abnormalities in SMZL has not been established yet. Results Bone marrow of a 78-year-old male patient with a 1 month history of umbilical abdominal pain, cough, pallor, vomiting, fever, pancytopenia, anemia and enhanced serum lactate dehydrogenase (LDH) level was studied by banding cytogenetics, refined by fluorescence in situ hybridization including array-proven multicolor banding. A complex karyotype involving, among others both chromosomes 13, was detected. An unbalanced translocation der(13)t(1;13)(q21;p11.2) led to partial trisomy of 1q21-qter and a dicentric dic(13)t(3;13)(p11.2;p11.2) caused partial trisomy of 3q11.2-qter. Besides there were inversion inv(1)(p12q12) and a balanced translocation t(9;14)(p13;q32.3) as yet unreported abnormalities in an adult SMZL case at diagnosis. The immunophenotype was consistent with marginal zone lymphoma according to World Health Organization (WHO) recommendations. Conclusions To the best of our knowledge, a comparable adult SMZL case with complex karyotype, anemia and elevated LDH was not previously reported. Besides the involvement of yet unreported genetic regions in SMZL, also this case is one of the rare examples for a malignancy with a stable dicentric chromosome.

Glutathione S-transferases (GSTs) gene polymorphisms were demonstrated to be associated with inter-individual variability of Imatinib mesylate (IM) response for chronic myeloid leukemia (CML) patients in a few studies; however, the results have been inconclusive. The aim of this study was to assess the role of such GSTs gene polymorphisms ( GSTT1 and GSTM1 ) in relation to IM treatment outcome in 96 Syrian CML in chronic phase (CP) patients. Screening of GSTM1 and GSTT1 genotypes (null or present of these genes) was determined by multiplex polymerase chain reaction. Our results revealed that a GSTM1 null genotype frequency was significantly higher in CML patients than control (reference group) (OR = 2.12, 95% CI: 1.24–3.7; p = 0.007) while the GSTT1 null had no significant effect on CML development (OR = 1.54, 95% CI: 0.83–2.9; p = 0.19). Dual GSTM1 and GSTT1 null were associated with the risk of CML development (OR = 3.6, 95% CI: 1.37–9.3; p = 0.01). The GSTM1 null significantly increased the risk of minimal cytogenetic response (p = 0.001). The similar trend was observed in patients with GSTT1 present/GSTM1 null genotypes (p = 0.009). The highest number of patients with minimal cytogenetic response was in the group treated with 400 mg of IM, while 600 and 800 mg of IM significantly decreased this frequency. Our results highlight the significance of GSTM1 null alone, or in combination with the GSTT1 gene null, significantly increased the likelihood of IM failure in the CML patients studied. Especially patients with minimal cytogenetic response and GSTM1 null suffered from IM treatment failure in case of low dosage IM.

Myelodysplastic syndrome (MDS) is a group of clonal stem cell disorders characterized by cytopenia, dysplasia in one or more cell lineages, and ineffective hematopoiesis. MDS is associated with high risk of progression to acute myeloid leukemia. At initial diagnosis, clonal cytogenetic aberrations are present in 40–70% of patients with de novo (primary) MDS and in 65–95% of patients with therapy-associated ones (t-MDS). Most commonly observed abnormalities present in MDS are monosomy 5 and 7, trisomy 8, deletions of long arm of chromosome 20 as well as complex karyotypes. Loss or gain of chromosomal material is known to be related to disease development and progression. In a de novo adult MDS case banding cytogenetics, refined by array-proven multicolor banding (aMCB) revealed a unique complex karyotype involving ten chromosomes that include del(5q), del(7q), deletions in parts of both chromosomes 10, and a dic(7;17). Interestingly, the dic(7;17) leads to monosomy of the tumor suppressor gene TP53 . The patient had an immunophenotype consistent with refractory anemia with excess blasts in transformation (RAEB-t) according to French–American–British (FAB) classification. To the best of our knowledge, a comparable adult MDS case associated with such a complex karyotype and loss of TP53 was not previously reported. As most of complex aberrations were found simultaneously in all studied malignant cells this may be a hint on an initial one step development of this complex rearrangement by chromothripsis.

