Detection of hemizygous deletions in genomic DNA from leukaemia specimens for the diagnosis of patients

Kees, Ursula R.; Terry, Philippa; Ford, Jette; Everett, J.P.; Murch, Ashleigh; Klerk, Nicholas de; Baker, David L.

doi:10.1016/j.leukres.2004.05.021

Cited by 7 publications

(8 citation statements)

References 22 publications

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“…Real-time Q-PCR is a precise and reproducible assay that has been successfully used in the measurement of genomic copy number changes in human tumors (Senchenko et al, 2003;Kees et al, 2005). In the present study, real-time Q-PCR was used to characterize the deletion patterns of 10 genes mapping to 22q12.3-q13.33, which were previously found to be underexpressed in pediatric ependymoma compared with normal brain controls by microarray analysis (Suarez-Merino et al, 2005).…”

Section: Discussionmentioning

confidence: 95%

Real‐time quantitative PCR analysis of pediatric ependymomas identifies novel candidate genes including TPR at 1q25 and CHIBBY at 22q12‐q13

Karakoula

Suárez-Merino

Ward

et al. 2008

Genes Chromosomes & Cancer

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Loss of chromosome 22 and gain of 1q are the most frequent genomic aberrations in ependymomas, indicating that genes mapping to these regions are critical in their pathogenesis. Using real-time quantitative PCR, we measured relative copy numbers of 10 genes mapping to 22q12.3-q13.33 and 10 genes at 1q21-32 in a series of 47 pediatric intracranial ependymomas. Loss of one or more of the genes on 22 was detected in 81% of cases, with RAC2 and C22ORF2 at 22q12-q13.1 being deleted most frequently in 38% and 32% of ependymoma samples, respectively. Combined analysis of quantitative-PCR with methylation-specific PCR and bisulphite sequencing revealed a high rate (>60% ependymoma) of transcriptional inactivation of C22ORF2, indicating its potential importance in the development of pediatric ependymomas. Increase of relative copy numbers of at least one gene on 1q were detected in 61% of cases, with TPR at 1q25 displaying relative copy number gains in 38% of cases. Patient age was identified as a significant adverse prognostic factor, as a significantly shorter overall survival time (P = 0.0056) was observed in patients <2 years of age compared with patients who were >2 years of age. Loss of RAC2 at 22q13 or amplification of TPR at 1q25 was significantly associated with shorter overall survival in these younger patients (P = 0.0492 and P = < 0.0001, respectively). This study identifies candidate target genes within 1q and 22q that are potentially important in the pathogenesis of intracranial pediatric ependymomas.

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Section: Discussionmentioning

confidence: 95%

Real‐time quantitative PCR analysis of pediatric ependymomas identifies novel candidate genes including TPR at 1q25 and CHIBBY at 22q12‐q13

Karakoula

Suárez-Merino

Ward

et al. 2008

Genes Chromosomes & Cancer

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“…Of the other 14 dogs (dogs nos. [15][16][17][18][19][20][21][22][23][24][25][26][27][28] showing TCRγ rearrangement, 11 dogs were diagnosed as having alimentary lymphoma, 1 with ALL and 2 with chronic lymphocytic leukemia (CLL). Primary tumor cell samples were obtained by endoscopy from dogs with the alimentary lymphoma, and by peripheral blood mononuclear cell (PbMC) separation by gradient centrifugation [43] from the dogs with ALL and CLL.…”

Section: Cells and Patient Samplesmentioning

confidence: 99%

“…Of these 3 genes, inactivation of p16 has been most frequently found in hematological malignancies, such as lymphoma [2,3,5,6,10,16,17,20,24,36,44], leukemia [13,18,19,22,30,38,42] and multiple myeloma [25,32] as well as other non-hematological malignancies of various types [25,32]. Inactivation of p16 results from 4 types of alterations, namely, homozygous deletion, promoter hypermethylation, loss of heterozygosity and point mutations.…”

