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Variations of BRAF mutant allele percentage in melanomas.

Hélias-Rodzewicz Z, Funck-Brentano E, Baudoux L, Jung CK, Zimmermann U, Marin C, Clerici T, Le Gall C, Peschaud F, Taly V, Saiag P, Emile JF - BMC Cancer (2015)

Bottom Line: FISH showed a polysomy of chromosome 7 in 13.6%, 35.3% and 54.5% of BRAF wild-type, heterozygous and non-heterozygous BRAF-mutated samples, respectively (P < 0.005).Amplification (5.6%) and loss (3.2%) of BRAF locus were rare.By contrast, chromosome 7 was disomic in 27/27 BRAF-mutated nevi.

View Article: PubMed Central - PubMed

Affiliation: EA4340, Versailles University, Boulogne-Billancourt, France. zofia.helias@aphp.fr.

ABSTRACT

Background: BRAF mutations are present in 40% of human skin melanomas. Mutated tumors with an increased percentage of BRAF mutant alleles (BRAF-M%) may have a better response to RAF/MEK inhibitors. We evaluated the BRAF-M% in melanomas, and the genetic causes of its variation.

Methods: BRAF-M% was quantified by pyrosequencing, real-time PCR (rtPCR) and/or picoliter-droplet PCR (dPCR). BRAF mutant expression was detected by immunohistochemistry. Chromosomal alterations were analyzed with fluorescence in situ hybridization (FISH), and single nucleotide polymorphism (SNP) arrays.

Results: BRAF-M% quantification obtained with pyrosequencing was highly correlated (R = 0.94) with rtPCR, and with dPCR. BRAF-M% quantified from DNA and RNA were also highly correlated (R = 0.98). Among 368 samples with >80% tumor cells, 38.6% had a BRAF (V600E) mutation. Only 66.2% cases were heterozygous (BRAF-M% 30 to 60%). Increased BRAF-M% (>60%) was observed in 19% of cases. FISH showed a polysomy of chromosome 7 in 13.6%, 35.3% and 54.5% of BRAF wild-type, heterozygous and non-heterozygous BRAF-mutated samples, respectively (P < 0.005). Amplification (5.6%) and loss (3.2%) of BRAF locus were rare. By contrast, chromosome 7 was disomic in 27/27 BRAF-mutated nevi.

Conclusions: BRAF-M% is heterogeneous and frequently increased in BRAF-mutant melanomas. Aneuploidy of chromosome 7 is more frequent in BRAF mutant melanomas, specifically in those with high BRAF-M%.

No MeSH data available.


Related in: MedlinePlus

Chromosome 7 alterations in human melanomas by FISH. Representative images of FISH with BRAF/chromosome 7 centromere probes in melanomas with different chromosome 7 alterations. a no alteration (disomy) but rare cells with chromosome 7 polysomy; b chromosome 7 polysomy; cBRAF amplification; d) chromosome 7 monosomy. White bar = 10 μm
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Fig2: Chromosome 7 alterations in human melanomas by FISH. Representative images of FISH with BRAF/chromosome 7 centromere probes in melanomas with different chromosome 7 alterations. a no alteration (disomy) but rare cells with chromosome 7 polysomy; b chromosome 7 polysomy; cBRAF amplification; d) chromosome 7 monosomy. White bar = 10 μm

Mentions: To elucidate mechanisms leading to BRAF-M% variation, we analyzed copy number alterations of chromosome 7 and BRAF locus. FISH was performed on TMA with two probes specific for the BRAF locus and for the chromosome 7 centromere. Among 125 samples, four types of chromosome 7 alterations were observed with BRAF probe RP11-121G9/centromere 7 (Fig. 2): no alteration (disomy), disomy but rare cells with polysomy, polysomy, and monosomy, which were respectively detected in 18.4 % (n = 23), 43.2 % (n = 54), 29.6 % (n = 37) and 3.2 % (n = 4) of cases. BRAF locus was amplified (6 to numerous BRAF copies) in 5.6 % of cases (n = 7).Fig. 2


Variations of BRAF mutant allele percentage in melanomas.