Background: Myelodysplastic syndromes (MDS) are subtypes of hematological disorders which are known to have partial bone marrow dysplasia, peripheral cytopenia, and later on an increased risk to develop acute myeloid leukemia. Chromosomal aberrations are detected in ~50% of cases of de novo MDS cases and the most common chromosomal abnormalities of this entity include complete or partial monosomy of chromosomes 5 and 7, partial deletion of 20q and 12p, trisomy 8, and 11q23 aberrations. A few primary and/or secondary MDS cases combined with other cancer have been reported. Case Presentation: We report here an adult MDS associated with squamous cell carcinoma (SCC). G-banding and array-proven multicolor banding (aMCB) revealed an unbalanced translocation der(7)t(1;7)(q21;q21), which led to 1q partial trisomy and 7q partial monosomy. Immunophenotype of this case was consistent with refractory anemia with excess of blasts (RAEB-2) according to World Health Organization (WHO) classification. Conclusions: As far as we know, this is the first adult MDS case associated with SCC and an unbalanced translocation t(1;7). Our patient received first cycle of azacitidine treatment and he showed bilateral pleural effusion as a secondary event. This toxicity is not limited to the first cycle as in previous MDS cases; our case is the first one to shown this toxicity as a secondary event of azacitidine treatment. As less than 10 cytogenetcially comparable cases without SCC were reported before in male MDS, we carefully conclude that this cytogenetic aberration may be a hint on a new gender associated MDS subgroup.

Bloom syndrome is a rare autosomal recessive disease, in which BLM gene is mutated, leading to genome instability and proneness to malignancy. It is characterized by short stature, sun-sensitive rash and immunodeficiency. We present a case of bloom syndrome with myelodysplasia complicated by acute myeloid leukaemia. This case has new ophthalmologic manifestations. We confirmed the diagnosis by detection of high rate of sister chromatid exchange. The patient received chemotherapy but did not tolerate it well and developed fungal pneumonia.

Background Chromosomal abnormalities are diagnostic and prognostic key factors in acute myeloid leukemia (AML) patients, as they play a central role for risk stratification algorithms. High hyperdiploidy (HH), a rare cytogenetic abnormality seen commonly in elder male AML patients, is normally categorized under AML with complex karyotype (CK). Accordingly, patients with HH generally are associated with low remission rates and a short overall survival. Case presentation Here we report a case of 21-year-old female, diagnosed with a de novo AML-M1 according to WHO classification and a CK at diagnosis. Cytogenetic, molecular cytogenetic approaches (standard fluorescence in situ hybridization (FISH), array-proven multicolor banding (aMCB)) and high resolution array comparative genomic hybridization (aCGH) analyses revealed a unique complex but still near diploid karyotype involving eleven chromosomes was identified. It included pentasomy 4, three yet unreported chromosomal aberrations t(1;2)(p35;p22), t(1;3)(p36.2;p26.2), and t(10;12)(p15.2;q24.11), and a combination of two cytogenetic events, yet unreported to appear in together, i.e. a reciprocal translocation t(1;3)(p36.2;p26.2) leading to EVI1/PRDM16 gene fusion, and monoallelic loss of tumor suppressor gene TP53. After successful chemotherapeutic treatment the patient experienced a relapse to AML-M1, and she developed secondary AML-M6 with tetraploidy and HH. Unfortunately, the young woman died 8.5 months after initial diagnosis. Conclusions To the best of our knowledge, a comparable adult AML associated with such a CK, coexistence of 3q rearrangements with loss of TP53 at diagnosis, and HH in secondary AML were not previously reported. Thus, the combination of the here seen chromosomal aberrations in adult primary AML seems to indicate for an adverse prognosis.

C677T polymorphism of the methylenetetrahydrofolate reductase ( MTHFR) gene was a risk factor for recurrent pregnancy loss (RPL), but few studies have confirmed a possible role of MTHFR A1298C polymorphism in RPL risk. This study was carried out to determine the influence of the MTHFR gene polymorphisms in RPL Syrian women. A case-control study was performed on 2 groups (106 healthy and 100 RPL women). The frequency of the MTHFR gene polymorphisms was determined by polymerase chain reaction based on restriction fragment length gene polymorphism. In the RPL group, the genotype frequencies of MTHFR C677T were CC (41%), CT (41%), and TT (18%), and in the control group, the frequencies were CC (62.2%), CT (36.7%), and TT (1%). Statistical analysis showed a homozygous TT genotype and T allele were significantly different in the RPL group ( P = .000003 and P = .000019, respectively). The genotype frequencies of MTHFR A1298C were AA (53%), AC (44%), and CC (8%) in the RPL group, whereas in the control group, these were AA (61.3%), AC (37.8%), and CC (1%). A significant difference in the CC genotype and C allelic frequencies in the RPL women was observed ( P = .014 and P = .064, respectively). The patients having compound heterozygous (677 CT/1298AC) were associated with an estimated 4.86-fold increase in risk of pregnancy loss compared to individuals with a wild type ( P = .012). Our findings indicate that RPL women with homozygous genotype for (C677T and A1298C) either alone or compound heterozygous genotypes have a high risk of pregnancy loss in Syrian women.

