The development of a mini-array for estimating the disease state of gastric adenocarcinoma by array CGH

Furuya, Tomoko; Uchiyama, Takanori; Adachi, Atsushi; Okada, Takae; Nakao, Motonao; Oga, Atsunori; Yang, Song Ju; Kawauchi, Shigeto; Sasaki, Kohsuke

doi:10.1186/1471-2407-8-393

Cited by 9 publications

(8 citation statements)

References 22 publications

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“…The array slides were scanned with a GenePix 4000A scanner (Axon Instruments, Union City, CA). The fluorescence images were analyzed using the Mac Viewer software program (Macrogen, Inc.) optimized for the analysis of the array as previously reported (17)(18)(19). Fluorescence spots were defined with the automatic grid feature and adjusted manually.…”

Section: Statistical Analysis Of Fish and Lsc Resultsmentioning

confidence: 99%

Genomic instability and DNA ploidy are linked to DNA copy number aberrations of 8p23 and 22q11.23 in gastric cancers

et al. 2010

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Abstract. The close relationship between chromosomal instability (CIN) and aneuploidy has been reported. The purpose of this study was to identify genomic aberrations present with CIN and aneuploidy in gastric cancers. FISH and image cytometry were applied to 27 sporadic gastric adenocarcinomas to identify CIN-positive tumors and to determine DNA ploidy, respectively. In addition, array-based comparative genomic hybridization was used to identify bacterial artificial chromosome clones that displayed differences in the frequency of copy number aberrations between CIN-positive and CIN-negative tumors, and between aneuploid and diploid tumors. There were many chromosomal regions with DNA copy number aberrations, some of which were nonrandom aberrations linked to the CIN phenotype and aneuploidy. A copy number loss of 22q11.23 was more frequent in CIN-positive cancers than in others (7/12 vs. 2/15, p<0.01) and in aneuploid cancers than in diploid cancers (8/16 vs. 1/11, p<0.05). The frequency of 22q11.23 loss differed significantly between CIN-positive and aneuploid tumors and between CIN-negative and diploid cancers (7/10 vs. 1/9, p<0.01). In contrast, a DNA copy number gain of 8p23.2 was detected in 6 out of 9 CINnegative/diploid cancers, but was not detected in CINpositive/aneuploid cancers (p<0.01). There were no cancers carrying both aberrations (22q11.23 loss and 8p23.2 gain). The present study indicates that a 22q11.23 loss and a 8p23.2 gain are markers for both CIN and aneuploidy. This is the first report describing an inverse relationship between the 22q11.23 loss and 8p23.2 gain in terms of genomic instability and DNA ploidy in gastric cancers.

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Section: Statistical Analysis Of Fish and Lsc Resultsmentioning

confidence: 99%

Genomic instability and DNA ploidy are linked to DNA copy number aberrations of 8p23 and 22q11.23 in gastric cancers

et al. 2010

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“…The clones with log 2 ratios exceeding ±0.25 were considered gain and loss of the copy number. A log 2 ratio >1.0 was defined as amplifications in this study (18)(19)(20).…”

Section: Methodsmentioning

confidence: 99%

“…The experiments were performed as previously described (18)(19)(20). Briefly, tumor DNA (500 ng) and gender-matched reference DNA (Promega, Madison, WI) were labeled with Cy5-and Cy3-dCTP (Perkin-Elmer Life Science, Inc., Waltham, MA), respectively, with a random primer labeling kit (BioPrine ® DNA Labelling System, Invitrogen, Carlsbad, CA).…”

Section: Methodsmentioning

confidence: 99%

DNA copy number aberrations associated with aneuploidy and chromosomal instability in breast cancers

