Publications


Bryndorf T, Kirchhoff M, Larsen J, Andreasson B, Bjerregaard B, Westh H, Rose H, Lundsteen C. The most common chromosome aberration detected by high-resolution comparative genomic hybridization in vulvar intraepithelial neoplasia is not seen in vulvar squamous cell carcinoma. Cytogenet Genome Res. In press. abstract

Kirchhoff M, Pedersen S, Kjeldsen E, Rose H, Dunø M, Kølvraa S, Lundsteen C (2004). A prospective study comparing HR-CGH and subtelomeric FISH for investigation of mentally retarded and dysmorphic individuals and an update of a study using only HR-CGH. Am J Med Genet. In press. abstract American Journal of Medical Genetics - Early view

Ottesen AM, Skakkebaek NE, Lundsteen C, Leffers H, Larsen J, Rajpert-De Meyts E (2003). High-resolution comparative genomic hybridization detects extra chromosome arm 12p material in most cases of carcinoma in situ adjacent to overt germ cell tumors, but not before the invasive tumor development. Genes Chromosomes Cancer. 38(2): 117-25. abstract

Kristensen TD, Wesenberg F, Jonsson OG, Carlsen NT, Forestier E, Kirchhoff M, Lundsteen C, Schmiegelow K (2003). High-resolution comparative genomic hybridisation yields a high detection rate of chromosomal aberrations in childhood acute lymphoblastic leukaemia. Eur J Haematol. 70(6): 363-72. abstract

Kirchhoff M, Rose H, Lundsteen C (2001). Comparative genomic hybridization in clinical genetics. J Med Genet. 38, 740. abstract

Kirchhoff M, Rose H, Gerdes T, Lundsteen C (2001). Påvisning af submikroskopiske kromosomfejl med komparativ genomisk hybridisering. Ugeskrift for læger. 163, 5652 abstract in English

Kirchhoff M, Rose H, Petersen BL, Maahr J, Gerdes T, Philip J, Lundsteen C (2001). Comparative genomic hybridization reveals non-random chromosomal aberrations in early preinvasive cervical lesions. Cancer Genet Cytogenet. 129, 47. abstract

Larsen J, Ottesen AM, Kirchhoff M, Lundsteen C, Larsen JK (2001): High resolution comparative genomic hybridization detects 7-8 megabasepair deletion in PCR amplified DNA. Anal Cell Pathol. 23, 61. abstract

Larsen J, Ottesen AM, Lundsteen C, Leffers H, Larsen JK (2001). Optimization of DOP-PCR amplification of DNA for high resolution comparative genomic hybridization Cytometry 44, 317. abstract

Andersen MK, Christiansen DH, Kirchhoff M, Pedersen-Bjergaard JP (2001). Duplication or amplification of chromosome band 1q23 including the MLL gene is a recurrent abnormality in therapy-related MDS and AML closely related to mutation of the p53 gene and to previous therapy with alkylating agents. Genes Chrom Cancer. 31, 33. abstract

Kirchhoff M., Rose H., Maahr J., Gerdes T., Bugge M., Tommerup N., Tumer Z., Lespinasse J., Jensen P.K., Wirth J. & Lundsteen C. (2000) High resolution comparative genomic hybridisation analysis reveals imbalances in dyschromosomal patients with normal or apparently balanced conventional karyotypes. Eur J Hum Genet. 8, 661. abstract

Larsen J., Kirchhoff M., Rose H., Gerdes T., Maahr J., Lundsteen C. & Larsen J.K. (1999) Improved sensitivity in comparative genomic hybridization analysis of DNA heteroploid cell mixtures after pre-enrichment of subpopulations by fluorescence activated cell sorting. Anal Cell Pathol. 19, 119. abstract

Kirchhoff M., Rose H., Petersen B.L., Maahr J., Gerdes T., Lundsteen C., Bryndorf T., Kryger-Baggesen N., Christensen L., Engelholm S.A. & Philip J. (1999) Comparative genomic hybridization reveals a recurrent pattern of chromosomal aberrations in severe dysplasia/carcinoma in situ of the cervix and in advanced-stage cervical carcinoma. Genes Chrom Cancer 24, 144. abstract

