Locus-specific Probes Research Articles

Molecular Cytogenetic Characterization of Rare but Repeatedly Observed Inversions in German Population

Introduction: The term inversion refers to an aberration caused by two breakage and fusion events found in one or both arms of a chromosome. The presence of such aberrations can but must not be associated with infertility or unbalanced products of conception. Normally, inversions are not associated with phenotypic alterations for the carrier. Despite the fact that most such inversions are de novo and unique, recurrent breakpoints have also been reported. Methods: Here two recurrent paracentric inversions in the long arm of chromosomes 11 and 12 and a pericentric one in chromosome 10 were studied in at least 10 unrelated (infertile) patients, each. Breakpoints were narrowed down by fluorescence in situ hybridization applying locus-specific bacterial artificial chromosome-derived probes. Results: Molecular cytogenetically identical breakpoints could be characterized for all three studied inversions. Pericentric inversion inv(10)(p11.21q21.2), previously reported to be of single origin and distributed mainly in Northern Europe, could be found to be present all over Germany, too. In the studied cases with paracentric inversion inv(11)(q21q23.3), recurrent breakpoints were found in all parts of Germany, as well; however, additional 2 cases with slightly different breakpoints were characterized besides. Most interestingly, inversion inv(12)(q14.1∼14.2q24.11∼24.13) had always the same recurrent breakpoints and presented an exclusive occurrence in North-Western part of Germany. Conclusion: Overall, (at least) three different cytogenetically detectable recurrent inversions were characterized here. This highlights that such events may be more frequent in human population than yet suggested. Accordingly, such events might even spread in (middle European) human population. Specific impact on reproduction and fitness of inversion carriers characterized here seems to be negligible. Nonetheless, such recurrent rearrangements need more attention as they may provide valuable information for genetic counseling in future.

Technical comparison of Abbott’s UroVysion® and Biocare’s CytoFISH urine fluorescence in situ hybridization (FISH) assays

BackgroundThis study aims to compare the technical performance of Abbott’s UroVysion and Biocare’s CytoFISH urine cytology probe panel and position the CytoFISH probe panel as an alternative to UroVysion. The CytoFISH probe panel was developed based on clinically sensitive chromosomes found to be amplified in bladder cancers, as well as a locus-specific probe also seen to be amplified in bladder tumors. After extensive testing comparing CytoFISH to UroVysion, we present here our findings for the two assays.Materials and methodsA total of 216 cases representing a mix of male (ages 36–99) and female (ages 46–91) patients were assayed with both probe sets. The CytoFISH and UroVysion probe panels were tested in accordance with the UroVysion procedure, as outlined in the manufacturer’s supplied package insert with the following exception: the probe volume used was 3µL for UroVysion and 5µL for CytoFISH.ResultsThe scoring used for the CytoFISH and UroVysion assays revealed a 95% concordance, suggesting that Biocare’s CytoFISH Test has at least the same clinical sensitivity and specificity as claimed by the Abbott UroVysion Kit. We found that the CytoFISH 5p15.2 locus-specific probe was easier to score than UroVysion’s 9p21 deletion.ConclusionThe high rate of concordance between the two assays suggests that Biocare’s CytoFISH assay is a robust alternative to Abbott’s UroVysion in the diagnosis and monitoring of bladder carcinoma.

Neoplastic Monocyte-Derived Fibrocytes Induce Bone Marrow Fibrosis in Patients with Primary Myelofibrosis

