Open Access Case report

A large de novo 9p21.3 deletion in a girl affected by astrocytoma and multiple melanoma

Simona Frigerio1, Vittoria Disciglio2, Siranoush Manoukian3, Bernard Peissel3, Gabriella Della Torre1, Andrea Maurichi4, Paola Collini5, Barbara Pasini36, Giacomo Gotti7, Andrea Ferrari7, Licia Rivoltini1, Maura Massimino7 and Monica Rodolfo1*

Author Affiliations

1 Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, Milan 20133, Italy

2 Department of Experimental Oncology and Molecular Medicine, Functional Genomics and Bioinformatics Core Facility, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, Milan 20133, Italy

3 Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy

4 Unit of Melanoma and Sarcoma, Department of Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy

5 Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy

6 Current address: Department of Medical Science, University of Turin, Turin, Italy

7 Pediatric Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy

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BMC Medical Genetics 2014, 15:59  doi:10.1186/1471-2350-15-59

Published: 17 May 2014

Additional files

Additional file 1:

Methods.

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Additional file 2: Table S1:

Primers of the microsatellite markers used in the study. Start and end positions are reported according to UCSC Genome Browser (NCBI Build 37, hg19).

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Additional file 3: Figure S1:

Microsatellite analysis revealing loss of the paternal allele in patient A and TS. Homozygosity or hemizygosity at microsatellite loci was analyzed by PCR and amplification products analyzed with the ABI Prism Peak Scanner Software.

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Additional file 4: Figure S2:

Results of MLPA of the 9p region in patient A, TS and parents. Results obtained with MLPA arrays for the 9p21 region ordered according to the genomic location of the probes. Gene dosage quotients for the 41 probes and relative ID numbers are shown, for patient A and TS in full bars, and for parents in empty bars. The deletion detected in the two sisters extends from CDKN2B to MLLT3 genes, and includes CDKN2A, MTAP, IFNA1, KLH9, IFNW1, and IFNB1 genes; in contrast, ELAV2 and TEK centromeric to CDKN2B and GLDC and DOCK8 telomeric to MLLT3 showed normal gene dosage quotients indicating retention of both gene copies.

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Additional file 5: Table S2:

List of chromosomal aberrations detected by aCGH (400K) in patient B not reported in the Database of Genomic Variants (http://dgv.tcag.ca/dgv/app/home?ref=GRCh37/hg19 webcite). CNVs in non coding regions were detected on 7p12.3, 7q11.22, 19q13.11 chromosomal regions. A large region on 14q11.2 contains genes poorly characterize functionally. CNVs on 4p14 and 16q24.3 involve genes of potential interest since they have been involved in the regulation of cell growth and death.

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Additional file 6: Figure S3:

Results of array-CGH of the 9p21.3 region in patient A and her twin sister. aCGH analysis showed an identical 9p21.3 deletion of ~ 2,135 Mb.

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