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The contribution of large genomic deletions at the CDKN2A locus to the burden of familial melanoma.

Lesueur F, de Lichy M, Barrois M, Durand G, Bombled J, Avril MF, Chompret A, Boitier F, Lenoir GM, French Familial Melanoma Study GroupBressac-de Paillerets B, Baccard M, Bachollet B, Berthet P, Bonadona V, Bonnetblanc JM, Caron O, Chevrant-Breton J, Cuny JF, Dalle S, Delaunay M, Demange L, De Quatrebarbes J, Doré JF, Frénay M, Fricker JP, Gauthier-Villars M, Gesta P, Giraud S, Gorry P, Grange F, Green A, Huiart L, Janin N, Joly P, Kérob D, Lasset C, Leroux D, Limacher JM, Longy M, Mansard S, Marrou K, Martin-Denavit T, Mateus C, Maubec E, Olivier-Faivre L, Orlandini V, Pujol P, Sassolas B, Stoppa-Lyonnet D, Thomas L, Vabres P, Venat L, Wierzbicka E, Zattara H - Br. J. Cancer (2008)

Bottom Line: All had been tested for CDKN2A and CDK4 point mutation, and 47 were found positive.Overall, genomic deletions represented 2.1% of total mutations in this series (1 of 48), confirming that they explain a very small proportion of CMM susceptibility.In addition, we excluded a new gene on 9p21, KLHL9, as being a major CMM gene.

View Article: PubMed Central - PubMed

Affiliation: Groupe Mélanome, Institut Gustave Roussy, FRE2939 CNRS-Université Paris-Sud, Villejuif, France.

ABSTRACT
Mutations in two genes encoding cell cycle regulatory proteins have been shown to cause familial cutaneous malignant melanoma (CMM). About 20% of melanoma-prone families bear a point mutation in the CDKN2A locus at 9p21, which encodes two unrelated proteins, p16(INK4a) and p14(ARF). Rare mutations in CDK4 have also been linked to the disease. Although the CDKN2A gene has been shown to be the major melanoma predisposing gene, there remains a significant proportion of melanoma kindreds linked to 9p21 in which germline mutations of CDKN2A have not been identified through direct exon sequencing. The purpose of this study was to assess the contribution of large rearrangements in CDKN2A to the disease in melanoma-prone families using multiplex ligation-dependent probe amplification. We examined 214 patients from independent pedigrees with at least two CMM cases. All had been tested for CDKN2A and CDK4 point mutation, and 47 were found positive. Among the remaining 167 negative patients, one carried a novel genomic deletion of CDKN2A exon 2. Overall, genomic deletions represented 2.1% of total mutations in this series (1 of 48), confirming that they explain a very small proportion of CMM susceptibility. In addition, we excluded a new gene on 9p21, KLHL9, as being a major CMM gene.

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Family tree of patient carrying the KLHL9 variant.
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fig5: Family tree of patient carrying the KLHL9 variant.

Mentions: For a second patient diagnosed with melanoma at the age of 54, and belonging to a different melanoma -prone pedigree, a dosage quotient close to 0.5 was obtained for a 9p probe specific of the 5′ end of the transcription unit of the single exon gene KLHL9 (Kelch-like 9, previously named KIAA1354), suggesting a hemizygous deletion in this gene located about 630 kb telomeric from CDKN2A (Figure 3). Subsequent direct sequencing of the entire exon led to the identification of a heterozygous nucleotidic variation (A>G) located 16 bp upstream of the START codon of KLHL9 (NM_018847), that prevents the ligation reaction of the two contiguous probes used for MLPA, for the G allele (Figure 4). Although the various in silico tools (PupaSuite, http://pupasuite.bioinfo.cipf.es/, CorePromoter,http://rulai.cshl.org/tools/genefinder/CPROMOTER/, TFSEARCH, http://www.cbrc.jp/research/db/TFSEARCH.html, TESS, http://www.cbil.upenn.edu/cgi-bin/tess/tess) did not suggest that the presence of the G allele would have direct functional effects on the activity of the promoter, this new variant was not described in the public SNPs databases (ENSEMBL, http://www.ensembl.org/, dbSNP, http://www.ncbi.nlm.nih.gov/SNP, and HAPMAP, http://www.hapmap.org/) and was absent in 188 unrelated controls from France (376 chromosomes). DNA was available for the two unaffected siblings of the patient, and MLPA and sequence analysis revealed that one of the patient's sisters, unaffected at age 62, also carried the –16 A>G allele. The father of the patient died of melanoma metastases to the brain at the age of 70, and his paternal grandmother had a suspicious pigmented lesion on her face and died of thyroid cancer at the age of 80. Unfortunately, material was not available for any of them, and co-segregation of the variant with skin lesion could not be investigated (Figure 5).


