Case study: WDR12 xQTL and AD GWAS¶

This notebook documents the analysis of xQTL case study on a targeted gene, WDR12.

  • Section 0: Sanity check
  • Section 1: Fine-mapping for xQTL and GWAS
  • Section 2: Multi-context colocalization with Bellenguez 2022
  • Section 3: Refinement of colocalized loci with other AD GWAS
  • Section 4: Assessment of multi-context xQTL effect sizes
  • Section 5: Multi-context causal TWAS (including conventional TWAS and MR)
  • Section 6: Context specific multi-gene fine-mapping
  • Section 7: Epigenomic QTL and their target regions
  • Section 8: Context focused validation in other xQTL data
  • Section 9: Non-linear effects of xQTL
  • Section 10: in silico functional studies in iPSC model
  • Section 11: Functional annotations of selected loci
  • Section 12: Candidate loci as trans-xQTL

Overview¶

FunGen-xQTL resource contains 67 xQTL contexts as well as 9 AD GWAS fine-mapped genome-wide. The overarching goal for case studies is to use these resource to raise questions and learn more about gene targets of interest.

Overall, a case study consists of the following aspects:

  • Check the basic information of the gene
  • Check the existing xQTL and integrative analysis results, roughly including
    • Summary table for univariate fine-mapping
    • Marginal association results
    • Multi-gene and multi-context fine-mapping
    • Multi-context colocalization with AD GWAS
    • TWAS, MR and causal TWAS
    • Integration with epigenetic QTL
    • Quantile QTL
    • Interaction QTL
    • Validation:
      • Additional xQTL data in FunGen-xQTL
      • Additional AD GWAS data-set already generated by FunGen-xQTL
    • In silico functional studies
      • Additional iPSC data-sets
    • Functional annotations of variants, particularly in relevant cellular contexts
  • Creative thinking: generate hypothesis, search in literature, raise questions to discuss

Computing environment setup¶

Interactive analysis will be done on AWS cloud powered by MemVerge. Please contact Gao Wang to setup accounts for you to start the analysis.

Please follow instructions on https://wanggroup.org/productivity_tips/mmcloud-interactive to configure your computing environment. Here are some additional packages you need to install after the initial configuration, in order to perform these analysis:

in terminal with bash:

micromamba install -n r_libs r-pecotmr

in R:

install.packages('BEDMatrix')

How to Use This Notebook¶

  1. Before you start: Load functions from cb_plot.R and utilis.R, located at <xqtl-paper>/codes/. These functions and resources are packaged to streamline the analysis and ensure everything is as clean as possible. And also the codes for ColocBoost under path /data/colocalization/colocboost/R.
  2. Inside of this notebook, use sed -i or Ctrl+F to replace the gene WDR12 with the gene you want to analyze.
  3. For detailed analysis in some sections, please refer to the corresponding analysis notebooks as indicated. These companion notebooks are available under this same folder. The rest of the tasks can be completed with a few lines of code, as demonstrated in this notebook.
  4. Similarly for the companion notebooks you should also use the sed -i or Ctrl+F replacing gene_name (WDR12 in this case) with the gene you want to investigate.

While using this notebook, you may need to generate three intermediate files from Sections 1 and 2, which will be useful for downstream analysis:

  • a. Section 1:
    • Fine-mapping contexts that indicate shared signals with AD, WDR12_finemapping_contexts.rds. This can be used as input for Section 8 the multi-cohort validation step
    • A subset of the xQTL-AD table, Fungen_xQTL_allQTL.overlapped.gwas.export.WDR12.rds. This can be used as input for Section 12.
  • b. Section 2: A variant list showing colocalization in cohorts we analyzed with ColocBoost, WDR12_colocboost_res.rds. this can be used as input for Sections 7, 9, 10, and 12.

Section 0: Sanity check¶

Check the basic information of the gene¶

  • To gain a preliminary understanding of this gene’s expression—specifically, whether it is cell-specific—can help us quickly determine if our results are consistent with expectations.