Kirchhoff M., Gerdes T., Maahr J., Rose H., Bentz M., Dohner H. & Lundsteen C. (1999) Deletions below 10 megabasepairs are detected in comparative genomic hybridization by standard reference intervals. Genes Chrom Cancer 25, 410. abstract

Kirchhoff M., Gerdes T., Rose H., Maahr J., Ottesen A.M. & Lundsteen C. (1998) Detection of chromosomal gains and losses in comparative genomic hybridization analysis based on standard reference intervals. Cytometry 31, 163. abstract

Ottesen A.M., Kirchhoff M., De-Meyts E.R., Maahr J., Gerdes T., Rose H., Lundsteen C., Petersen P.M., Philip J. & Skakkebaek N.E. (1997) Detection of chromosomal aberrations in seminomatous germ cell tumours using comparative genomic hybridization. Genes Chrom Cancer 20, 412. abstract

Kirchhoff M., Gerdes T., Maahr J., Rose H. & Lundsteen C. (1997) Automatic correction of the interfering effect of unsuppressed interspersed repetitive sequences in comparative genomic hybridization analysis. Cytometry 28, 130. abstract

Bryndorf T., Kirchhoff M., Rose H., Maahr J., Gerdes T., Karhu R., Kallioniemi A., Christensen B., Lundsteen C. & Philip J. (1995) Comparative genomic hybridization in clinical cytogenetics. Am J Hum Genet. 57, 1211. abstract

Lundsteen C., Maahr J., Christensen B., Bryndorf T., Bentz M., Lichter P. & Gerdes T. (1995) Image analysis in comparative genomic hybridization. Cytometry 19, 42. abstract

 


Abstracts

Lundsteen C., Maahr J., Christensen B., Bryndorf T., Bentz M., Lichter P. & Gerdes T. (1995) Image analysis in comparative genomic hybridization. Cytometry 19, 42.
Keywords: Human/Image Processing,Computer-Assisted/methods/In Situ Hybridization,Fluorescence/Karyotyping/Software/Support,Non-U.S.Gov't/Tumor Cells,Cultured/analysis/genetics/Dna/Metaphase/Fluorescence/Chromosomes
Abstract: Comparative genomic hybridization (CGH) is a new technique by which genomic imbalances can be detected by combining in situ suppression hybridization of whole genomic DNA and image analysis. We have developed software for rapid, quantitative CGH image analysis by a modification and extension of the standard software used for routine karyotyping of G-banded metaphase spreads in the Magiscan chromosome analysis system. The DAPI-counterstained metaphase spread is karyotyped interactively. Corrections for image shifts between the DAPI, FITC, and TRITC images are done manually by moving the three images relative to each other. The fluorescence background is subtracted. A mean filter is applied to smooth the FITC and TRITC images before the fluorescence ratio between the individual FITC- and TRITC-stained chromosomes is computed pixel by pixel inside the area of the chromosomes determined by the DAPI boundaries. Fluorescence intensity ratio profiles are generated, and peaks and valleys indicating possible gains and losses of test DNA are marked if they exceed ratios below 0.75 and above 1.25. By combining the analysis of several metaphase spreads, consistent findings of gains and losses in all or almost all spreads indicate chromosomal imbalance. Chromosomal imbalances are detected either by visual inspection of fluorescence ratio (FR) profiles or by a statistical approach that compares FR measurements of the individual case with measurements of normal chromosomes. The complete analysis of one metaphase can be carried out in approximately 10 minutes.



Bryndorf T., Kirchhoff M., Rose H., Maahr J., Gerdes T., Karhu R., Kallioniemi A., Christensen B., Lundsteen C. & Philip J. (1995) Comparative genomic hybridization in clinical cytogenetics. Am J Hum Genet. 57, 1211.
Keywords: Chromosome Aberrations/genetics/Comparative Study/Cytogenetics/methods/Human/In Situ Hybridization,Fluorescence/Karyotyping/Nucleic Acid Hybridization/Support,Non-U.S.Gov't/analysis/Trisomy/Chromosomes
Abstract: We report the results of applying comparative genomic hybridization (CGH) in a cytogenetic service laboratory for (1) determination of the origin of extra and missing chromosomal material in intricate cases of unbalanced aberrations and (2) detection of common prenatal numerical chromosome aberrations. A total of 11 fetal samples were analyzed. Seven cases of complex unbalanced aberrations that could not be identified reliably by conventional cytogenetics were successfully resolved by CGH analysis. CGH results were validated by using FISH with chromosome-specific probes. Four cases representing common prenatal numerical aberrations (trisomy 21, 18, and 13 and monosomy X) were also successfully diagnosed by CGH. We conclude that CGH is a powerful adjunct to traditional cytogenetic techniques that makes it possible to solve clinical cases of intricate unbalanced aberrations in a single hybridization. CGH may also be a useful adjunct to screen for euchromatic involvement in marker chromosomes. Further technical development may render CGH applicable for routine aberration screening.



Kirchhoff M., Gerdes T., Maahr J., Rose H. & Lundsteen C. (1997) Automatic correction of the interfering effect of unsuppressed interspersed repetitive sequences in comparative genomic hybridization analysis. Cytometry 28, 130.
Keywords: Algorithms/Chromosome Aberrations/Chromosomes,Human,Pair 2/Chromosomes,Human,Pair 21/Dna/analysis/Female/Human/Image Processing,Computer-Assisted/In Situ Hybridization,Fluorescence/methods/Repetitive Sequences,Nucleic Acid/Support,Non-U.S.Gov't/X Chromosome
Abstract: Comparative genomic hybridization (CGH) is a relatively new technique whose application is increasing. The method has mostly been employed for detection of chromosome aberrations in cancers, and a large amount of data in this field is accumulating. At the same time, efforts are made to improve the technique in order to increase the sensitivity and the generation of reliable results. Based on experimental data, we have developed a computer algorithm for eliminating some of the interfering effects of unsuppressed repetitive sequences in CGH analysis, and thereby improved our CGH analysis system.



Ottesen A.M., Kirchhoff M., De-Meyts E.R., Maahr J., Gerdes T., Rose H., Lundsteen C., Petersen P.M., Philip J. & Skakkebaek N.E. (1997) Detection of chromosomal aberrations in seminomatous germ cell tumours using comparative genomic hybridization. Genes Chrom Cancer 20, 412.
Keywords: Chromosome Aberrations/genetics/Chromosome Banding/Chromosome Deletion/DNA,Neoplasm/analysis/Genes,Structural,Neoplasm/Human/Karyotyping/Male/Neoplasm Staging/Nucleic Acid Hybridization/Seminoma/pathology/Support,Non-U.S.Gov't/Testicular Neoplasms/Genome/Dna/Chromosomes
Abstract: Comparative genomic hybridization (CGH) was used to evaluate tissue specimens from 16 seminomas in order to elucidate the pathogenesis of germ cell tumours in males. A characteristic pattern of losses and gains within the entire genomes was detected in 94% of the seminomas by comparing the ratio profiles of the tumours with a standard of cytogenetically normal genomic DNA. Losses represented 43% of the total number of alterations often affecting chromosomes and chromosome arms 4, 5, 11, 13q, and 18q. Gains amounted to 57% and were often observed on 1q, 7, 8, 12, 14q, 15q, 21q, and 22q. Aberrations of 12p and 21q appeared most consistently. Results from CGH analysis displayed no relationship to the clinical stages of the malignancy. Some rare aberrations appeared, however, only in clinical stage II and in tumours showing relapse in the contralateral testis following orchiectomy, although the alterations were not present in all of the tumours in question. Losses of 16q13-21 and gains of 9q22.1-22.2 were demonstrated in both groups, while loss of 16p12 and gains of 6p21 and 6q23.3-24 were detected in the latter group as well. In conclusion, a specific pattern of chromosomal alterations was demonstrated in the seminomas by improved detection criteria, which increased specificity and sensitivity. The rare aberrations, which appeared only in tumours in improved detection criteria, which increased specificity and sensitivity. The rare aberrations, which appeared only in tumours in clinical stage II and relapsed tumours, may be linked to tumour progression, invasiveness, and bilateral disease.