The contribution of large genomic deletions at the CDKN2A locus to the burden of familial melanoma.

Lesueur F, de Lichy M, Barrois M, Durand G, Bombled J, Avril MF, Chompret A, Boitier F, Lenoir GM, French Familial Melanoma Study GroupBressac-de Paillerets B, Baccard M, Bachollet B, Berthet P, Bonadona V, Bonnetblanc JM, Caron O, Chevrant-Breton J, Cuny JF, Dalle S, Delaunay M, Demange L, De Quatrebarbes J, Doré JF, Frénay M, Fricker JP, Gauthier-Villars M, Gesta P, Giraud S, Gorry P, Grange F, Green A, Huiart L, Janin N, Joly P, Kérob D, Lasset C, Leroux D, Limacher JM, Longy M, Mansard S, Marrou K, Martin-Denavit T, Mateus C, Maubec E, Olivier-Faivre L, Orlandini V, Pujol P, Sassolas B, Stoppa-Lyonnet D, Thomas L, Vabres P, Venat L, Wierzbicka E, Zattara H - Br. J. Cancer (2008)

Family tree of patient carrying the KLHL9 variant.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2480975&req=5

fig5: Family tree of patient carrying the KLHL9 variant.
Mentions: For a second patient diagnosed with melanoma at the age of 54, and belonging to a different melanoma -prone pedigree, a dosage quotient close to 0.5 was obtained for a 9p probe specific of the 5′ end of the transcription unit of the single exon gene KLHL9 (Kelch-like 9, previously named KIAA1354), suggesting a hemizygous deletion in this gene located about 630 kb telomeric from CDKN2A (Figure 3). Subsequent direct sequencing of the entire exon led to the identification of a heterozygous nucleotidic variation (A>G) located 16 bp upstream of the START codon of KLHL9 (NM_018847), that prevents the ligation reaction of the two contiguous probes used for MLPA, for the G allele (Figure 4). Although the various in silico tools (PupaSuite, http://pupasuite.bioinfo.cipf.es/, CorePromoter,http://rulai.cshl.org/tools/genefinder/CPROMOTER/, TFSEARCH, http://www.cbrc.jp/research/db/TFSEARCH.html, TESS, http://www.cbil.upenn.edu/cgi-bin/tess/tess) did not suggest that the presence of the G allele would have direct functional effects on the activity of the promoter, this new variant was not described in the public SNPs databases (ENSEMBL, http://www.ensembl.org/, dbSNP, http://www.ncbi.nlm.nih.gov/SNP, and HAPMAP, http://www.hapmap.org/) and was absent in 188 unrelated controls from France (376 chromosomes). DNA was available for the two unaffected siblings of the patient, and MLPA and sequence analysis revealed that one of the patient's sisters, unaffected at age 62, also carried the –16 A>G allele. The father of the patient died of melanoma metastases to the brain at the age of 70, and his paternal grandmother had a suspicious pigmented lesion on her face and died of thyroid cancer at the age of 80. Unfortunately, material was not available for any of them, and co-segregation of the variant with skin lesion could not be investigated (Figure 5).

Bottom Line: All had been tested for CDKN2A and CDK4 point mutation, and 47 were found positive.Overall, genomic deletions represented 2.1% of total mutations in this series (1 of 48), confirming that they explain a very small proportion of CMM susceptibility.In addition, we excluded a new gene on 9p21, KLHL9, as being a major CMM gene.

View Article: PubMed Central - PubMed

Affiliation: Groupe Mélanome, Institut Gustave Roussy, FRE2939 CNRS-Université Paris-Sud, Villejuif, France.

ABSTRACT
Mutations in two genes encoding cell cycle regulatory proteins have been shown to cause familial cutaneous malignant melanoma (CMM). About 20% of melanoma-prone families bear a point mutation in the CDKN2A locus at 9p21, which encodes two unrelated proteins, p16(INK4a) and p14(ARF). Rare mutations in CDK4 have also been linked to the disease. Although the CDKN2A gene has been shown to be the major melanoma predisposing gene, there remains a significant proportion of melanoma kindreds linked to 9p21 in which germline mutations of CDKN2A have not been identified through direct exon sequencing. The purpose of this study was to assess the contribution of large rearrangements in CDKN2A to the disease in melanoma-prone families using multiplex ligation-dependent probe amplification. We examined 214 patients from independent pedigrees with at least two CMM cases. All had been tested for CDKN2A and CDK4 point mutation, and 47 were found positive. Among the remaining 167 negative patients, one carried a novel genomic deletion of CDKN2A exon 2. Overall, genomic deletions represented 2.1% of total mutations in this series (1 of 48), confirming that they explain a very small proportion of CMM susceptibility. In addition, we excluded a new gene on 9p21, KLHL9, as being a major CMM gene.

Show MeSH
Related in: MedlinePlus