Useful websites:

  1. check gene function, (immune) cell type specificity, tissue specifity, protein location: https://www.proteinatlas.org
  2. check gene position and structure: https://www.ncbi.nlm.nih.gov/gene/
  3. other collective information: https://www.genecards.org

Check the existing results which are inputs to this analysis¶

Check the existing results which are inputs to this analysis¶

In [1]:
# If an error occurs while sourcing scripts, it might be because your get() returned NULL. 
#Please restart the kernel or click the R kernel in the upper right corner to resolve the issue.
source('../../codes/cb_plot.R')
source('../../codes/utilis.R')

for(file in list.files("/data/colocalization/colocboost/R", pattern = ".R", full.names = T)){
          source(file)
        }
gene_name = 'WDR12'

dir.create(paste0('plots/', gene_name), recursive = T)
In [2]:
target_gene_info <- get_gene_info(gene_name = gene_name)
target_gene_info
$gene_info
A data.table: 1 x 14
region_id#chrstartendTSSLD_matrix_idLD_sumstats_idLD_sumstats_id_oldTADB_indexTADB_idgene_startgene_endsliding_windowsgene_name
<chr><chr><dbl><dbl><int><chr><chr><chr><chr><chr><int><int><chr><chr>
ENSG00000138442chr2201874261204014798203014797chr2:201677542-203951659,chr2:203951659-2072543192_201677542-203951659,2_203951659-2072543192_201677542-203951659,2_203951659_207254319TADB_217,TADB_218,TADB_219chr2_199844239_203567751,chr2_201265735_204961577,chr2_202936762_207159509203014798202874261chr2:196447744-202229406,chr2:196804592-203567751,chr2:198867396-204961577,chr2:199844239-207159509,chr2:201265735-209854503,chr2:202936762-211266074WDR12
$target_LD_ids
A matrix: 1 x 2 of type chr
chr2:201677542-203951659chr2:203951659-207254319
$target_sums_ids
A matrix: 1 x 2 of type chr
2_201677542-2039516592_203951659-207254319
$gene_region
'chr2:201874261-204014798'
$target_TAD_ids
A matrix: 1 x 3 of type chr
chr2_199844239_203567751chr2_201265735_204961577chr2_202936762_207159509
In [2]:
target_gene_info <- get_gene_info(gene_name = gene_name)
target_gene_info
$gene_info
A data.table: 1 x 14
region_id#chrstartendTSSLD_matrix_idLD_sumstats_idLD_sumstats_id_oldTADB_indexTADB_idgene_startgene_endsliding_windowsgene_name
<chr><chr><dbl><dbl><int><chr><chr><chr><chr><chr><int><int><chr><chr>
ENSG00000138442chr2201874261204014798203014797chr2:201677542-203951659,chr2:203951659-2072543192_201677542-203951659,2_203951659-2072543192_201677542-203951659,2_203951659_207254319TADB_217,TADB_218,TADB_219chr2_199844239_203567751,chr2_201265735_204961577,chr2_202936762_207159509203014798202874261chr2:196447744-202229406,chr2:196804592-203567751,chr2:198867396-204961577,chr2:199844239-207159509,chr2:201265735-209854503,chr2:202936762-211266074WDR12
$target_LD_ids
A matrix: 1 x 2 of type chr
chr2:201677542-203951659chr2:203951659-207254319
$target_sums_ids
A matrix: 1 x 2 of type chr
2_201677542-2039516592_203951659-207254319
$gene_region
'chr2:201874261-204014798'
$target_TAD_ids
A matrix: 1 x 3 of type chr
chr2_199844239_203567751chr2_201265735_204961577chr2_202936762_207159509
In [3]:
gene_id = target_gene_info$gene_info$region_id
chrom = target_gene_info$gene_info$`#chr`
In [4]:
source('../../codes/utilis.R')
expression_in_rosmap_bulk(target_gene_info)
No description has been provided for this image

Section 1: Fine-mapping for xQTL and GWAS¶

see notebook

In [15]:
region_p
No description has been provided for this image

Bellenguez et al GWAS signals has many overlap with CS from other xQTL sources. This motivates us to look further. The figure above shows the ranges of CS to give us a loci level idea. Below, we show the variants in those CS, color-coding the variants that are shared between them in the same color. In particular, AD GWAS signals are also captured by a few xQTL data, although at this point we don't have formal statistical (colocalization) evidences for these observations yet.

