Pattern Of Chromosomal Aberrations Research Articles

Frequency and pattern of chromosomal abnormalities in acute myeloid leukemia from Western India: A retrospective study

Chromosomal abnormalities play an important role in diagnosis and prognosis of hematological diseases. The aim of the present study was to study the pattern and frequency of chromosomal aberrations in acute myeloid leukemia (AML) subgroups from western India. A retrospective study was conducted through evaluating laboratory proforma which were filled during 2005 to 2014 for diagnosis and treatment of AML subjects. We have studied chromosomal aberrations in 282 subjects with AML from western India. AML patients were sub-grouped according to FAB classification. Cytogenetic study using conventional cytogenetics (GTG-banding) and Fluorescence in situ hybridization (FISH) was carried out using FISH probes (AML1/ETO, PML/RARA, CBFB). Student's t test for continuous variables and Pearson's Chi-squared test for categorical variables were used to identify the relationship between variables. Cytomorphological study revealed AML- M3 as most frequent (32.3%) group followed by AML-M2 (25.2%) and AML-M4 (19.9%). Chromosomal abnormalities were identified in 145 (51.42%) of the total AML cases. A high frequency (38.6%) of chromosomal abnormalities was identified in AML-M3 subgroup as compared to AML-M2 (31%) and AML-M4 (20.6%). Cytogenetic study is important for the diagnosis and management of the AML patients. Our study identified chromosomal abnormalities in AML subgroups with varied frequencies. It is important in diagnosis and monitoring of the disease. As younger AML patients were more affected in our study, etiological factors such as environmental factors need to be studied. Combination of conventional cytogenetics and FISH has an advantage of identifying high frequency of chromosomal aberrations in AML patients.

The Pattern of Chromosome Aberrations and Molecular Markers in the Population of Hematological Patients Diagnosed at the University Clinical Center Tuzla

Introduction: Besides cardiovascular, malignant diseases are one of the leading causes of death in Bosnia and Herzegovina. At the top of this list are hematological diseases. This research aimed to identify cytogenetic and molecular biomarkers in patients treated for different types of hematological neoplasms. Methods: The retrospective study included 1600 samples of patients with different hematological diseases in the period from January 2006 to May 2022. The Polymerase Chain Reaction (RT-PCR) method was used to determine the presence of genetic rearrangements and to confirm the findings of conventional cytogenetic analysis. Results: Chromosomal aberrations were found in 739 (46,18%) patients. Using the RT-PCR technique, positive cases were increased by 1,5%. The BCR-ABL fusion gene was present in e14-a2 transcript form in 73% of samples, e13-a2 isoform in 21%, e1-a2 in 2%, while e14-a2/e1-a2 transcript coexpression was present in a percentage of 4% of the samples. The PML-RARa fusion gene was found in the form of bcr 1 transcripts in 21%, bcr2 32% and bcr3 59% of the samples. In twelve cases A type of the CBFB-MYH11 fusion transcript was detected. The MLL-AF4 fusion was found in only one case. Conclusion: The obtained percentages of frequency of individual molecular gene isoforms are in accordance with the results of most other researchers. This refers to the Balkan population and the Caucasian ethnic group.

Prognostic impact of copy number alterations and tumor mutational burden in carcinoma of unknown primary.

Chromosomal aberrations are known to drive metastatic spread, but their profile is still elusive in carcinoma of unknown primary (CUP). Therefore, the aim of this study was to characterize the chromosomal aberration pattern in CUP depending on histological and clinical features and to assess its prognostic impact together with chromothripsis, tumor mutational burden (TMB), microsatellite instability (MSI), and mutational profiles as potential prognostic biomarkers. Chromosomal aberrations and chromothripsis were detected by methylation-based copy number variation (CNV) analysis, whereas TMB and MSI were calculated based on large next-generation sequencing (NGS) panels. Putative primaries were assigned by consensus between two independent oncologists. CNV losses varied depending on putative primaries and were more abundant in patients harboring TP53 mutations and/or deletions 17p. CNV loss was prognostically adverse in localized CUP treated with surgery and/or radiotherapy, but not in disseminated poor-risk CUP treated with palliative chemotherapy. CNV loss also worsened the prognosis in squamous cell CUP. Chromothripsis was detected in 18/59 (30.5%) patients without prognostic effect. TMB was highest in cases with MSI, squamous cell histology, and with lung, anal or cervical putative primaries. Overall, CNV, chromothripsis, TMB, and MSI profiles in CUP are reminiscent of biological characteristics known from other cancer entities without a unifying CUP-specific signature. Markedly, high-level CNV loss is an adverse predictive biomarker in localized but not disseminated chemotherapy-treated CUP. This implies that chromosomal losses drive CUP progression, but also increase susceptibility to chemotherapy, with both effects apparently leveling out in disseminated CUP.

