Detection Of Chromosomal Changes Research Articles

In vitro fertilization and preimplantation genetic testing methods in infertility treatment of a woman with karyotype 46,XX,ins(13;4)(q34;p14p15.3),inv(4)(p14q12). Case report

The frequency of structural chromosomal transpositions can range from 1.8 to 8% among patients with reproductive disorders. There are several types of the rarest chromosomal abnormalities: insertion (insertion of a chromosomal region) and inversion (rotation of a chromosome region). This article describes a clinical case of the infertility treatment using assisted reproductive technologies in a woman with a rare chromosomal abnormality: simultaneous insertion and inversion of chromosomes 46, XX, ins (13;4)(q34;p14p15.3), inv(4)(p14q12). The structure and frequency of chromosomal aberrations were determined by high-throughput sequencing in preimplantation embryos. The result of the sequencing analysis showed that unbalanced variants for a known pathology were detected in 9 (56.3%) out of 16 observations, while in 6 (37%) only for a pathology known in the karyotype and in 3 (19%) they were presented simultaneously with the pathology of other chromosomes or with mosaicism. According to the results of the study, in preimplantation embryos, where one of the parents had chromosomal abnormalities, in addition to unbalanced variants, there is aneuploidy of other chromosomes not involved in the known pathology. They are described in 3 (21%) out of 14 observations of all identified pathology. In this regard, patients with aberrations in the karyotype are recommended, whenever possible, to carry out preimplantation genetic testing of structural rearrangements by methods allowed to analyze all chromosomes simultaneously. For example, high-throughput sequencing on the Illumina platform may become an alternative for prenatal diagnostics, which is performed in fertile couples with high risk of having a child with hereditary or congenital disorders. In the case of detection of chromosomal changes in the fetus, patients are faced with a number of ethical issues related to the necessity for medical abortion, which may contradict their religious and moral convictions.

Detection of chromosomal changes in chronic lymphocytic leukemia using classical cytogenetic methods and FISH: application of rich mitogen mixtures for lymphocyte cultures

One of the research methods of prognostic value in chronic lymphocytic leukemia (CLL) is cytogenetic analysis. This method requires the presence of appropriate B-cell mitogens in cultures in order to...

Detection of Chromosomal Abnormalities with Different In Situ Hybridisation Techniques--the Usefulness in the Qualification of Cancer Patients for Molecularly-Targeted Therapies.

Proper qualification of patients with cancer for an effective treatment regiment is essential to rationalize therapy benefit and costs. The early detection of genetic disorders that are responsible for the stimulation of uncontrolled cancer cells proliferation makes it possible to select agroup of patients with ahigh probability of response to molecularly-targeted therapy. Data has shown that careful analysis of genes mutation using different PCR and sequencing techniques or chromosomal aberrations using in situ hybridization (ISH) techniques have apredictive value for drug targeted therapy. Overexpression of receptors and gene amplification has been reported in various cancers. Their detection is still aconsiderable challenge, which is connected with the unsatisfactory quality of DNA and low mutated cells percentage compared to cells with no genetic abnormalities in tested material. Different techniques of standardization were performed to prevent false negative results and to increase the sensitivity of qualitative and quantitative evaluation of chromosomal abnormalities. Immunohistochemistry (IHC) technique is useful in the screening of receptor expression in paraffin-embedded tissue samples in different malignant diseases. Whereas ISH techniques, especially fluorescence in situ hybridization (FISH), are now considered the diagnostic gold standard method in detection chromosomal aberrations. Moreover, molecular biology techniques, which are using molecular probes and real-time PCR and quantitative PCR techniques, were also applied for the detection of chromosomal changes. In order to identify the best genetic marker for treatment regiment, it is important to compare results of different studies, which are evaluating the sensitivity of diagnostic techniques and treatment response after asuitable selection factors based on genetic aberrations profile.

SNP-Arrays: a Routine Cytogenetic Tool In Chronic Lymphocytic Leukemia ?.