In [17]:
pip_p
No description has been provided for this image

Section 2: Multi-context colocalization with Bellenguez 2022¶

This is done using ColocBoost. The most updated version of ColocBoost results are under path s3://statfungen/ftp_fgc_xqtl/analysis_result/ColocBoost/2024_9/

In [4]:
cb_res <- readRDS(paste0("/data/analysis_result/ColocBoost/2024_9/",gene_id,"_res.rds") )
In [4]:
cb_res <- readRDS(paste0("/data/analysis_result/ColocBoost/2024_9/",gene_id,"_res.rds") )
In [9]:
cb <- plot_cb(cb_res = cb_res, cex.pheno = 1.5, x.phen = -0.2)
No description has been provided for this image
In [10]:
pdf('plots/WDR12/sec2.colocboost_res.pdf', width = 10, height = 5)
replayPlot(cb$p)
dev.off()
pdf: 2
In [11]:
# colocalized variants
cb_res_table
A data.frame: 3 x 8
colocalized phenotypespurity# variantshighest VCPcolocalized indexcolocalized variantsmax_abs_z_variantcset_id
<chr><dbl><dbl><dbl><chr><chr><chr><chr>
DLPFC; AC; PCC 1.0000000 20.499535143873; 4215 chr2:202906576:G:A; chr2:203001075:CGTGTGTGTGTGT:TGTGTGTGTGTGT chr2:202906576:G:Acoloc_sets:Y7_Y8_Y9:CS1
Exc; DLPFC; AC; PCC; PCC_productive0.9567232 60.270743603599; 3650; 3608; 3627; 3906; 4061 chr2:202841064:G:C; chr2:202856022:G:A; chr2:202843584:A:G; chr2:202916162:TTTTATTTATTTA:TTTTATTTA; chr2:202850250:G:C; chr2:202959815:CAA:CA chr2:202841064:G:Ccoloc_sets:Y5_Y7_Y8_Y9_Y16:CS3
DLPFC; AC; PCC 0.8976547360.060942573544; 3554; 3574; 3630; 3632; 3727; 3779; 3829; 3864; 3931; 3769; 3912; 3547; 3708; 3774; 3909; 3753; 3903; 3546; 3954; 3839; 4262; 4196; 4225; 4253; 4254; 4261; 4324; 3970; 4033; 4038; 4082; 4110; 4145; 3840; 4367chr2:202825664:G:A; chr2:202828836:C:G; chr2:202834693:G:T; chr2:202850789:C:T; chr2:202850905:G:T; chr2:202874289:C:T; chr2:202886008:C:G; chr2:202896851:A:G; chr2:202903616:C:T; chr2:202928093:C:T; chr2:202916348:C:T; chr2:202918486:T:C; chr2:202898078:CA:C; chr2:202826558:A:G; chr2:202827287:A:G; chr2:202867547:T:C; chr2:202884669:C:CTTT; chr2:202878969:A:G; chr2:202883871:A:G; chr2:203018272:C:CT; chr2:202914796:C:A; chr2:202898079:AC:CC; chr2:203056547:A:G; chr2:202996143:G:C; chr2:203003634:T:A; chr2:203013429:C:T; chr2:203014780:A:G; chr2:203017975:C:A; chr2:202935324:TTATATA:TTA; chr2:203040452:G:T; chr2:202940311:A:G; chr2:202953852:A:G; chr2:202955052:A:T; chr2:202964301:T:A; chr2:202969678:C:G; chr2:202980923:T:Cchr2:202825664:G:Acoloc_sets:Y7_Y8_Y9:CS2
In [12]:
# effect sign for each coloc sets
get_effect_sign_csets(cb_res)
$`coloc_sets:Y7_Y8_Y9:CS1`
A data.frame: 2 x 4
variantsDLPFCACPCC
<chr><dbl><dbl><dbl>
chr2:202906576:G:Achr2:202906576:G:A -3.935098-6.13314-6.250894
chr2:203001075:CGTGTGTGTGTGT:TGTGTGTGTGTGTchr2:203001075:CGTGTGTGTGTGT:TGTGTGTGTGTGT-3.935098-6.13314-6.250894
$`coloc_sets:Y5_Y7_Y8_Y9_Y16:CS3`
A data.frame: 6 x 6
variantsExcDLPFCACPCCPCC_productive
<chr><dbl><dbl><dbl><dbl><dbl>
chr2:202841064:G:Cchr2:202841064:G:C 6.46886811.416258.8015225.8238005.651822
chr2:202856022:G:Achr2:202856022:G:A 6.46886811.416258.8015225.8238005.651822
chr2:202843584:A:Gchr2:202843584:A:G 6.55977711.245948.6842805.8238005.651822
chr2:202850250:G:Cchr2:202850250:G:C 6.67487211.328908.7121865.6801945.572117