Progressive bone marrow (BM) fibrosis is a defining feature of primary myelofibrosis (PMF). The extent of BM fibrosis has been closely associated with the clinical manifestations of advanced disease, including anemia and thrombocytopenia, rendering it an important prognostic indicator. Mesenchymal stromal cells (MSCs) have long been regarded as the exclusive inducer of BM fibrosis. However, using xenograft and transgenic animal models, we and other investigators demonstrated that neoplastic monocyte-derived fibrocytes independently contribute to the induction of BM fibrosis in PMF. Notably, our data revealed that PMF fibrocytes but not MSCs, carry pro-fibrotic signaling pathways that are absent in healthy individuals' fibrocytes or MSCs. Despite these findings, the precise contribution of BM fibrocytes and MSCs to the induction of BM fibrosis in patients with PMF remains elusive. To determine which of two subsets of collagen-producing cells are the main contributors to the induction of BM fibrosis in PMF, we analyzed BM biopsies of patients with PMF and assessed whether their distribution spatially correlated with areas of fibrosis. We analyzed formalin-fixed paraffin-embedded BM trephine biopsies obtained from previously untreated patients with PMF (n = 85) and age-matched healthy donors (n = 6). Using a 7-plexed fluorescence immunohistochemistry (IHC) in conjunction with hematoxylin/eosin, Masson's trichrome, and Gomorri's silver stains we analyzed those BM biopsy specimens. To ensure comprehensive assessment, we imaged serial whole-tissue sections from each patient at 400x resolution, meticulously aligning and carefully correcting for bone trabeculae and any artifacts. To quantitate the spatial distribution of individual cells, collagen fibers, and reticulin fibers, we developed a set of analytical algorithms based on a U-Net neural network in Visiopharm software. Our analysis revealed a 6-fold higher density of fibrocytes, defined as CD45 +/CD68 +/procollagen type I + cells, in the BM of patients with PMF ( P=0.0003) compared to normal controls. By contrast, the number of MSCs, defined as CD45 -/CD90 +/CD105 + cells, in the PMF BM was not different from the number of MSCs in normal BM. After dividing the area of each BM biopsy into a 100 μm regular hexagonal grid, the observed spatial distribution of fibrocytes strongly and positively correlated with the areas covered by reticulin and collagen fibers ( P<0.0001 in both). Furthermore, spatial analysis showed that increased densities of fibrocytes were associated with an increased number of fibrotic cellular zones in the BM tissue of PMF patients. To investigate the clonality of PMF BM fibrocytes, we conducted DNA in situ hybridization (ISH) analysis, employing two sets of locus-specific probe pairs. The DNA-ISH analysis provided valuable insights, revealing that fibrocytes obtained from PMF patients with trisomy 9 or 20q deletion carried the same corresponding cytogenetic abnormalities, indicating that PMF fibrocytes indeed originate from the neoplastic PMF clone. Because increased peripheral blood monocyte counts, commonly detected in patients with PMF, are associated with a poor prognosis, we sought to determine the potential correlation between BM fibrocyte and circulating monocyte counts. As expected, we found a significant positive correlation between BM fibrocyte counts and the percentage of circulating monocytes ( P=0.001). Moreover, we also found that fibrocyte numbers correlated with the levels of the plasma cytokines pentraxin 3, known to induce the differentiation of monocytes into fibrocytes, and matrix metalloproteinase 2, as assessed by using magnetic immunoassay, suggesting that neoplastic fibrocytes induce BM fibrosis in PMF and that fibrocyte quantification could serve as a valuable indicator of disease severity and prognosis. Taken together, our quantitative imaging analysis of BM biopsy tissue from treatment naïve PMF patients revealed that neoplastic fibrocytes, rather than MSCs, are the main contributors to the induction of BM fibrosis in PMF. Our findings underscore the importance of BM fibrocytes in the pathogenesis of PMF and warrant further investigation to identify novel therapeutic agents that will either inhibit fibrocyte differentiation or block their pro-fibrotic function.

Abstract 4351: Multiplex detection of G12/G13 KRAS mutations with an electrochemiluminescent hybridization assay

Abstract Purpose: Oncogenic Kirsten rat sarcoma virus (KRAS) mutations are the most prevalent cancer mutations in all human tumors. Also, genotyping the KRAS gene has become increasingly important with the emergence of new evidence highlighting differences in downstream signaling pathways, tumor microenvironment composition, treatment responses and prognoses linked to specific single nucleotide polymorphisms (SNPs) in the G12 or G13 codons. FDA approval of G12C-specific anti-KRAS drugs highlights the importance of the development of reliable SNP assays to interrogate the mutation status in a tumor sample. Currently available genotyping assays are based on NGS, PCR, or ddPCR. These methods can be time-consuming, costly, suffer from amplification bias, or require follow-up testing or bioinformatics skills to analyze. Building on Meso Scale Discovery’s (MSD) existing technology, we aimed to develop a method for the identification of eight KRAS SNPs located on the G12-G13 codons in a single reaction. Methods: Ten-spot, 96-well N-PLEX plates were used for the study. SNP-specific upstream probes carrying unique 5′ leader sequences complementary to spot-specific captures on the N-PLEX plates were designed for eight KRAS genotypes (WT, G12R, G12C, G12S, G12A, G12D, G12V, G13D). Locus-specific downstream probes were 5’ phosphorylated for ligation and 3’ biotinylated for detection. Synthetic DNA targets were used as assay calibrators, and commercially available FFPE reference samples were tested for validation. DNA (10 ng) was PCR amplified with primers flanking the KRAS mutation sites. A multiplexed mixture of upstream and downstream probes was hybridized to the amplicons, and 30 cycles of ligation was performed using DNA ligase in a thermal cycler. Samples were subsequently hybridized to spot-specific capture oligonucleotides on the surface of the assay plates and detected with SULFO-TAG labeled streptavidin. Electrochemiluminescence readout was collected on an MSD imager. Results: Optimization of probe concentrations and ligation temperature was performed to maximize signal-to-background ratios and assay specificity. Spike recovery experiments using artificial target DNA showed successful identification of KRAS mutant genotypes at spike levels as low as 0.1% over wild-type background. Validation experiments with gDNA extracted from FFPE reference samples confirmed that the multiplex SNP assay can accurately differentiate eight KRAS genotypes in samples with >0.4% tumor burden. Conclusion: These data highlight a novel approach to simultaneously identify eight KRAS genotypes from 10 ng of DNA input in a single reaction within 4-5 hours. The assay is capable of identifying double mutants and can provide a semiquantitative assessment of tumor burden without the need for follow-up testing. Citation Format: Annamaria Szabolcs, Timothy J. Break, Isaac H. Shin, Seth B. Harkins, Jacob N. Wohlstadter. Multiplex detection of G12/G13 KRAS mutations with an electrochemiluminescent hybridization assay. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4351.

