Supplementary Tables 1-7 and Figures 1-5 from Germline Genetic Variants and Lung Cancer Survival in African Americans

Abstract

<p>SUPPLEMENTAL TABLE 1. Summary of the five previously reported lung cancer survival GWAS variants examined in the present study. SUPPLEMENTAL TABLE 2. Descriptive characteristics of African Americans with NSCLC participating in the KCI/WSU and UCSF studies. SUPPLEMENTAL TABLE 3. Allele frequency for the five variants previously associated with lung cancer survival in the NHGRIEBI GWAS Catalog in the SCCS (N=275), KCI/WSU (N=312), and UCSF (N=284) populations. Allele frequencies are also presented for the ASW 1000 Genomes African American reference population and for the 1000 Genomes reference population that matches the racial/ethnic group of the original discovery population (CEU or CHB). SUPPLEMENTAL TABLE 4. Adjusted multivariable Cox proportional hazards model results for African Americans with incident non-small cell lung cancer participating in the Southern Community Cohort Study (N=264) for the five candidate SNPs previously associated with lung cancer survival from the NHGRI GWAS catalog. SUPPLEMENTAL TABLE 5. Stage-stratified multivariable Cox proportional hazards results for the association of rs1878022 and overall survival in the SCCS and pooled KCI/WSU and UCSF populations. SUPPLEMENTAL TABLE 6. Allele frequency for common variants associated survival in the SCCS (N=275), KCI/WSU (N=312), and UCSF (N=284) populations. Allele frequencies are also presented for the ASW 1000 Genomes African American reference population. SUPPLEMENTAL TABLE 7. Adjusted multivariable Cox proportional hazards results for African Americans with incident non-small cell lung cancer participating in the Southern Community Cohort Study (N=264) for common variants assayed by the Illumina HumanExome BeadChip v1.1. SUPPLEMENTAL FIGURE 1. Flow chart of quality control (QC) for the SCCS genotyping data. SUPPLEMENTAL FIGURE 2. Distribution of stage at diagnosis across the SCCS (N=286), KCI/WSU (N=316), and UCSF (N=298.) SUPPLEMENTAL FIGURE 3. Global genetic ancestry estimates for African Americans with NSCLC participating in the (A) SCCS, (B) KCI/WSU, and (C) UCSF study populations.SUPPLEMENTAL FIGURE 4. Linkage disequilibrium (LD) patterns +/-10kb surrounding the CMKLR1 gene region in the YRI and CEU populations (A and B, respectively) from 1000 Genomes (phase 3). LD patterns surrounding rs1878022 (denoted by black arrow) are presented as inserts. 1000 Genomes data and Haploview software were utilized to display r2 values (filters:Hardy-Weinberg p-value > 0.001, genotyping efficiency > 90%, and minor allele frequency >0.05).SUPPLEMENTAL FIGURE 5. H3K4me1 and H3K27Ac histone modification marks surrounding rs1878022 in the CMKLR1 gene, visualized using the UCSC Genome Browser. Marks in (A) are specific to normal human lung fibroblast (NHLF) cell lines from the ENCODE project. Marks in (B) are for all cell lines (GM12878, H1-hESC, HSMM, HUVEC, K562, NHEK, and NHLF) in the ENCODE project.</p>