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Multiple breast cancer risk variants are associated with differential transcript isoform expression in tumors.

Caswell JL, Camarda R, Zhou AY, Huntsman S, Hu D, Brenner SE, Zaitlen N, Goga A, Ziv E - Hum. Mol. Genet. (2015)

Bottom Line: A subset of these SNPs are associated with quantitative expression of nearby genes, but the functional effects of the majority remain unknown.Six SNPs were associated with differential transcript expression of seven nearby genes at FDR < 0.05 (BABAM1, DCLRE1B/PHTF1, PEX14, RAD51L1, SRGAP2D and STXBP4).Lastly, at two loci, we identified the likely causal SNP for the alternative splicing event, and at one, functionally validated the effect of that SNP on alternative splicing using a minigene reporter assay.

View Article: PubMed Central - PubMed

Affiliation: Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center and, Department of Medicine, Division of Medical Oncology, Stanford University, Stanford, CA, USA and caswell@stanford.edu.

No MeSH data available.


Related in: MedlinePlus

Alternative splice site usage in BABAM1 exon 2 based on rs8170 genotype. (A) Relative expression of RSEM reconstructed BABAM1 transcript uc002nfu decreases and uc002nfv increases with rs8170 risk genotype. (B) LocusZoom plot (23) displaying −log10P-values for the association of each SNP within the window with BABAM1 uc002nfv transcript expression by position. (C) Locations of all candidate SNPs, defined as SNPs with r2 > 0.6 with rs8170, or LD unknown but splicing QTL association P-value of <1 × 10−6. SNPs are colored red if r2 > 0.8 and orange if r2 > 0.6. Screenshot from http://genome.ucsc.edu (24). (D) The locus of rs10424178, the presumed causal SNP. The two alternative 3′ splice sites are highlighted in red, and the two alternative branch points as identified by Human Splicing Finder (25) are highlighted in blue. The minor allele of rs10424178 (T) is in high LD with the risk allele of rs8170. Screenshot from http://genome.ucsc.edu (24). (E) Results of a six replicates of a minigene reporter vector assay, transfecting the major allele (C) or minor allele (T) of rs10424178. In each well, the lower band represents the shorter BABAM1 exon 2, as included in transcript uc002nfu, and the upper band represents the longer BABAM1 exon 2, as included in transcript uc002nfv; the identities of the bands were confirmed by sequencing. The percentages shown below each well are the intensity of the lower band divided by the sum of the intensities of the lower band and the upper band. In all six replicates, the percentage of the total bands represented by the shorter BABAM1 exon 2 is higher for the major allele than that for the minor (risk) allele.
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DDV432F3: Alternative splice site usage in BABAM1 exon 2 based on rs8170 genotype. (A) Relative expression of RSEM reconstructed BABAM1 transcript uc002nfu decreases and uc002nfv increases with rs8170 risk genotype. (B) LocusZoom plot (23) displaying −log10P-values for the association of each SNP within the window with BABAM1 uc002nfv transcript expression by position. (C) Locations of all candidate SNPs, defined as SNPs with r2 > 0.6 with rs8170, or LD unknown but splicing QTL association P-value of <1 × 10−6. SNPs are colored red if r2 > 0.8 and orange if r2 > 0.6. Screenshot from http://genome.ucsc.edu (24). (D) The locus of rs10424178, the presumed causal SNP. The two alternative 3′ splice sites are highlighted in red, and the two alternative branch points as identified by Human Splicing Finder (25) are highlighted in blue. The minor allele of rs10424178 (T) is in high LD with the risk allele of rs8170. Screenshot from http://genome.ucsc.edu (24). (E) Results of a six replicates of a minigene reporter vector assay, transfecting the major allele (C) or minor allele (T) of rs10424178. In each well, the lower band represents the shorter BABAM1 exon 2, as included in transcript uc002nfu, and the upper band represents the longer BABAM1 exon 2, as included in transcript uc002nfv; the identities of the bands were confirmed by sequencing. The percentages shown below each well are the intensity of the lower band divided by the sum of the intensities of the lower band and the upper band. In all six replicates, the percentage of the total bands represented by the shorter BABAM1 exon 2 is higher for the major allele than that for the minor (risk) allele.

Mentions: After excluding the six problematic associations, six raSNPs were associated with exon, junction or whole-transcript expression of seven genes (Table 1). Four of the six loci replicated at P < 0.05 in the smaller set of 109 ER-negative tumors from TCGA (Table 1), three at FDR < 0.05. We identified one SNP associated with exon skipping (rs11552449-DCLRE1B), two SNPs associated with alternative splice site usage (rs6504950-STXBP4 and rs8170-BABAM1) (Figs 2 and 3), three SNPs associated with more complex exon usage patterns (rs11552449-PHTF1, rs616488-PEX14 and rs999737-RAD51L1) and one SNP associated only with an exon–exon junction, which could represent an unannotated alternative splice site or other unannotated pattern of exon usage (rs11249433-SRGAP2D).Table 1.


