Skip to content

Commit

Permalink
feat: added curation for PPR569774
Browse files Browse the repository at this point in the history
  • Loading branch information
@ireneisdoomed
ireneisdoomed committed Nov 15, 2022
1 parent 412f207 commit 4f3484a
Show file tree
Hide file tree
Showing 2 changed files with 26 additions and 1 deletion.
5 changes: 4 additions & 1 deletion docs/gene_burden.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -28,4 +28,7 @@ Associations of 497 genes with traits from the UK Biobank. The data has been par
Associations of 60 genes with autism were identified by analyzing de novo and rare inherited variants from WES and WGS data. The data is pulled from the results of the meta analysis described in the Supplementary Table 9 of their publication (https://www.nature.com/articles/s41588-022-01148-2). Only associations with a p-value < 2.5 × 10−6 are included.

### Fat distributionn Publication
16 genes associated with fat distribution (BMI-adjusted WHR) were identified by analysing missense variants from WES data. Most of them with a protective direction of effect. The data is pulled from the Table 1 of their publication (https://www.nature.com/articles/s41467-022-32398-7.pdf). Only associations with a p-value < 3.6 × 10−7 are included.
16 genes associated with fat distribution (BMI-adjusted WHR) were identified by analysing missense variants from WES data. Most of them with a protective direction of effect. The data is pulled from the Table 1 of their publication (https://www.nature.com/articles/s41467-022-32398-7.pdf). Only associations with a p-value < 3.6 × 10−7 are included.