Alveolar rhabdomyosarcoma: novel surrogate markers associated with oncogenic translocation

Anomalies of the FOXO1 gene in alveolar rhabdomyosarcoma are associated with a worse clinical prognosis, which determines the high value of studying the status of this gene when choosing a therapy strategy. The «gold standard» for determining FOXO1 gene rearrangements is currently the fluorescent in situ hybridization (FISH) technique. Study of the relationship between canonical FOXO1 translocation and immunohistochemical expression of new surrogate markers in alveolar rhabdomyosarcoma to determine their predictive value. 139 cases of rhabdomyosarcoma were retrospectively studied. The study used tissue matrix technology (TMA). On sections obtained from TMA blocks, the FISH technique was implemented using the locus-specific probe MetaSystems XL FOXO1 Break Apart (Metasystems, Germany). Immunohistochemical studies were performed on similar sections from TMA blocks with OLIG2 (Cell Marque Antibodies, clone 211F1.1) and MUC4 (Cell Marque Antibodies, clone 8G7) antibodies. The final expression analysis and statistical processing using a 2x2 contingency table and Fisher's exact test passed 111 cases (76 without FOXO1 rearrangement and 35 with rearrangement). The specificity of OLIG2 and MUC4 expression for FOXO1-rearranged alveolar rhabdomyosarcoma was 85.53% and 80.26%, respectively (p<0.01). The present study confirms the high predictive value of the expression of surrogate markers OLIG2 and MUC4 in determining the genetic status of alveolar rhabdomyosarcoma, which makes it possible to predict with high specificity the detection of the FOXO1 gene rearrangement.

Цитогенетическая диагностика хронических лимфопролиферативных заболеваний с применением локусспецифичных флуоресцентных зондов

Цитогенетическое исследование клеток костного мозга или периферической крови у лиц с лимфопролиферативными заболеваниями является обязательным и необходимым. Результаты помогают врачу с ранней диагностикой заболевания и выбором тактики лечения. Современные молекулярно-цитогенетические подходы, основанные на применении локусспецифичных флуоресцентных зондов (метод FISH), дают возможность быстро получить точную информацию о наличии или отсутствии наиболее распространенных мутаций при определенных нозологиях. Целью настоящей работы является анализ собственных данных цитогенетического обследования c применением «коктейля» из 5 локусспецифичных флуоресцентных зондов лиц с лимфопролиферативными заболеваниями, большая часть которых имела диагноз хронический лимфолейкоз. Цитогенетическое исследование было проведено 16 пациентам в период с 2014 г. по 2022 г. в лаборатории радиационной генетики ФГБУН УНПЦ РМ. Использовали коктейль локусспецифичных зондов: ATM (11q22)/TP53 (17p13), DLEU (13q14)/LAMP (13q34) и cen 12 (12p11.1;12q11.1). 75% обследованных лиц были носителями мутаций. Наиболее часто встречались мутации del17p13 (50%), del13q14 (50%). Считаем, что при наличии у пациента мутации в 13q14 необходимо провести дополнительно исследование на del 13q14.2 (RB1). The cytogenetic assay of bone marrow or peripheral blood cells in persons with lymphoproliferative diseases is mandatory and necessary. The results help a doctor with the diagnosis of the disease and the choice of treatment tactics as early as possible after the patient’s visit to the hematologist. Modern molecular cytogenetic approaches based on the use of locus-specific fluorescent probes (FISH method) make it possible to quickly and accurately obtain information about the presence or absence of the most common mutations. The aim of this work is to analyze our cytogenetic data given with a “cocktail” of 5 locus-specific fluorescent probes in individuals with lymphoproliferative diseases, most of whom were diagnosed with CLL. A cytogenetic study was conducted in 16 patients in the period 2014 - 2022 in the Laboratory of Radiation Genetics of the URCRM. A cocktail of locus-specific probes was used: ATM (11q22)/TP53 (17p13) and DLEU (13q14)/LAMP (13q34) and cen 12 (12p11.1;12q11.1). Seventy five percent of the examined individuals were carriers of mutations. The most common mutations were del17p13 (50%), del13q14 (50%). We believe that if a patient has a mutation in 13q14, it is necessary to conduct an additional study on del13q14.2 (RB1).