Multiple breast cancer risk variants are associated with differential transcript isoform expression in tumors.

Caswell JL, Camarda R, Zhou AY, Huntsman S, Hu D, Brenner SE, Zaitlen N, Goga A, Ziv E - Hum. Mol. Genet. (2015)

Alternative splice site usage in BABAM1 exon 2 based on rs8170 genotype. (A) Relative expression of RSEM reconstructed BABAM1 transcript uc002nfu decreases and uc002nfv increases with rs8170 risk genotype. (B) LocusZoom plot (23) displaying −log10P-values for the association of each SNP within the window with BABAM1 uc002nfv transcript expression by position. (C) Locations of all candidate SNPs, defined as SNPs with r2 > 0.6 with rs8170, or LD unknown but splicing QTL association P-value of <1 × 10−6. SNPs are colored red if r2 > 0.8 and orange if r2 > 0.6. Screenshot from http://genome.ucsc.edu (24). (D) The locus of rs10424178, the presumed causal SNP. The two alternative 3′ splice sites are highlighted in red, and the two alternative branch points as identified by Human Splicing Finder (25) are highlighted in blue. The minor allele of rs10424178 (T) is in high LD with the risk allele of rs8170. Screenshot from http://genome.ucsc.edu (24). (E) Results of a six replicates of a minigene reporter vector assay, transfecting the major allele (C) or minor allele (T) of rs10424178. In each well, the lower band represents the shorter BABAM1 exon 2, as included in transcript uc002nfu, and the upper band represents the longer BABAM1 exon 2, as included in transcript uc002nfv; the identities of the bands were confirmed by sequencing. The percentages shown below each well are the intensity of the lower band divided by the sum of the intensities of the lower band and the upper band. In all six replicates, the percentage of the total bands represented by the shorter BABAM1 exon 2 is higher for the major allele than that for the minor (risk) allele.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4664170&req=5

DDV432F3: Alternative splice site usage in BABAM1 exon 2 based on rs8170 genotype. (A) Relative expression of RSEM reconstructed BABAM1 transcript uc002nfu decreases and uc002nfv increases with rs8170 risk genotype. (B) LocusZoom plot (23) displaying −log10P-values for the association of each SNP within the window with BABAM1 uc002nfv transcript expression by position. (C) Locations of all candidate SNPs, defined as SNPs with r2 > 0.6 with rs8170, or LD unknown but splicing QTL association P-value of <1 × 10−6. SNPs are colored red if r2 > 0.8 and orange if r2 > 0.6. Screenshot from http://genome.ucsc.edu (24). (D) The locus of rs10424178, the presumed causal SNP. The two alternative 3′ splice sites are highlighted in red, and the two alternative branch points as identified by Human Splicing Finder (25) are highlighted in blue. The minor allele of rs10424178 (T) is in high LD with the risk allele of rs8170. Screenshot from http://genome.ucsc.edu (24). (E) Results of a six replicates of a minigene reporter vector assay, transfecting the major allele (C) or minor allele (T) of rs10424178. In each well, the lower band represents the shorter BABAM1 exon 2, as included in transcript uc002nfu, and the upper band represents the longer BABAM1 exon 2, as included in transcript uc002nfv; the identities of the bands were confirmed by sequencing. The percentages shown below each well are the intensity of the lower band divided by the sum of the intensities of the lower band and the upper band. In all six replicates, the percentage of the total bands represented by the shorter BABAM1 exon 2 is higher for the major allele than that for the minor (risk) allele.
Mentions: After excluding the six problematic associations, six raSNPs were associated with exon, junction or whole-transcript expression of seven genes (Table 1). Four of the six loci replicated at P < 0.05 in the smaller set of 109 ER-negative tumors from TCGA (Table 1), three at FDR < 0.05. We identified one SNP associated with exon skipping (rs11552449-DCLRE1B), two SNPs associated with alternative splice site usage (rs6504950-STXBP4 and rs8170-BABAM1) (Figs 2 and 3), three SNPs associated with more complex exon usage patterns (rs11552449-PHTF1, rs616488-PEX14 and rs999737-RAD51L1) and one SNP associated only with an exon–exon junction, which could represent an unannotated alternative splice site or other unannotated pattern of exon usage (rs11249433-SRGAP2D).Table 1.

Bottom Line: A subset of these SNPs are associated with quantitative expression of nearby genes, but the functional effects of the majority remain unknown.Six SNPs were associated with differential transcript expression of seven nearby genes at FDR < 0.05 (BABAM1, DCLRE1B/PHTF1, PEX14, RAD51L1, SRGAP2D and STXBP4).Lastly, at two loci, we identified the likely causal SNP for the alternative splicing event, and at one, functionally validated the effect of that SNP on alternative splicing using a minigene reporter assay.

View Article: PubMed Central - PubMed

Affiliation: Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center and, Department of Medicine, Division of Medical Oncology, Stanford University, Stanford, CA, USA and caswell@stanford.edu.

No MeSH data available.


Related in: MedlinePlus