Noninvasive Prenatal Test Results Indicative of Maternal Malignancies: A Nationwide Genetic and Clinical Follow-Up Study.

Noninvasive prenatal testing (NIPT) for fetal aneuploidy screening using cell-free DNA derived from maternal plasma can incidentally raise suspicion for cancer. Diagnostic routing after malignancy suspicious-NIPT faces many challenges. Here, we detail malignancy suspicious-NIPT cases, and describe the clinical characteristics, chromosomal aberrations, and diagnostic routing of the patients with a confirmed malignancy. Clinical lessons can be learned from our experience. Patients with NIPT results indicative of a malignancy referred for tumor screening between April 2017 and April 2020 were retrospectively included from a Dutch nationwide NIPT implementation study, TRIDENT-2. NIPT profiles from patients with confirmed malignancies were reviewed, and the pattern of chromosomal aberrations related to tumor type was analyzed. We evaluated the diagnostic contribution of clinical and genetic examinations. Malignancy suspicious-NIPT results were reported in 0.03% after genome-wide NIPT, and malignancies confirmed in 16 patients (16/48, 33.3%). Multiple chromosomal aberrations were seen in 23 of 48 patients with genome-wide NIPT, and a malignancy was confirmed in 16 patients (16/23, 69.6%). After targeted NIPT, 0.005% malignancy suspicious-NIPT results were reported, in 2/3 patients a malignancy was confirmed. Different tumor types and stages were diagnosed, predominantly hematologic malignancies (12/18). NIPT data showed recurrent gains and losses in primary mediastinal B-cell lymphomas and classic Hodgkin lymphomas. Magnetic resonance imaging and computed tomography were most informative in diagnosing the malignancy. In 231,896 pregnant women, a low percentage (0.02%) of NIPT results were assessed as indicative of a maternal malignancy. However, when multiple chromosomal aberrations were found, the risk of a confirmed malignancy was considerably high. Referral for extensive oncologic examination is recommended, and may be guided by tumor-specific hallmarks in the NIPT profile.

Delayed Puberty in Girls with Primary Amenorrhea: A Report of Cases

Background:Female puberty starts when the pituitary hormone producing follicle-stimulating hormone (FSH) and luteinizing hormone (LH), which will stimulate the ovaries to produce estrogen. Delayed puberty with primary amenorrhea in female is the lack of breast development followed by the absence of menses 3 years after the initiation of breast development. Sex chromosomes have an important role in determining the sex, germ cell differentiation of foetus, and reproductive functions of an offspring, thus, sex chromosomal aberrations frequently cause primary amenorrheaCase presentation: We report two delayed puberty cases with the chief complain of primary amenorrhea. Both cases showed hypoplasia of uterus and ovaries on pelvic imaging and hormonal assay showed low of FSH. The first case was gonadal dysgenesis with 46,XX karyotype and low level of estrogen and the second case was a turner syndrome with 45,X karyotype and normal level of estrogen. Conclusion:This study reported delayed puberty with primary amenorrhea cases due to different chromosomal aberration pattern which have similar clinical features. Therefore, cytogenetic examination is needed for any primary amenorrhea cases in order to accomplish the confirmatory diagnosis and for the clinicians to make a correct intervention and treatment.

The prevalence and patterns of chromosome abnormalities in newborns with major congenital anomalies: A retrospective study from Saudi Arabia.

Congenital anomalies are a worldwide health problem that places a burden on the family and society. Chromosome abnormalities are one of the leading causes for congenital anomalies in newborns. Despite the remarkable development in cytogenetic services in the past years, still there are limited data from Middle East countries. The current study aimed to evaluate the prevalence and patterns of chromosomal aberrations in newborns admitted to the neonatal intensive care unit (NICU) with major congenital anomalies at Medina province in the western region of Saudi Arabia. Out of 2,541 live births, 150 newborns were selected based on the presence of major birth defects. Demographic and clinical data were collected from hospital medical records and statistically analyzed. The prevalence of major congenital anomalies was 10.7/1,000 live births (95% CI: 9.076- 12.583). The most common congenital anomalies in descending order were congenital heart disease, musculoskeletal and chromosome abnormalities. The birth prevalence of chromosome abnormalities was 4.22/1,000 live births (95% CI: 3.211-5.441). The most common chromosome abnormality was Down syndrome-nondisjunction type (66%). Advanced parental age was strongly associated with chromosome aberrations (p < 0.001) while consanguinity was evident in cases with normal karyotype (p < 0.001). High birth prevalence of chromosome abnormalities in newborns with congenital anomalies in Al Madinah was evident and advanced parental age is a potential risk factor. A local registry system for congenital anomalies is highly recommended to provide proper health services to high risk families.