AbstractAbstract 4611 Background:Chronic lymphocytic leukemia (B-CLL) is the most common adult leukemia in Western countries, and is characterized by a highly variable clinical course. Interphase fluorescent in situ hybridization (I-FISH) has been able to identify chromosomal abnormalities in ~80% of B-CLL, including deletions at 13q, 11q, 17p and trisomy 12, which has proven to be prognostic indicators for disease progression and survival. Although recent immunostimulatory methods have substantially improved analysis via conventional metaphase cytogenetics (CC), detection of chromosome changes is limited by the low mitotic activity of CLL cells in vitro. High-density single nucleotide polymorphism (SNP) arrays are commercially available technologies, which allow genome-wide detection of allelic copy number gains or losses, and loss-of-heterozygosity (LOH) regions. Aims:To assess whether SNP-arrays are more sensitive than I-FISH and CC to detect specific chromosomal abnormalities associated with prognosis in B-CLL, i.e. del13q, del11q, del17p and tri12. Methods:Blood samples from 24 patients with B-CLL at diagnosis were tested in parallel by I-FISH, CC and SNP-array. FISH: blood smear samples were hybridized with 4 probes, in order to detect deletions at 17p13.1, 11q22.3, 13q14.3, and trisomy 12 [respectively LSI p53, ATM, D13S319 and centromeric CEP12 probes, Abbott]. In normal lymphocytes, an average of 6.7% nuclei showed one signal (truncated nuclei), and we defined the cut-off level for detection of a deletion at 11% (mean+3SD). The cut-off for detection of tri12 was defined at 5% (mean+3SD). CC: blood lymphocytes are cultivated for 72 hours with immunostimulants (DSP30 and IL-2) and metaphases analyzed according to standard procedures. SNP-arrays: DNA samples (200 ng) were hybridized on the Illumina HumanCNV370-quad v3 BeadChips, which assess 373,397 markers with a median marker spacing of 4.9 kb (mean 7.8 kb). The I-Scan system was used to scan the BeadChips (primary data). GenomeStudio 1010 v1 and CNVPartition 2.4.4 package were used to process primary data and identify chromosomal deletions/amplifications and LOH regions. Results:I-FISH identified deletions at 13q (15-95% of nuclei; mean=51%), 11q (35-54%; mean=43%) and trisomy 12 (32-49%; mean=37%) in 17 (71%) [including 2 cases of biallelic deletions], 3 (12.5%) and 4 (17%) cases, respectively. No del17p was detected. Five B-CLL cases presented associated FISH abnormalities. SNP-arrays identified all changes (100%) detected by I-FISH (del13q, median size: 13 Mb – range, 0.49–50 Mb; del11q, median size: 39 Mb – range, 34.8–42 Mb]. However, SNP-arrays showed 5 additional deletions at 13q14.3. Three patients had cryptic deletions (~52 to 82 kb), not detected by the FISH LSI D13S319 probe (~130 kb) or CC, and two others had large deletions (1.1 and 33.3 Mb) but with one signal below the cut-off of 11% by I-FISH (therefore considered as negative- both had normal CC). In these two cases, tumor cell enrichment before I-FISH allowed the detection of the deletion. In one case with del13q and tri12 (30% of nuclei by FISH), an additional del11q was also detected by SNP-array and CC (in 5/24 mitoses). The size of this deletion was 37.8 Mb and involved the cytogenetic bands 11q14.1 to 11q23.2 (including ATM). In addition, SNP-arrays enabled to define more precisely the size and location of the abnormalities. For instance, in one case with tri12 (as identified by the centromeric FISH probe), a partial trisomy of chromosome 12 short arm was indeed detected by SNP-array. No 17p abnormality was detected by SNP-array (either deletion or LOH). Only one of the 24 samples had no abnormality by SNP, I-FISH or CC for the loci studied. Conclusions:Despites using a relatively low density SNP-array (~370,000 markers), a higher sensitivity of Illumina BeadChips was observed. “SNP+/FISH negative” cases can be explained by either cryptic deletions or low leukemic cell content (< cut-off level). “SNP+/CC negative” cases can be explained by either a higher resolution, or the presence of normal mitosis in excess following stimulation. Higher density SNP-arrays (> 5 million markers) may be used to improve the assay sensitivity, especially regarding del13q14 which seems to be present in a great majority of our cases. Our study confirms usefulness of SNP-arrays for prognostic evaluation of B-CLL patients at diagnosis, and suggests the use of this assay as a routine procedure. [Display omitted] Disclosures:No relevant conflicts of interest to declare.