Kawauchi¹

2010

Oncol Rep

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Abstract. Biological characteristics of a tumor are primarily affected by its genomic alterations. It is thus important to ascertain whether there are genomic changes linked with DNA ploidy and/or chromosomal instability (CIN). In the present study, using fresh-frozen samples of 46 invasive breast cancers, laser scanning cytometry, array-based comparative genomic hybridization, and chromosome fluorescence in situ hybridization were performed to assess DNA ploidy, DNA copy number aberrations (DCNAs), and CIN status. Both ploidy and CIN status were examined in 36 tumors, resulting in 23 aneuploid/CIN + tumors, 1 aneuploid/ CIN -, 2 diploid/CIN + , and 10 diploid/CIN -tumors. Comparison of the aCGH data with the DNA ploidy and CIN status identified cytogenetically 11 characteristic breast cancers with distinctive DCNAs. The 11 tumors were classified into two types; one type is diploid/CIN -phenotype containing 4 DCNAs, and the other aneuploid/CIN + phenotype containing 7 DCNAs. In 30 (65.2%) of the 36 breast cancers, the status of DNA ploidy and CIN depended on the type of DCNAs. Furthermore, the DNA ploidy phenotype depended on the dominant type of DCNAs even in tumors with a mixture of multiple DCNAs of one type and a single DCNA of the other type. Tumors with multiple DCNAs of both types represented aneuploidy and over three quarters of breast cancers carry at least one type of the DCNAs. These results suggested that, in breast cancers, the status of DNA ploidy and CIN was likely to determine at the beginning of carcinogenesis.

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“…In fact, to detect DNA copy number aberrations, aCGH has been used to examine many cancers and cancer cell lines for diagnosis and prognosis [3][4][5][6][7]. Moreover, in Korea an aCGH chip was approved for use to diagnose hereditary diseases and inherent chromosomal disorders, such as Down syndrome and Turner's syndrome, which are caused by chromosomal aberrations [Korean Food and Drug Administration (KFDA; http://www.macrogen.com/eng/macrogen/press_ list.jsp)].…”

Section: Introductionmentioning

confidence: 99%

Use of BAC array CGH for evaluation of chromosomal stability of clinically used human mesenchymal stem cells and of cancer cell lines

et al. 2010

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Array-based comparative genomic hybridization (aCGH) using bacterial artificial chromosomes (BAC) is a powerful method to analyze DNA copy number aberrations of the entire human genome. In fact, CGH and aCGH have revealed various DNA copy number aberrations in numerous cancer cells and cancer cell lines examined so far. In this report, BAC aCGH was applied to evaluate the stability or instability of cell lines. Established cell lines have greatly contributed to advancements in not only biology but also medical science. However, cell lines have serious problems, such as alteration of biological properties during long-term cultivation. Firstly, we investigated two cancer cell lines, HeLa and Caco-2. HeLa cells, established from a cervical cancer, showed significantly increased DNA copy number alterations with passage time. Caco-2 cells, established from a colon cancer, showed no remarkable differences under various culture conditions. These results indicate that BAC aCGH can be used for the evaluation and validation of genomic stability of cultured cells. Secondly, BAC aCGH was applied to evaluate and validate the genomic stabilities of three patient's mesenchymal stem cells (MSCs), which were already used for their treatments. These three MSCs showed no significant differences in DNA copy number aberrations over their entire chromosomal regions. Therefore, BAC aCGH is highly recommended for use for a quality check of various cells before using them for any kind of biological investigation or clinical application.

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The development of a mini-array for estimating the disease state of gastric adenocarcinoma by array CGH

Cited by 9 publications

References 22 publications

Genomic instability and DNA ploidy are linked to DNA copy number aberrations of 8p23 and 22q11.23 in gastric cancers

Genomic instability and DNA ploidy are linked to DNA copy number aberrations of 8p23 and 22q11.23 in gastric cancers

DNA copy number aberrations associated with aneuploidy and chromosomal instability in breast cancers

Use of BAC array CGH for evaluation of chromosomal stability of clinically used human mesenchymal stem cells and of cancer cell lines

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