Background The translocation t(1;19)(q23;p13), which results in the TCF3-PBX1 chimeric gene, is one of the most frequent rearrangements observed in B cell acute lymphoblastic leukemia. It appears in both adult and pediatric patients with B cell acute lymphoblastic leukemia at an overall frequency of 3 to 5%. Most cases of pre-B cell acute lymphoblastic leukemia carrying the translocation t(1;19) have a typical immunophenotype with homogeneous expression of CD19, CD10, CD9, complete absence of CD34, and at least diminished CD20. Moreover, the translocation t(1;19) correlates with known clinical high risk factors, such as elevated white blood cell count, high serum lactate dehydrogenase levels, and central nervous system involvement; early reports indicated that patients with translocation t(1;19) had a poor outcome under standard treatment. Case presentation We report the case of a 15-year-old Syrian boy with pre-B cell acute lymphoblastic leukemia with abnormal karyotype with a der(19)t(1;19)(q21.1;p13.3) and two yet unreported chromosomal aberrations: an interstitial deletion 6q12 to 6q26 and a der(13)t(1;13)(q21.1;p13). According to the literature, cases who are translocation t(1;19)-positive have a significantly higher incidence of central nervous system relapse than patients with acute lymphoblastic leukemia without the translocation. Of interest, central nervous system involvement was also seen in our patient. Conclusions To the best of our knowledge, this is the first case of childhood pre-B cell acute lymphoblastic leukemia with an unbalanced translocation t(1;19) with two additional chromosomal aberrations, del(6)(q12q26) and t(1;13)(q21.3;p13), which seem to be recurrent and could influence clinical outcome. Also the present case confirms the impact of the translocation t(1;19) on central nervous system relapse, which should be studied for underlying mechanisms in future.

The t(3;12)(q26;p13) translocation is a recurrent chromosomal aberration observed in myeloid malignancies. The translocation results in the generation of the ETV6/myelodysplastic syndrome 1 (MDS1)/ectopic viral integration site 1 (EVI1) fusion gene. However, the present case report is the first to present this rearrangement in acute myelogeneous leukemia (AML)-M4. Notably, this case is the first report of AML-M4 with an initial trisomy 8 and secondary acquired t(3;12)(q26;p13). Cells harboring the t(3;12) translocation were found to exhibit a higher proliferative capacity than cells with pure trisomy 8, which is consistent with the role of the ETV6/MDS1/EVI1 fusion transcript in the development and progression of malignancy.

Background Follicular lymphoma (FL) is one of the most common B-cell non-Hodgkin’s lymphoma (NHL). A subset of FL cases transform into more aggressive malignancies, most often to diffuse large B-cell lymphoma (DLBCL); in addition, lymphoblastic lymphoma and acute lymphoblastic leukemia (ALL) have also been rarely reported. The most common cytogenetic abnormalities associated with FL are translocation t(14;18)(q32;q21) with BCL2 rearrangements, present in 80–90% of all FL. However, that translocation alone is insufficient to cause FL and additional genomic events specifically leading to this kind of disease are still to be determined. The most frequently reported secondary changes are gains of chromosomes 7p or 7q, Xp, 12q and 18q, as well as losses on 6q and mutations within BCL2 and/or BCL6 genes. The presence of additional genomic aberrations, in particular 17p and 6q deletions is more frequent in grade 2 and 3 FL patients and correlated with shorter survival and a higher rate of transformation into DLBCL. Case presentation We describe here, an adult FL grade 2 patient that had transformed to B-ALL at diagnosis. Banding cytogenetics, refined by multi-color fluorescence in situ hybridization including array-proven multicolor banding revealed a unique complex karyotype involving eleven chromosomes, translocation t(X;20)(p21.3;q11.2), translocation t(3;20)(q26.2;q12), and a dicentric dic(17;18). Interestingly, the dicentric chromosome led to monosomy of the tumor suppressor gene TP53. The case had an immunophenotype consistent with follicular center cell lymphoma according to the World Health Organization (WHO) recommendations. Conclusions To the best of our knowledge, a comparable adult FL grade 2 case that transformed to B-ALL associated with such a complex karyotype and loss of TP53 was not previously reported. Most of complex aberrations were found simultaneously in approximately 85% of studied malignant cells and the remained cells studied were non-clonal; mechanisms explaining this may be either multiple-step mechanisms or single step in sense of chromothripsis. Trial registration Identifying number: 3842. Registered 09 July 2012.

