Tommy Gerdes

DETECTION OF CHROMOSOMAL GAINS AND LOSSES IN COMPARATIVE GENOMIC HYBRIDIZATION ANALYSIS BASED ON STANDARD REFERENCE INTERVALS

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.

Deletions below 10 megabasepairs are detected in comparative genomic hybridization by standard reference intervals

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. Genes Chromosomes Cancer 25:410–413, 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

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. Genes Chromosomes Cancer 24:144–150, 1999.

Increased Number of Sex Chromosomes Affects Height in a Nonlinear Fashion: A Study of 305 Patients With Sex Chromosome Aneuploidy

Tall stature and eunuchoid body proportions characterize patients with 47,XXY Klinefelter syndrome, whereas patients with 45,X Turner syndrome are characterized by impaired growth. Growth is relatively well characterized in these two syndromes, while few studies describe the growth of patients with higher grade sex chromosome aneuploidies. It has been proposed that tall stature in sex chromosome aneuploidy is related to an overexpression of SHOX, although the copy number of SHOX has not been evaluated in previous studies. Our aims were therefore: (1) to assess stature in 305 patients with sex chromosome aneuploidy and (2) to determine the number of SHOX copies in a subgroup of these patients (n = 255) these patients and 74 healthy controls. Median height standard deviation scores in 46,XX males (n = 6) were −1.2 (−2.8 to 0.3), +0.9 (−2.2 to +4.6) in 47,XXY (n = 129), +1.3 (−1.8 to +4.9) in 47,XYY (n = 44), +1.1 (−1.9 to +3.4) in 48,XXYY (n = 45), +1.8 (−2.0 to +3.2) in 48,XXXY (n = 9), and −1.8 (−4.2 to −0.1) in 49,XXXXY (n = 10). Median height standard deviation scores in patients with 45,X (n = 6) were −2.6 (−4.1 to −1.6), +0.7 (−0.9 to +3.2) in 47,XXX (n = 40), −0.6 (−1.9 to +2.1) in 48,XXXX (n = 13), and −1.0 (−3.5 to −0.8) in 49,XXXXX (n = 3). Height increased with an increasing number of extra X or Y chromosomes, except in males with five, and in females with four or five sex chromosomes, consistent with a nonlinear effect on height.

Computer-assisted prenatal aneuploidy screening for chromosome 13, 18, 21, X and Y based on multiplex ligation-dependent probe amplification (MLPA).

In routine prenatal diagnostics we used a commercial multiplex ligation-dependent probe amplification (MLPA) kit for aneuploidy screening for chromosomes 13, 18, 21, X and Y. We present the results of 1593 consecutive prenatal samples analysed and diagnosed prior to knowledge of the G-banding analysis during 8-month routine use of computer-assisted MLPA aneuploidy screening. In total, 27 aneuploidies were detected. There were no false positive results while two false negative results could be explained by a placental mosaicism and a partial monosomy, respectively. In total, 3.2% of the samples were inconclusive. We conclude that automatic computer assisted MLPA is a rapid, simple and reliable method for detection of aneuploidies in prenatal diagnostics.

Detection of chromosomal aberrations in seminomatous germ cell tumours using comparative genomic hybridization

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 clinical stage II and relapsed tumours, may be linked to tumour progression, invasiveness, and bilateral disease. Genes Chromosomes Cancer 20:412–418, 1997.

High resolution comparative genomic hybridisation analysis reveals imbalances in dyschromosomal patients with normal or apparently balanced conventional karyotypes.

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.

Comparative genomic hybridization reveals non-random chromosomal aberrations in early preinvasive cervical lesions

We performed CGH analysis on 34 cervical lesions, which included 8 cases of koilocytosis, 6 mild dysplasias and 20 moderate dysplasias. Chromosome aberrations were detected in 11 cases of which 9 were moderate dysplasias. A total of 55 chromosome arms were involved. The most frequent aberrations were losses of 5p and Xq, each of which was present in 5/34 cases. Gain of 3q was 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.

Automatic correction of the interfering effect of unsuppressed interspersed repetitive sequences in comparative genomic hybridization analysis

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.

Multiplex ligation-dependent probe amplification (MLPA) in prenatal diagnosis : experience of a large series of rapid testing for aneuploidy of chromosomes 13, 18, 21, X, and Y

Multiplex ligation‐dependent probe amplification (MLPA) is a relatively new method for rapid prenatal diagnosis of common aneuploidies, and larger series to evaluate its performance remain to be reported.