chr2:202916162:TTTTATTTATTTA:TTTTATTTAchr2:202916162:TTTTATTTATTTA:TTTTATTTA6.90660111.132198.6495165.8024655.120113
chr2:202959815:CAA:CAchr2:202959815:CAA:CA 6.58607811.018128.5258775.6167775.637198
$`coloc_sets:Y7_Y8_Y9:CS2`
A data.frame: 36 x 4
variantsDLPFCACPCC
<chr><dbl><dbl><dbl>
chr2:202825664:G:Achr2:202825664:G:A 8.610602 8.759280 5.897966
chr2:202828836:C:Gchr2:202828836:C:G 8.610602 8.759280 5.897966
chr2:202834693:G:Tchr2:202834693:G:T 8.610602 8.759280 5.897966
chr2:202850789:C:Tchr2:202850789:C:T 8.610602 8.759280 5.897966
chr2:202850905:G:Tchr2:202850905:G:T 8.610602 8.759280 5.897966
chr2:202874289:C:Tchr2:202874289:C:T 8.610602 8.759280 5.897966
chr2:202886008:C:Gchr2:202886008:C:G 8.610602 8.759280 5.897966
chr2:202896851:A:Gchr2:202896851:A:G 8.610602 8.759280 5.897966
chr2:202903616:C:Tchr2:202903616:C:T 8.610602 8.759280 5.897966
chr2:202928093:C:Tchr2:202928093:C:T 8.610602 8.759280 5.897966
chr2:202883871:A:Gchr2:202883871:A:G 8.698313 8.592295 5.845422
chr2:202918486:T:Cchr2:202918486:T:C 8.639583 8.631226 5.845422
chr2:202827287:A:Gchr2:202827287:A:G 8.563309 8.646358 5.845422
chr2:202867547:T:Cchr2:202867547:T:C 8.563309 8.646358 5.845422
chr2:202884669:C:CTTTchr2:202884669:C:CTTT 8.563309 8.646358 5.845422
chr2:202916348:C:Tchr2:202916348:C:T 8.459777 8.443372 5.959266
chr2:202878969:A:Gchr2:202878969:A:G 8.563887 8.548605 5.840398
chr2:202914796:C:Achr2:202914796:C:A 8.435272 8.287633 5.937400
chr2:202826558:A:Gchr2:202826558:A:G 8.382462 8.646358 5.845422
chr2:202935324:TTATATA:TTAchr2:202935324:TTATATA:TTA 8.539323 8.587844 5.581173
chr2:202898078:CA:Cchr2:202898078:CA:C 8.334125 8.515161 5.896910
chr2:203018272:C:CTchr2:203018272:C:CT 8.112531 8.739257 5.670492
chr2:202996143:G:Cchr2:202996143:G:C 8.274524 8.651068 5.679455
chr2:203003634:T:Achr2:203003634:T:A 8.260394 8.651068 5.679455
chr2:203013429:C:Tchr2:203013429:C:T 8.260394 8.651068 5.679455
chr2:203014780:A:Gchr2:203014780:A:G 8.260394 8.651068 5.679455
chr2:203017975:C:Achr2:203017975:C:A 8.260394 8.651068 5.679455
chr2:203040452:G:Tchr2:203040452:G:T 8.260394 8.651068 5.679455
chr2:202940311:A:Gchr2:202940311:A:G 8.464034 8.617185 5.615000
chr2:202953852:A:Gchr2:202953852:A:G 8.464034 8.617185 5.615000
chr2:202955052:A:Tchr2:202955052:A:T 8.464034 8.617185 5.615000
chr2:202964301:T:Achr2:202964301:T:A 8.464034 8.617185 5.615000
chr2:202969678:C:Gchr2:202969678:C:G 8.464034 8.617185 5.615000
chr2:202980923:T:Cchr2:202980923:T:C 8.464034 8.617185 5.615000
chr2:202898079:AC:CCchr2:202898079:AC:CC -7.989343-8.357625-5.896910
chr2:203056547:A:Gchr2:203056547:A:G 7.302074 8.645431 5.679455
In [13]:
# LD between coloc sets
get_between_purity_simple(cb_res, gene.name = gene_id, path = '/data/colocalization/QTL_data/eQTL/')
A matrix: 3 x 5 of type chr
coloc_csets_1coloc_csets_2min_abs_cormax_abs_cormedian_abs_cor
coloc_sets:Y7_Y8_Y9:CS1 coloc_sets:Y5_Y7_Y8_Y9_Y16:CS30.04666487297005630.050175603913272 0.0476588716079472
coloc_sets:Y7_Y8_Y9:CS1 coloc_sets:Y7_Y8_Y9:CS2 0.042877456385991 0.04849151524101620.0476704953046012
coloc_sets:Y5_Y7_Y8_Y9_Y16:CS3coloc_sets:Y7_Y8_Y9:CS2 0.469795574415134 0.522660476572075 0.508064572013709