Colorectal cancer (CRC) is considered to be the third most common cancer worldwide, and it is the fourth most common cause of cancer deaths. CRC is described as multifactorial disease. Among others, Glutathione S-transferases are known to act pro-carcinogenic in CRCs, however, they are needed for the conjugation between chemotherapeutics and a wide spectrum of xenobiotics. In this study, 70 patients with CRC and 85 healthy volunteers without any cancer history were genotyped. Polymorphism genotypes for the genes GSTP1, GSTT1 and GSTM1 were studied by polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) and/or multiplex polymerase chain reaction. Our finding showed a significant risk for CRC associated with GSTP1 heterozygous Ile/Val (OR = 1.8; 95% CI: 0.93–3.44; p = 0.009), while GSTP1 Val/Val homozygous was observed only in the CRC patients. Significant differences in the frequency of GSTM1- and GSTT1-null genotypes were found. The GSTT1-null genotype was higher in CRC group (34.3%) than in control group (12.9%) (OR = 3.5; 95% CI: 1.57–7.83; p = 0.001). The GSTM1-null was higher in CRC cases (42.8%) compared with control group (21.1%) (OR = 2.79; 95% CI: 1.38–5.64; p = 0.003). Individuals carrying combined, both GSTM1/GSTT1-null genotype, were associated with an estimated 7.56-fold higher risk to form CRC than those having GSTM1/GSTT1-present genotype. Individuals carrying combined three genotypes of GSTM1-null/GSTT1-null/ heterozygous Ile/Val genotype for GSTP1 were associated with an estimated 21.63-fold higher risk to be CRC than those carrying GSTM1-present/GSTT1-present/ Ile/Ile genotype of the GSTP1 (OR = 21.63; 95% CI: 2.39–195.82; p = 0.001). Also, individuals with combined three genotypes of GSTM1-null/GSTT1-present/ heterozygous Ile/Val genotype for GSTP1 were associated with an estimated 13.9-fold higher risk to be CRC than those carrying GSTM1-present/GSTT1-present/ Ile/Ile genotype of the GSTP1 (OR = 13.9; 95% CI: 2.60–74.35; p = 0.0007). Overall, the results of this pilot study in 70 patients revealed that the GSTM1-null genotype, alone or in combination with GSTT1-null genotype, GSTP1-heterozygous is associated with enhanced risk for CRC in Syrian population.

Constitutional chromosomal abnormalities are an important cause of miscarriage, infertility, congenital anomalies and mental retardation in humans. Pericentric inversions of the human Y-chromosome [inv(Y)] are rather common and show an estimated incidence of 0.6-1:1,000 in males in the general population. Most of the reported cases with inv(Y) are familial. For carriers of pericentric inversions the risk of mental retardation or multiple abortions is not apparently increased and there is no relation with abnormal phenotypic features. Polymerase chain reaction (PCR) analysis to detect microdeletions along the Y-chromosome as well as cytogenetic and fluorescence in situ hybridization (FISH) analysis were done to delineate the characteristics of an inv(Y) in a Syrian family. Thus, we present a detailed molecularcytogenetic characterization of a father and his two sons having an inv(Y)(p11. 2q11.221~q11.222) with varying mental retardation features but otherwise normal phenotype

The so-called Philadelphia (Ph) chromosome is present in more than 90% of chronic myeloid leukemia (CML) cases. Amplification or duplication of the BCR-ABL gene has been found to be one of the key factors leading to drug resistance to imatinib mesylate (IM). In the present study, we identified the presence of isodicentric Ph chromosomes [idic(Ph)] in an IM-resistant patient. Fluorescence in situ hybridization (FISH) analysis on metaphase chromosomes confirmed the heterogeneity and amplification of the fused BCR-ABL gene. FISH analysis superimposed on G-banding confirmed the presence of idic(Ph) chromosomes. Reverse transcription-polymerase chain reaction (RT-PCR) products revealed the presence of the BCR-ABL fusion transcript b3a2. The idic(Ph) chromosomes in CML were shown to be fused at the satellite regions of the short arms. The patient did not respond to IM chemotherapy and did not achieve remission. In this study, the impact of the idic(Ph) chromosomes on genomic instability, heterogeneity and amplification of the BCR-ABL gene in IM-resistant patients is discussed.

The so-calledPhiladelphia(Ph) chromosome is present in more than 90% of chronic myeloid leukemia (CML) cases. It results in juxtaposition of the 5' part of the BCR gene on chromosome 22 and the 3' part of the ABL1 gene on chromosome 9. An additional acquired monosomy 7 or deletion of 7q is associated with poor prognosis in a variety of myeloid disorders. Here we report a novel Ph chromosome positive CML case with a ring chromosome 7 [r(7)]. Immunophenotyping was compatible with CML, although 4.5% of total leucocytes appeared like acute myelogeneous leukemia (AML) subtype M2. The r(7) was characterized in detail by array-proven multicolor banding (aMCB), the latter being of enormous significance to characterize breakpoint regions in detail. Underlying mechanisms and prognostic are discussed, as ring chromosomes are rare cytogenetic abnormalities in hematopoietic malignancies.

The aim of this study was to search the BCR/ABL 1 fusion gene in 45 chronic myeloid leukemia (CML) Syrian patients using nested reverse transcription polymerase chain reaction (RT-PCR) and compare our results with those of conventional cytogenetics and molecular cytogenetics methods.45 bone marrow or peripheral blood samples from untreated CML patients in chronic phase (CP) were obtained at diagnosis, and analyzed by nested RT-PCR, conventional cytogenetics and molecular cyto-genetics methods.45 patients examined were positive for some type of BCR/ABL1 fusion gene rearrangement. Out of 45 studied CML patients, 23 (51.1%) expressed b3a2 fusion transcript, 21 (46.7%) b2a2 transcript, and 1 (2.2%) a rare b2a3 transcript. No patient co-expressed both b3a2/b2a2 types.The distribution BCR-ABL1 transcript types found in Syria were similar to that of Indian Far-Eastern, African or European populations and the M-BCR rearrangement types were not dependent on white blood count (WBC), platelet count, hemoglobin level or gender of the patients. Overall, we could show that patients with b3a2 rearrangements were younger than patients with b2a2 transcripts, thus our young patients may have a worse prognosis.

Infertility is an important health issue affecting numerous couples. Approximately 30-50% of the cases of male infertility is due to unknown reasons. The main genetic factors involved in male infertility are chromosomal abnormalities and Y chromosome microdeletions within the Yq11 region. The genes controlling spermatogenesis located in the Yq11 region are termed azoospermia factor genes (AZF). Klinefelter syndrome (KS) is the most common of the chromosomal anomalies in the infertile male. AZF microdeletions on the Y chromosome are the most frequent genetic cause of male infertility. Screening for microdeletions in the AZFa, b and c regions of the Y chromosome showed a marked variation among different studies. The present study aimed to investigate the prevalence of such deletions in Syrian men. A total of 162 infertile males (97 azoospermic, 49 oligospermic and 16 severely oligospermic) were screened for chromosomal abnormalities and Y chromosome microdeletions using 28 markers in the AZF region. Twenty (12.34%) patients had chromosomal rearrangements, 17 of them showed sex chromosome abnormalities (11 of 17 patients within the azoospermic group had a KS of 64.7%), 2 patients had apparently balanced autosomal rearrangements, while 1 patient had an inversion. Of the 162 infertile men, 46 patients (28.4%) had Y chromosome microdeletions within the AZF-regions. Most frequently hit were the AZFc (34.8%), followed by the AZFbc, AZFa, AZFac, AZFbc, AZFb, AZFd, AZFab, AZFad, AZFbd, AZFabc and the AZFbcd. Combined AZF deletions involving three regions with chromosomal abnormalities were observed in one case. The higher frequency of AZF deletions in our study was comparable with frequencies in other countries and regions of the world, possibly due to the elevated number of the sequence-tagged site (STS) markers used for this screening.

The so-called Philadelphia (Ph) chromosome is found in over 90% of cases of chronic myeloid leukemia (CML). Of these cases, 2-10% demonstrate complex translocations involving a third chromosome in addition to chromosomes 9 and 22. Since the majority of CML cases are currently treated with imatinib, variant rearrangements tend to have no specific prognostic significance, although the mechanisms involved in resistance to therapy have yet to be investigated. This study evaluated a CML case with complex chromosomal aberrations not previously observed. A four-chromosome translocation involving chromosomal regions including 11p11.2 and 20q11.21 in addition to 9q34 and 22q11 was characterized in detail using array-proven multicolor banding (aMCB), a technique which has proven to be of significance in characterizing breakpoint regions in detail. Underlying mechanisms and prognostic factors are discussed.

(1) Background: T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy of thymocytes with multiple genetic abnormalities, accounting for 15% and 25% of newly diagnosed cases of ALL in children and adults, respectively. Notably, T-ALL has a 3-fold higher incidence in males. Cytogenetically detectable structural or numerical chromosomal abnormalities are detected in ~50% of ALL cases. Such aberrations have a prognostic significance. High hyperdiploidy (51–65 chromosomes, HeH) is an established genetic subtype of B-cell ALL (B-ALL), which is associated with good survival and an excellent outcome. Furthermore, the most commonly acquired chromosomes in HeH are +4, +6, +10, +14, +17, +18, +21 and +X. However, the mechanism for chromosomal gains in ALL and their role in leukemogenesis are still ambiguous. (2) Methods: Banding cytogenetics, and molecular cytogenetics using whole chromosome paints and array-proven multicolor banding (aMCB) were used on chromosomal preparations together with immunophenotyping of the bone marrow cells. (3) Results: A HeH karyotype including a balanced translocation t(X;5) was detected in an, according to World Health Organization (WHO) classification, de novo childhood cortical-T-ALL case. (4) Conclusions: To the best of our knowledge, a childhood T-ALL case associated with a HeH karyotype was not previously reported. Even though an involvement of cytoband Xq26 in a rearrangement has already been observed, here a rearrangement involving Xq26 in a male ALL case was seen for the first time, suggesting a gender association, but not limitation of this cytogenetic ALL subgroup.

