Supplemental Material for Newman et al., 2018

<div>Supplementary figures, tables and files for Newman et. al, 2018, "Event Analysis: using transcript events to improve estimates of abundance in RNA-seq data", G3, manuscript# G3/2018/200373R1.</div><div><br></div><div>Additional File 1 contains Supplementary Figures 1-6 and Supplementaty Table 1</div><div><br></div><div>Supplementary File 1 contains the results of simulations to compare the Event Analysis approach to STAR (for junction detection) and iReckon (for transcript identification).</div><div><br></div><div>Supplementary File 2 contains the results of applying Event Analysis to eXpress, and the results of using iReckon to identify possible transcripts in the mouse neural data used in the study.<br></div><div><br></div><div>Supplementary File 3 contains the results of comparing Event Analysis (using Bowtie or SOAP2 as the aligner) against STAR for benchmarking junction detection using the mouse neural data. Results are benchmarked against the set of junctions observed in PacBio-sequenced transcripts in the mouse neural data.<br></div><div><br></div><div>Supplementary File 4 contains the comparison between Event Analysis and iReckon for the mouse neural data, benchmarked against PacBio-sequenced transcripts.</div

Additional file 1: of Systemic therapy for breast cancer and risk of subsequent contralateral breast cancer in the WECARE Study

Table S1. Characteristics of patients diagnosed with ER/PR-positive first breast cancer enrolled in the WECARE I and II Study. Table S2. Risk ratios of contralateral breast cancer associated with different aspects of tamoxifen use among participants diagnosed with ER/PR positive first breast cancer in the WECARE I and II Study. Table S3. Risk ratios of ER-positive and ER-negative contralateral breast cancer associated with different aspects of tamoxifen use among participants diagnosed with ER/PR-positive first breast cancer in the WECARE I and II Study. Table S4. Risk ratios of contralateral breast cancer associated with tamoxifen use by patient and tumor characteristics among participants diagnosed with ER/PR positive first breast cancer in the WECARE I and II Study. (DOCX 59 kb

Additional file 1 of A genome-wide association study of contralateral breast cancer in the Women’s Environmental Cancer and Radiation Epidemiology Study

Additional file 1. Description of methods for the current study

Additional file 1: Table S1. of Hormone receptor status of a first primary breast cancer predicts contralateral breast cancer risk in the WECARE study population

Association between first breast cancer HR status and CBC, among women not receiving tamoxifen for first diagnosis. In the WECARE Study population of women who had not received tamoxifen for their first breast cancer diagnosis, having an ER-negative first breast cancer or a PR-negative first breast cancer statistically significantly increased the risk of CBC. (DOCX 19 kb

Association signal at the mapping intervals flanking rs34593439 and rs7553711.

<p>Association scores at 15q25.1 (panel A) and 1q25.1 (panel B). Genotyped (diamonds) and imputed (circles) SNPs are indicated and the top genotyped SNP in the interval is outlined in orange. A SNP in 15q25.1 previously associated with Diabetes is outlined in blue. The degree of red color in each diamond or circle indicates the strength of LD with the top SNP (on a scale shown in the legend at the upper left hand corner of the plot). The X-axis shows the chromosome and physical distance (kb) from the human genome reference sequence (hg19), the left Y-axis shows the negative base ten logarithm of the p-value and the right Y-axis shows recombination rate (cM/Mb) as a navy line. The genome-wide significance threshold (P<5×10⁻⁸) is given by the dashed grey line. Genes in the regions are annotated at the bottom as green arrows. Also indicated in 1q25.1 is a ∼130 kb region with no SNPs on the ImmunoChip.</p

Non-HLA narcolepsy risk variant loci reaching genome-wide significance.

<p>Chr.: Chromosome; BP: position according to NCBI build 36 (Hg18) coordinates; MAF_N: minor allele frequency in narcolepsy (_N) and controls (_C); P: P value according to variance component model (EMMAX). EMMAX does not provide OR (Odds Ratio) or adjusted allele frequencies, therefore MAF, OR, and 95% confidence intervals (CI) were calculated with Plink on subset of 8,474 samples with the greatest PCA homogeneity (see Figure S2; EV 11.21<0.004, EV 4.12<0.01).</p

Manhattan Plot of association statistics.

<p>The significance threshold used (blue line) was P = 5×10⁻⁸; The insets depict plots of 1) association results in a broad region encompassing the HLA locus (chr 6:24,067–35,474 kb) that were excluded from the present analysis (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003270#s3" target="_blank">Methods</a>) and 2) QQ plot of results for 109,777 markers after excluding a 1 Mb window surrounding the associated loci (λ = 1.004). The inflation statistic for all 111,240 tested markers is 1.04.</p

Sample collections.

*<p>Numbers of samples by country of origin are listed in the <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003270#s3" target="_blank">Methods</a> section.</p><p>Case cohort names represent location of genotyping, and do not reflect country of origin of samples.</p