Novel genomic alterations and clonal evolution in chronic lymphocytic leukemia revealed by representational oligonucleotide microarray analysis (ROMA)

Grubor, Vladimir; Krasnitz, A.; Troge, Jennifer; Meth, Jennifer; Lakshmi, B.; Kendall, Jude; Yamrom, Boris; Alex, Garrick; Pai, Deepa; Navin, Nicholas E.; Hufnagel, Lisa A.; Lee, Yoonha; Cook, Kerry; Allen, Sheila; Kanti, R.; Damle, Rajendra N.; Calissano, Carlo; Chiorazzi, Nicholas; Wigler, Michael; Esposito, Diane

doi:10.1182/blood-2008-05-158865

Cited by 95 publications

(68 citation statements)

References 46 publications

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“…CNVs identified by CGH and array technology have the potential to directly or indirectly impact the susceptibility of a healthy individual to cancer, for example by varying the gene dosage of tumor suppressors or oncogenes (14,27). However, many discrepancies exist among previous studies which used high-resolution approaches to screen CNVs (28)(29)(30)(31)(32). Thus, validation of such CNVs using a large number of clinical samples is required.…”

Section: Discussionmentioning

confidence: 99%

Coexistence of copy number increases of ZNF217 and CYP24A1 in colorectal cancers in a Chinese population

Fang

Xiong²,

Zhang³

et al. 2010

Oncology Letters

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Abstract. Evidence suggests that the amplification of chromosome 20q13 is common in colorectal cancers (CRCs). Certain candidate oncogenes located in this region are reported to be associated with tumorigenesis of the gastrointestinal tract. The functional impact of such regions should be extensively investigated in a large number of clinical samples. In this study, 145 CRC samples with matched adjacent normal tissues were collected from a Chinese population for copy number variation (CNV) analysis. Our results showed that both the copy numbers of 25-hydroxy vitamin D3 24-hydroxylase (CYP24A1) and zinc-finger protein 217 (ZNF217) were amplified in a relatively high percentage of CRC samples (51.1 and 60%, respectively). The mRNA expression levels of both CYP24A1 and ZNF217 were found to have increased in the collected CRC samples as compared to the matched adjacent normal tissues. ZNF217, but not CYP24A1, showed a positive correlation between copy number increases and mRNA overexpression. These findings suggest the potential role of CNVs of certain oncogenes in CRCs.

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Section: Discussionmentioning

confidence: 99%

Coexistence of copy number increases of ZNF217 and CYP24A1 in colorectal cancers in a Chinese population

Fang

Xiong²,

Zhang³

et al. 2010

Oncology Letters

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“…The similarity scores were segmented into contiguous regions matching one or the other parental line using a segmentation algorithm based on the Kolmogorov Smirnov (KS) test statistic (Grubor et al 2009). Segmentation values less than 0.4 and greater than 0.6 were rounded to zero and one, respectively.…”

Section: Rils Switching Methylation Statementioning

confidence: 99%

The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA

et al. 2013

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The maize genome, with its large complement of transposons and repeats, is a paradigm for the study of epigenetic mechanisms such as paramutation and imprinting. Here, we present the genome-wide map of cytosine methylation for two maize inbred lines, B73 and Mo17. CG (65%) and CHG (50%) methylation (where H = A, C, or T) is highest in transposons, while CHH (5%) methylation is likely guided by 24-nt, but not 21-nt, small interfering RNAs (siRNAs). Correlations with methylation patterns suggest that CG methylation in exons (8%) may deter insertion of Mutator transposon insertion, while CHG methylation at splice acceptor sites may inhibit RNA splicing. Using the methylation map as a guide, we used low-coverage sequencing to show that parental methylation differences are inherited by recombinant inbred lines. However, frequent methylation switches, guided by siRNA, persist for up to eight generations, suggesting that epigenetic inheritance resembling paramutation is much more common than previously supposed. The methylation map will provide an invaluable resource for epigenetic studies in maize.

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“…Novel small aberrations have recently been reported in CLL, although with low recurrence either within or between studies. 4,9 This discrepancy between different array studies is probably highly influenced by the differential design of microarrays applied. 8 Overall survival was investigated in relation to the hierarchal model of known recurrent alterations, which verified the clinical impact of these prognostic markers (Figure 2a).…”

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confidence: 99%

Large but not small copy-number alterations correlate to high-risk genomic aberrations and survival in chronic lymphocytic leukemia: a high-resolution genomic screening of newly diagnosed patients

et al. 2009

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Novel genomic alterations and clonal evolution in chronic lymphocytic leukemia revealed by representational oligonucleotide microarray analysis (ROMA)

Cited by 95 publications

References 46 publications

Coexistence of copy number increases of ZNF217 and CYP24A1 in colorectal cancers in a Chinese population

Coexistence of copy number increases of ZNF217 and CYP24A1 in colorectal cancers in a Chinese population

The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA

Large but not small copy-number alterations correlate to high-risk genomic aberrations and survival in chronic lymphocytic leukemia: a high-resolution genomic screening of newly diagnosed patients

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