Here, different colors refer to different 95% Colocalization Sets (CoS, a metric developed in ColocBoost indicating that there is 95% probabilty that this CoS captures a colocalization event). We only included ROSMAP data for this particular ColocBoost analysis. In this case, we observe cell specific eQTL, bulk sQTL colocalization on ROSMAP data with AD as two separate CoS, suggesting two putative causal signals. We did not detect colocalization with pQTL of statistical significance although from Section 1 there are some overlap with pQTL signals in fine-mapping CS, the overlapped variants in CS have small PIP.

Section 3: Refinement of colocalized loci with other AD GWAS¶

Here we refine the colocalization with other AD GWAS to iron out any heterogeniety between studies (heterogeniety can come from many sources), to get additional candidate loci from these more heterogenous sources as candidates to study.

In [14]:
AD_cohorts <- c('AD_Jansen_2021', 'AD_Bellenguez_EADB_2022', 'AD_Bellenguez_EADI_2022',
             'AD_Kunkle_Stage1_2019', 'AD_Wightman_Excluding23andMe_2021',
             'AD_Wightman_ExcludingUKBand23andME_2021', 'AD_Wightman_Full_2021')
cb_ad <- plot_cb(cb_res = cb_res, cex.pheno = 1.5, x.phen = -0.2, add_gwas = TRUE, gene_id = gene_id, cohorts = AD_cohorts)

No pvalue cutoff. Extract all variants names.No pvalue cutoff. Extract all variants names.No pvalue cutoff. Extract all variants names.No pvalue cutoff. Extract all variants names.No pvalue cutoff. Extract all variants names.No pvalue cutoff. Extract all variants names.No pvalue cutoff. Extract all variants names.
No description has been provided for this image
In [15]:
pdf('plots/WDR12/sec3.colocboost_res_allad.pdf', width = 10, height = 5)
replayPlot(cb_ad$p)
dev.off()
pdf: 2

Section 4: Assessment of multi-context xQTL effect sizes¶

Option 1: ColocBoost + MASH¶

Use colocboost variants and check for mash posterior contrast to see if the effect size are shared or specific or even opposite. Advantage is that colocboost result is AD GWAS informed; issue is that marginal posterior effects is not always the joint

In [16]:
mash_p <- mash_plot(gene_name = 'WDR12')

options(repr.plot.width = 10, repr.plot.height = 10)

for (mash_p_tmp in mash_p) {
    print(mash_p_tmp)
}

Option 2: mvSuSiE¶

Use mvSuSiE multicontext fine-mapping results --- the bubble plot to check posterior effects. Issue is that we don't have this results yet, and this is limited to one cohort at a time, without information from AD.

We should go for option 1 by default and if we want to make claim about opposite effect size we double-check with mvSuSiE multicontext analysis.

Section 5: Multi-context causal TWAS (including conventional TWAS and MR)¶

The most updated version of cTWAS analysis are under path s3://statfungen/ftp_fgc_xqtl/analysis_result/cTWAS/

TWAS results¶

We report TWAS from all contexts and methods from the pipeline. Here we will filter it down to the best performing methods and only keep contexts that are significant.