Background Chronic myeloid leukemia (CML) is a myeloproliferative disorder characterized by the presence of a derivative chromosome 22 [der(22)] commonly called Philadelphia chromosome (Ph). The Ph chromosome is a product of the reciprocal translocation t(9;22)(q34.1;q11.2). Additional genetic changes occur in less than 10 % of CML cases at the time of diagnosis and other genetic changes are seen in 60–80 % of the cases in advanced disease. Even though deletions in chromosome 9 are not rare findings in advanced phase-CML, del(9)(p23p11.1) as sole additional abnormality detected by fluorescence in situ hybridization (FISH) technique, to our knowledge has not been described in the literature. Results A complete cytogenetic and molecular cytogenetic analysis, molecular biology method (reverse transcription polymerase chain reaction (RT-PCR)), and immunophenotype confirmed to be a CML case in blast crisis (BC). It revealed del(9)(p23p11.1) as sole abnormality detected by FISH technique besides Ph chromosome, which leads to monoallely of tumor suppressor gene CDKN2A (cyclin-dependent kinase inhibitor 2A) before Imatinib mesylate (IM) treatment. Conclusions The patient did not demonstrate a good response to IM treatment. The underlying mechanisms and prognostic implications of these cytogenetic abnormalities are discussed.

Chronic myelogenous leukemia (CML) is characterized by the Philadelphia (Ph) chromosome created by the reciprocal translocation t(9:22)(q34;q11), resulting in the chimeric gene breakpoint cluster region (BCR)-Abelson (ABL). Variant Ph chromosome translocations involving chromosomes other than 9 and 22 occur in 5-10% of CML cases. In the present study, a novel case of a Ph chromosome-positive CML in the chronic phase (CP) is reported, with a three-way Ph translocation involving three chromosomal regions, 9q34, 10p11.2 and 22q11.2, in addition to the loss of the Y chromosome, where the latter was a secondary abnormality. Since the majority of CML cases are currently treated with imatinib, variant rearrangements generally have no specific prognostic significance, although the mechanisms involved in resistance to therapy have yet to be investigated. The underlying mechanisms and prognostic implications of these cytogenetic abnormalities are discussed in the present study.

The so-called Philadelphia (Ph) chromosome is present in more than 90% of chronic myeloid leukemia (CML) patients. Approximately, 5–10% of these patients show complex translocations involving a third chromosome in addition to chromosomes 9 and 22. Since at present the majority of CML cases are treated with imatinib, variant rearrangements do not exhibit specific prognostic significance. However, events of therapy resistance remain to be studied. In this study, we report a unique case of CML exhibiting an uncommon t(21;22)(p12;q11). This translocation has been characterized by fluorescence in situ hybridization (FISH) and array-proven multicolor banding (aMCB). Using specific probes for the BCR and ABL genes, results of FISH showed a three-way variant Philadelphia translocation (9;22;21)(q34;q11;p12) with a BCR/ABL fusion residing on the der(22) and the 3′BCR region translocated on the short arm of the derivative chromosome 21. In addition, the aMCB technique is significant in the detection of the breakpoints of genetic changes. The underlying mechanisms and prognostic significance of these changes are discussed.

T-cell prolymphocytic leukemia (T-PLL) is a rare and aggressive subtype of chronic lymphocytic leukemia. Usually it presents in older people with a median age of 61 years. T-PLL is characterized by elevated white blood cell (WBC) count with anemia and thrombocytopenia, hepatosplenomegaly, and lymphadenopathy; less common findings are skin infiltration and pleural effusions. The most frequent chromosomal abnormalities in T-PLL include 14q11.2, chromosome 8, and 11q rearrangements. Also deletions in the short arm of a chromosome 9 are reported in ~30% of T-PLL together with other aberrations. Here we report a childhood T-PLL case with a de novo del(9)(p13) as sole acquired anomaly leading to monosomy of the tumor suppressor gene CDKN2A (cyclin-dependent kinase inhibitor 2A). Also, to the best of our knowledge this is the first case of a childhood T-PLL with this aberration.

In the present study, we investigated the associations of polymorphisms in cytochrome P450 gene (CYP1A1), glutathione S-transferase genes (GSTM1 and GSTT1) with chronic myelogenous leukemia (CML). A total of 126 patients with CML and 172 healthy volunteers were genotyped, and the DNA was isolated from their blood samples. The polymorphisms were assessed by polymerase chain reaction (PCR) restriction fragment length polymorphism-based methods and multiplex PCR. Logistic regression analyses showed significant risk of CML associated with CYP1A1 Val allele [odds ratio (OR) 3.3, 95 % confidence intervals (CI) 1.96–5.53], (p < 0.0001) while CYP1A1 Val/Val homozygotes were observed only in the CML patients. There was statistically significant difference in the frequency of GSTM1 and GSTT1 null genotypes. The GSTT1-null genotype was slightly higher in 27 % of CML cases and 16.7 % of controls (OR 1.98, 95 % CI 1.12–3.5) (p < 0.020). The GSTM1 null was higher in 42.8 % of CML cases and 22.7 % of controls (OR 2.55, 95 % CI 1.54–4.22) (p < 0.00024). The individuals carrying CYP1A1 Ile/Val (AG) and GSTM1 null genotype have 9.9 times higher risk to be CML than those carrying CYP1A1 Ile/Ile (AA) and GSTM1 present genotype (OR 9.9, 95 % CI 2.7–36.3) (p < 0.0001). This suggests that the association of the GSTM1 null genotype, either alone or in combination with GSTT1 null, with CYP1AI heterozygous leads to the CML risk.