Newly established gastrointestinal cancer cell lines retain the genomic and immunophenotypic landscape of their parental cancers

Human cancer cell lines are frequently used as model systems to study molecular mechanisms and genetic changes in cancer. However, the model is repeatedly criticized for its lack of proximity to original patient tumors. Therefore, understanding to what extent cell lines cultured under artificial conditions reflect the phenotypic and genomic profiles of their corresponding parental tumors is crucial when analyzing their biological properties. To directly compare molecular alterations between patient tumors and derived cell lines, we have established new cancer cell lines from four patients with gastrointestinal tumors. Tumor entities comprised esophageal cancer, colon cancer, rectal cancer and pancreatic cancer. Phenotype and genotype of both patient tumors and derived low-passage cell lines were characterized by immunohistochemistry (22 different antibodies), array-based comparative genomic hybridization and targeted next generation sequencing (48-gene panel). The immunophenotype was highly consistent between patient tumors and derived cell lines; the expression of most markers in cell lines was concordant with the respective parental tumor and characteristic for the respective tumor entities in general. The chromosomal aberration patterns of the parental tumors were largely maintained in the cell lines and the distribution of gains and losses was typical for the respective cancer entity, despite a few distinct differences. Cancer gene mutations (e.g., KRAS, TP53) and microsatellite status were also preserved in the respective cell line derivates. In conclusion, the four examined newly established cell lines exhibited a phenotype and genotype closely recapitulating their parental tumor. Hence, newly established cancer cell lines may be useful models for further pharmacogenomic studies.

Significance of cytogenetic-risk categories and refined international prognostic scoring system for overall survival in primary myelofibrosis: A single-center experience

Abstract Background/Aim. Primary myelofibrosis (PMF) is a chronic, malignant hematological disease characterized by a leucoerythroblastic blood picture, anisopoikilocytosis teardrop- shaped erythrocytes, different degrees of bone marrow fibrosis and hepatosplenomegaly due to extramedullary hematopoiesis. Among genetic specificities of the disease, those that stand out are chromosomal aberrations in pathological, myeloid blood cells. The aim of this study was to examine the prognostic significance of clinical, hematologic and cytogenetic parameters in PMF. Methods. A retrospective study included 144 patients with PMF. Karyotypes were analyzed using conventional cytogenetic methods. Results. The chromosome examinations were successful in 126 (88%) patients and failed in the remainder ones (12%). Karyotype was abnormal in 36/126 (29%) subjects at presentation. The most frequent changes included +9, 13q- and 20q- (28%). Other abnormalities were: aberrations of chromosome 18 and 16, deletions (9q-, 12p-, 7q-, 5q-, 6q-, 8q-), trisomies (+1q, +8, +10, +21), monosomies (-7, -11), 3q inversion and loss of Y chromosome. We detected four novel balanced translocations in PMF: t(17;22)(q11;q13), t(15;17)(q22;q25), t(9;12)(q22;q24) and t(2;4)(q21;p16), one constitutional translocation-rob(13;14)(q10;q10) and some new karyotype anomalies ? deletion of both homologues, hyperdiploidy and the coexistence of unrelated pathological clones. Conclusion. Chromosomal aberrations had a significant influence on overall survival of patients with PMF according to the refined cytogenetic-risk of the International Prognostic Scoring System (Refined CIPSS) (p = 0.004). Our patients matched the pattern of chromosome aberrations usually observed in PMF but some newly registered, balanced translocations and other rare karyotype anomalies were recorded as well.

Fumarate hydratase deficient renal cell carcinoma: Chromosomal numerical aberration analysis of 12 cases

Hereditary leiomyomatosis and renal cell carcinoma-associated renal cell carcinoma (HLRCC)/fumarate hydratase deficient renal cell carcinoma (FHRCC) is defined by molecular genetic changes (mutation/LOH in fumarate hydratase (FH) gene). We investigated chromosomal numerical aberration pattern (CNV) in FHRCC/HLRCC using array comparative genomic hybridization analysis and low pass whole genome sequencing. Genetic analysis was successfully completed in 12 tumors. Most common chromosomal aberrations detected were a complete or partial loss of chromosome 4 (5/12 cases), chromosome 15 (4/12 cases), and chromosomes 9, 13, and 14 (each in 3/12 cases), as well as a complete or partial gain of chromosome 17 (in 4/12 cases). No chromosomal losses or gains were detected in 4 cases. Copy number variation pattern in FHRCC/HLRCC appears to be highly variable and does not provide a useful diagnostic tool in identifying these cases. Immunohistochemical staining and especially molecular genetic evaluation of FH gene mutations/LOH remain the gold standard in identifying FHRCC/HLRCC.

