cDNA array-CGH profiling identifies genomic alterations specific to stage and MYCN-amplification in neuroblastoma

Qing-Rong Chen; Bilke, Sven; Wei, Jun S.; Whiteford, Craig C.; Cenacchi, Nicola; Krasnoselsky, Alexei L.; Greer, Braden T.; Chang-Gue Son; Westermann, Frank; Berthold, Frank; Schwab, Manfred; Catchpoole, Daniel; Khan, Javed
January 2004
BMC Genomics;2004, Vol. 5, p1
Academic Journal
Background: Recurrent non-random genomic alterations are the hallmarks of cancer and the characterization of these imbalances is critical to our understanding of tumorigenesis and cancer progression. Results: We performed array-comparative genomic hybridization (A-CGH) on cDNA microarrays containing 42,000 elements in neuroblastoma (NB). We found that only two chromosomes (2p and 12q) had gene amplifications and all were in the MYCN amplified samples. There were 6 independent non-contiguous amplicons (10.4-69.4 Mb) on chromosome 2, and the largest contiguous region was 1.7 Mb bounded by NAG and an EST (clone: 757451); the smallest region was 27 Kb including an EST (clone: 241343), NCYM, and MYCN. Using a probabilistic approach to identify single copy number changes, we systemically investigated the genomic alterations occurring in Stage 1 and Stage 4 NBs with and without MYCN amplification (stage 1-, 4-, and 4+). We have not found genomic alterations universally present in all (100%) three subgroups of NBs. However we identified both common and unique patterns of genomic imbalance in NB including gain of 7q32, 17q21, 17q23-24 and loss of 3p21 were common to all three categories. Finally we confirm that the most frequent specific changes in Stage 4+ tumors were the loss of 1p36 with gain of 2p24-25 and they had fewer genomic alterations compared to either stage 1 or 4-, indicating that for this subgroup of poor risk NB requires a smaller number of genomic changes are required to develop the malignant phenotype. Conclusions: cDNA A-CGH analysis is an efficient method for the detection and characterization of amplicons. Furthermore we were able to detect single copy number changes using our probabilistic approach and identified genomic alterations specific to stage and MYCN amplification.


Related Articles

  • IgA in the horse: cloning of equine polymeric Ig receptor and J chain and characterization of recombinant forms of equine IgA. Lewis, M. J.; Wagner, B.; Irvine, R. M.; Woof, J. M. // Mucosal Immunology (1933-0219);Nov2010, Vol. 3 Issue 6, p610 

    As in other mammals, immunoglobulin A (IgA) in the horse has a key role in immune defense. To better dissect equine IgA function, we isolated complementary DNA (cDNA) clones for equine J chain and polymeric Ig receptor (pIgR). When coexpressed with equine IgA, equine J chain promoted efficient...

  • Asymmetric somatic hybridization induces point mutations and indels in wheat. Mengcheng Wang; Chun Liu; Tian Xing; Yanxia Wang; Guangmin Xia // BMC Genomics;10/17/2015, Vol. 16, p1 

    Background: Allopolyploid genome needs wide structural variation to deal with genomic shock. The introgression line, generated via asymmetric somatic hybridization, is introgressed with a minimum of exogenous chromatin, which also leads to genomic shock to induce genetic variation. However, the...

  • Positional and functional mapping of a neuroblastoma differentiation gene on chromosome 11. De Preter, Katleen; Vandesompele, Jo; Menten, Björn; Carr, Philippa; Fiegler, Heike; Edsjö, Anders; Carter, Nigel P; Yigit, Nurten; Waelput, Wim; Van Roy, Nadine; Bader, Scott; Påhlman, Sven; Speleman, Frank // BMC Genomics;2005, Vol. 6, p97 

    Background: Loss of chromosome 11q defines a subset of high-stage aggressive neuroblastomas. Deletions are typically large and mapping efforts have thus far not lead to a well defined consensus region, which hampers the identification of positional candidate tumour suppressor genes. In a...

  • Expressed sequence tags from Peromyscus testis and placenta tissue: Analysis, annotation, and utility for mapping. Weston Glenn, Julie L.; Chin-Fu Chen; Lewandowski, Adrienne; Chun-Huai Cheng; Ramsdell, Clifton M.; Bullard-Dillard, Rebecca; Jianguo Chen; Dewey, Michael J.; Glenn, Travis C. // BMC Genomics;2008, Vol. 9, Special section p1 

    Background: Mice of the genus Peromyscus are found in nearly every habitat from Alaska to Central America and from the Atlantic to the Pacific. They provide an evolutionary outgroup to the Mus/Rattus lineage and serve as an intermediary between that lineage and humans. Although Peromyscus has...

  • Identification of a novel gene NCRMS on chromosome 12q21 with differential expression between Rhabdomyosarcoma subtypes. Agnes S. Chan; Thorner, Paul S.; Squire, Jeremy A.; Zielenska, Maria // Oncogene;5/2/2002, Vol. 21 Issue 19, p3029 

    Focuses on a study which identified the novel gene non-coding RNA in rhabdomyosarcoma (NCRMS) on chromosome 12q21. Gene expression between the RMS subtypes; Confirmation of differential expression of selected representational difference analysis products; Isolation of full-length complementary...

  • Genomic organization and chromosomal mapping of ELKS, a gene rearranged in a papillary thyroid carcinoma. Yokota, T.; Nakata, T.; Minami, S.; Inazawa, J.; Emi, M. // Journal of Human Genetics;2000, Vol. 45 Issue 1, p6 

    Abstract We recently isolated a novel cDNA, designated ELKS, that was fused to RET cDNA in a papillary thyroid carcinoma. Its encoded polypeptide sequence was rich in glutamic acid (E), leucine (L), lysine (K), and serine (S), and was characterized by the presence of nine alpha-helical...

  • Molecular epigenetics of Angelman syndrome. Lalande, M.; Calciano, M. A. // Cellular & Molecular Life Sciences;Apr2007, Vol. 64 Issue 7/8, p947 

    Angelman syndrome (AS) is a neurogenetic disorder characterized by severe mental retardation, ataxia, seizures, EEG abnormalities and bouts of inappropriate laughter. AS individuals fail to inherit a normal active maternal copy of ubiquitin protein ligase E3A (UBE3A). UBE3A is subject to genomic...

  • The Staurotypus Turtles and Aves Share the Same Origin of Sex Chromosomes but Evolved Different Types of Heterogametic Sex Determination. Kawagoshi, Taiki; Uno, Yoshinobu; Nishida, Chizuko; Matsuda, Yoichi // PLoS ONE;Aug2014, Vol. 9 Issue 8, p1 

    Reptiles have a wide diversity of sex-determining mechanisms and types of sex chromosomes. Turtles exhibit temperature-dependent sex determination and genotypic sex determination, with male heterogametic (XX/XY) and female heterogametic (ZZ/ZW) sex chromosomes. Identification of sex chromosomes...

  • Uncoupling Antisense-Mediated Silencing and DNA Methylation in the Imprinted Gnas Cluster. Williamson, Christine M.; Ball, Simon T.; Dawson, Claire; Mehta, Stuti; Beechey, Colin V.; Fray, Martin; Teboul, Lydia; Dear, T. Neil; Kelsey, Gavin; Peters, Jo // PLoS Genetics;Mar2011, Vol. 7 Issue 3, preceding p1 

    No abstract available.


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics