Detection of chromosomal gains and losses in comparative genomic hybridization analysis based on standard reference intervals

Kirchhoff, Maria; Gerdes, Tommy; Rose, Hanne; Maahr, Jan; Ottesen, Anne Marie; Lundsteen, Claes

doi:10.1002/(sici)1097-0320(19980301)31:3<163::aid-cyto3>3.3.co;2-1

Cited by 62 publications

(93 citation statements)

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“…Imbalances were scored as a deviation from the standard reference interval CGH ratio profiles at 99.5% confidence intervals. 16 The CGH results were verified either by re-examination of G-banded highquality chromosomes (band level above 600) or by BACbased fluorescence in situ hybridisation (FISH) analysis. 7 Array-CGH For array-CGH, a BAC/PAC clone set consisting of approximately 3500 clones with an average interclonal distance of 1 Mb was obtained from the Wellcome Trust Sanger Institute (UK).…”

Section: Hr-cghsupporting

confidence: 81%

“…The finding of a terminal deletion combined with a subterminal duplication suggests that the mechanism might have been a breakage -fusionbridge cycle after 7q arm fusion. 20 In two patients with small but visible imbalances (Table 2), the HR-CGH software excluded the subtelomeric regions from the imbalance, 16 for example, case 72, where a terminal 19q duplication that appeared to be interstitial (Figure 3a) and, case 74, where the HR-CGH software suppressed the terminal part of a 22q13 deletion. This demonstrates that HR-CGH software may overlook even visible subtelomeric imbalances.…”

Section: Resultsmentioning

confidence: 99%

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Array-CGH fine mapping of minor and cryptic HR-CGH detected genomic imbalances in 80 out of 590 patients with abnormal development

et al. 2008

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During a 6-year period, 590 patients suspected of having a minor or cryptic genomic imbalance as the cause of mental retardation with dysmorphic signs þ /À malformations have been investigated with highresolution comparative genomic hybridisation (HR-CGH) in our diagnostic laboratory. Thirty-six patients had a small chromosomal aberration detected by routine karyotyping, and 554 patients had a normal G-banded karyotype. In the latter group, a genomic imbalance was detected by HR-CGH in 40 patients (7.2%): 29 deletions, 3 duplications, 4 unbalanced translocations, and 4 occult trisomy mosaicisms. When microarray-based comparative genomic hybridisation (array-CGH) became available, all HR-CGH-positive samples were also investigated by 1 Mb resolution array-CGH for more precise mapping. From the 514 patients with normal HR-CGH findings, a subset of 20 patients with particularly high suspicion of having a chromosomal imbalance was selected for array-CGH. In four of them (20%), an imbalance was detected: three deletions and one duplication. Of note, 73 out of the 80 array-CGH mapped patients had a de novo chromosomal rearrangement (91%). Taken together, this work provides phenotype -genotype information on 80 patients with minor and cryptic chromosomal imbalances.

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Section: Hr-cghsupporting

confidence: 81%

Section: Resultsmentioning

confidence: 99%

Array-CGH fine mapping of minor and cryptic HR-CGH detected genomic imbalances in 80 out of 590 patients with abnormal development

et al. 2008

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“…16,17 Third, previous studies usually scored the alterations with a resolution that is far behind the power of CGH counting a specific genetic change as an imbalance of the entire chromosome arm. This is understandable because of the complexity of the statistical analysis if each chromosomal subregion is analyzed separately.…”

Section: Discussionmentioning

confidence: 99%

Genetic Imbalances with Impact on Survival in Head and Neck Cancer Patients

Bockmühl

Schlüns

Küchler

et al. 2000

The American Journal of Pathology

113

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Chromosomal imbalances in 113 primary head and neck squamous cell carcinomas (HNSCCs) determined by comparative genomic hybridization were correlated with patients survival using custom-made computer software which enabled the assessment of individual chromosomal loci. The Kaplan-Meier analysis revealed that overrepresentations of 2q12, 3q21-29, 6p21.1, 11q13, 14q23, 14q24, 14q31, 14q32, 15q24, 16q22, and deletions of 8p21-22 and 18q11.2 were significantly associated with both shorter disease-free interval and disease-specific survival in this tumor collective. Multivariate Cox proportional hazards regression models consistently identified the gains of 3q21-29, 11q13, and the loss of 8p21-22 as independent prognostic markers carrying a higher significance than the nodal status as the only clinicopathological parameter with statistical importance. In addition, these three markers allowed a molecular dissection of the patients with low clinical risk (pN0 and pT2 tumors). Thus, the genomic data being derived from the evaluation of primary HNSCC enabled a stratification of the patients into subgroups with different survival highlighting the necessity of a genetically based tumor classification for refining diagnosis and treatment of HNSCC patients. (Am J Pathol , :369 -375)

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“…A negative (normal vs normal) and a positive control were included in every set of experiments. In all, 10 cells of each of 10 normal vs normal hybridisations were used to establish the normal ratio profile with 99% confidence intervals (Kirchhoff et al, 1998). Copy number gains or losses were scored whenever the test and reference 99% confidence intervals did not overlap.…”

Section: Comparative Genomic Hybridisationmentioning

confidence: 99%

Assessment of clonal relationships in ipsilateral and bilateral multiple breast carcinomas by comparative genomic hybridisation and hierarchical clustering analysis

et al. 2004

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The issue of whether multiple, ipsilateral or bilateral, breast carcinomas represent multiple primary tumours or dissemination of a single carcinomatous process has been difficult to resolve, especially for individual patients. We have addressed the problem by comparative genomic hybridisation analysis of 26 tumours from 12 breast cancer patients with multiple ipsilateral and/or bilateral carcinoma lesions. Genomic imbalances were detected in 25 of the 26 (96%) tumours. Using the genomic imbalances detected in these 26 lesions as well as those previously found by us in an independent series of 35 unifocal breast carcinomas, we compared a probabilistic model for likelihood of independence with unsupervised hierarchical clustering methodologies to determine the clonal relatedness of multiple tumours in breast cancer patients. We conclude that CGH analysis of multiple breast carcinomas followed by unsupervised hierarchical clustering of the genomic imbalances is more reliable than previous criteria to determine the tumours' clonal relationship in individual patients, that most ipsilateral breast carcinomas arise through intramammary spreading of a single breast cancer, and that most patients with bilateral breast carcinomas have two different diseases.

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Detection of chromosomal gains and losses in comparative genomic hybridization analysis based on standard reference intervals

Cited by 62 publications

References 0 publications

Array-CGH fine mapping of minor and cryptic HR-CGH detected genomic imbalances in 80 out of 590 patients with abnormal development

Array-CGH fine mapping of minor and cryptic HR-CGH detected genomic imbalances in 80 out of 590 patients with abnormal development

Genetic Imbalances with Impact on Survival in Head and Neck Cancer Patients

Assessment of clonal relationships in ipsilateral and bilateral multiple breast carcinomas by comparative genomic hybridisation and hierarchical clustering analysis

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