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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

Percent of tumours with mutations by pathway group and clinical factors.The percent of tumours with NCAM1 (red square), collagen (blue diamond), and ECM (green triangle) pathway mutations were plotted by lymph node status and tumour stage for all mutations (solid lines), and splicing mutations alone (dashed line).
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f5: Percent of tumours with mutations by pathway group and clinical factors.The percent of tumours with NCAM1 (red square), collagen (blue diamond), and ECM (green triangle) pathway mutations were plotted by lymph node status and tumour stage for all mutations (solid lines), and splicing mutations alone (dashed line).

Mentions: NCAM1, collagen, and ECM pathway mutations were assessed in tumours, stratifying by lymph node status and tumour stage (Fig. 5). The percentage of tumours with NCAM1-related pathway splicing mutations was increased in N0 (110 localized tumours) and N1 (84 tumours with lymph node involvement), as well as Stage I (37) and II tumours (140). Advanced lymph node involvement and tumour stage were not associated with increased numbers of collagen and ECM pathway splicing mutations, but rather a decrease in the percent of tumours with these pathways mutations in advanced stages was observed. A multiple factor analysis (MFA; Table 3) was performed to assess contributions of the number of NCAM1-related pathway mutations per tumour (both protein coding and splicing), clinical parameters including stage (AJCC tumour stage, lymph node status and metastasis stage), receptor status (HER2, PR, and ER positivity), and patient outcome (relapsed, living/deceased). NCAM1-related pathway mutations were either absent (n = 213), harbored a single mutation (n = 117), or two or more mutations (n = 112) per tumour. The MFA components containing NCAM1-related pathway mutations were moderately correlated with both tumour stage and receptor status, and accounted for 11% of the variance.


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

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

Percent of tumours with mutations by pathway group and clinical factors.The percent of tumours with NCAM1 (red square), collagen (blue diamond), and ECM (green triangle) pathway mutations were plotted by lymph node status and tumour stage for all mutations (solid lines), and splicing mutations alone (dashed line).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f5: Percent of tumours with mutations by pathway group and clinical factors.The percent of tumours with NCAM1 (red square), collagen (blue diamond), and ECM (green triangle) pathway mutations were plotted by lymph node status and tumour stage for all mutations (solid lines), and splicing mutations alone (dashed line).
Mentions: NCAM1, collagen, and ECM pathway mutations were assessed in tumours, stratifying by lymph node status and tumour stage (Fig. 5). The percentage of tumours with NCAM1-related pathway splicing mutations was increased in N0 (110 localized tumours) and N1 (84 tumours with lymph node involvement), as well as Stage I (37) and II tumours (140). Advanced lymph node involvement and tumour stage were not associated with increased numbers of collagen and ECM pathway splicing mutations, but rather a decrease in the percent of tumours with these pathways mutations in advanced stages was observed. A multiple factor analysis (MFA; Table 3) was performed to assess contributions of the number of NCAM1-related pathway mutations per tumour (both protein coding and splicing), clinical parameters including stage (AJCC tumour stage, lymph node status and metastasis stage), receptor status (HER2, PR, and ER positivity), and patient outcome (relapsed, living/deceased). NCAM1-related pathway mutations were either absent (n = 213), harbored a single mutation (n = 117), or two or more mutations (n = 112) per tumour. The MFA components containing NCAM1-related pathway mutations were moderately correlated with both tumour stage and receptor status, and accounted for 11% of the variance.

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