The well-known typical fusion gene BCR/ABL is observed in connection with a complex translocation event in 5–8% of cases of chronic myeloid leukemia (CML). The present study described an exceptional CML case with complex chromosomal aberrations not previously observed. Aberrations included a translocated BCR to the derivative chromosome 2 [der(2)] that also involved a four-chromosome translocation, implying chromosomal regions 1p32 and 2q21, besides 9q34 and 22q11.2, which were characterized by molecular cytogenetics.

Here we report an unusual case of Chronic Myelogeneous Leukemia (CML) developing towards an Acute Myelogeneous Leukemia subtype M5 (AML-M5). The chromosomal constitution was at (final) stage of AML-M5: Philadelphia chromosome positivity with multiple trisomies, a double t (9; 22) (q34; q11) and an AML1/MDS1/EVI1 (AME) fusion transcript resulting from a t (3; 21) (q26; q22). The latter translocation was detectable first in blast phase of CML and remained present in AML-M5 stage. Overall, four chromosomal analyses were done within 19 months, describing the ongoing karyotypic evolution during this transformation. Unfortunately this exceptional patient did not respond to Imatinib- (IM) or Nilotinib-therapy. These finding May by a first hint that CML-patients acquiring a t (3; 21) (q26; q22) might be appropriate to bone marrow transplantation rather than for IM-therapy.

Chronic myelogenous leukemia (CML) is characterized by the Philadelphia (Ph) chromosome, created by a reciprocal translocation t(9:22)(q34;q11) which forms the chimeric gene, BCR-ABL. Variant Ph chromosome translocations involving chromosomes other than 9 and 22 have been identified in 5–10% of CML cases. Four-way Ph chromosome translocations are an extremely rare event in myeloid malignancies and the phenotypic consequences of such rearrangements have not been investigated. Deletions in chromosome 9 are known to be associated with a poor prognosis. In the present study, a novel case of Ph chromosome-positive CML in blast crisis is reported. A four-way Ph translocation was identified, involving five chromosomal regions, 9p21, 9q34, 12p13.3, 20q11.2 and 22q11.2, as well as an unbalanced translocation, der(7)t(7;8)(p11.2;q11.2). Since the majority of CML cases are currently treated with imatinib, variant rearrangements in general have no specific prognostic significance, although the mechanisms involved in resistance to therapy have yet to be investigated. In the present case, multiple partial deletions, including ABL and ASS genes on chromosome 9, the region 7p11.2 to 7pter, 8q11.2 to 8pter and two regions on chromosome 12, were identified. An additional Ph chromosome was also detected. Immunophenotyping indicated that the patient had biphenotypic leukemia. The patient did not respond positively to imatinib chemotherapy and died for unknown reasons, one month after diagnosis. The underlying mechanisms and prognostic implications of these cytogenetic abnormalities are discussed.

The Philadelphia (Ph) chromosome is present in more than 90% of patients suffering from chronic myeloid leukemia (CML). It is the product of a reciprocal translocation between the long arms of chromosomes 9 and 22, resulting in the transfer of the 3′ portion of the proto-oncogene ABL from 9q34 to the 5′ portion of the breakpoint cluster region (BCR) on 22q11. Currently, most CML cases are treated with Imatinib and variant rearrangements are thought to have no specific prognostic significance, although the events of therapy resistance have not yet been studied. In this study we report a novel case of CML exhibiting an uncommon t(2;7)(p13.1;p21.3) besides t(9;22)(q34;q11). This unusual translocation has been characterized by fluorescence in situ hybridization (FISH) and array-proven multicolor banding (aMCB), the latter being extremely significant in characterizing breakpoint regions in detail. The underlying mechanisms and prognostic implications of this cytogenetic abnormality are discussed in this study.