First Comprehensive Characterization of Phayre's Leaf-Monkey (Trachypithecus phayrei) Karyotype.

The chromosomal homologies of human (Homo sapiens—HSA) and Trachypithecus phayrei (TPH—Phayre’s leaf-monkey, family Cercopithecidae) have previously been studied by using classical chromosome staining/banding and fluorescence in situ hybridization (FISH) from the 1970s to 1990s. In this study, we carried out molecular cytogenetics applying human multicolor banding (MCB), locus-specific, and human heterochromatin-specific probes to establish the first detailed chromosomal map of TPH, which was not available until now. Accordingly, it was possible to precisely determine evolutionary-conserved breakpoints (ECBs) and the orientation of evolutionary-conserved segments compared to HSA. It could be shown that five chromosomes remained completely unchanged between these two species, and 16 chromosomes underwent only intrachromosomal changes. In addition, 50 ECBs that failed to be resolved in previous reports were exactly identified and characterized in this study. It could also be shown that 43.5% of TPH centromere positions were conserved and 56.5% were altered compared to HSA. Interestingly, 82% ECBs in TPH corresponded to human fragile sites. Overall, this study is an essential contribution to future studies and reviews on chromosomal evolution in Cercopithecidae.

Prenatal Diagnosis of Small Supernumerary Marker Chromosome 10 by Array-Based Comparative Genomic Hybridization and Microdissected Chromosome Sequencing.

Interpreting the clinical significance of small supernumerary marker chromosomes (sSMCs) in prenatal diagnosis is still an urgent problem in genetic counselling regarding the fate of a pregnancy. We present a case of prenatal diagnosis of mosaic sSMC(10) in a foetus with a normal phenotype. Comprehensive cytogenomic analyses by array-based comparative genomic hybridization (aCGH), sSMC microdissection with next-generation sequencing (NGS) of microdissected library, fluorescence in situ hybridization (FISH) with locus-specific and telomere-specific DNA probes and quantitative real-time PCR revealed that sSMC(10) had a ring structure and was derived from the pericentromeric region of chromosome 10 with involvement of the 10p11.21-p11.1 and 10q11.21-q11.23 at 1.243 Mb and 7.173 Mb in size, respectively. We observed a difference in the length of sSMC(10) between NGS data of the DNA library derived from a single copy of sSMC(10), and aCGH results that may indicate instability and structural mosaicism for ring chromosomes in foetal cells. The presence of a 9 Mb euchromatin region in the analysed sSMC(10) did not lead to clinical manifestations, and a healthy girl was born at term. We suggest that the ring structure of sSMCs could influence sSMC manifestations and should be taken into account in genetic counselling during prenatal diagnosis.

Association between Angiopoietin-2 Gene Polymorphisms and Susceptibility to Coronary Artery Disease.

Angiopoietin-2 (Angpt2) is associated with the progression of coronary artery disease (CAD). This research aimed to investigate the possible association between single nucleotide polymorphisms (SNPs) of ANGPT2 and CAD. This research was performed in a hospital from the eastern region of China. From February 2019 to June 2019, 222 patients with CAD were newly diagnosed and 403 healthy controls were confirmed by physical examinations. The distribution frequency of five SNPs of the ANGPT2 (rs11137037, rs2442598, rs12674822, rs1823375, and rs734701) in all participants was analyzed by real-time polymerase chain reaction (PCR) with SNP locus-specific probes. Our data showed that the participants with the TT genotype of rs2442598 were at reduced risk of CAD compared with wild-types (adjusted odds ratio [AOR] = 0.511, 95% CI: 0.283-0.923). The participants with the AC and AC+CC genotypes of rs11137037 were at greater risk of CAD compared to wild-types (AOR = 1.754, 95% CI: 1.140-2.699; AOR = 1.731, 95% CI: 1.165-2.573, respectively). In addition, carriers of the GG+TT genotypes of rs12674822, showed more significant high-density lipoprotein than those of GG genotype, in addition, carriers of the GG+TT genotypes of rs12674822, showed more significant high-density lipoprotein than those of GG genotype (P=0.037). These findings, as well as analysis of the haplotype, clearly indicate that ANGPT2 SNPs were highly correlated with susceptibility to CAD among the Han Chinese population.

Differential Cytogenetic Pattern of Splenic Marginal Zone B-Cell Lymphoma CD5 Positive Versus CD5 Negative. Preliminary Results.