Kirchhoff M., Gerdes T., Rose H., Maahr J., Ottesen A.M. & Lundsteen C. (1998) Detection of chromosomal gains and losses in comparative genomic hybridization analysis based on standard reference intervals. Cytometry 31, 163.
Keywords: Chromosome Aberrations/Dna/analysis/Female/Human/Image Processing,Computer-Assisted/In Situ Hybridization,Fluorescence/standards/Karyotyping/Male/Sensitivity and Specificity/Support,Non-U.S.Gov't/genetics/Software
Abstract: Criteria for detection of chromosome aberrations by Comparative Genomic Hybridization (CGH) are not standardized and improvement of this part of the analysis is of paramount importance to the applicability of the technique. The aim of this work was to suggest CGH detection criteria that increase the specificity and sensitivity and at the same time include chromosome regions previously excluded from CGH analysis. We analyzed 33 hybridizations with normal DNA and modified our CGH software in order to use a selection of these normal analyses as a model for interpretation of analyses of unknown samples. This approach was successfully tested on 14 samples with known aberrations.



Kirchhoff M., Gerdes T., Maahr J., Rose H., Bentz M., Dohner H. & Lundsteen C. (1999) Deletions below 10 megabasepairs are detected in comparative genomic hybridization by standard reference intervals. Genes Chrom Cancer 25, 410.
Keywords: Chromosome Aberrations/Chromosome Abnormalities/genetics/Comparative Study/DNA,Neoplasm/isolation & purification/Human/In Situ Hybridization,Fluorescence/Nucleic Acid Hybridization/methods/Reference Standards/Sequence Deletion/Support,Non-U.S.Gov't/analysis/Chromosomes
Abstract: Comparative genomic hybridization (CGH) is a widely used technique for studying chromosomal imbalances. The sensitivity of the technique is, however, relatively low. Deletions down to a size of 10-12 Mbp have been detected by the use of fixed diagnostic thresholds. In this study, we applied standard reference intervals as detection criteria on a number of deletions in the range of 3 Mbp to 14-18 Mbp. All deletions were detected. Thus, detection by standard reference intervals confers a considerably higher sensitivity to CGH analysis compared to fixed diagnostic thresholds.



Kirchhoff M., Rose H., Petersen B.L., Maahr J., Gerdes T., Lundsteen C., Bryndorf T., Kryger-Baggesen N., Christensen L., Engelholm S.A. & Philip J. (1999) Comparative genomic hybridization reveals a recurrent pattern of chromosomal aberrations in severe dysplasia/carcinoma in situ of the cervix and in advanced-stage cervical carcinoma. Genes Chrom Cancer 24, 144.
Keywords: Carcinoma in Situ/genetics/Carcinoma,Squamous Cell/Cervix Dysplasia/Cervix Neoplasms/Chromosome Aberrations/Chromosomes,Human/Comparative Study/Female/Human/Neoplasm Recurrence,Local/Nucleic Acid Hybridization/methods/Support,Non-U.S.Gov't
Abstract: We analyzed 17 cases of dysplasia/carcinoma in situ (CIS) of the cervix and 29 advanced-stage cervical squamous cell carcinomas by comparative genomic hybridization (CGH). A comparable recurrent pattern of aberrations was detected in both preinvasive and invasive cases, although the total number of aberrations was much higher in the latter category. The most consistent chromosomal gain was mapped to chromosome arm 3q in 35% of preinvasive cases and in 72% of invasive cases. Chromosome aberrations were detected in 13/17 preinvasive cases with a total of 61 involved chromosome arms. In the invasive cases, frequent gains also occurred on 1q (45%), 8q (41%), 15q (41%), 5p (34%), and Xq (34%), and frequent losses were mapped to chromosome arms 3p (52%), 11q (48%), 13q (38%), 6q (38%), and 4p (34%). A recurrent pattern of aberrations has not previously been described in preinvasive lesions of the cervix. Our finding is surprising considering that only few preinvasive lesions are expected to progress to invasive cancer.