In [17]:
plot_TWAS_res(gene_id = gene_id, gene_name = gene_name)
No description has been provided for this image

MR results¶

This is only available for genes that are deemed significant in TWAS and have summary statistics available for effect size and standard errors in GWAS, in addition to z-scores --- current version does not support z-scores although we will soon also support z-scores in MR using MAF from reference panel.

cTWAS results¶

To be updated soon.

Section 6: Context specific multi-gene fine-mapping¶

A quick analysis: using the xQTL-AD summary table (flatten table)¶

We extract from xQTL-AD summary table the variants to get other genes also have CS with the variants shared by target gene and AD.

In [18]:
multigene_flat <- get_multigene_multicontext_flatten('Fungen_xQTL_allQTL.overlapped.gwas.export.WDR12.rds', sQTL = 'no_MSBB')
multigene_flat
A data.frame: 18 x 6
gene_id#chrstartendgene_namecontexts
<chr><chr><int><int><chr><chr>
ENSG00000003393chr2201782111201782112ALS2 BM_22_MSBB_eQTL,ROSMAP_AC_sQTL
ENSG00000055044chr2202265735202265736NOP58 MiGA_GTS_eQTL,MiGA_THA_eQTL,ROSMAP_PCC_sQTL
ENSG00000064012chr2201233442201233443CASP8 ROSMAP_AC_sQTL,ROSMAP_PCC_sQTL
ENSG00000115993chr2201451499201451500TRAK2 Knight_eQTL,ROSMAP_AC_sQTL
ENSG00000116030chr2202238598202238599SUMO1 ROSMAP_AC_sQTL,ROSMAP_PCC_sQTL
ENSG00000118257chr2205681989205681990NRP2 DLPFC_Bennett_pQTL
ENSG00000138380chr2202912213202912214CARF AC_DeJager_eQTL,ROSMAP_DLPFC_sQTL
ENSG00000138439chr2202634968202634969FAM117B ROSMAP_AC_sQTL,ROSMAP_DLPFC_sQTL
ENSG00000138443chr2203328279203328280ABI2 STARNET_eQTL
ENSG00000144426chr2203014878203014879NBEAL1 AC_DeJager_eQTL,Exc_mega_eQTL,ROSMAP_PCC_sQTL,ROSMAP_DLPFC_sQTL
ENSG00000155749chr2201357397201357398FLACC1 ROSMAP_DLPFC_sQTL
ENSG00000155755chr2201643569201643570TMEM237 ROSMAP_AC_sQTL,ROSMAP_PCC_sQTL
ENSG00000163596chr2202871765202871766ICA1L Ast_DeJager_eQTL,ROSMAP_PCC_sQTL,ROSMAP_DLPFC_sQTL
ENSG00000163599chr2203867770203867771CTLA4 MiGA_SVZ_eQTL
ENSG00000173166chr2203535334203535335RAPH1 MSBB_BM36_pQTL,ROSMAP_AC_sQTL,ROSMAP_PCC_sQTL,STARNET_eQTL
ENSG00000182329chr2202073254202073255KIAA2012ROSMAP_AC_sQTL
ENSG00000196290chr2200889326200889327NIF3L1 MiGA_SVZ_eQTL
ENSG00000204217chr2202376326202376327BMPR2 MiGA_GTS_eQTL,ROSMAP_AC_sQTL,ROSMAP_DLPFC_sQTL

Other genes implicated are PROC and HS6ST1 in MiGA cohort which may share causal eQTL with WDR12. Further look into the data-set --- using these genes as targets and repeating what we did above for WDR12 --- might be needed to establish a more certain conclusion.

Alternatively, we may be able to apply a multi-gene statistical fine-mapping test on WDR12 region to find these genes, as you will see in the section below.

A statistically solid approach: mvSuSiE multi-gene analysis¶

This multi-gene fine-mapping analysis was done for each xQTL context separately. We will need to check the results for all contexts where this gene has an xQTL, in order to identify if there are other genes also sharing the same xQTL with this target gene. We included other genes in the same TAD window along with this gene, and extended it into a sliding window approach to include multiple TADs just in case. You need to check the sliding windows belongs to that gene (TSS) on analysis repo.