Background. Splenic marginal zone B-cell lymphoma (SMZBCL) is a low-grade B-cell lymphoma, characterized by splenomegaly with or without circulating villous lymphocytes in peripheral blood. The SMZBCL immunophenotype is B-cell antigen positive. A minority of cases (<20%) express CD5 antigen which is related with an aggressive clinical course. There is not a specific cytogenetic aberration, although the most frequently recurrent abnormalities are trisomy 3, deletion at 7q22–7q35 and involvement of chromosomes 1 and 8; P53 is rarely implicated. Some controversial cases CD5 positive with t(11;14)(q13;q32) have been reported. The objective of this study is to identificate the cytogenetic pattern in cases CD5 positive and negative.Patients and methods.We studied 40 patients with SMZBCL, 31 CD5 negative and 9 CD5 positive. The diagnosis of SMZBCL was ascertained in all cases after studying morphologically and immunologically peripheral blood and splenectomy specimens. We performed conventional cytogenetics and FISH. Chromosome analysis was carried out from peripheral blood, lymph nodes or from the spleen with TPA mitogen and incubated for 72 hours at 37°C. FISH was made using centromeric probes (chromosomes 3 and 12) and locus specific probes (7q31 and 17p13). Statistic analysis to differentiate the cytogenetic pattern by the CD5 expression was made by the Fisher test.Results.We identified a cytogenetic alteration in 28 of 40 (70%) cases. No patient showed a translocation t(11;14)(q13;q32). In the CD5 negative group of patients, 10/31 (32.3%) presented a normal karyotype, 6/31 (19.4%) trisomy 3, 10/31 (32.3%) deletion 7q and 5/31 (16.1%) other abnormalities. No patient presented deletion 17p13 (P53). In the CD5 positive group of patients, 2/9 (22.2%) presented a normal karyotype, 3/9 (33.3%) trisomy 3, 2/9 (22.2%) deletion 17p13 (P53) and 2/9 (22.2%) other alterations. In no patient deletion 7q was found. Statistic analysis revealed significative differences between the two groups of patients (p=0.028).Conclusions. In our series there is a different cytogenetic pattern between CD5 positive and CD5 negative SMZBCL patients: 1.Deletion 7q is frequently described in CD5 negative SMZBCL while deletion 17p13 is not identified in this group of patients. 2.Deletion 17p13 is detected in CD5 positive SMZBCL patients. 3.The aggressive course of the CD5 positive SMZBCL referred in the literature could be explained by the finding of the alteration of P53. Further cases have to be described in order to validate these preliminary findings.

UroVysion fluorescence in situ hybridization in urothelial carcinoma: a narrative review and future perspectives.

The number of patients with urothelial carcinoma (UC) is high, with a corresponding demand for detecting UC easily and non-invasively. Cystoscopy and urine cytology, with widely known diagnostic accuracies, are the gold standards for identifying UC originating from the bladder. However, cystoscopy or other tests, such as ureteroscopy or retrograde pyelography, are uncomfortable for patients. Tests for urinary biomarkers are expected to satisfy the demand for less invasive tests that will benefit patients with anxiety for invasive tests such as cystoscopy or ureteroscopy. Although several urinary biomarkers have been reported to support the diagnosis or follow-up of UC, their use in the clinic is uncommon. The UroVysion test examines urinary biomarkers using a multitarget, multicolor fluorescence in situ hybridization (FISH) assay. The test uses exfoliated cells found in urine and is a mixture of centromeric fluorescent denatured chromosome enumeration probes for chromosomes 3, 7, and 17 (labelled stratum red, spectrum green and spectrum aqua, respectively), and a locus-specific identifier probe for 9p21 (spectrum gold). It is used for the initial diagnosis of patients with hematuria or the monitoring of patients previously diagnosed with bladder cancer. Almost 20 years have passed since UroVysion was approved by the U.S. Food and Drug Administration, and so this is a well-established test. However, room exists for further research, with numerous reports on this test having been recently published. In order to update our knowledge, we herein present a brief overview of UroVysion and its features that follows the latest findings as they relate to UC.

Clinical Cytogenetics of the Dog: A Review.

Simple SummaryThe cytogenetic analysis of dogs is mainly focused on the diagnosis of disorders of sex development (DSD) and cancers. Unfortunately, the study of canine chromosomes is a challenging task due a high chromosome number (2n = 78) and the one-arm morphology of all autosomes. For years, the application of conventional cytogenetic techniques, Giemsa staining and G and DAPI (4′,6-diamidino-2-phenylindole) bandings, allowed the identification of sex chromosome aneuploidies and centric fusions. An advanced clinical cytogenetic diagnosis is also needed due to the fact that the dog is a valuable animal model in biomedical research. The application of hybridization methods, such as fluorescence in situ hybridization (FISH) and array comparative genome hybridization (aCGH), facilitated the detection of other chromosomal rearrangements. It can be foreseen that a wide use of modern molecular techniques (e.g., SNP microarray and next generation sequencing) will substantially extend the knowledge on canine chromosome mutations.The dog is an important companion animal and has been recognized as a model in biomedical research. Its karyotype is characterized by a high chromosome number (2n = 78) and by the presence of one-arm autosomes, which are mostly small in size. This makes the dog a difficult subject for cytogenetic studies. However, there are some chromosome abnormalities that can be easily identified, such as sex chromosome aneuploidies, XX/XY leukocyte chimerism, and centric fusions (Robertsonian translocations). Fluorescence in situ hybridization (FISH) with the use of whole-chromosome painting or locus-specific probes has improved our ability to identify and characterize chromosomal abnormalities, including reciprocal translocations. The evaluation of sex chromosome complement is an important diagnostic step in dogs with disorders of sex development (DSD). In such cases, FISH can detect the copy number variants (CNVs) associated with the DSD phenotype. Since cancers are frequently diagnosed in dogs, cytogenetic evaluation of tumors has also been undertaken and specific chromosome mutations for some cancers have been reported. However, the study of meiotic, gamete, and embryo chromosomes is not very advanced. Knowledge of canine genome organization and new molecular tools, such as aCGH (array comparative genome hybridization), SNP (single nucleotide polymorphism) microarray, and ddPCR (droplet digital PCR) allow the identification of chromosomal rearrangements. It is anticipated that the comprehensive use of chromosome banding, FISH, and molecular techniques will substantially improve the diagnosis of chromosome abnormalities in dogs.

