Optimizing DOP-PCR for universal amplification of small DNA samples in comparative genomic hybridization

Kuukasjärvi, Tuula; Tanner, Minna; Pennanen, Sari; Karhu, Ritva; Visakorpi, Tapio; Isola, Jorma

doi:10.1002/(sici)1098-2264(199702)18:2<94::aid-gcc3>3.0.co;2-w

Cited by 121 publications

(39 citation statements)

References 14 publications

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“…Briefly, areas of interest (2 -3 mm 2 ) were microdissected from paraffin-embedded formalinfixed tissue sections and digested with proteinase K. MCF7 cellline DNA and reference control DNAs from peripheral blood lymphocytes were extracted using a Progenome kit (Progen, Ipswich, Australia). DOP -PCR was performed on all reference and tumour samples and MCF-7 control DNA as previously described by Kuukasjarvi et al (1997). The CGH result using DOP -PCR amplified MCF-7 control showed all the same changes as an intra-laboratory MCF-7 standard CGH profile using nonamplified DNA.…”

Section: Cgh Methodsmentioning

confidence: 99%

Genetic aberrations detected by comparative genomic hybridisation in vulvar cancers

Hammet

et al. 2002

Br J Cancer

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Squamous cell carcinoma of the vulva is a disease of significant clinical importance, which arises in the presence or absence of human papillomavirus. We used comparative genomic hybridisation to document non-random chromosomal gains and losses within human papillomavirus positive and negative vulvar cancers. Gain of 3q was significantly more common in human papillomavirus-positive cancers compared to human papillomavirus-negative cancers. The smallest area of gain was 3q22 -25, a chromosome region which is frequently gained in other human papillomavirus-related cancers. Chromosome 8q was more commonly gained in human papillomavirus-negative compared to human papillomavirus-positive cancers. 8q21 was the smallest region of gain, which has been identified in other, non-human papillomavirus-related cancers. Chromosome arms 3p and 11q were lost in both categories of vulvar cancer. This study has demonstrated chromosome locations important in the development of vulvar squamous cell carcinoma. Additionally, taken together with previous studies of human papillomaviruspositive cancers of other anogenital sites, the data indicate that one or more oncogenes important in the development and progression of human papillomavirus-induced carcinomas are located on 3q. The different genetic changes seen in human papillomavirus-positive and negative vulvar squamous cell carcinomas support the clinicopathological data indicating that these are different cancer types.

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Section: Cgh Methodsmentioning

confidence: 99%

Genetic aberrations detected by comparative genomic hybridisation in vulvar cancers

Hammet

et al. 2002

Br J Cancer

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“…A number of different labeling techniques were tested: (a) standard nick translation (Langer et al, 1981), (b) standard DOP-PCR (Kuukasjarvi et al, 1997;Telenius et al, 1992), (c) cisplatinum-fluorochrome coupling (KREATECH, Amsterdam, Netherlands), and (d) linker-adapter-PCR (Klein et al, 1999). Cisplatinumfluorochrome compounds resulted in high signal intensities but yielded an unsatisfactory reproducibility of signal ratios.…”

Section: Preparation Of Test and Control Dnamentioning

confidence: 99%

Automated Screening for Genomic Imbalances using Matrix-Based Comparative Genomic Hybridization

Weßendorf

Fritz

Wrobel

et al. 2002

Laboratory Investigation

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SUMMARY:Genome-wide screening for chromosomal imbalances using comparative genomic hybridization (CGH) revealed a wealth of data on previously unrecognized tumor-specific genomic alterations. CGH to microarrays of DNA, an approach termed matrix-CGH, allows detection of genomic imbalances at a much higher resolution. We show that matrix CGH is also feasible from small tissue samples requiring universal amplification of genomic DNA. Because widespread application of matrix-CGH experiments using large numbers of DNA targets demands a high degree of automation, we have developed a protocol for a fully automated procedure. The use of specialized instrumentation for the generation of DNA chips, their hybridization, scanning, and evaluation required numerous alterations and modifications of the initial protocol. We here present the elaboration and testing of automated matrix-CGH. A chip consisting of 188 different genomic DNA fragments, cloned in bacterial artificial chromosome (BAC) or P1-derived artificial chromosome (PAC) vectors and immobilized in replicas of 10, was used to assess the performance of the automated protocol in determining the gene dosage variations in tumor cell lines COLO320-HSR, HL60, and NGP. Although ratios of matrix-CGH were highly concordant with results of chromosomal CGH (85%), the dynamic range of the matrix-CGH ratios was highly superior. Investigation of the two amplicons on 8q24 in COLO320-HSR and HL60, containing the MYC gene, revealed a homogeneous amplicon in COLO320-HSR but a heterogeneous amplification pattern in HL60 cells. Although control clones for normalization of the signal ratios can be predicted in cases with defined chromosomal aberrations, in primary tumors such data are often not available, requiring alternative normalization algorithms. Testing such algorithms in a primary high-grade B-cell lymphoma, we show the feasibility of this approach. With the matrix-CGH protocol presented here, robust and reliable detection of genomic gains and losses is accomplished in an automated fashion, which provides the basis for widespread application in tumor and clinical genetics. (Lab Invest 2002, 82:47-60).