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confidence: 99%

Simultaneous Inactivation of the <i>p16, p15</i> and <i>p14</i> Genes Encoding Cyclin-Dependent Kinase Inhibitors in Canine T-Lymphoid Tumor Cells

et al. 2013

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AbSTRACT. The p16, p15 and p14 genes are widely known as tumor suppressor genes in human medicine. Although a large number of genetic and epigenetic aberrations in these genes have been reported in human malignancies, canine malignancies have not been well analyzed on the aberrations of these genes. In this study, the full-length complementary DNA (cDNA) of the canine p16 gene was cloned using the 5' and 3' rapid amplification of cDNA ends methods. Based on the sequence data, primers specific for p16, p15 and p14 were designed. Using these primers, the expression of p16, p15 and p14 mRNAs could be individually evaluated by reverse transcriptase polymerase chain reaction. Genomic aberrations were also examined using genomic polymerase chain reaction. Two of the 6 canine lymphoid tumor cell lines did not express detectable levels of p16, p15 and p14 mRNAs, and wide-ranging deletions in the p15-p14-p16 genomic locus were suspected. Wide-ranging deletions were also speculated in 2 of 14 dogs with T-cell lymphoid tumors. On the other hand, similar failure of amplification suggesting wide-ranging deletions were not observed in any of the 14 dogs with b-cell lymphoma. Deletion of the p15-p14-p16 genomic locus could be one of the molecular aberrations in canine lymphoid tumor cells.

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“…The various percentages of patients with loss of the CDKN2A allele may result from different age of patients. CDKN2A deletions were also detected using different technique:~8-44% of patients (Southern blot),~17-53% (RT-PCR) and in 31-73% of patients (Q-PCR) [10,16,[27][28][29].…”

Section: F -Female; M -Male; Ir -Intermediate Risk; Sr -Standard Riskmentioning

confidence: 99%

“…Some authors observed both deletion types in an equal percentage of patients [8,9]. Others found biallelic deletions in a higher number of patients than the monoallelic ones and some authors found biallelic deletions in a lower number of patients [7,27,30,31]. Conversion of monoallelic into biallelic deletion requires additional time; therefore biallelic deletions might be more likely in adults.…”

Section: F -Female; M -Male; Ir -Intermediate Risk; Sr -Standard Riskmentioning

confidence: 99%

Allelic loss of selected tumor suppressor genes in acute lymphoblastic leukemia in children

Studniak¹,

Maloney²,

Ociepa³

et al. 2013

pjp

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Defect in function of tumor suppressor genes may lead to initiation/progression of leukemias. RB1, CDKN2A and TP53 gene alterations are found in acute lymphoblastic leukemia (ALL) in children. Data showing a contribution of these alterations to the pathomechanism of leukemias are contradictory and their impact on a disease course still remains undefined. The main aim of the study was to identify and the characterize of RB1, CDKN2A and TP53 allele loss in ALL children patients at diagnosis. 46 children with de novo ALL were examined. Fluorescent in situ hybridization was performed on bone marrow smear preparations. We demonstrated that at least one of three investigated deletions occurred statistically more frequently in T-lineage leukemia patients (p = 0.044); this was the most frequent in respect to RB1 gene (p = 0.054). Additionally, at least one of the examined deletions was observed statistically more frequently in patients with WBC above 20 000/µl (p = 0.043), this was the most frequent for CDKN2A gene (p = 0.066). Presented results seem to give an evidence that deletions of RB1 and CDKN2A genes may contribute to the development of hyperleukocytic type of T-lineage ALL in children, nevertheless this observation needs further investigations.

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Detection of hemizygous deletions in genomic DNA from leukaemia specimens for the diagnosis of patients

Cited by 7 publications

References 22 publications

Real‐time quantitative PCR analysis of pediatric ependymomas identifies novel candidate genes including TPR at 1q25 and CHIBBY at 22q12‐q13

Real‐time quantitative PCR analysis of pediatric ependymomas identifies novel candidate genes including TPR at 1q25 and CHIBBY at 22q12‐q13

Simultaneous Inactivation of the <i>p16, p15</i> and <i>p14</i> Genes Encoding Cyclin-Dependent Kinase Inhibitors in Canine T-Lymphoid Tumor Cells

Allelic loss of selected tumor suppressor genes in acute lymphoblastic leukemia in children

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