Detection of chromosome changes in pathology archives: an application of microwave-assisted fluorescence in situ hybridization to human carcinogenesis studies

Pathology archives provide unique and abundant opportunities to investigate human carcinogenesis and identify potential targets for cancer therapy. Microwaving was introduced into various procedures used in histopathology two decades ago, although the precise mechanisms underlying its effectiveness in any of the procedures, including antigen retrieval, acceleration of fixation and nucleic acid hybridization, are not known. Since microwaving was first applied to fluorescence in situ hybridization (FISH), many pathologists and researchers have enjoyed the benefits of excellent preservation of histological structures as well as good retrieval of FISH signals by this method. Microwave-assisted fluorescence in situ hybridization (MW-FISH) has proved to be especially useful in retrospective investigations of tissues fixed and preserved for long periods of time, and the success rates in the randomly selected pathology archives have been greater (70-95%) than by the conventional protocol (</=40%) The MW-FISH protocol and current availability of human genome information together with information on a variety of other histopathological attributes have paved the way to exploration of specific, large-scale genomic changes in human tumor tissue, even in the incipient stage. In practice, this protocol is very useful for retrospective surveillance of amplicons in tumor tissue by using hundreds of bacterial artificial chromosome clones and many specimens in the form of a tissue microarray. Effective retrieval of specific genome-wide amplicon profiles from human tumors stored unaware in ordinary pathology laboratories would help to further stratify tumors so that individually tailored treatment strategies would become feasible in clinical settings.

Genome-wide loss of heterozygosity and copy number alteration in esophageal squamous cell carcinoma using the Affymetrix GeneChip Mapping 10 K array

BackgroundEsophageal squamous cell carcinoma (ESCC) is a common malignancy worldwide. Comprehensive genomic characterization of ESCC will further our understanding of the carcinogenesis process in this disease.ResultsGenome-wide detection of chromosomal changes was performed using the Affymetrix GeneChip 10 K single nucleotide polymorphism (SNP) array, including loss of heterozygosity (LOH) and copy number alterations (CNA), for 26 pairs of matched germ-line and micro-dissected tumor DNA samples. LOH regions were identified by two methods – using Affymetrix's genotype call software and using Affymetrix's copy number alteration tool (CNAT) software – and both approaches yielded similar results. Non-random LOH regions were found on 10 chromosomal arms (in decreasing order of frequency: 17p, 9p, 9q, 13q, 17q, 4q, 4p, 3p, 15q, and 5q), including 20 novel LOH regions (10 kb to 4.26 Mb). Fifteen CNA-loss regions (200 kb to 4.3 Mb) and 36 CNA-gain regions (200 kb to 9.3 Mb) were also identified.ConclusionThese studies demonstrate that the Affymetrix 10 K SNP chip is a valid platform to integrate analyses of LOH and CNA. The comprehensive knowledge gained from this analysis will enable improved strategies to prevent, diagnose, and treat ESCC.

Molecular Cytogenetic Study of Immunofluorescently Labeled Plasma Cells and Prognostic Significance of Clonal Chromosomal Aberrations in Multiple Myeloma.