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“…These ®ndings bear two interesting implications: (1) allelotyping can be e ciently used for amplicon mapping; (2) AI observed on a number of chromosomal sites in breast cancer could in fact correspond to gains of genetic material. This may explain the discrepancy shown between allelotyping and CGH studies on chromosome 1q, where multiple SROs have been described while CGH showed the existence of several regions of gains (Benitez et al, 1997;Isola et al, 1995;Kuukasjarvi et al, 1997;Munn et al, 1995).…”

Section: Molecular Cytogenetics Studymentioning

confidence: 99%

17q21-q25 aberrations in breast cancer: combined allelotyping and CGH analysis reveals 5 regions of allelic imbalance among which two correspond to DNA amplification

et al. 1999

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Chromosome 17q is frequently rearranged in breast cancer. Allelotyping studies have proposed the existence of at least four regions of allelic imbalance (AI). Here we present a study combining allelotyping using 19 CA repeat markers mapping in the 17q21 ± 25 region and molecular cytogenetics (CGH and FISH). Allelotyping was undertaken on 178 pairs of cognate tumor and normal DNA in order to determine the number of regions of AI and de®ne the shortest overlaps. AI ranged from 34 ± 54% of the informative cases according to the marker and, overall, 66% of the tumors presented AI at one of the markers tested. Analysis of the patterns of imbalances revealed at least ®ve common regions of imbalance respectively de®ned by markers: D17S855, which is intragenic of BRCA1 (SRO 1), D17S1607 (SRO 2), D17S1855 (SRO 3), between D17S789 and D17S785 (SRO 4) and D17S784 (SRO 5). In order to characterize the nature of the genetic events revealed by allelotyping we performed CGH analysis on a subset of 43 tumors presenting variable patterns of imbalance. CGH showed that AI at 17q could represent four di erent types of genetic events: loss of chromosome 17, gain of 17q, gain of 17q22 ± q24, loss of 17q11 ± q21 and/ or 17q25 ± qter. Some of these anomalies could occur concomitantly within the same tumor. Since 35% of the tumors analysed by CGH presented gains, these data indicated that AI at 17q were not solely indicative of losses of genetic material and could also represent DNA ampli®cation. Gains were most commonly observed in the 17q23 ± q24 regions. This suggested that AI in SRO 2 and SRO 3 corresponded to DNA ampli®cation. To assess this, we isolated BAC clones by PCR screening for markers D17S1607 and D17S1855 and used these in FISH experiments on six breast tumor cell lines and 14 breast cancer specimens. FISH results showed that both D17S1607 and D17S1855 were frequently involved in DNA ampli®cation (8 ± 30 copies). Altogether, our data show that allelotyping can be e ciently used in amplicon mapping. Clinico-pathological correlations indicated that imbalance at 17q preferentially occurred in high grade, PR-and ERBB2 ampli®ed tumors.

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Optimizing DOP-PCR for universal amplification of small DNA samples in comparative genomic hybridization

Cited by 121 publications

References 14 publications

Genetic aberrations detected by comparative genomic hybridisation in vulvar cancers

Genetic aberrations detected by comparative genomic hybridisation in vulvar cancers

Automated Screening for Genomic Imbalances using Matrix-Based Comparative Genomic Hybridization

17q21-q25 aberrations in breast cancer: combined allelotyping and CGH analysis reveals 5 regions of allelic imbalance among which two correspond to DNA amplification

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