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Splicing mutation analysis reveals previously unrecognized pathways in lymph node-invasive breast cancer.

Dorman SN, Viner C, Rogan PK - Sci Rep (2014)

Bottom Line: Of the 5,206 putative mutations identified, exon skipping, leaky or cryptic splicing was confirmed for 988 variants.Pathway enrichment analysis of the mutated genes revealed mutations in 9 NCAM1-related pathways, which were significantly increased in samples with evidence of lymph node metastasis, but not in lymph node-negative tumours.We suggest that comprehensive reporting of DNA sequencing data should include non-trivial splicing analyses to avoid missing clinically-significant deleterious splicing mutations, which may reveal novel mutated pathways present in genetic disorders.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada.

ABSTRACT
Somatic mutations reported in large-scale breast cancer (BC) sequencing studies primarily consist of protein coding mutations. mRNA splicing mutation analyses have been limited in scope, despite their prevalence in Mendelian genetic disorders. We predicted splicing mutations in 442 BC tumour and matched normal exomes from The Cancer Genome Atlas Consortium (TCGA). These splicing defects were validated by abnormal expression changes in these tumours. Of the 5,206 putative mutations identified, exon skipping, leaky or cryptic splicing was confirmed for 988 variants. Pathway enrichment analysis of the mutated genes revealed mutations in 9 NCAM1-related pathways, which were significantly increased in samples with evidence of lymph node metastasis, but not in lymph node-negative tumours. We suggest that comprehensive reporting of DNA sequencing data should include non-trivial splicing analyses to avoid missing clinically-significant deleterious splicing mutations, which may reveal novel mutated pathways present in genetic disorders.

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Related in: MedlinePlus

Significantly mutated breast cancer genes with validated splicing mutations.TP53, KMT2C and CDH1 gene lengths are displayed with both exons (thick lines/boxes) and introns (thin horizontal lines), along with the location of all splicing mutations. Diamond markers denote cryptic mutations, natural splice site mutations are indicated by a circle and the colour of the marker corresponds with breast cancer tumour subtype. Mutations validated by Veridical are found above the gene, and those mutations not assessed or not validated are below.
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f2: Significantly mutated breast cancer genes with validated splicing mutations.TP53, KMT2C and CDH1 gene lengths are displayed with both exons (thick lines/boxes) and introns (thin horizontal lines), along with the location of all splicing mutations. Diamond markers denote cryptic mutations, natural splice site mutations are indicated by a circle and the colour of the marker corresponds with breast cancer tumour subtype. Mutations validated by Veridical are found above the gene, and those mutations not assessed or not validated are below.

Mentions: The most commonly mutated genes with splicing mutations were also found by MuSiC to be significantly mutated in these tumours (n = 13, FDR < 0.05), and at least one third of the mutations were validated with RNA-Seq data (Table 2). In TP53, which exhibited the highest density of splicing mutations (Fig. 2), 18 of 23 (78%) predicted variants were validated to cause aberrant splicing (p ≤ 0.05). All of the validated mutations exhibited statistically significant intron inclusion, and, in three instances, also resulted in exon skipping.


Splicing mutation analysis reveals previously unrecognized pathways in lymph node-invasive breast cancer.

Dorman SN, Viner C, Rogan PK - Sci Rep (2014)

Significantly mutated breast cancer genes with validated splicing mutations.TP53, KMT2C and CDH1 gene lengths are displayed with both exons (thick lines/boxes) and introns (thin horizontal lines), along with the location of all splicing mutations. Diamond markers denote cryptic mutations, natural splice site mutations are indicated by a circle and the colour of the marker corresponds with breast cancer tumour subtype. Mutations validated by Veridical are found above the gene, and those mutations not assessed or not validated are below.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4231324&req=5

f2: Significantly mutated breast cancer genes with validated splicing mutations.TP53, KMT2C and CDH1 gene lengths are displayed with both exons (thick lines/boxes) and introns (thin horizontal lines), along with the location of all splicing mutations. Diamond markers denote cryptic mutations, natural splice site mutations are indicated by a circle and the colour of the marker corresponds with breast cancer tumour subtype. Mutations validated by Veridical are found above the gene, and those mutations not assessed or not validated are below.
Mentions: The most commonly mutated genes with splicing mutations were also found by MuSiC to be significantly mutated in these tumours (n = 13, FDR < 0.05), and at least one third of the mutations were validated with RNA-Seq data (Table 2). In TP53, which exhibited the highest density of splicing mutations (Fig. 2), 18 of 23 (78%) predicted variants were validated to cause aberrant splicing (p ≤ 0.05). All of the validated mutations exhibited statistically significant intron inclusion, and, in three instances, also resulted in exon skipping.

Bottom Line: Of the 5,206 putative mutations identified, exon skipping, leaky or cryptic splicing was confirmed for 988 variants.Pathway enrichment analysis of the mutated genes revealed mutations in 9 NCAM1-related pathways, which were significantly increased in samples with evidence of lymph node metastasis, but not in lymph node-negative tumours.We suggest that comprehensive reporting of DNA sequencing data should include non-trivial splicing analyses to avoid missing clinically-significant deleterious splicing mutations, which may reveal novel mutated pathways present in genetic disorders.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada.

ABSTRACT
Somatic mutations reported in large-scale breast cancer (BC) sequencing studies primarily consist of protein coding mutations. mRNA splicing mutation analyses have been limited in scope, despite their prevalence in Mendelian genetic disorders. We predicted splicing mutations in 442 BC tumour and matched normal exomes from The Cancer Genome Atlas Consortium (TCGA). These splicing defects were validated by abnormal expression changes in these tumours. Of the 5,206 putative mutations identified, exon skipping, leaky or cryptic splicing was confirmed for 988 variants. Pathway enrichment analysis of the mutated genes revealed mutations in 9 NCAM1-related pathways, which were significantly increased in samples with evidence of lymph node metastasis, but not in lymph node-negative tumours. We suggest that comprehensive reporting of DNA sequencing data should include non-trivial splicing analyses to avoid missing clinically-significant deleterious splicing mutations, which may reveal novel mutated pathways present in genetic disorders.

Show MeSH
Related in: MedlinePlus