Finding of clonal chromosomal aberrations in plasma cells is considered as one of the most important and independent prognostic factor in patients with multiple myeloma (MM). The most frequent and reliable cytogenetic indicators are chromosome 13q deletions (intermediate or moderately adverse prognosis), and translocations involving the immunoglobulin heavy chain gene (IgH) at 14q32 region. IgH gene is involved in translocations with different partner genes and these rearrangements are related to a very poor prognosis. The only exception is translocation t(11;14)(q13;q32) which is often connected with longer overall survival and therefore considered to be a favorable prognostic factor. The aim of the study was to assess the frequency of the most important chromosomal aberrations in immunofluorescently labeled plasma cells of patients with MM by interphase fluorescence in situ hybridization (I-FISH), and to evaluate their prognostic significance.During the last two years we examined 128 newly diagnosed patients with MM by conventional G-banding technique and by I-FISH. We focused on detection of aberrations of 13q, IgH gene rearrangements, and t(11;14)(q13;q32) translocation. I-FISH was done by locus-specific DNA probes (Abbott-Vysis, Des Plaines, Illinois, USA). Fifteen patients with complex karyotype were re-examined by multicolor FISH (mFISH, MetaSystems GmbH, Altlussheim, Germany). G-banding revealed abnormal karyotypes in 25% of patients, I-FISH detected chromosomal abberations in 82.8% cases. Abberations of chromosome 13 were found in plasma cells of 84 patients (65,6%), the incidence was: del(13)(q14) in 11%, monosomy 13 in 40%, combination of del(13)(q14)/monosomy 13 in 8%, and other aberrations of chromosome 13 in 7% of cases. Aberrations of IgH gene were proved in 82 patients (64%). t(11;14)(q13;q32) was seen in fourteen patients (11%) and other translocations affecting 14q32 region in 19 patients (15%). Besides translocations, different variations of total and/or partial deletions of IgH gene were detected in 28 cases (22%). In nine patients (7%) we found clones with translocation and deletion of 14q32 simultaneously, twelve patients (9%) had other IgH aberrations. Univariate statistical testing showed aberrations of 13q (p=0.042), and IgH gene rearrangments (translocations except t(11;14)(q13;q32) or deletions; p=0.007) to be associated with significantly shorter progression-free survival. The worst prognosis in our cohort was for 18 patients with combination of chromosome 13 anomalies together with rearrangements of IgH gene (p=0.049). Method of immunofluorescent labeling of plasma cells allows higher detection of chromosomal changes by I-FISH technique and therefore correct prognosis of the disease can be done.

Cytogenetic and Molecular Analysis of 12 Cases of Primary Cutaneous Marginal Zone Lymphomas

Primary low-grade B-cell lymphomas of the skin are separated into marginal zone and follicle center lymphomas according to the recent World Health Organization-European Organization for Research and Treatment of Cancer classification, with distinct histologic and immunohistochemical profiles. Some cases remain difficult to distinguish. The degree of relationship with their extracutaneous counterparts is currently being investigated on clinical, histologic and molecular grounds. Cytogenetic analysis using fluorescence in situ hybridization was performed on 12 frozen samples of infiltrated skin that had been classified as marginal zone lymphoma (MZL). Chromosomal changes known to be recurrently observed in systemic MZL of the mucosa-associated lymphoid tissue type, and in follicular center lymphoma were analyzed. These included trisomy for chromosomes 3, 7, 12, and 18 as well as t(14;18) IGH/BCL2, t(14;18) IGH/MLT1, and t(11;18) API2/MLT1 translocations. Complementary molecular search of IGH/BCL2 rearrangement using a polymerase chain reaction technique and of API2/MLT1 mRNA expression by reverse transcriptase-polymerase chain reaction were performed. Two cases showed evidence of trisomy 3 at levels varying from 14% to 20% of the analyzed cells. No other chromosomal abnormalities were found with those techniques in the remaining cases. These results demonstrate that known recurrent chromosomal abnormalities rarely occur in primary cutaneous MZLs and suggest the possibility of a variety of initial oncogenic events leading to a common downstream pathway. These data also underline that fluorescence in situ analysis on routine skin punch biopsies represents a reliable tool for the detection of chromosomal changes, but requires consistent dermal infiltration.