### Parkinson Publication
9 genes associated with Parkinson disease were identified by analysing rare variants from WES and WGS data of different cohorts. The data is curated from Table 1 (data about the population) and Table 2 and 3 (https://www.medrxiv.org/content/10.1101/2022.11.08.22280168v1.full). We report the results of the meta analyses when they show exome wide significance, otherwise we show the significant result on the independent sample.
22 changes: 22 additions & 0 deletions gene_burden/curated_evidence.tsv
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7958,3 +7958,25 @@ REGENERON "" TMPRSS6 Mean corpuscular volume (30040) EFO_0004526 1.96e-38 1.96 -
REGENERON "" OBSCN Impedance of arm left (23110) HP_0000924 6.82e-13 6.82 -13 "" -0.03 -0.017 -0.024 "" EUR HANCESTRO_0005 UK Biobank 450k GCST90078913 424014 424014 44590.0 "" ADD-WGR-FIRTH_M3.1 Burden test carried out with pLOFs and deleterious missense variants with a MAF smaller than 1%. 34662886 ""
REGENERON "" UGT1A3 Total bilirubin (30840) EFO_0004570 2.91e-14 2.91 -14 "" 0.114 0.193 0.154 "" EUR HANCESTRO_0005 UK Biobank 450k GCST90079041 410431 410431 2103.0 "" ADD-WGR-FIRTH_M3.1 Burden test carried out with pLOFs and deleterious missense variants with a MAF smaller than 1%. 34662886 ""
REGENERON "" LCORL Standing height (50) EFO_0004339 2.95e-32 2.95 -32 "" 0.45 0.629 0.54 "" EUR HANCESTRO_0005 UK Biobank 450k GCST90079277 430070 430070 161.0 "" ADD-WGR-FIRTH_M1.1 Burden test carried out with pLOF variants with a MAF smaller than 1%. 34662886 ""
"" GBA ENSG00000177628 parkinson disease MONDO_0005180 1,46E-21 1,46 -21 "" "" "" "" "" EUR HANCESTRO_0005 "" "" 65535 13885 "" "" meta-analysis Meta-analysis of burden tests carried out with missense variants with a MAF smaller than 1% PPR569774 ""
"" GBA ENSG00000177628 parkinson disease MONDO_0005180 1,32E-22 1,32 -22 "" "" "" "" "" EUR HANCESTRO_0005 "" "" 65535 13885 "" "" meta-analysis Meta-analysis of burden tests carried out with variants of high or moderate impact with a MAF smaller than 1% PPR569774 ""
"" GBA ENSG00000177628 parkinson disease MONDO_0005180 9,12E-22 9,12 -22 "" "" "" "" "" EUR HANCESTRO_0005 "" "" 65535 13885 "" "" meta-analysis Meta-analysis of burden tests carried out with variants predicted to be deleterious or LOF and with a MAF smaller than 1% PPR569774 ""
"" GBA ENSG00000177628 parkinson disease MONDO_0005180 4,48E-12 4,48 -12 "" "" "" "" "" EUR HANCESTRO_0005 "" "" 65535 13885 "" "" meta-analysis Meta-analysis of burden tests carried out with missense variants with a MAF smaller than 0.1% PPR569774 ""
"" GBA ENSG00000177628 parkinson disease MONDO_0005180 4,87E-16 4,87 -16 "" "" "" "" "" EUR HANCESTRO_0005 "" "" 65535 13885 "" "" meta-analysis Meta-analysis of burden tests carried out with variants of high or moderate impact with a MAF smaller than 0.1% PPR569774 ""
"" GBA ENSG00000177628 parkinson disease MONDO_0005180 1,20E-14 1,2 -14 "" "" "" "" "" EUR HANCESTRO_0005 "" "" 65535 13885 "" "" meta-analysis Meta-analysis of burden tests carried out with variants predicted to be deleterious or LOF and with a MAF smaller than 0.1% PPR569774 ""
"" LRRK2 ENSG00000188906 parkinson disease MONDO_0005180 7,15E-07 7,15 -7 "" "" "" "" "" EUR HANCESTRO_0005 "" "" 58834 7184 "" "" meta-analysis Meta-analysis of burden tests carried out with missense variants with a MAF smaller than 1% PPR569774 ""
"" LRRK2 ENSG00000188906 parkinson disease MONDO_0005180 7,23E-07 7,23 -7 "" "" "" "" "" EUR HANCESTRO_0005 "" "" 58834 7184 "" "" meta-analysis Meta-analysis of burden tests carried out with variants of high or moderate impact with a MAF smaller than 1% PPR569774 ""
"" LRRK2 ENSG00000188906 parkinson disease MONDO_0005180 2,49E-07 2,49 -7 "" "" "" "" "" EUR HANCESTRO_0005 "" "" 58834 7184 "" "" meta-analysis Meta-analysis of burden tests carried out with variants predicted to be deleterious or LOF and with a MAF smaller than 1% PPR569774 ""
"" B3GNT3 ENSG00000179913 parkinson disease MONDO_0005180 4,40E-09 4,4 -9 "" "" "" "" "" EUR HANCESTRO_0005 "" "" 65535 13885 "" "" meta-analysis Meta-analysis of burden tests carried out with pLOF variants and with a MAF smaller than 1% PPR569774 ""
"" B3GNT3 ENSG00000179913 parkinson disease MONDO_0005180 4,40E-09 4,4 -9 "" "" "" "" "" EUR HANCESTRO_0005 "" "" 58834 7184 "" "" meta-analysis Meta-analysis of burden tests carried out with pLOF variants and with a MAF smaller than 0.1% PPR569774 ""
"" CAPN10 ENSG00000142330 parkinson disease MONDO_0005180 3,60E-07 3,6 -7 "" "" "" "" "" EUR HANCESTRO_0005 "" "" 58834 7184 "" "" meta-analysis Meta-analysis of burden tests carried out with pLOF variants and with a MAF smaller than 1% PPR569774 ""
"" CAPN10 ENSG00000142330 parkinson disease MONDO_0005180 3,60E-07 3,6 -7 "" "" "" "" "" EUR HANCESTRO_0005 "" "" 58834 7184 "" "" meta-analysis Meta-analysis of burden tests carried out with pLOF variants and with a MAF smaller than 0.1% PPR569774 ""
"" AUNIP ENSG00000127423 parkinson disease MONDO_0005180 1,54E-08 1,54 -8 "" "" "" "" "" EUR HANCESTRO_0005 "" "" 58834 7184 "" "" meta-analysis Meta-analysis of burden tests carried out with variants of high or moderate impact with a MAF smaller than 0.1% PPR569774 ""
"" AUNIP ENSG00000127423 parkinson disease MONDO_0005180 1,64E-08 1,64 -8 "" "" "" "" "" EUR HANCESTRO_0005 "" "" 58834 7184 "" "" meta-analysis Meta-analysis of burden tests carried out with pLOF variants and with a MAF smaller than 0.1% PPR569774 ""
"" AUNIP ENSG00000127423 parkinson disease MONDO_0005180 2,12E-07 2,12 -7 "" "" "" "" "" EUR HANCESTRO_0005 "" "" 58834 7184 "" "" meta-analysis Meta-analysis of burden tests carried out with variants predicted to be deleterious or LOF and with a MAF smaller than 0.1% PPR569774 ""
"" TREML1 ENSG00000161911 parkinson disease MONDO_0005180 3,58E-07 3,58 -7 "" "" "" "" "" EUR HANCESTRO_0005 "" "" 65535 13885 "" "" meta-analysis Meta-analysis of burden tests carried out with variants of high or moderate impact with a MAF smaller than 0.1% PPR569774 ""
"" OR1G1 ENSG00000183024 parkinson disease MONDO_0005180 6,58E-07 6,58 -7 "" "" "" "" "" EUR HANCESTRO_0005 UK Biobank 200k "" 4131 668 "" "" skat-o SKAT-O test carried out with variants predicted to be deleterious or LOF and with a MAF smaller than 1% PPR569774 ""
"" OR1G1 ENSG00000183024 parkinson disease MONDO_0005180 6,58E-07 6,58 -7 "" "" "" "" "" EUR HANCESTRO_0005 UK Biobank 200k "" 4131 668 "" "" skat-o SKAT-O test carried out with variants predicted to be deleterious or LOF and with a MAF smaller than 0.1% PPR569774 ""
"" TUBA1B ENSG00000123416 parkinson disease MONDO_0005180 9,48E-07 9,48 -7 "" "" "" "" "" EUR HANCESTRO_0005 UK Biobank 200k "" 34978 6033 "" "" skat-o SKAT-O test carried out with variants of high or moderate impact with a MAF smaller than 1% PPR569774 ""
"" TUBA1B ENSG00000123416 parkinson disease MONDO_0005180 9,48E-07 9,48 -7 "" "" "" "" "" EUR HANCESTRO_0005 UK Biobank 200k "" 34978 6033 "" "" skat-o SKAT-O test carried out with variants of high or moderate impact with a MAF smaller than 0.1% PPR569774 ""
"" ADH5 ENSG00000197894 parkinson disease MONDO_0005180 3,13E-07 3,13 -7 "" "" "" "" "" EUR HANCESTRO_0005 UK Biobank 200k "" 6748 1105 "" "" skat-o SKAT-O test carried out with variants predicted to be deleterious or LOF and with a MAF smaller than 1% PPR569774 ""

0 comments on commit 4f3484a

Please sign in to comment.