21. A case of acute myeloid leukemia with gain of two copies of neocentromeric chromosome 11

Neocentromeres are ectopic centromeres that arise on a chromosome at a location that is normally not centromeric [1]. Since the discovery of the first human neocentromere in 1993, more than 90 cases of constitutional supernumerary marker chromosomes containing neocentromeres have been documented. However, neocentromere formation has only been observed in three tumor categories including lipomatous tumors, lung carcinoma and acute myeloid leukemia (AML) [2]. In AML, neocentromeric chromosomes have been described in three cases: a derivative r(8) [3], inv dup(10q) [4] and neo(1)[5]. Here we report a neocentromeric chromosome 11 in a 76 year-old female with AML. Chromosome analysis of unstimulated peripheral blood revealed an abnormal clone with two extra copies of a neocentromeric chromosome 11: 48,XX,+11,+11,iso(11)(qter->q22->neo->q22->q13::q13->qter)x2[19]/46,XX[1]. FISH analysis using an α-satellite probe specific for centromere 11 and locus specific probe for 11q23 (MLL locus) indicated that these two neocentromeres do not have the genomic sequence of centromere 11. This abnormal clone has four copies of chromosome 11: two structurally normal chromosomes 11 and two structurally abnormal neocentromeric chromosomes 11. In sum, this leads to a total of six copies of 11q. Partial gain of chromosome 11q, containing the unrearranged mixed lineage leukaemia (MLL) gene is a rare but recurrent anomaly in myeloid malignancies. However, gain of 11q in the form of a neocentromeric chromosome 11 has not been described previously. Further study on the interaction between kinetochore protein and this active neocentromere will provide evidence about the mechanism of a functional neocentromere formation.

Ancient Origin of Two 5S rDNA Families Dominating in the Genus Rosa and Their Behavior in the Canina-Type Meiosis.

The genus Rosa comprises more than 100 woody species characterized by intensive hybridization, introgression, and an overall complex evolutionary history. Besides many diploid species (2n = 2x = 14) polyploids ranging from 3x to 10x are frequently found. Here we analyzed 5S ribosomal DNA in 19 species covering two subgenera and the major sections within subg. Rosa. In addition to diploids and polyploids with regular meiosis, we focused on 5x dogroses (Rosa sect. Caninae), which exhibit an asymmetric meiosis differentiating between bivalent- and univalent-forming chromosomes. Using genomic resources, we reconstructed 5S rDNA units to reveal their phylogenetic relationships. Additionally, we designed locus-specific probes derived from intergenic spacers (IGSs) and determined the position and number of 5S rDNA families on chromosomes. Two major 5S rDNA families (termed 5S_A and 5S_B, respectively) were found at variable ratios in both diploid and polyploid species including members of the early diverging subgenera, Rosa persica and Rosa minutifolia. Within subg. Rosa species of sect. Rosa amplified the 5S_A variant only, while taxa of other sections contained both variants at variable ratios. The 5S_B family was often co-localized with 35S rDNA at the nucleolar organizer regions (NOR) chromosomes, whereas the co-localization of the 5S_A family with NOR was only exceptionally observed. The allo-pentaploid dogroses showed a distinct distribution of 5S rDNA families between bivalent- and univalent-forming chromosomes. In conclusion, two divergent 5S rDNA families dominate rose genomes. Both gene families apparently arose in the early history of the genus, already 30 myrs ago, and apparently survived numerous speciation events thereafter. These observations are consistent with a relatively slow genome turnover in the Rosa genus.

FrenchFISH: Poisson Models for Quantifying DNA Copy Number From Fluorescence In Situ Hybridization of Tissue Sections.

