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Polygenic Risk Score
usage:
python3 tapes.py sort -i ./input_annottated_multi.vcf -o ./output_folder/ --prs "Alzheimer's disease" --prs_num 200
or
python3 tapes.py analyse -i ./main_report.txt -o ./prs_report.txt --prs "Asthma" --prs_num 40
By using the option --prs (see here for a list of diseases and number of SNPs associated) with the --analyse or -sort option, you will generate a report containing the genotype for the cohort samples and the public 1000genomephase3 samples for specific SNPs associated with a trait (extracted from GWAS Catalog).
--prs-num is used to specify the number of public samples to compare to (default = 100 and maximum = 3000)
Warning This function can be quite slow if a lot of SNPs are getting interrogated.
| snpid | INFOS | AB_sample | AC_sample | AE_sample | AQ_sample | … | 1000GENOMES:phase_3:HG00233 | 1000GENOMES:phase_3:HG00234 | 1000GENOMES:phase_3:HG00235 | 1000GENOMES:phase_3:HG00236 | 1000GENOMES:phase_3:HG00261 | 1000GENOMES:phase_3:HG00262 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| rs2641348 | {'beta': 0.121336270987748, 'gene': 'NR', 'ci': '[1.09-1.17]', 'freq': '0.89'} | 0/0 | 0/0 | 0/0 | 1/1 | … | 0/0 | 0/0 | 0/0 | 0/1 | 0/0 | 0/1 |
| rs2241880 | {'beta': 0.37156355643248296, 'gene': 'ATG16L1', 'ci': '[1.27-1.64]', 'freq': '0.55'} | 0/1 | 0/1 | 0/0 | 1/1 | … | 0/1 | 0/1 | 1/1 | 0/1 | 0/0 | 0/0 |
| rs34856868 | {'beta': 0.19250816336218, 'gene': 'BTBD8', 'ci': '[1.13-1.29]', 'freq': '0.97'} | 0/0 | 0/0 | 0/0 | 0/0 | … | 0/1 | 0/0 | 0/0 | 0/1 | 0/1 | 0/0 |
| rs4077515 | {'beta': 0.25464221837358103, 'gene': 'CARD9, SNAPC4', 'ci': '[NR]', 'freq': 'NR'} | 0/0 | 0/0 | 1/1 | 0/1 | … | 0/1 | 0/1 | 0/1 | 0/1 | 0/1 | 0/0 |
| rs10781499 | {'beta': 0.167095391502335, 'gene': 'NR', 'ci': '[1.16-1.21]', 'freq': '0.4263'} | 0/0 | 0/0 | 1/1 | 0/1 | … | 0/1 | 0/1 | 0/1 | 0/1 | 0/1 | 0/1 |
| rs9868809 | {'beta': 0.116971239572422, 'gene': 'NR', 'ci': '[1.09-1.16]', 'freq': '0.1036'} | 0/0 | 0/1 | 0/0 | 0/0 | … | 0/0 | 0/0 | 0/1 | 0/0 | 0/0 | 0/0 |
| rs3742130 | {'beta': 0.094611026362598, 'gene': 'NR', 'ci': '[1.07-1.13]', 'freq': '0.78'} | 0/1 | 0/0 | 0/1 | 0/1 | … | 0/1 | 0/0 | 0/0 | 0/0 | 0/1 | 0/0 |
| rs11465804 | {'beta': 0.916290731874155, 'gene': 'IL23R', 'ci': '[NR]', 'freq': '0.93'} | 0/0 | 0/0 | 0/0 | 0/0 | … | 0/0 | 0/0 | 0/0 | 0/0 | 0/0 | 0/1 |
| rs11209026 | {'beta': 1.15688119679209, 'gene': 'IL23R', 'ci': '[2.91-3.44]', 'freq': 'NR'} | 0/0 | 0/0 | 0/0 | 0/0 | … | 0/0 | 0/0 | 0/0 | 0/0 | 0/0 | 0/1 |