In [19]:
sliding_windows <- target_gene_info$gene_info$sliding_windows %>% strsplit(., ',') %>% unlist %>% as.character
sliding_windows
  1. 'chr2:196447744-202229406'
  2. 'chr2:196804592-203567751'
  3. 'chr2:198867396-204961577'
  4. 'chr2:199844239-207159509'
  5. 'chr2:201265735-209854503'
  6. 'chr2:202936762-211266074'

The most updated version of mvSuSiE multi-gene results are under path s3://statfungen/ftp_fgc_xqtl/analysis_result/mvsusie_multi_gene_test/multi_gene/ Currently it is still WIP. You can revisit this later when we prompt you to. Here is an example for WDR12:

In [20]:
mnm_gene <- list()
for (window in sliding_windows) {
    mnm_gene_tmp <- NULL
    mnm_gene_tmp <- tryCatch(
        readRDS(paste0('/data/analysis_result/mvsusie_multi_gene/multi_gene/ROSMAP_multi_gene.', window, '.mnm.rds')),
        error = function(e) NULL
    )
    
    if (!is.null(mnm_gene_tmp)) {
        if(target_gene_info$gene_info$region_id %in% mnm_gene_tmp$mvsusie_fitted$condition_names){
        tryCatch({
            p <- mvsusieR::mvsusie_plot(mnm_gene_tmp$mvsusie_fitted, sentinel_only = F, add_cs = T)
            print(p)  # This ensures the plot is displayed in JupyterLab
        }, error = function(e) NULL)
        } else {
            message('There is mnm result for sliding window ',window,', but not include target gene ', gene_name, ' in CS')
        }
        mnm_gene <- append(mnm_gene, list(mnm_gene_tmp))
    }
}

In this case, there is no statistical evidence for WDR12 sharing any of its xQTL with other genes in ROSMAP Microglia data we looked into; although we have not analyzed MiGA this way yet (which showed some potential signals from the quick analysis above).

Section 7: Epigenomic QTL and their target regions¶

fsusie, see notebook

Generate a crude plot to determined whether the story is interesting¶

This is a crude version of the case study plot which shows the fsusie Effect (colored line), the gene body (black arrow), the epi-QTL (large dots with the same color as the effects) and ADGWAS cs position (small red dots).

Only produce the refine plot if we can see either:

  1. There are sharing snp between epi-QTL and AD CS
  2. There are the AD CS located within one of the effect range
  3. The crude plot suggest something interesting
In [9]:
options(repr.plot.width = 40, repr.plot.height = 40)

 ggplot() + theme_bw() + facet_grid(cs_coverage_0.95 + study + region ~ ., labeller = labeller(.rows = function(x) gsub("([_:,-])", "\n", x)), scale = "free_y") +

      theme(text = element_text(size = 20), strip.text.y = element_text(size = 25, angle = 0.5)) +
     # xlim(view_win) +
      ylab("Estimated effect") +
   #   geom_line(data = haQTL_df %>% mutate(study = "haQTL effect") %>% filter(CS == 5),
    #            aes_string(y = "fun_plot", x = "x", col = "CS"), size = 4, col = "#00AEEF") +
  geom_line(data = effect_of_interest ,
                aes_string(y = "fun_plot", x = "x", col = "cs_coverage_0.95"), size = 2) +  
    geom_point(data = effect_of_interest ,
                aes_string(y = "pip", x = "pos", col = "cs_coverage_0.95"), size = 10) +
    theme(text = element_text(size = 40), strip.text.y = element_text(size = 15, angle = 0.5), 
            axis.text.x = element_text(size = 40), axis.title.x = element_text(size = 40)) +
      xlab("Position") +
      ylab("Estimated\neffect") +
      geom_segment(arrow = arrow(length = unit(1, "cm")), aes(x = gene_start, xend = gene_end, y = 1, yend = 1), size = 6,
                  data = tar_gene_info$gene_info, alpha = 0.3) +
      geom_text(aes(x = (gene_start + gene_end) / 2, y = 1 , label = gene_name), size = 10, 
              data = tar_gene_info$gene_info)+
        geom_point(aes(x = pos, y = pip  ) ,color = "red", data = flatten_table%>%filter( str_detect(study,"AD_") , cs_coverage_0.95 != 0  )%>%mutate(AD_study = study%>%str_replace_all("_","\n" ))%>%select(-study,-region,-cs_coverage_0.95) )
No description has been provided for this image