Larsen J., Kirchhoff M., Rose H., Gerdes T., Maahr J., Lundsteen C. & Larsen J.K. (1999) Improved sensitivity in comparative genomic hybridization analysis of DNA heteroploid cell mixtures after pre-enrichment of subpopulations by fluorescence activated cell sorting. Anal Cell Pathol. 19, 119.
Keywords: Analysis/Dna/Fluorescence/Cytogenetic Analysis/Cells/Lymphocytes/K562 Cells
Abstract: Cytogenetic analysis of solid tumors with comparative genomic hybridization (CGH) is hampered by the dilution of DNA from individual tumor subpopulations with DNA from other cells. We investigated to what extent this dilution effect can be alleviated using fluorescence activated cell sorting (flow sorting) of experimental DNA heteroploid cell mixtures prior to CGH. From mixtures of normal lymphocytes with triploid K-562 cells the individual components were sorted according to stemline DNA content and processed by CGH in comparison with pure K-562 samples and the original mixtures. Compared with 30 autosome copy number imbalances found in pure K-562 samples, a mixture with 32% K-562 cells showed 16 imbalancies, and none were detected in mixtures with 13% or 5% K-562 cells. In contrast, 29, 22 and 23 imbalances were detected in K-562 nuclei sorted from the 32%, 13% and 5% mixtures, respectively. This indicate that CGH analysis of flow sorted DNA aneuploid subpopulations enables a specific cytogenetic analysis of the individual subclones in a DNA heteroploid cell population.



Kirchhoff M., Rose H., Maahr J., Gerdes T., Bugge M., Tommerup N., Tumer Z., Lespinasse J., Jensen P.K., Wirth J. & Lundsteen C. (2000) High resolution comparative genomic hybridisation analysis reveals imbalances in dyschromosomal patients with normal or apparently balanced conventional karyotypes. Eur J Hum Genet. 8, 661.
Keywords: Abnormalities/genetics/Case Report/Chromosome Aberrations/Chromosome Abnormalities/Chromosome Banding/Comparative Study/Dna/analysis/DNA Probes/Female/Fetus/Fluorescent Dyes/metabolism/Genetic Screening/Human/In Situ Hybridization,Fluorescence/Karyotyping/Male/Mental Retardation/Nucleic Acid Hybridization/methods/Support,Non-U.S.Gov't/Genome
Abstract: A sensitive technique is needed for screening whole genome imbalances in dyschromosomal patients when G-banding shows normal karyotypes or apparently balanced translocations. In this study we performed highly sensitive comparative genomic hybridisation analysis on a number of such cases and revealed chromosomal imbalances in all.



Andersen MK, Christiansen DH, Kirchhoff M, Pedersen-Bjergaard JP (2001). Duplication or amplification of chromosome band 11q23 including the MLL gene is a recurrent abnormality in therapy-related MDS and AML closely related to mutation of the p53 gene and to previous therapy with alkylating agents. Genes Chrom Cancer. 31, 33.
Abstract: Gene amplification is a rare phenomenon in acute leukemia, but recently amplification of specific chromosome bands containing genes rearranged in leukemia-specific balanced chromosome translocations has been reported in a few cases. We detected duplication or amplification of chromosome band 11q23 with 3-7 copies of the MLL gene by fluorescence in situ hybridization in 12 out of 70 unselected patients with therapy-related myelodysplasia or acute myeloid leukemia (17%). In all but one case, the supernumerary copies of MLL were located to previously unidentified marker chromosomes or unbalanced translocations. In 4 of the 12 patients, 2-6 copies were located together on the same chromosome arm representing amplification, 7 patients had single, extra duplicated copies of MLL, whereas both amplification and duplication were observed in the same cell in 1 patient. Comparative genomic hybridization demonstrated gain of varying, often large parts of 11q in five patients. The MLL gene was shown to be unrearranged in all 12 patients. Seven out of eight patients with duplication or amplification of MLL had mutations of TP53. Patients with supernumerary copies of MLL were in general older (P = 0.007) and had a shorter survival (P < 0.001) compared to other patients. Duplication or amplification of MLL was significantly associated with a complex karyotype (P = 0.002), with deletion or loss of 5q (P = 0.001), and with prior therapy with alkylating agents. These results support the existence of a specific genetic pathway in t-MDS and t-AML with many previously unidentified chromosome aberrations demonstrated to represent extra copies of parts of 11q, including the unrearranged MLL gene.