| rs12103 | {'beta': 0.078861086757506, 'gene': 'NR', 'ci': '[1.05-1.11]', 'freq': '0.1834'} | 0/1 | 1/1 | 1/1 | 0/1 | … | 1/1 | 1/1 | 0/1 | 1/1 | 0/0 | 1/1 |
| rs3764147 | {'beta': 0.22314355131421, 'gene': 'Unknown', 'ci': '[NR]', 'freq': '0.22'} | 0/1 | 0/0 | 0/0 | 0/0 | … | 0/1 | 0/0 | 0/0 | 0/0 | 0/1 | 0/1 |
| rs516246 | {'beta': 0.114575853697663, 'gene': 'NR', 'ci': '[1.1-1.15]', 'freq': '0.4652'} | 0/1 | 1/1 | 0/1 | 0/1 | … | 0/1 | 0/1 | 0/1 | 0/0 | 0/0 | 0/1 |
| rs1042058 | {'beta': 0.074774578493767, 'gene': 'NR', 'ci': '[1.05-1.1]', 'freq': '0.6'} | 0/1 | 0/0 | 1/1 | 1/1 | … | 1/1 | 0/1 | 0/1 | 0/1 | 0/1 | 0/0 |
| rs2066847 | {'beta': 1.38379123090177, 'gene': 'NOD2', 'ci': '[NR]', 'freq': '0.02'} | 0/0 | 0/0 | 0/0 | 0/0 | … | 0/0 | 0/0 | 0/0 | 0/0 | 0/0 | 0/0 |
| rs2476601 | {'beta': 0.27002713721306, 'gene': 'PTPN22', 'ci': '[NR]', 'freq': '0.9'} | 0/1 | 1/1 | 1/1 | 1/1 | … | 0/0 | 0/0 | 0/0 | 0/0 | 0/0 | 0/1 |
| rs2024092 | {'beta': 0.14766368469731697, 'gene': 'NR', 'ci': '[1.13-1.19]', 'freq': '0.2162'} | 0/0 | 0/1 | 0/1 | 0/0 | … | 0/0 | 0/0 | 0/1 | 0/0 | 0/0 | 0/0 |
| rs3792109 | {'beta': 0.32208349916911305, 'gene': 'ATG16L1', 'ci': '[NR]', 'freq': 'NR'} | 0/1 | 0/1 | 0/0 | 1/1 | … | 0/1 | 0/1 | 1/1 | 0/1 | 0/0 | 0/0 |
| rs34687326 | {'beta': 0.165514438477573, 'gene': 'SLAMF8', 'ci': '[1.12–1.24]', 'freq': '0.9'} | 1/1 | 0/0 | 0/1 | 0/0 | … | 0/0 | 0/0 | 0/0 | 0/0 | 0/1 | 0/0 |
| rs6596 | {'beta': 1.31788462314897, 'gene': 'SNX20', 'ci': '[3.10-4.49]', 'freq': 'NR'} | 0/1 | 0/0 | 0/0 | 0/1 | … | 0/1 | 0/1 | 0/0 | 0/0 | 0/1 | 0/0 |
| rs3810936 | {'beta': 0.19062035960864998, 'gene': 'TNFSF8, TNFSF15', 'ci': '[1.15-1.27]', 'freq': '0.682'} | 1/1 | 1/1 | 0/1 | 1/1 | … | 0/0 | 0/1 | 0/0 | 0/1 | 0/0 | 0/1 |
| rs4246905 | {'beta': 0.135098651332732, 'gene': 'NR', 'ci': '[1.12-1.17]', 'freq': '0.72'} | 1/1 | 1/1 | 0/1 | 1/1 | … | 0/0 | 0/1 | 0/0 | 0/1 | 0/0 | 0/1 |
| rs1292053 | {'beta': 0.09118541190616197, 'gene': 'NR', 'ci': '[1.07-1.12]', 'freq': '0.442'} | 0/0 | 0/1 | 1/1 | 0/1 | … | 0/1 | 0/1 | 0/1 | 0/1 | 0/1 | 0/1 |
| rs12720356 | {'beta': 0.143323418868969, 'gene': 'NR', 'ci': '[1.11-1.2]', 'freq': '0.08572'} | 0/0 | 0/0 | 0/0 | 0/0 | … | 0/0 | 0/0 | 0/0 | 0/1 | 0/0 | 0/0 |
| rs7076156 | {'beta': 0.173953307123438, 'gene': 'ADO, ZNF365, ERG2', 'ci': '[1.10-1.30]', 'freq': '0.751'} | 0/1 | 1/1 | 1/1 | 1/1 | … | 0/1 | 0/1 | 0/0 | 0/1 | 0/1 | 0/0 |
| Mean PRS of cases | 3.440069989 | |||||||||||
| Mean PRS of controls | 2.771992909 | |||||||||||
| p-value | 0.003571013 |