Genomic analysis of Korean patients with advanced prostate cancer by use of a comprehensive next-generation sequencing panel and low-coverage, whole-genome sequencing

PurposeTo analyze the characteristics of somatic mutations and copy number alterations (CNAs) in Korean patients with advanced prostate cancer (PCa) by use of the Oncomine Comprehensive Panel (ThermoFisher Scientific) and low-coverage, whole-genome sequencing (LC-WGS).Materials and MethodsWe retrospectively analyzed PCa tissues obtained from 14 patients with advanced PCa (metastatic tumor, 12 [85.7%]; nonmetastatic castration-resistant PCa, 1 [7.1%]; pT3b, 1 [7.1%]) from 2009 to 2017. The Oncomine Comprehensive Panel included a total of 143 genes. Moreover, LC-WGS was performed to detect CNAs of the entire genome. Two plasma samples matched with tumor tissues were analyzed using LC-WGS to compare the chromosomal aberration patterns between circulating tumor DNA and tumor tissue.ResultsGenetic alterations were most frequently observed in the androgen receptor (AR) (42.9%, n=6/14), TP53 (14.3%, n=2/14), and PTEN (14.3%, n=2/14) genes in the Oncomine panel. AR amplification was the most common CNA (35.7%, n=5/14). As a result of LC-WGS, CNAs were confirmed in about 92.9% (n=13/14) of the samples in regions Xq12, 8q24.21, and 11q13.3 (gains) and in regions 6q16.1, 8p23.1, 10q25.1, 16q24.2, 18q12.3, Xq25, and Xq26.3 (losses). All CNAs identified in the Oncomine panel matched the results of LC-WGS. Additionally, LC-WGS of two plasma samples that matched tumor tissues revealed that CNA patterns of plasma samples (circulating tumor DNA) were very similar to those detected in tumor samples.ConclusionsOur data showed that the characteristics of mutations and CNAs in Korean patients with advanced PCa were similar to those observed in previous studies.

Circulating Cell-Free DNA-Diagnostic and Prognostic Applications in Personalized Cancer Therapy.

Genomic analyses in oncologic care allow for the development of more precise clinical laboratory tests that will be critical for personalized pharmacotherapy. Traditional biopsy-based approaches are limited by the availability of sequential tissue specimens to detect resistance. Blood-based genomic profiling ("liquid biopsy") is useful for longitudinal monitoring of tumor genomes and can complement biopsies. Tumor-associated mutations can be identified in cell-free tumor DNA (ctDNA) from patient blood samples and used for monitoring disease activity. The US Food and Drug Administration approved a liquid biopsy test for EGFR-activating mutations in patients with non-small-cell lung cancer as a companion diagnostic for therapy selection. ctDNA also allows for the identification of mutations selected by treatment such as EGFR T790M in non-small-cell lung cancer. ctDNA can also detect mutations such as KRAS G12V in colorectal cancer and BRAF V600E/V600K in melanoma. Chromosomal aberration pattern analysis by low-coverage whole genome sequencing is a new, broader approach. Genomic imbalances detected in cell-free DNA (cfDNA) can be used to compute a copy number instability (CNI) score. In clinical studies, it was demonstrated that the change in CNI score can serve as an early predictor of therapeutic response to chemotherapy/immunotherapy of many cancer types. In multivariable models, it could be shown that the CNI score was superior to clinical parameters for prediction of overall survival in patients with head and neck cancer. There is emerging evidence for the clinical validity of ctDNA testing regarding identification of candidates for targeted therapies, prediction of therapeutic response, early detection of recurrence, resistance mutation detection, measuring genetic heterogeneity, tumor burden monitoring, and risk stratification. Improvement of sensitivity to detect tumors at very early stages is difficult due to insufficient mutant DNA fraction of ≤0.01%. Further developments will include validation in prospective multicenter interventional outcome studies and the development of digital platforms to integrate diagnostic data.

Genetic causes of reproductive problems in the Bosnian women population

Background: The causes of infertility and recurrent spontaneous abortions are diverse and numerous – including non-genetic and genetic factors – whereby the importance of genetic factors in pathogenesis of infertility is becoming more and more common. Chromosomal abnormalities and genetic defects can cause reproduction failures, and for this reason genetic analysis can play an important role in reproductive problems research.Aims and Objective: This study aims to determine the type and frequency of chromosomalaberrations in the female population sample, as well as to determine if the difference between groups with and without chromosomal aberrations was statistically significant.Materials and Methods: One hundred women aged 15-46 were included in the study, allhaving different reproductive disorder diagnoses and requiring karyotype analysis in the Sarajevo Medical Faculty Genetic Center. Cytogenetic analysis was performed on the peripheral blood, which was cultured for four days, using GTG banding forchromosomalanalysis.Results: Out of 100 women included in the study, an abnormal karyotype was found in 16 of them (16%). The difference between the frequency of normal and abnormal karyotype in women with reproductive problems identified in this study was found to be statistically significant. The pattern of chromosomal aberrations was similar to that reported in the previous cytogenetic studies with similar inclusion criteria.Conclusion: This fact should be taken in the consideration in order to estimate true etiology of reproductive problems and it is a valuable information in the process of genetic counseling and decision making in assisted reproductive technology.Asian Journal of Medical Sciences Vol.9(5) 2018 12-16