Jacob Larsen, Anne Marie Ottesen, Claes Lundsteen, Henrik Leffers, and Jørgen K. Larsen (2001). Optimization of DOP-PCR amplification of DNA for high resolution comparative genomic hybridization analysis. Cytometry 44, 317.
Key words: PCR, Comparative genomic hybridization
Abstract: Background: Whole genome amplification of minute samples of DNA for the use in CGH analysis has found wide spread use, but the method has not been well validated.
Methods: Four different protocols for degenerate oligonucleotide primed polymerase chain reaction (DOP-PCR) and fluorescence labelling were applied to test DNA from normal cells and K-562 cells, and the DNA products were used for CGH analysis.
Results: The DOP-PCR amplified DNA from each protocol produced hybridizations with different qualities. These could primarily be seen as differences in background staining and signal/noise ratios, but also in the characteristic deviations of normal/normal hybridizations. One DOP-PCR-protocol was further investigated. We observed concordance between CGH results using unamplified and DOP-PCR amplified DNA. An example of an analysis of an invasive carcinoma of the breast supports the practical value of this approach.
Conclusions: DOP-PCR amplified DNA is applicable for high resolution CGH, the results being similar to those of CGH using unamplified DNA.



Larsen J, Ottesen AM, Kirchhoff M, Lundsteen C, Larsen JK (2001). High resolution comparative genomic hybridization detects 7-8 megabasepair deletion in PCR amplified DNA. Anal Cell Pathol.23.
Key words: High resolution comparative genomic hybridization, DOP-PCR, B-cell leukemia
Abstract: We investigated if any change in spatial resolution of comparative genomic hybridization analysis could be detected when using DNA amplified by degenerate oligonucleotide primed PCR (DOP-PCR) as opposed to the use of unamplified DNA. Five DNA samples from B-cell leukemias with small 11q deletions were amplified by DOP-PCR and analysed by means of high resolution comparative genomic hybridization (HR-CGH) for the evaluation of aberration size detection limit. By means of HR-CGH, we found the detection limit of DOP-PCR CGH for deletions to be between 3 Mbp and 7-8 Mbp.



Kirchhoff M, Rose H, Petersen BL, Maahr J, Gerdes T, Philip J, Lundsteen C (2001). Comparative genomic hybridization reveals non-random chromosomal aberrations in early preinvasive cervical lesions. Cancer Genet Cytogenet. 129, 47.
Keywords: Carcinoma in Situ/genetics/Carcinoma,Squamous Cell/Cervix Dysplasia/Cervix Neoplasms/Chromosome Aberrations/Chromosomes,Human/Comparative Study/Female/Human/Neoplasm Recurrence,Local/Nucleic Acid Hybridization/methods/
Abstract: We performed CGH analysis on 34 cervical lesions, which included eight cases of koilocytosis, six mild dysplasias and 20 moderate dysplasias. Chromosome aberrations were detected in 11 cases of which nine were moderate dysplasias. A total of 55 chromosome arms were involved. The most frequent aberrations were losses of chromosomes 5p and Xq which were each present in 5/34 cases. Gain of chromosome 3q were detected in two moderate dysplasias. This aberration is the most frequent copy number change in advanced-stage cervical carcinoma. A considerable number of the aberrations found in the preinvasive cases of this study are frequently present in invasive cervical tumors. The presence of apparently non-random chromosome aberrations in early preinvasive cervical lesions has not previously been described.



Kirchhoff M, Rose H, Gerdes T, Lundsteen C (2001). Påvisning af submikroskopiske kromosomfejl med komparativ genomisk hybridisering. Ugeskrift for læger. 163. 5652.
Summary in English: The purpose was to detect chromosome abnormalities in dysmorphic and mentally retarded individuals with normal karyotypes by means of comparative genomic hybridization (CGH). Material and methods: 144 individuals with normal karyotype underwent CGH-analysis with a new detection technique where fixed limits are replaced by dynamic standard reference intervals, which reveals an improved resolution and thereby detects smaller chromosome abnormalities. Sixteen small abnormalities (11%) were found. Eleven were interstitial deletions or duplications, which can not be detected by screening with other cytogenetic techniques. Three were terminal deletions or duplications, one was a terminal unbalanced translocation and one was a low frequent mosaic. CGH-analysis using dynamic standard reference intervals is a new objective and quantitative method suitable for screening for small chromosome abnormalities that can not be seen by conventional chromosome analysis. It is recommended that the method is used to investigate dysmorphic and mentally retarded individuals in whom abnormalities are not found by ordinary karyotyping.



