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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

Frequency of chromosome 7 aberrations in BRAF mutant melanoma (n = 125) and melanocytic nevi groups (n = 33).Histogram representation of prevalence of chromosome 7 abnormalities evaluated by FISH in 115 melanomas depending on the amounts of V600E mutation, in 10 melanomas with BRAF exon 15 mutations different from V600E and in 33 melanocytic nevi. WT – wild-type, HETR – heterozygous, MUT – mutation
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Fig3: Frequency of chromosome 7 aberrations in BRAF mutant melanoma (n = 125) and melanocytic nevi groups (n = 33).Histogram representation of prevalence of chromosome 7 abnormalities evaluated by FISH in 115 melanomas depending on the amounts of V600E mutation, in 10 melanomas with BRAF exon 15 mutations different from V600E and in 33 melanocytic nevi. WT – wild-type, HETR – heterozygous, MUT – mutation

Mentions: We then compared BRAF mutation allele quantity and chromosome 7 copy number changes (Additional file 6). Disomy of chromosome 7 - or only few cells with polysomy - were detected in 78 % (n = 46/59) of BRAF wild-type samples, but in only 47 % (n = 31/66) of BRAF mutants; however the difference didn’t reached statistical significance (P = 0.08). Quantification of BRAF-M% was not validated in samples with mutations other than V600E (n = 10/66). Correlation with FISH showed a polysomy of chromosome 7 in 13.6 % (n = 8/59), 35.3 % (n = 12/34) and 54.5 % (n = 12/22) of wild-type, heterozygous and non-heterozygous samples, respectively (P < 0.05) (Fig. 3). Furthermore, none of the 22 non-heterozygous cases, versus 33.9 % (n = 20/59) of the BRAF WT group, were diploid (P < 0.05). Among the 22 non-heterozygous samples, six had low BRAF-M% (Additional file 6). Six of the 10 samples with other BRAF mutations had a polysomy of chromosome 7.Fig. 3


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)

Frequency of chromosome 7 aberrations in BRAF mutant melanoma (n = 125) and melanocytic nevi groups (n = 33).Histogram representation of prevalence of chromosome 7 abnormalities evaluated by FISH in 115 melanomas depending on the amounts of V600E mutation, in 10 melanomas with BRAF exon 15 mutations different from V600E and in 33 melanocytic nevi. WT – wild-type, HETR – heterozygous, MUT – mutation
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig3: Frequency of chromosome 7 aberrations in BRAF mutant melanoma (n = 125) and melanocytic nevi groups (n = 33).Histogram representation of prevalence of chromosome 7 abnormalities evaluated by FISH in 115 melanomas depending on the amounts of V600E mutation, in 10 melanomas with BRAF exon 15 mutations different from V600E and in 33 melanocytic nevi. WT – wild-type, HETR – heterozygous, MUT – mutation
Mentions: We then compared BRAF mutation allele quantity and chromosome 7 copy number changes (Additional file 6). Disomy of chromosome 7 - or only few cells with polysomy - were detected in 78 % (n = 46/59) of BRAF wild-type samples, but in only 47 % (n = 31/66) of BRAF mutants; however the difference didn’t reached statistical significance (P = 0.08). Quantification of BRAF-M% was not validated in samples with mutations other than V600E (n = 10/66). Correlation with FISH showed a polysomy of chromosome 7 in 13.6 % (n = 8/59), 35.3 % (n = 12/34) and 54.5 % (n = 12/22) of wild-type, heterozygous and non-heterozygous samples, respectively (P < 0.05) (Fig. 3). Furthermore, none of the 22 non-heterozygous cases, versus 33.9 % (n = 20/59) of the BRAF WT group, were diploid (P < 0.05). Among the 22 non-heterozygous samples, six had low BRAF-M% (Additional file 6). Six of the 10 samples with other BRAF mutations had a polysomy of chromosome 7.Fig. 3

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