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Characterization of DNA variants in the human kinome in breast cancer.

Agarwal D, Qi Y, Jiang T, Liu X, Shi W, Wali VB, Turk B, Ross JS, Fraser Symmans W, Pusztai L, Hatzis C - Sci Rep (2015)

Bottom Line: We detected 1561 unique, non-synonymous variants in kinase genes in the 92 cases, and 74 unique variants in 43 kinases that were predicted to have major functional impact on the protein.We also observed that a higher proportion of histologic grade 1 and 2 cases had high functional impact variants in the SCYL2 gene compared with grade 3 cases.Our findings indicate that individual breast cancers harbor a substantial number of potentially functionally important nucleotide variations in kinase genes, most of which are present in unique combinations and include both somatic and germline functional variants.

View Article: PubMed Central - PubMed

Affiliation: Department of Breast Medical Oncology of Yale University, New Haven, CT, USA.

ABSTRACT
Kinases play a key role in cancer biology, and serve as potential clinically useful targets for designing cancer therapies. We examined nucleic acid variations in the human kinome and several known cancer-related genes in breast cancer. DNA was extracted from fine needle biopsies of 73 primary breast cancers and 19 metastatic lesions. Targeted sequencing of 518 kinases and 68 additional cancer related genes was performed using the SOLiD sequencing platform. We detected 1561 unique, non-synonymous variants in kinase genes in the 92 cases, and 74 unique variants in 43 kinases that were predicted to have major functional impact on the protein. Three kinase groups--CMGC, STE and TKL--showed greater mutational load in metastatic compared to primary cancer samples, however, after correction for multiple testing the difference was significant only for the TKL group (P = 0.04). We also observed that a higher proportion of histologic grade 1 and 2 cases had high functional impact variants in the SCYL2 gene compared with grade 3 cases. Our findings indicate that individual breast cancers harbor a substantial number of potentially functionally important nucleotide variations in kinase genes, most of which are present in unique combinations and include both somatic and germline functional variants.

No MeSH data available.


Related in: MedlinePlus

Schematic of the process for determining whether a nucleotide variant is of high functional impact (HFI).An HFI variant (i) was predicted to be in the high or medium functional importance category by the Mutation Assessor (MA) and at least one other functional predictor, or (ii) it was a stop-gain (nonsense) variant, or (iii) a stop-loss variant, or (iv) a frame-shifting indel.
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f1: Schematic of the process for determining whether a nucleotide variant is of high functional impact (HFI).An HFI variant (i) was predicted to be in the high or medium functional importance category by the Mutation Assessor (MA) and at least one other functional predictor, or (ii) it was a stop-gain (nonsense) variant, or (iii) a stop-loss variant, or (iv) a frame-shifting indel.

Mentions: All sequenced paired end reads from each barcoded sample were processed by the Applied Biosystems BioScope™ software (version 1.3) using the diBayes and small.indel models to call single nucleotide variants (SNVs) and small insertions or deletions (indels). The reference genome used in this analysis was GRCh37 (hg19). We used ANNOVAR13 to annotate the SNVs and indels based on their genomic locations. The functional impact of the variants was determined by using the Mutation Assessor (MA, http://mutationassessor.org/)14, a kinase specific functional variant predictor score (KSS) that provides a deleterious versus non deleterious prediction15 and by SIFT1617. SIFT scores of <0.05 were considered to represent a deleterious variant. A nucleotide variant was called high functional impact (HFI) if (i) it was predicted to be in the high or medium functional importance category by the MA and at least one other predictor, or (ii) it was a stop-gain (nonsense) variant, or (iii) a stop-loss variant, or (iv) a frame-shifting indel (Fig. 1). At the gene level, we called a gene affected, and designated as a variant kinase, if it had at least one nucleotide variant categorized as HFI1518. Variants were also annotated by COSMIC and dbSNP/1000 human genome annotation. The number of HFI-variant genes per sample were compared between different breast cancer subtypes and response groups using the Fisher’s exact test. To determine statistical significance, the p-values were adjusted for multiple testing using the Bonferroni correction.