Genome-Wide Analysis of Interchromosomal Interaction Probabilities Reveals Chained Translocations and Overrepresentation of Translocation Breakpoints in Genes in a Cutaneous T-Cell Lymphoma Cell Line.

In classical models of tumorigenesis, the accumulation of tumor promoting chromosomal aberrations is described as a gradual process. Next-generation sequencing-based methods have recently revealed complex patterns of chromosomal aberrations, which are beyond explanation by these classical models of karyotypic evolution of tumor genomes. Thus, the term chromothripsis has been introduced to describe a phenomenon, where temporarily and spatially confined genomic instability results in dramatic chromosomal rearrangements limited to segments of one or a few chromosomes. Simultaneously arising and misrepaired DNA double-strand breaks are also the cause of another phenomenon called chromoplexy, which is characterized by the presence of chained translocations and interlinking deletion bridges involving several chromosomes. In this study, we demonstrate the genome-wide identification of chromosomal translocations based on the analysis of translocation-associated changes in spatial proximities of chromosome territories on the example of the cutaneous T-cell lymphoma cell line Se-Ax. We have used alterations of intra- and interchromosomal interaction probabilities as detected by genome-wide chromosome conformation capture (Hi-C) to infer the presence of translocations and to fine-map their breakpoints. The outcome of this analysis was subsequently compared to datasets on DNA copy number alterations and gene expression. The presence of chained translocations within the Se-Ax genome, partly connected by intervening deletion bridges, indicates a role of chromoplexy in the etiology of this cutaneous T-cell lymphoma. Notably, translocation breakpoints were significantly overrepresented in genes, which highlight gene-associated biological processes like transcription or other gene characteristics as a possible cause of the observed complex rearrangements. Given the relevance of chromosomal aberrations for basic and translational research, genome-wide high-resolution analysis of structural chromosomal aberrations will gain increasing importance.

Monosomal karyotype in myeloid neoplasias: a literature review.

In 2008, the concept of the monosomal karyotype (MK) in adult acute myeloid leukemia (AML) patients was introduced, defined by the presence of a chromosomal aberration pattern characterized by the presence of at least two autosomal monosomies or of one monosomy plus one or more structural aberrations (not including loss of a chromosome). We present a systematic review of the literature about the influence of the MK on the outcome of patients affected by myeloid malignancies (AML, myelodysplastic syndromes, and primary myelofibrosis). For this review, a comprehensive literature search using the term “monosomal karyotype” was performed, considering articles listed in MEDLINE. This analysis of the literature confirms the negative prognostic impact on survival of the MK in myeloid neoplasias. The detrimental effect of MK on AML patients’ outcome is independent of other variables, including adverse cytogenetic features, supporting the identification of this entity as a challenging subgroup of patients with distinct biologic and clinical features.

Warthin-like papillary renal cell carcinoma: Clinicopathologic, morphologic, immunohistochemical and molecular genetic analysis of 11 cases.

Oncocytic papillary renal cell carcinoma (PRCC) is a distinct subtype of PRCC, listed as a possible new variant of PRCC in the 2016 WHO classification. It is composed of papillae aligned by large single-layered eosinophilic cells showing linearly arranged oncocytoma-like nuclei. We analyzed clinicopathologic, morphologic, immunohistochemical and molecular-genetic characteristics of 11 oncocytic PRCCs with prominent tumor lymphocytic infiltrate, morphologically resembling Warthin's tumor. The patients were predominantly males (8/11, 73%), with an average age of 59years (range 14-76), and a mean tumor size of 7cm (range 1-22cm). Tumors had the features of oncocytic PRCCs with focal pseudostratification in 8/11 cases and showed dense stromal inflammatory infiltration in all cases. Papillary growth pattern was predominant, comprising more than 60% of tumor volume. Tubular and solid components were present in 5 and 3 cases, respectively. Uniform immunohistochemical positivity was found for AMACR, PAX-8, MIA, vimentin, and OSCAR. Tumors were mostly negative for carboanhydrase 9, CD117, CK20, and TTF-1. Immunohistochemical stains for DNA mismatch repair proteins MLH1 and PMS2 were retained in all cases, while MSH2 and MSH6 were negative in 1 case. Tumor infiltrating lymphocytes (TILs) consisted of both B and T cells. Chromosomal copy number variation analysis showed great variability in 5 cases, ranging from a loss of one single chromosome to complex genome rearrangements. Only one case showed gains of chromosomes 7 and 17, among other aberrations. In 4 cases no numerical imbalance was found. Follow up data was available for 9 patients (median 47.6months, range 1-132). In 6 patients no lethal progression was noted, while 3 died of disease. In conclusion, Warthin-like PRCC is morphologically very close to oncocytic PRCC, from which it differs by the presence of dense lymphoid stroma. Chromosomal numerical aberration pattern of these tumors is variable; only one case showed gains of chromosomes 7 and 17. Warthin-like PRCC is a potentially aggressive tumor since a lethal outcome was recorded in 3/9 cases.