Hélias-Rodzewicz Z, Funck-Brentano E, Baudoux L, Jung CK, Zimmermann U, Marin C, Clerici T, Le Gall C, Peschaud F, Taly V, Saiag P, Emile JF - BMC Cancer (2015)

Chromosome 7 alterations in human melanomas by FISH. Representative images of FISH with BRAF/chromosome 7 centromere probes in melanomas with different chromosome 7 alterations. a no alteration (disomy) but rare cells with chromosome 7 polysomy; b chromosome 7 polysomy; cBRAF amplification; d) chromosome 7 monosomy. White bar = 10 μm
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4491198&req=5

Fig2: Chromosome 7 alterations in human melanomas by FISH. Representative images of FISH with BRAF/chromosome 7 centromere probes in melanomas with different chromosome 7 alterations. a no alteration (disomy) but rare cells with chromosome 7 polysomy; b chromosome 7 polysomy; cBRAF amplification; d) chromosome 7 monosomy. White bar = 10 μm
Mentions: To elucidate mechanisms leading to BRAF-M% variation, we analyzed copy number alterations of chromosome 7 and BRAF locus. FISH was performed on TMA with two probes specific for the BRAF locus and for the chromosome 7 centromere. Among 125 samples, four types of chromosome 7 alterations were observed with BRAF probe RP11-121G9/centromere 7 (Fig. 2): no alteration (disomy), disomy but rare cells with polysomy, polysomy, and monosomy, which were respectively detected in 18.4 % (n = 23), 43.2 % (n = 54), 29.6 % (n = 37) and 3.2 % (n = 4) of cases. BRAF locus was amplified (6 to numerous BRAF copies) in 5.6 % of cases (n = 7).Fig. 2

Bottom Line: FISH showed a polysomy of chromosome 7 in 13.6%, 35.3% and 54.5% of BRAF wild-type, heterozygous and non-heterozygous BRAF-mutated samples, respectively (P < 0.005).Amplification (5.6%) and loss (3.2%) of BRAF locus were rare.By contrast, chromosome 7 was disomic in 27/27 BRAF-mutated nevi.

View Article: PubMed Central - PubMed

Affiliation: EA4340, Versailles University, Boulogne-Billancourt, France. zofia.helias@aphp.fr.

ABSTRACT

Background: BRAF mutations are present in 40% of human skin melanomas. Mutated tumors with an increased percentage of BRAF mutant alleles (BRAF-M%) may have a better response to RAF/MEK inhibitors. We evaluated the BRAF-M% in melanomas, and the genetic causes of its variation.

Methods: BRAF-M% was quantified by pyrosequencing, real-time PCR (rtPCR) and/or picoliter-droplet PCR (dPCR). BRAF mutant expression was detected by immunohistochemistry. Chromosomal alterations were analyzed with fluorescence in situ hybridization (FISH), and single nucleotide polymorphism (SNP) arrays.

Results: BRAF-M% quantification obtained with pyrosequencing was highly correlated (R = 0.94) with rtPCR, and with dPCR. BRAF-M% quantified from DNA and RNA were also highly correlated (R = 0.98). Among 368 samples with >80% tumor cells, 38.6% had a BRAF (V600E) mutation. Only 66.2% cases were heterozygous (BRAF-M% 30 to 60%). Increased BRAF-M% (>60%) was observed in 19% of cases. FISH showed a polysomy of chromosome 7 in 13.6%, 35.3% and 54.5% of BRAF wild-type, heterozygous and non-heterozygous BRAF-mutated samples, respectively (P < 0.005). Amplification (5.6%) and loss (3.2%) of BRAF locus were rare. By contrast, chromosome 7 was disomic in 27/27 BRAF-mutated nevi.

Conclusions: BRAF-M% is heterogeneous and frequently increased in BRAF-mutant melanomas. Aneuploidy of chromosome 7 is more frequent in BRAF mutant melanomas, specifically in those with high BRAF-M%.

No MeSH data available.


Related in: MedlinePlus