Summary. We have carried out comparative genomic hybridization (CGH) analysis on archival biopsy material from a series of 30 UK mantle cell lymphomas. The most frequent aberrations were gains of 3q (21 cases), 6p (19 cases), 7q (8 cases), 12p (8 cases), 12q (9 cases) and 17q11q21 (8 cases), and losses of 1p13p32 (10 cases), 5p13p15.3 (9 cases), 6q14q27 (11 cases), 8p (7 cases), 11q13q23 (8 cases) and 13q (18 cases). Nineteen cases (63%) had a common region of amplification at 3q28q29, which was highly amplified in three cases, suggesting the presence of a mantle cell lymphoma (MCL)‐related oncogene in this region. There was a minimal common region of deletion at 6q25q26 in nine cases (30%). No MCL‐specific locus has previously been identified on chromosome 6 and this region may contain a tumour suppressor gene specifically implicated in the development of this subtype of lymphoma. An increased number of chromosome aberrations, gain of Xq and loss of 17p were all significantly associated with a worse prognosis. A greater understanding of the genetics of mantle cell lymphoma may allow the identification of prognostic factors which will aid the identification of appropriate treatment regimens.

The purpose of this study was to identify novel areas of genomic copy number change associated with transformation from follicular lymphoma (FL) to diffuse large B cell lymphoma (DLBL). DNA was extracted from tumour cells micro-dissected from paraffin- embedded tissue sections in 24 patients with FL and subsequent transformation to DLBL and 18 patients with de novo DLBL. Tumour DNA was compared to reference DNA using comparative genomic hybridization. Abnormalities common to all 3 groups were gains on chromosomes 4q, 5q, 7q, 11q and X and losses on 3p, 8p and 10q. Copy number changes seen in both transformed and de novo DLBL and not seen in FL were gains on 2p and losses on 1q, 15q and Xq. Gains on 2q, 6p, 7p and 17q and losses on 5p and 8q were specific to transformed DLBL cases. Gain on 12q12-14 was found in 52% of the transformed DLBL cases and was never seen in its follicular counterpart. Patterns of genomic copy number change associated with specific clinical events in NHL have been demonstrated and suggest that gains on 2q, 6p, 7p, 12q and 17q and losses on 5p and 8q may be important in the transformation from low to high-grade disease. © 2001 Cancer Research Campaign http://www.bjcancer.com

This investigation aimed to identify patterns of copy number change in colorectal tumor progression from adenoma to liver metastasis. Fifty-three microdissected sub-regions from 17 cases of colorectal cancer were assigned to one of six histopathologically defined categories: coexisting adenoma, tumor above the muscularis layer, tumor within the muscularis layer, tumor extending through the bowel wall to serosal fat, lymph node metastasis, and liver metastasis. Microdissected samples were treated by a microwave processing step and then used as templates for universal PCR amplification. PCR products were fluorophore labeled and subjected to comparative genomic hybridization. Copy number changes were found in all samples, and every chromosome arm (excluding acrocentric short arms) was affected. More losses than gains were detected, but there were no significant differences between the numbers of changes seen in each category. Each individual sample revealed unique changes, additional to those shared within each case. The most frequently observed gains were of X and 12q. The most common losses were of 8p, 16p, 9p, 15q, 18q, and 10q. Nominally significant associations were observed between metastatic tumor and loss of 12q24.1 or 10p13-14, non-metastatic tumor and loss of 8q24.1, tumor extending to serosal fat and loss of 6q24-25 or gain of 4q11-13, tumor extending to serosal fat and metastatic lesions and loss of 4q32-34 or 22q11-12, and adenoma and loss of 15q24. Loss of 4q32-34 remained highly significant after correction for multiple testing. Adenoma was the only category not to show loss of 17p. These data reveal a genetically heterogeneous picture of tumor progression, with a small number of changes associated with advanced disease.

Polymerase chain reaction (PCR) techniques are used increasingly for the diagnosis of Mycobacterium tuberculosis infection and can be used on the DNA obtained from both frozen and formalin fixed, paraYn wax embedded tissues. However, the extraction of DNA by means of the conventional phenol/chloroform method is time consuming and requires the use of potentially dangerous chemical reagents. This paper describes a method based upon the use of magnetic beads for the extraction of M tuberculosis DNA from both routinely formalin fixed, paraffin wax embedded tissues and frozen tissues. Magnetic bead extracted DNA from brain, lymph node, and lung tissues collected from patients with human immunodeficiency virus and tuberculosis was compared with that extracted using the phenol/ chloroform method. The magnetic bead extraction procedure requires less than two hours, including the time necessary to dewax the tissue sections. In all cases, the DNA extracted with both methods was amplified successfully by PCR for the M tuberculosis IS6110 sequence. Magnetic bead DNA extraction can be used on both frozen and archival tissues: the method is reliable, simple, sensitive, and rapid; in addition, it does not use hazardous procedures or specialised laboratory equipment and can be used for routine DNA isolation from various human tissues. (J Clin Pathol: Mol Pathol 1999;52:158-160) Keywords: magnetic beads; paraYn wax embedded tissue; DNA extraction for Mycobacterium tuberculosisOver the past few years, the polymerase chain reaction (PCR) has been widely used to identify the genomic sequences of a number of microorganisms from various biological fluids and tissues, including samples processed routinely for histopathological examination, although the fixation and processing steps reduce the eYciency of extraction and the integrity of nucleic acids. 1 The most widely used method for extracting DNA from formalin fixed, paraYn wax embedded blocks requires tissue lysis with proteinase K, followed by phenol/chloroform extraction, and ethanol precipitation. However, this procedure is relatively long and exposes the operators to potentially dangerous reagents. Alternative methods for the extraction of DNA from fresh and/or paraYn wax embedded samples have been proposed, based upon diVerent chemical principles. [2][3][4][5][6] We report here the results of a method based upon the use of magnetic beads (Dynabeads; Dynal, Oslo, Norway) for the extraction of DNA from formalin fixed, paraYn wax embedded tissues and frozen tissues, which has been used previously on human whole blood, bone marrow, and cultured cells. 2 The process relies upon cell lysis to release the DNA and its subsequent adsorption to the surface of the Dynabeads and does not require specialised laboratory equipment. To compare magnetic bead extraction with a conventional phenol/chloroform method, we amplified the DNA extracted from both formalin fixed and frozen tissues of culture confirmed cases of tuberculosis with a nested PCR (nPCR) method for a sequence from t...