Kirchhoff M, Rose H, Lundsteen C (2001). Comparative genomic hybridization in clinical genetics. J Med Genet. 38. 740
Keywords: Comparative genomic hybridization; chromosome analysis; chromosome aberrations; dyschromosomal
Abstract: For a number of years we have used high resolution comparative genomic hybridization as a diagnostic tool in our clinical cytogenetic laboratory. The present survey show the results of 159 clinical cases of which 39 (24.5%) were found to be abnormal. Among 50 dyschromosomal individuals with normal conventional karyotype eight (16%) had small deletions or amplifications of which five were interstitial. The eight abnormalities were all confirmed by either FISH or reinspection of the karyotype. Among 25 dyschromosomal individuals carrying an apparently balanced de novo translocations four had a deletion in a translocation breakpoint and two had deletions else where in the genome. Seventeen of 19 complicated rearrangements were clarified by HR-CGH. A supernumary small marker chromosome occurring with low frequency and the breakpoint of a mosaic of a r(18) could not be clarified. Three of 19 abnormalities could not be confirmed by HR-CGH. Two of these were DiGeorge syndrome and one was a case of Williams syndrome which had deletions that apparently were below the resolution of HR-CGH. However, we were able to confirm the deletions in one case of Angelmann and one case of Prader-Willi syndrome in which the deletions are about 3-5 Mb. We conclude that HR-CGH should be used as follows: 1) dyschromosomal individuals where normal karyotyping has failed to reveal abnormalities, 2) dyschromosomal individuals carrying apparently balanced de novo translocations, 3) apparently balanced de novo translocations detected prenatally and 4) for clarification of complicated structural rearrangements.



Kristensen TD, Wesenberg F, Jonsson OG, Carlsen NT, Forestier E, Kirchhoff M, Lundsteen C, Schmiegelow K (2003). High-resolution comparative genomic hybridisation yields a high detection rate of chromosomal aberrations in childhood acute lymphoblastic leukaemia. Eur J Haematol. 70(6): 363-72.
Abstract: BACKGROUND: Cytogenetic aberrations are of prognostic significance in childhood acute lymphoblastic leukaemias and a high detection rate could improve the biological understanding and classification of these diseases. METHODS: Bone-marrow samples from 92 children with acute lymphoblastic leukaemia were studied by high-resolution comparative genomic hybridisation (HRCGH) using dynamic standard reference intervals that enhance both specificity and sensitivity in the detection of aberrations. RESULTS: In 80 patients (87%) HRCGH revealed a total of 405 aberrations, mostly whole chromosome gains (n = 265) and partial losses (n = 80). The 25 leukaemias with a gain of more than five whole chromosomes by HRCGH harboured only 7% of all losses. With G-band karyotyping 59 patients (64%) had aberrations. HRCGH revealed more aberrations per patient than did G-band karyotyping (median: 3 vs. 1, P = 0.005), revealed aberrations in 27 of the 34 patients for whom the G-band karyotyping failed or was found to be normal, and specifically revealed more 9p losses (21% vs. 5%, P < 0.005), 12p losses (12% vs. 2%, P < 0.05) and 17q gains (11% vs. 1%, P < 0.01). Compared to the present study, the frequency of patients with aberrant karyotypes was significantly lower in previous conventional CGH studies (64% vs. 87%, P < 0.0001), as was the rate of partial aberrations per patient (1.1% vs. 1.7, P < 0.001), particularly with fewer 6q losses, 9p losses and 17q gains detected. CONCLUSION: HRCGH is superior to conventional CGH as an adjunct to G-band karyotyping as it detects recurrent aberrations at a significantly higher rate than both these techniques.