Homozygosity of Mutated Calreticulin in Myeloproliferative Neoplasms By an Acquired Chromosome 19p UPD Is Associated with Deletions in the Long Arm of Chromosome 5 and SF3B1 Mutations

Background: CALR is mutated in about 70% of patients with essential thrombocythemia and primary myelofibrosis lacking mutations in JAK2 and MPL. High mutational loads (≥ 60%) are seen less frequently in CALR mutated cases than in JAK2 or MPL mutated cases. Especially for JAK2 uniparental disomy (UPD) of 9p24 is commonly detected leading to homozygosity of JAK2V617F and progressive disease. Until now, in CALR mutated patients UPD has only rarely been detected and data on these cases are scant.Aim: (1) Detection of cases with CALR UPD in a cohort of MPN cases with high CALR mutation loads and/or progressive disease, (2) cytogenetic and molecular genetic characterization of these cases in comparison to CALR mutated patients without UPD.Patients and Methods: Overall 50 cases with a CALR mutation were analyzed by genomic arrays (SurePrint G3 ISCA CGH+SNP Microarray, Agilent, Waldbronn, Germany). Caseswere selected as follows: (1) mutation load ≥ 60% determined by gene scan analysis (n=26), (2) progressive disease (accelerated phase: n=7, blast crisis: n=5) according to cytomorphology and/or (3) displaying mutations in ASXL1, SRSF2, EZH2 and/or IDH1/2 as markers for progression (n=12). Additionally, amplicon next-generation sequencing was performed to detect mutations in ASXL1, CBL, DNMT3A, EZH2, IDH1/2, KRAS, NRAS, RUNX1, SF3B1, SRSF2, TET2, TP53 and U2AF1. Variants of unknown significance were excluded from statistical analysis.Results: 11/50 cases (22%) with UPD were identified by array CGH. While the type 1 (c.1099_1150del52) CALR mutation was the most frequent mutation in cases without UPD (25/39, 64%), type 1 mutation was rare in CALR UPD cases (1/11, 9%; p=0.009). Thus, in cases with UPD, mainly the type 2 (c.1154_1155insTTGTC) mutation (5/11, 45%) and rare mutation types were detected (5/11, 45%). Of note, the only case with CALR UPD showing the type 1 mutation was found to harbor a TET2 mutation and UPD encompassing 4q23q28, which includes the TET2 gene. As the CALR mutation load was clearly lower compared to the TET2 mutation load (50% vs. 100%), the CALR mutation might only belong to a subclone in this case.Cases with CALR UPD showed a higher mutation load than cases without UPD (mean: 77% vs. 48%, p<0.001) and presented more frequently with MPN in acceleration (5/11, 46% vs. 6/39, 15%, p=0.048). Almost all of the patients (4/5, 80%) in accelerated phase with UPD showed a mutation load ≥60%.The remaining case was the patient with concomitant TET2 and CALR UPD.Regarding chromosomal aberrations, del(13q) (12/50, 24%), del(5q) (9/50, 18%), del(20q) (6/50, 12%) and gain of 1q (5/50, 10%), have been detected as recurrent abnormalities by array CGH analyses in the total cohort. Del(5q) showed a trend to be more frequent in cases with UPD (4/11, 36% vs. 5/39, 13%; p=0.093). Corresponding to the advanced disease state of the selected cohort, mutation analyses revealed a high frequency of ASXL1 mutations (44%), followed by mutations in TET2 (19%), EZH2 (13%), TP53 (13%), U2AF1 (9%), NRAS (9%) and SF3B1 (7%). Interestingly, SF3B1 mutations were exclusively detected in cases with CALR UPD (3/11, 27% vs. 0/34, 0%; p=0.012), whereas ASXL1 mutations tended to be more frequent in cases without UPD (19/37, 51% vs. 2/11, 18%, p=0.083). TP53 mutations were also detected more often in the subgroup of cases with CALR UPD, although this was not statistically significant (3/11, 27% vs. 3/35, 9%). Additionally, TP53 mutations showed a significant correlation to del(5q) (TP53 mutation in cases with del(5q): 5/9, 56% vs. TP53 mutation in cases without del(5q): 1/37, 3%, p=0.001). Comparison of the CALR mutation loads with mutation loads of accompanying mutations revealed that in most cases, the CALR mutation is found in the main clone.Conclusions: In cases with high CALR mutation loads and/or progressive disease UPD of 19p13 is rather common (22%). These cases show a distinct pattern of chromosomal aberrations and additional molecular mutations, as they are associated with del(5q) and mutations in SF3B1 and TP53, whereas ASXL1 mutations are less frequent. Due to the limited number of cases, these results have to be verified in future analyses. DisclosuresStengel:MLL Munich Leukemia Laboratory: Employment. Meggendorfer:MLL Munich Leukemia Laboratory: Employment. Kern:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Jeromin:MLL Munich Leukemia Laboratory: Employment.