Characterization of DNA variants in the human kinome in breast cancer.

Agarwal D, Qi Y, Jiang T, Liu X, Shi W, Wali VB, Turk B, Ross JS, Fraser Symmans W, Pusztai L, Hatzis C - Sci Rep (2015)

Schematic of the process for determining whether a nucleotide variant is of high functional impact (HFI).An HFI variant (i) was predicted to be in the high or medium functional importance category by the Mutation Assessor (MA) and at least one other functional predictor, or (ii) it was a stop-gain (nonsense) variant, or (iii) a stop-loss variant, or (iv) a frame-shifting indel.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4588561&req=5

f1: Schematic of the process for determining whether a nucleotide variant is of high functional impact (HFI).An HFI variant (i) was predicted to be in the high or medium functional importance category by the Mutation Assessor (MA) and at least one other functional predictor, or (ii) it was a stop-gain (nonsense) variant, or (iii) a stop-loss variant, or (iv) a frame-shifting indel.
Mentions: All sequenced paired end reads from each barcoded sample were processed by the Applied Biosystems BioScope™ software (version 1.3) using the diBayes and small.indel models to call single nucleotide variants (SNVs) and small insertions or deletions (indels). The reference genome used in this analysis was GRCh37 (hg19). We used ANNOVAR13 to annotate the SNVs and indels based on their genomic locations. The functional impact of the variants was determined by using the Mutation Assessor (MA, http://mutationassessor.org/)14, a kinase specific functional variant predictor score (KSS) that provides a deleterious versus non deleterious prediction15 and by SIFT1617. SIFT scores of <0.05 were considered to represent a deleterious variant. A nucleotide variant was called high functional impact (HFI) if (i) it was predicted to be in the high or medium functional importance category by the MA and at least one other predictor, or (ii) it was a stop-gain (nonsense) variant, or (iii) a stop-loss variant, or (iv) a frame-shifting indel (Fig. 1). At the gene level, we called a gene affected, and designated as a variant kinase, if it had at least one nucleotide variant categorized as HFI1518. Variants were also annotated by COSMIC and dbSNP/1000 human genome annotation. The number of HFI-variant genes per sample were compared between different breast cancer subtypes and response groups using the Fisher’s exact test. To determine statistical significance, the p-values were adjusted for multiple testing using the Bonferroni correction.

Bottom Line: We detected 1561 unique, non-synonymous variants in kinase genes in the 92 cases, and 74 unique variants in 43 kinases that were predicted to have major functional impact on the protein.We also observed that a higher proportion of histologic grade 1 and 2 cases had high functional impact variants in the SCYL2 gene compared with grade 3 cases.Our findings indicate that individual breast cancers harbor a substantial number of potentially functionally important nucleotide variations in kinase genes, most of which are present in unique combinations and include both somatic and germline functional variants.

View Article: PubMed Central - PubMed

Affiliation: Department of Breast Medical Oncology of Yale University, New Haven, CT, USA.

ABSTRACT
Kinases play a key role in cancer biology, and serve as potential clinically useful targets for designing cancer therapies. We examined nucleic acid variations in the human kinome and several known cancer-related genes in breast cancer. DNA was extracted from fine needle biopsies of 73 primary breast cancers and 19 metastatic lesions. Targeted sequencing of 518 kinases and 68 additional cancer related genes was performed using the SOLiD sequencing platform. We detected 1561 unique, non-synonymous variants in kinase genes in the 92 cases, and 74 unique variants in 43 kinases that were predicted to have major functional impact on the protein. Three kinase groups--CMGC, STE and TKL--showed greater mutational load in metastatic compared to primary cancer samples, however, after correction for multiple testing the difference was significant only for the TKL group (P = 0.04). We also observed that a higher proportion of histologic grade 1 and 2 cases had high functional impact variants in the SCYL2 gene compared with grade 3 cases. Our findings indicate that individual breast cancers harbor a substantial number of potentially functionally important nucleotide variations in kinase genes, most of which are present in unique combinations and include both somatic and germline functional variants.

No MeSH data available.


Related in: MedlinePlus