Cell Line Data Base: structure and recent improvements towards molecular authentication of human cell lines

Romano, Paolo; Manniello, A.; Aresu, Ottavia; Armento, Massimiliano; Cesaro, Michela; Parodi, Brunella

doi:10.1093/nar/gkn730

Cited by 128 publications

(99 citation statements)

References 11 publications

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“…The cell lines were authenticated by using the panel of 11 STRs (AmpFlSTR SGM Plus; Applied Biosystems). The number of repeats for each locus was verified in the CLIMA database (13).…”

Section: Human Crc Tissue Samples and Human Crc Cell Linesmentioning

confidence: 99%

Intermediate- and Low-Methylation Epigenotypes Do Not Correspond to CpG Island Methylator Phenotype (Low and -Zero) in Colorectal Cancer

Karpiński

Walter

Szmida

et al. 2013

Cancer Epidemiology, Biomarkers &Amp; Prevention

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Background: Most recent genome-wide studies on the CpG island methylation in colorectal cancer (CRC) have led to the discovery of at least 3 distinct methylation clusters. However, there remains an uncertainty whether the CRC clusters identified in these studies represent compatible phenotypes.Methods: We carried out comprehensive genome-scale DNA methylation profiling by Illumina Infinium HumanMethylation27 of 21 DNA pools that represent 84 CRC samples divided according to their high-, intermediate-, and low-methylation epigenotypes (HME, IME, and LME, respectively) and 70 normal-adjacent colonic tissues. We have also examined the relationship among 3 epigenotypes and chromosomal gains and deletions (assessed by Comparative Genomic Hybridization) in a group of 100 CRC samples.Results: The HME subgroup showed features associated with CpG island methylator phenotype -high (CIMP-high) including methylation of specific CpG sites (CpGs) as well as significantly lower mean number of chromosomal imbalances when compared with other epigenotypes. The IME subgroup displayed the lowest number of methylated CpGs (717 vs. 2,399 and 2,679 in HME and LME, respectively) and highest mean number of chromosomal imbalances when compared with HME (P, 0.001) and LME (P, 0.004). A comparison between the methylation profiles of 3 epigenotypes revealed more similarities between the HME and LME (1,669 methylated CpGs overlapped) than HME and IME (673 methylated CpGs overlapped).Conclusion: Our results provide evidence that IME and LME CRCs show opposite features to those that have been previously attributed to CIMP-low and CIMP-0 CRCs.Impact: These discrepancies should be considered when interpreting the data from a particular epigenotyping method. Cancer Epidemiol Biomarkers Prev; 22(2); 201-8. Ó2012 AACR.

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“…The cell lines were authenticated by using the panel of 11 STRs (AmpFlSTR SGM Plus; Applied Biosystems). The number of repeats for each locus was verified in the CLIMA database (13).…”

Section: Human Crc Tissue Samples and Human Crc Cell Linesmentioning

confidence: 99%

Intermediate- and Low-Methylation Epigenotypes Do Not Correspond to CpG Island Methylator Phenotype (Low and -Zero) in Colorectal Cancer

Karpiński

Walter

Szmida

et al. 2013

Cancer Epidemiology, Biomarkers &Amp; Prevention

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“…CLDB (Romano, 2009) and its hypertextual version HyperCLDB 7 are a long established service, offering information on human and animal cell lines since 1990. Included in CLDB, are data on 6 http://bioinformatics.istge.it/cldb/cldb.php 7 http://bioinformatics.istge.it/hypercldb/ availability of cell lines in some of the most well known European collections and in many Italian research laboratories, together with their main biological characterisation.…”

Section: Methodsmentioning

confidence: 99%

EMBnet.journal 19 Suppl. B

journal¹

2013

EMBnet j.

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“…CLDB (Romano, 2009) and its hypertextual version HyperCLDB 7 are a long established service, offering information on human and animal cell lines since 1990. Included in CLDB, are data on availability of cell lines in some of the most well known European collections and in many Italian research laboratories, together with their main biological characterisation.…”

Section: Methodsmentioning

confidence: 99%

Towards a semantic wiki for human and animal cell lines

Romano

Bolser

2013

EMBnet j.

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Wiki systems have emerged as a social network tool able to stimulate users to contribute to the collaborative building of a common knowledge base. Some of the specific aims of wikis for biology (bio-wikis) include collaborative efforts for the development and sharing of knowledge, the annotation of database contents, and the creation of database contents. Indeed, the increasing volumes of biological data cannot be adequately managed by the existing centralised databases and database curators. On the contrary, information and data must be exchanged by the whole community. Special features may be required to adapt to the specificity of biological data. Moreover, integration with the most relevant biological databases must be implemented. In this context, Semantic technologies promise to be of paramount relevance. In this abstract, we present a preliminary analysis for the implementation of a semantic wiki system for human and animal cell lines derived from the Cell Line Data Base (CLDB) and tightly connected to external relevant resources.

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Cell Line Data Base: structure and recent improvements towards molecular authentication of human cell lines

Cited by 128 publications

References 11 publications

Intermediate- and Low-Methylation Epigenotypes Do Not Correspond to CpG Island Methylator Phenotype (Low and -Zero) in Colorectal Cancer

Intermediate- and Low-Methylation Epigenotypes Do Not Correspond to CpG Island Methylator Phenotype (Low and -Zero) in Colorectal Cancer

EMBnet.journal 19 Suppl. B

Towards a semantic wiki for human and animal cell lines

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