Cystic and necrotic papillary renal cell carcinoma: prognosis, morphology, immunohistochemical, and molecular-genetic profile of 10 cases.

Conflicting data have been published on the prognostic significance of tumor necrosis in papillary renal cell carcinoma (PRCC). Although the presence of necrosis is generally considered an adverse prognostic feature in PRCC, we report a cohort of 10 morphologically distinct cystic and extensively necrotic PRCC with favorable biological behavior. Ten cases of type 1 PRCC with a uniform morphologic pattern were selected from the 19 500 renal tumors, of which 1311 were PRCCs in our registry. We focused on precise morphologic diagnosis supported by immunohistochemical and molecular-genetic analysis. Patients included 8 men and 2 women with an age range of 32-85 years (mean, 62.6 years). Tumor size ranged from 6 to 14 cm (mean, 9.4 cm). Follow-up data were available in 7 patients, ranging from 0.5 to 14 years (mean, 4 years). All tumors were spherical, cystic, and circumscribed by a thick fibrous capsule, filled with hemorrhagic/necrotic contents. Limited viable neoplastic tissue was present only as a thin rim in the inner surface of the cyst wall, consistent with type 1 PRCC. All cases were positive for AMACR, OSCAR, CAM 5.2, HIF-2, and vimentin. Chromosome 7 and 17 polysomy was found in 5 of 9 analyzable cases, 2 cases demonstrated chromosome 7 and 17 disomy, and 1 case showed only chromosome 17 polysomy. Loss of chromosome Y was found in 5 cases, including 1 case with disomic chromosomes 7 and 17. No VHL gene abnormalities were found. Papillary renal cell carcinoma type 1 can present as a large hemorrhagic/necrotic unicystic lesion with a thick fibroleiomyomatous capsule. Most cases showed a chromosomal numerical aberration pattern characteristic of PRCC. All tumors followed a nonaggressive clinical course. Large liquefactive necrosis should not necessarily be considered an adverse prognostic feature, particularly in a subset of type 1 PRCC with unilocular cysts filled with necrotic/hemorrhagic material.

Morphological, immunohistochemical, and chromosomal analysis of multicystic chromophobe renal cell carcinoma, an architecturally unusual challenging variant.

Chromophobe renal cell carcinoma (ChRCC) is typically composed of large leaf-like cells and smaller eosinophilic cells arranged in a solid-alveolar pattern. Eosinophilic, adenomatoid/pigmented, or neuroendocrine variants have also been described. We collected 10 cases of ChRCC with a distinct multicystic pattern out of 733 ChRCCs from our registry, and subsequently analyzed these by morphology, immunohistochemistry, and array comparative genomic hybridization. Of the 10 patients, 6 were males with an age range of 50-89years (mean 68, median 69). Tumor size ranged between 1.2 and 20cm (mean 5.32, median 3). Clinical follow-up was available for seven patients, ranging 1-19years (mean 7.2, median 2.5). No aggressive behavior was documented. We observed two growth patterns, which were similar in all tumors: (1) variable-sized cysts, resembling multilocular cystic neoplasm of low malignant potential and (2) compressed cystic and tubular pattern with slit-like spaces. Raisinoid nuclei were consistently present while necrosis was absent in all cases. Half of the cases showed eosinophilic/oncocytic cytology, deposits of pigment (lipochrome) and microcalcifications. The other half was composed of pale or mixed cell populations. Immunostains for epithelial membrane antigen (EMA), CK7, OSCAR, CD117, parvalbumin, MIA, and Pax 8 were positive in all tumors while negative for vimentin, TFE3, CANH 9, HMB45, cathepsin K, and AMACR. Ki67 immunostain was positive in up to 1% of neoplastic cells. Molecular genetic examination revealed multiple chromosomal losses in two fifths analyzable tumors, while three cases showed no chromosomal numerical aberrations. ChRCC are rarely arranged in a prominent multicystic pattern, which is probably an extreme form of the microcystic adenomatoid pigmented variant of ChRCC. The spectrum of tumors entering the differential diagnosis of ChRCC is quite different from that of conventional ChRCC. The immunophenotype of ChRCC is identical with that of conventional ChRCC. Chromosomal numerical aberration pattern was variable; no chromosomal numerical aberrations were found in three cases. All the cases in this series have shown an indolent and non-aggressive behavior.

