Supplementary material
Supplementary material
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Files in this Data Supplement:
- Supplementary material -
1. Methods
Patient and control subjects
Genotyping and quality control
SNP selection and statistical analysis
mRNA isolation from BAL cells and RT-PCR (BAL panel I)
2. Results
Known risk loci in screening panel A (GWAS)
Cell composition in BAL panel II
3. Figures
Figure E1: Study design
Figure E2: Density plot of �outlier detection�-analysis
Figure E3: Signal intensity plots in the GWAS for the 99 SNPs selected for validation
Figure E4: Quantile-quantile (Q-Q) plot of the association test statistic
Figure E5: Disease association of SNPs in the chromosome 6p22.33�p21.32 region
Figure E6: Regional plot of the fine-mapped region around the lead SNP
Figure E7: Electropherogram for the two novel SNPs detected by Sanger sequencing
Figure E8: Expression of the eight candidate genes
Figure E9: Quantitative analysis of OS9 expression rs1050045
Figure E10: Percentage of alveolar macrophages in BALs
Figure E11: CD4+/CD8+ T lymphocytes in the BAL
4. Tables
Table E1: SNPs used in the backward model selection in a logistic regression model
Table E2: Primer used for the detection of variants in the OS9 regions
Table E3: RT-PCR primer used for tissue-specific expression and BAL panel I
Table E4: Primer used for quantification of OS9 mRNA expression (BAL panel II)
Table E5: Results of the GWAS and of the validation stage
Table E6: Results for the 53 SNPs genotyped to fine-map 12q13.3-q14.1 in panel C
Table E7: Results of the haplotype analysis
Table E8: Prediction of SNP function
5. References