Section 8: Context focused validation in other xQTL data¶

see notebook

add fake version for now, so you don't have to refer to above link

Background: our "discovery set" is ROSMAP but we have additional "validation" sets including:

  • STARNET
  • MiGA
  • KnightADRC
  • MSBB
  • metaBrain
  • UKB pQTL

TODO:

  • Get from Carlos WashU CSF based resource (pQTL and metabolomic QTL)

This section shows verification of findings from these data-sets. In principle we should check them through sections 1-6 more formally. In practice we will start with colocalization via colocboost --- since our study is genetics (variant and loci level) focused. We can selectively follow them up for potentially intereting validations. We therefore only demonstrate validation via colocboost as a starting point.

In [5]:
finempping_contexts <- readRDS(paste0(gene_name, '_finemapping_contexts.rds')) # from sec1
In [5]:
finempping_contexts <- readRDS(paste0(gene_name, '_finemapping_contexts.rds')) # from sec1
In [6]:
finempping_contexts <- get_norosmap_contexts(finempping_contexts)
In [7]:
cb_contexts <- plot_cb(cb_res = cb_res, cex.pheno = 1.5, x.phen = -0.2, add_QTL = TRUE, cohorts = finempping_contexts, gene_id = gene_id)

No pvalue cutoff. Extract all variants names.No pvalue cutoff. Extract all variants names.
No description has been provided for this image

Section 9: Non-linear effects of xQTL¶

see notebook

APOE interaction¶

In [10]:
options(repr.plot.width=6, repr.plot.height=6)

ggplot(WDR12_int_res, aes(x = variant_id, y = qvalue_interaction)) +
  geom_point(alpha = 0.7, size = 6) +
  labs(title = "qvalue for WDR12 csets in interaction association nalysis",
       x = "Gene Name",
       y = "qvalue_interaction",
       size = "qvalue_interaction") +
  theme_minimal(base_size = 14) +
  theme(panel.background = element_blank(),
        panel.grid.major = element_line(color = "grey80"),
        legend.position = NULL,
        axis.text.x = element_text(angle = 45, hjust = 1))  + ylim(0,1)
  # scale_color_manual(values = colorRampPalette(brewer.pal(8, "Set1"))(length(unique(flat_var$gene_name))))
ggsave('plots/WDR12/sec11.interaction_association_WDR12_lessPIP25.pdf', height = 5, width = 8)
No description has been provided for this image

In conclusion, there is no interaction QTL with APOE identified.

Section 10: in silico functional studies in iPSC model¶

see notebook

In [11]:
vars_p
In [13]:
apoe_p

Section 11: Functional annotations of selected loci¶

see notebook

TODO

  • Touch base with Ryan on the snATAC annotations
  • Run this by Pavel to see if there are additional comments on how we do this
In [ ]:

Section 12: Candidate loci as trans-xQTL¶

see notebook

In [9]:
options(repr.plot.width=12, repr.plot.height=6)
if(!is.null(flat_var)){
   p =  ggplot(flat_var, aes(x = gene_name, y = pip, size = pip)) +
      geom_point(alpha = 0.7) +
      labs(title = paste0("PIP values for trans fine mapped Genes in ", gene_name ," csets with AD"),
           x = "Gene Name",
           y = "PIP",
           size = "PIP",
           color = "CS Coverage 0.95 Min Corr") +
      theme_minimal(base_size = 14) +
      theme(panel.background = element_blank(),
            panel.grid.major = element_line(color = "grey80"),
            legend.position = NULL,
            axis.text.x = element_text(angle = 45, hjust = 1))  
      # scale_color_manual(values = colorRampPalette(brewer.pal(8, "Set1"))(length(unique(flat_var$gene_name))))
    ggsave(paste0('plots/WDR12/sec12.trans_fine_mapping_',gene_name,'.pdf'),p, height = 5, width = 8)
    p
    } else{
    message('There are no detectable trans signals for ', gene_name)
}

Creative thinking: generate hypothesis, search in literature, raise questions to discuss¶

You can now generate some preliminary hypotheses based on the above results. Next, you should search for evidence in the literature to support or refine these hypotheses and identify additional analyses needed to confirm them.