PURPOSEChromosomal aberration and DNA copy number change are robust hallmarks of cancer. The gold standard for detecting copy number changes in tumor cells is fluorescence in situ hybridization (FISH) using locus-specific probes that are imaged as fluorescent spots. However, spot counting often does not perform well on solid tumor tissue sections due to partially represented or overlapping nuclei.MATERIALS AND METHODSTo overcome these challenges, we have developed a computational approach called FrenchFISH, which comprises a nuclear volume correction method coupled with two types of Poisson models: either a Poisson model for improved manual spot counting without the need for control probes or a homogeneous Poisson point process model for automated spot counting.RESULTSWe benchmarked the performance of FrenchFISH against previous approaches using a controlled simulation scenario and tested it experimentally in 12 ovarian carcinoma FFPE-tissue sections for copy number alterations at three loci (c-Myc, hTERC, and SE7). FrenchFISH outperformed standard spot counting with 74% of the automated counts having < 1 copy number difference from the manual counts and 17% having < 2 copy number differences, while taking less than one third of the time of manual counting.CONCLUSIONFrenchFISH is a general approach that can be used to enhance clinical diagnosis on sections of any tissue by both speeding up and improving the accuracy of spot count estimates.

FISH Diagnostics of Chromosomal Translocation with the Technology of Synthesis of Locus-Specific DNA Probes Based on Long-Range PCR

Detection of translocations in subtelomeric regions of chromosomes is a serious diagnostic problem, because they are difficult to determine by conventional cytogenetics with G banding. The aim of this work was the development of the technology of DNA probe synthesis for unique sequences of subtelomeric chromosome regions based on long-range PCR using the clinical case of determining the parental origin of unbalanced translocation between chromosomes 5 and 8. The unbalanced translocation der(5)t(5;8)(р15.33;q24.22) in a proband with physical, motor, intellectual, and speech development delay and in his sibling with speech and intellectual development delay as well, which was previously identified by array comparative genomic hybridization (aCGH), was confirmed by FISH. A balanced translocation 46,XX,t(5;8)(p15.33;q24.22) was detected in the mother’s karyotype using the created locus-specific DNA probe. This chromosome aberration was not detected by G banding of metaphase chromosomes. The father’s karyotype was normal according to FISH results. The method presented here makes it possible to create locus-specific DNA probes in a molecular cytogenetic laboratory using long-range PCR for the rapid diagnosis of cryptic chromosomal rearrangements.

Association of chromosome 7 aneuploidy measured by fluorescence in situ hybridization assay with muscular invasion in bladder cancer.

BackgroundThe preoperative prediction of muscular invasion status is important for adequately treating bladder cancer (BC) but nevertheless, there are some existing dilemmas in the current preoperative diagnostic accuracy of BC with muscular invasion. Here, we investigated the potential association between the fluorescence in situ hybridization (FISH) assay and muscular invasion among patients with BC. A cytogenetic‐clinical nomogram for the individualized preoperative differentiation of muscle‐invasive BC (MIBC) from non‐muscle‐invasive BC (NMIBC) is also proposed.MethodsAll eligible BC patients were preoperatively tested using a FISH assay, which included 4 sites (chromosome‐specific centromeric probe [CSP] 3, 7, and 17, and gene locus‐specific probe [GLP]‐p16 locus). The correlation between the FISH assay and BC muscular invasion was evaluated using the Chi‐square tests. In the training set, univariate and multivariate logistic regression analyses were used to develop a cytogenetic‐clinical nomogram for preoperative muscular invasion prediction. Then, we assessed the performance of the nomogram in the training set with respect to its discriminatory accuracy and calibration for predicting muscular invasion, and clinical usefulness, which were then validated in the validation set. Moreover, model comparison was set to evaluate the discrimination and clinical usefulness between the nomogram and the individual variables incorporated in the nomogram.ResultsMuscular invasion was more prevalent in BC patients with positive CSP3, CSP7 and CSP17 status (OR [95% CI], 2.724 [1.555 to 4.774], P < 0.001; 3.406 [1.912 to 6.068], P < 0.001 and 2.483 [1.436 to 4.292], P = 0.001, respectively). Radiology‐determined tumor size, radiology‐determined clinical tumor stage and CSP7 status were identified as independent risk factors of BC muscular invasion by the multivariate regression analysis in the training set. Then, a cytogenetic‐clinical nomogram incorporating these three independent risk factors was constructed and was observed to have satisfactory discrimination in the training (AUC 0.784; 95% CI: 0.715 to 0.853) and validation (AUC 0.743; 95% CI: 0.635 to 0.850) set. The decision curve analysis (DCA) indicated the clinical usefulness of our nomogram. In models comparison, using the receiver operator characteristic (ROC) analyses, the nomogram showed higher discriminatory accuracy than any variables incorporated in the nomogram alone and the DCAs also identified the nomogram as possessing the highest net benefits at wide range of threshold probabilities.ConclusionCSP7 status was identified as an independent factor for predicting muscular invasion in BC patients and was successfully incorporated in a clinical nomogram combining the results of the FISH assay with clinical risk factors.