Ottesen AM, Skakkebaek NE, Lundsteen C, Leffers H, Larsen J, Rajpert-De Meyts E (2003). High-resolution comparative genomic hybridization detects extra chromosome arm 12p material in most cases of carcinoma in situ adjacent to overt germ cell tumors, but not before the invasive tumor development. Genes Chromosomes Cancer. 38(2): 117-25.
Abstract: High-resolution comparative genomic hybridization (HR-CGH) analysis was performed on DNA purified from laser-capture microdissected carcinoma in situ (CIS) cells from nine cases of CIS, either from tissue without any invasive tumor or from testicular parenchyma adjacent to seminoma, nonseminoma, or a combined germ cell tumor. Before CGH analysis, DNA was amplified by degenerate oligonucleotide primed PCR (DOP-PCR) and directly labeled with a mixture of FITC-dUTP and FITC-dCTP. CGH analysis revealed extra chromosome arm 12p material in six out of seven cases with CIS adjacent to overt tumors, but only a diminutive gain of 12q was noted in one of the two cases of CIS without invasive elements. In addition, gains of parts of chromosome 8 (3/7) and losses of chromosome 5 (2/7) were demonstrated in CIS adjacent to invasive tumors. Gains of parts of chromosome 7 were found in CIS adjacent to seminoma (4/4), whereas relative gains of chromosome 15 were identified in some cases of CIS adjacent to seminoma and in isolated CIS in comparison to CIS adjacent to nonseminoma. Our data seem to indicate that extra 12p material is not present in the "dormant" CIS cell before development of an invasive tumor. The gain of extra chromosome 12 material may not be an early event in the neoplastic transformation, but is most likely associated with a more malignant progression of the CIS cell.



Kirchhoff M, Pedersen S, Kjeldsen E, Rose H, Dunø M, Kølvraa S, Lundsteen C. A prospective study comparing HR-CGH and subtelomeric FISH for investigation of mentally retarded and dysmorphic individuals and an update of a study using only HR-CGH. Am J Med Genet. In press.
Abstract: In a prospective study 94 mentally retarded and dysmorphic individuals with normal conventional karyotypes were investigated by both subtelomeric FISH and high resolution CGH (HR-CGH) in order to compare the potential of the two techniques in this application. A total of 9.6% abnormalities were found with HR-CGH and subtelomeric FISH, with HR-CGH detecting 8.5% (95% CI: 4.4-15.9) and FISH 3.2% (95% CI: 1.2-9.0). Thus, the techniques complemented each other, however, the diagnostic yield appeared higher of HR-CGH than of subtelomeric FISH, as most aberrations were interstitial. Another 330 mentally retarded and dysmorphic individuals with normal conventional karyotypes were investigated by HR-CGH on a routine basis. When added to the analyses of the prospective study a total of 51/424 (12%; 95% CI: 9.3-15.5) abnormalities were found, of which the majority were interstitial. We conclude that HR-CGH is well suited for routine screening for cryptic chromosomal imbalances in patients with mental retardation and dysmorphic features. It is likely that the use of the technique in this application will reinforce the effort of defining new syndromes.



Bryndorf T, Kirchhoff M, Larsen J, Andreasson B, Bjerregaard B, Westh H, Rose H, Lundsteen C. The most common chromosome aberration detected by high-resolution comparative genomic hybridization in vulvar intraepithelial neoplasia is not seen in vulvar squamous cell carcinoma. Cytogenet Genome Res. In press.
Abstract:We analyzed genetic changes in condylomas (4 cases), vulvar intraepithelial neoplasia I-III (VIN I-III, 11 cases), and primary vulvar squamous cell carcinomas (VSCC, 10 cases) by high-resolution comparative genomic hybridization (HR-CGH) and flowcytometry. All samples were also human papilloma virus (HPV) -genotyped. Gain of chromosome 1, the aberration most often seen in VIN III (67 %), was not seen in HPV-positive or ?negative VSCCs (0 %). Both VIN III and VSCC frequently showed gain of 3q (56 % and 70 %, re-spectively). The VIN III samples often demonstrated gain of 20q (56%), and 20p (44%), and the VSCC samples gain of 8q (60%), and loss of 3p (50%), and 8p (40%). None of the 4 most frequent changes in the VSCC samples occurred exclusively in the HPV-positive or -negative samples. As expected, we did not find any cytogenetic changes in condylomas and nearly no changes in VIN I-II.




Home to HR-CGH - www.chromosomelab.dk
Copyright: Dept. of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark   -   Last revised: July 12, 2005