Fluorescent in situ hybridization (FISH) on the veterinary diagnostic field

Proceeding deals with of genomic changes detectable by FISH . The DSD syndrom in Yorkshire terrier 78,XY t (Y-;6p+) was observed by the use of X and Y FISH WCP probes. Following results indicated numerous genomic changes in cancers. Using comparative genomic hybridization numerous chromosomal rearrangements were detected, which indicated the heterogeneity in tumour growth. In Bernese Mountain Dog bitch,8 loses on chromosomes and gains on 18 different of chromosomes were detected. The last study was focused on chromosomal position and nucleotide sequencing of the LCA5L exons. Those were analysed in cattle of BTA1q44, sheep OAR1q43 and of CHI1q44 in the goats. Keywords: fluorescent in situ hybridization, FISH, veterinary diagnostics References ALARM, M. R. et al. (2007) Male pseudohermafroditism in dogs: three case reports. Veterinarni Medicina 52 pp.74- 78. Hallermann, C . et al. (2004) Chromosomal Aberration Patterns Differ in Subtypes of Primary Cutaneous B Cell Lymphomas. J. Invest. Dermatol. 122 pp. 1495–1502. D’Haese, J . G. et al .(2005) Chromosomal aberrations in follicular non-Hodgkin lymphomas of Japanese patients, detected with comparative genomic hybridization and polymerase chain reaction analysis. Cancer Genet. Cytogenet. 162 pp. 107–114. Di MEO, G.P. et al. ( 2006) Mapping of 11 genes by FISH to BTA2, BBU2q, OAR2q and CHI2, and comparison with HSA2q. Anim. Genet. 2006; 37 pp. 299-300. NAFSTRoM K . et al .(2007). Effective treatment for the canine RPE65null mutation, a hereditary retinal dystrophy comparable to human Leber’s congenital amaurosis. In: Retinal degenerations: biology, diagnostics, and therapeutics. 1st edn. Humana Press Inc., Totowa, New Jersey, pp. 415-431. Schibler L . et al. (2009) Molecular cytogenetics and comparative mapping in goats (Capra hircus, 2n=60). Cytogenet. Genome Res .126 pp 77-85. Streubel, B . et al. (2003) T(14;18)(q32;q21) involving IGH andMALT1 is a frequent chromosomal aberration in MALT lymphoma. Blood 101 pp . 2335–2339 .

Genes encoding members of the JAK-STAT pathway or epigenetic regulators are recurrently mutated in T-cell prolymphocytic leukaemia.

T-cell prolymphocytic leukaemia (T-PLL) is an aggressive leukaemia. The primary genetic alteration in T-PLL are the inv(14)(q11q32)/t(14;14)(q11;q32) leading to TRD/TRA-TCL1A fusion, or the t(X;14)(q28;q11) associated with TRD/TRA-MTCP1 fusion. However, additional cooperating abnormalities are necessary for emergence of the full neoplastic phenotype. Though the pattern of secondary chromosomal aberrations is remarkably conserved, targets of the changes are largely unknown. We analysed a cohort of 43 well-characterized T-PLL for hotspot mutations in the genes JAK3, STAT5B and RHOA. Additionally, we selected a subset of 23 T-PLL cases for mutational screening of 54 genes known to be recurrently mutated in T-cell and other haematological neoplasms. Activating mutations in the investigated regions of the JAK3 and STAT5B genes were detected in 30% (13/43) and 21% (8/39) of the cases, respectively, and were mutually exclusive. Further, we identified mutations in the genes encoding the epigenetic regulators EZH2 in 13% (3/23), TET2 in 17% (4/23) and BCOR in 9% (2/23) of the cases. We confirmed that the JAK-STAT pathway is a major mutational target, and identified epigenetic regulators recurrently mutated in T-PLL. These findings complement the mutational spectrum of secondary aberrations in T-PLL and underscore the potential therapeutical relevance of epigenetic regulators in T-PLL.