Complex karyotype with cryptic FUS gene rearrangement and deletion of NR3C1 and VPREB1 genes in childhood B-cell acute lymphoblastic leukemia: A case report.

B-cell acute lymphoblastic leukemia (B-ALL) is a hematopoietic malignancy characterized by overproduction of immature B-lymphoblasts. B-ALL is the most common pediatric tumor and remains the leading cause of mortality in children and adolescents. Molecular and cytogenetic analyses of B-ALL revealed recurrent genetic and structural genomic alterations which are routinely applied for diagnosis, prognosis and choice of treatment regimen. The present case report describes a 4-year-old female diagnosed with B-ALL. GTG-banding at low resolution revealed an abnormal clone with 46,XX,?t(X;19)(q13;q13.3),der(9) besides normal cells. Molecular cytogenetics demonstrated a balanced translocation between chromosomes 16 and 19, and an unbalanced translocation involving chromosomes 5 and 9. A locus-specific probe additionally identified that the FUS gene in 16p11.2 was split and its 5' region was translocated to subband 19q13.33, whereas the 3' region of the FUS gene remained on the derivative chromosome 16. Overall, this complex karyotype included four different chromosomes and five break events. Further analyses, including array-comparative genomic hybridization, additionally revealed biallelic deletion of the tumor suppressor genes CDKN2A/B, and deletion of the NR3C1 and VPREB1 genes. The patient passed away under treatment due to sepsis.

Использование трофобластов цервикального канала для неинвазивной пренатальной детекции частых анеуплоидий

The article presents an experience of isolation of trophoblast cells from cervical samples of pregnant women and demonstrates a possibility of determining aneuploid cells in cervical samples using FISH analysis. Objective. To study methods of effective isolation and reliable detection of trophoblasts for genetic pathology analysis. Patients and methods. The participants of the study were three pregnant women, who according to the findings of the combined first trimester screening test were referred to the group with a high risk for fetal aneuploidy. The terms of gestation varied from 12 to 14 wks. Immunocytochemical detection of trophoblast cells was performed with FITC-labelled HLA-G antibodies. FISH was performed with the use of locus-specific DNA probes on chromosomes 13/21 and a DNA probe on chromosome 18 centromere. The chromosome set of a fetus was verified by the results of standard cytogenetic analysis of semi-direct chromosome preparations from cytotrophoblast cells obtained by chorionic villi biopsy. Results. HLA-G-positive cells were found in all examined cytological specimens. FISH analysis with the use of DNA probes on chronomomes, whose trisomies are compatible with live birth, detected aneuploid cells in all three cases. Conclusion. The use of cervical trophoblasts for noninvasive collection of information about the genetic status of the developing fetus at present needs further study of effective and reliable methods of their isolation, detection and analysis. Key words: aneuploidy, throphoblast cells, NIPT, prenatal diagnosis, HLA-G

Abstract 2898: Stochastic variation in gene expression is selected during clonal evolution of spontaneous mouse mammary tumors

Abstract Molecular and cellular diversity in cancer cells enables evolutionary processes that govern tumor progression and contributes to treatment failures, but the mechanisms governing this variability remain incompletely understood. We previously described tumor-specific epigenetic alterations in DNA devoid of canonical CpG methylation sites throughout the genomes of spontaneous breast tumors which arise in genetically uniform, yet heterozygous, [FVB X BALB/c MMTV-NeuT+] F1 mice. Those changes were detected in purified tumor DNA using a template-assisted quantitative ligation assay employing locus-specific and SNP-specific oligonucleotide genotyping probes, and the assay was subsequently shown to be sensitive to epigenetic modifications of the templates. We now describe losses of heterozygosity similarly distributed throughout the transcriptomes of tumors in this same model. We quantified expressed alleles across a population of clonal tumors and tested each expressed variant for the occurrence of allelic ratio outliers. The results revealed variegated patterns of expression in hundreds of genes, highly significantly enriched in pathways typically co-opted by tumors (Molecular Mechanisms of Cancer, P &amp;lt; 10-10, IPA analysis). An astounding 87% (2634 of 3044) of expressed genes that could be measured using this approach were represented in at least one tumor. Furthermore, the frequency of these outliers in any one individual tumor was found to correlate strongly with the transcriptional repression of an additional large set of non-polymorphic genes. These findings reveal underappreciated, latent mechanisms driving sporadic errors in epigenetic programming that promote repression of a multiple cis-linked transcripts. This genome-wide molecular chaos presents as dysregulated cellular homeostasis and is the foundation for heritable diversity as tumors evolve. Citation Format: Sara J. Felts, Xiaojia Tang, Virginia P. Van Keulen, Krishna R. Kalari, Larry R. Pease. Stochastic variation in gene expression is selected during clonal evolution of spontaneous mouse mammary tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2898.