Reduced Replication: A Call to ARMS

In this issue of Cell, Lemoine et al. monitor chromosome instability in yeast cells with reduced levels of an essential replicative DNA polymerase. The authors identify a hotspot for chromosome aberrations reminiscent of fragile sites in human cells. This hotspot is composed of inverted Ty elements, which lead to a double-strand break under conditions of limited replication.

A novel 5q11.2 deletion detected by microarray comparative genomic hybridisation in a child referred as a case of suspected 22q11 deletion syndrome

The 22q11 deletion syndrome (22q11DS) is a developmental syndrome comprising of heart, palate, thymus and parathyroid glands defects. Individuals with 22q11DS usually carry a 1.5- to 3-Mb heterozygous deletion on chromosome 22q11.2. However, there are many patients with features of 22q11DS without a known cause from conventional karyotype and FISH analysis. Six patients with features of 22q11DS, a normal chromosomal and FISH 22q11 analysis, were selected for investigation by microarray genomic comparative hybridisation (array CGH). Array-CGH is a powerful technology enabling detection of submicroscopic chromosome duplications and deletions by comparing a differentially labelled test sample to a control. The samples are co-hybridised to a microarray containing genomic clones and the resulting ratio of fluorescence intensities on each array element is proportional to the DNA copy number difference. No chromosomal changes were detected by hybridisation to a high resolution array representing chromosome 22q. However, one patient was found to have a 6-Mb deletion on 5q11.2 detected by a whole genome 1-Mb array. This deletion was confirmed with fluorescence in-situ hybridisation (FISH) and microsatellite marker analysis. It is the first deletion described in this region. The patient had tetralogy of Fallot, a bifid uvula and velopharyngeal insufficiency, short stature, learning and behavioural difficulties. This case shows the increased sensitivity of array CGH over detailed karyotype analysis for detection of chromosomal changes. It is anticipated that array CGH will improve the clinician's capacity to diagnose congenital syndromes with an unknown aetiology.

Molecular pathology of the prostate carcinoma. Academic playground or guide for diagnosis or therapy planning?

No effective therapy exists for late-stage hormone-refractory prostate cancer. It would therefore be important to better understand the biological basis of prostate cancer progression. Since cancer is based on genetic alterations, detection of chromosomal changes can pinpoint critical genes and highlight mechanisms of cancer development and progression. Studies by comparative genomic hybridization (CGH) identified recurrent chromosomal aberrations across the progression from organ-confined to late-stage hormonerefractory cancer. These include frequent losses at 8p, 6q, 13q and 18q suggesting relevant tumor-suppressor genes on these chromosomal arms. In contrast, several genes with oncogenic function are likely to reside on 8 q, which is frequently gained in advance stages. Importantly, there are several high-level amplifications in hormone-refractory and metastatic prostate cancers including Xq11-12, 1q21-25, 8q21, 8q24, and 10q22 that may pinpoint to potent oncogenes. The high-level amplification of the androgene receptor at Xq11-12 is a paradigm as to how molecular cytogenetics can elucidate the molecular mechanisms of hormone-refractory growth. Target gene identification of amplifications may lead to new diagnostic tools and therapies of advanced prostate cancer.

Contribution of Comparative Genomic Hybridization and Fluorescence in situ Hybridization to the Detection of Chromosomal Abnormalities in B-Cell Chronic Lymphocytic Leukemia

Background: B-chronic lymphocytic leukemia (B-CLL), the most common type of leukemia in Western Europe and the United States, is characterized by clonal chromosomal abnormalities detected in almost half of the studied patients. The precise determination of chromosomal changes helps to indicate the prognosis and to understand the pathogenesis of CLL. Methods and Patients: We applied conventional cytogenetics (CC), FISH and comparative genomic hybridization (CGH) to the investigation of clonal abnormalities in 88 B-CLL patients at the time of diagnosis. Results: By using CC of bone marrow cells without any stimulation, non-random chromosomal changes were found in 17 (19%) of 88 patients.The employment of FISH and CGH revealed chromosomal changes in additional 33 patients, thus increasing the detection rate of chromosomal abnormalities to 57%. The most common abnormalities detected in our patients included deletions of 13q in 16 cases (18%), followed by trisomy of chromosome 12 in 12 patients (13%), deletions of 11q in 10 patients (11%) and deletions of 17p in 10 patients (11%). A statistically significant correlation between higher disease activity and the presence of deletions 11q and 17p was observed. Conclusion: The addition of FISH and CGH to CC in 88 B-CLL patients improved the detection of clonal chromosomal changes from 19 to 57%. The most frequent chromosomal change was deletion of 13q14 (18%). Deletions of 11q23 and 17p13 were found in patients with higher clinical disease activity. Our results underline the importance of employing FISH and CGH techniques in CLL patients. CC without any stimulation has a low detection rate and is not suggested for detection of chromosomal changes in CLL.