Abnormalities involving sex chromosomes account for approximately 0.5% of live births. The phenotypes of individuals with mosaic cell lines that exhibit structural aberrations of the X and Y chromosomes are variable and difficult to predict. Phenotypes associated with sex chromosome mosaicism vary from females with Turner syndrome to males with infertility, and include individuals with ambiguous genitalia. In this study, we report a 17-year-old male with phenotypic features of Klinefelter syndrome with an isodicentric Y chromosome and a final karyotype of 45,X[4]/46,X,idic(Y)(q11.21)[95]/47,XX,+idic(Y)(q11.21)[1]. Application of high resolution molecular cytogenetic techniques as well as molecular studies revealed two copies of the sex-determining region of Y chromosome (SRY) gene and two centromers. Additionally, the breakpoint in Yq11.21 was narrowed down between positions 13.4 and 14.3 MB (hg18). We present a patient with partial disomy of Ypter to Yq11.21 in the majority of the patient cells, showing phenotypic features of Klinefelter syndrome. The syndrome may have occurred due to a more prominent presence of the cell line 47,XX,+idic(Y)(q11.21) detected only once in 1% of the peripheral blood cells. This finding may prove helpful in similar cases with symptoms of Klinefelter syndrome, but which exhibit an absence of the cell line 47,XXY in peripheral blood.

Small supernumerary marker chromosomes (sSMCs) are present in ~2.6x10⁶ individuals worldwide. Concerning their clinical consequences as well as their chromosomal origin and shape, sSMCs are a heterogeneous group of derivative chromosomes; 70% of sSMC carriers are clinically normal. In the present study, we report on a female with mosaicism (45%) of a de novo sSMC derived from chromosome 7, in which the observed clinical signs do not correspond to comparable cases in the literature. She is clinically normal apart from problems in gender determination, a uterus without ovaries and an external penis, pointing overall towards an adrenogenital syndrome (AGS). 21-Hydroxylase deficiency (21-OHD) is the most common cause of AGS. A corresponding analysis for underlying mutations in the CYP21A2 gene revealed a homozygous mutation c.518T>A (p.Ile173Asn) inherited from both non-related parents. Overall, in this study, we report a unique case of female pseudohermaphroditism, classified as a simple virilization form of 21-OHD having an additional minute-shaped chromosome 7 [min(7)(:p11.1->q11.23:)]. Notably, AGS was due to a mutation in the CYP21A2 gene located on chromosome 6. This is a further example that detection of an sSMC does not always resolve the clinical case.

Background Myelodysplastic syndrome (MDS) represents a group of clonal hematological disorders characterized by progressive cytopenia, and reflects to defects in erythroid, myeloid and megakaryocytic maturation. MDS is more frequently observed in older aged patients with cytogenetic abnormalities like monosomy of chromosome(s) 5 and/or 7. In 50% of de novo MDS cases, chromosomal aberrations are found and rearrangements involving the retinoblastoma (RB1) gene in 13q14 are found. Results Here, we are presenting a case report of a rare biclonal MDS with a karyotype of 45, XY,-4, der(6)t(4;6)(p15.1;p21.3), der(8)t(4;8)(q31.2;q22), t(13;16)(q21.3;p11.2)11/45, XY, der(7)t(7;13)(p22.2~22.3;q21.3),-13 9. The patient was diagnosed according to WHO classification as refractory anemia with excess of blasts (RAEB-II). Immunophenotyping was positive for CD11b, CD11c, CD10, CD13, CD15, CD16 and CD33. Conclusion We report, a novel and cytogenetically rare case of a biclonal MDS with complex chromosomal aberrations and deletion of RB1-gene in both clones. These findings are associated with a poor prognosis as the patient died 3 months after diagnosis.

Acute lymphoblastic leukemia (ALL) is the most common childhood malignancy. Approximately 84% of cases of ALL are classified as B-precursor ALL, 14% of cases are T-cell and 2% of cases are B-cell (B-)ALL. About one third of B-ALL cases show an abnormal karyotype. Combining data obtained by immunophenotyping, karyotyping and molecular cytogenetic analyses allows for a better understanding of this heterogeneous disease. This study reports an exceptional B-ALL case with a poor prognosis and unique complex chromosomal aberrations not previously observed, i.e., a translocation involving the six chromosomal regions 1q42, 4q21, 4q24, 4q35 (twice), 8q22 and 10p15.3 besides 9q34 and 22q11.2.

The reciprocal translocation t(9;22)(q34;q11), leading to the formation of two fusion genes, BCR/ABL and ABL/BCR, is found in 90-95% of cases with chronic myeloid leukemia (CML). ABL-BCR expression does not correlate with prognosis, as assessed by cytogenetic response, since the ABL/BCR gene is expressed in only a proportion of CML patients. This study examined an exceptional BCR/ABL-positive CML case with inversion in 9q22q34 leading to the absence of ABL/BCR. Moreover, an unbalanced translocation between chromosomes 10 and 17 which caused deletion of the TP53 gene was identified. The TP53 gene plays a potential role in CML progression, and loss of TP53 may be regarded as a poor prognostic factor.