Importance of using comparative genomic hybridization to improve detection of chromosomal changes in childhood acute lymphoblastic leukemia

We used comparative genomic hybridization (CGH) and conventional cytogenetics (CC) to define chromosomal changes and to evaluate the usefulness of CGH in 65 patients having childhood acute lymphoblastic leukemia (ALL). Subsequently, fluorescence in situ hybridization (FISH) was used to evaluate the CGH and cytogenetic results. Comparative genomic hybridization revealed DNA copy number changes in 49 (75%) patients (including 7 patients with unsuccessful cytogenetics and 2 patients with normal karyotype). A total of 85 losses and 195 gains were detected. The most commonly gained chromosomes were 21 (35%), X (31%), 18 (27%), 10 (26%), 6 (25%), 17 (25%), 4 (23%), and 14 (22%). Losses were most frequently observed on chromosomes 9p (18%) and 12p (11%). Other losses were detected on chromosomes 13q (9%), 6q (9%), 7p (8%), and chromosome X (6%). Conventional cytogenetics revealed chromosomal changes in 53 (82%) patients. The employment of CGH and FISH together with CC analysis revealed chromosomal changes in 62 (95%) of the childhood ALL patients investigated. The CGH completed CC results in 36 patients; in 9 patients, the changes escaped detection without using CGH. The results of our study were compared to 6 other CGH studies previously reported. Our observations underline the benefits of supplementing routine cytogenetic investigation in childhood ALL by FISH and CGH, because small unbalanced changes may escape detection when conventional cytogenetics is the only diagnostic method used.

Detection of chromosomal changes by interphase cytogenetics in biopsies of recurrent astrocytomas and oligodendrogliomas.

Recently, lineage-specific genetic pathways of tumor progression have been suggested in both oligodendrogliomas and astrocytomas. Aberrations consistently reported in gliomas include chromosomes 1, 7, 10, 17 and 19. Identification of specific genetic damage may have important clinical consequences, because oligodendrogliomas, unlike astrocytomas, are responsive to chemotherapy. Genetic alterations specific for tumor type and tumor progression were investigated in 5 pairs of recurrent astrocytomas and 8 pairs of recurrent oligodendrogliomas by means of interphase in situ hybridization (ISH) to paraffin-embedded, formalin-fixed tissue sections. A set of DNA probes specific for the centromeric regions of chromosomes 1, 7, 10, 17, X and Y was applied. Since LOH studies on oligodendrogliomas have revealed losses in the region of 1p32-1p36, a DNA probe specific for the 1p36.3 locus was included. Hybridization with the 1p36.3 probe revealed loss of 1p in 5 of the 8 oligodendroglioma recurrences, the aberration being present in the primary tumors in 2 cases. In none of the astrocytomas was loss of 1p observed. Numerical aberrations were found in one astrocytoma pair (+7) and in the second biopsy of an oligodendroglioma (+7, -10). Aneuploidy was found by in situ hybridization in 8 of the 13 tumor pairs. Detection of aberrations in the 1p36.3 locus by interphase in situ hybridization to paraffin-embedded, formalin-fixed tumors may become a very useful tool in delineation of oligodendroglial from astrocytic genotypes, directing tumor specific therapy. The technique may be of crucial importance in tumor cases in which histologic criteria of lineage are not obvious.