Case study: APOC1 xQTL and AD GWAS¶

This notebook documents the analysis of xQTL case study on a targeted gene, APOC1.

  • 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 APOC1 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 (APOC1 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, APOC1_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.APOC1.rds. This can be used as input for Section 12.
  • b. Section 2: A variant list showing colocalization in cohorts we analyzed with ColocBoost, APOC1_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 = 'APOC1'

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>
ENSG00000130208chr19418400004796000044914246chr19:41137068-42346101,chr19:42346101-44935906,chr19:44935906-46842901,chr19:46842901-4859013619_41137068-42346101,19_42346101-44935906,19_44935906-46842901,19_46842901-4859013619_41137068-42346101,19_42346101_44935906,19_44935906_46842901,19_46842901_48590136TADB_1261,TADB_1262chr19_40837074_46645602,chr19_43631573_488863154491424744919349chr19:29228289-44527222,chr19:31719752-46645602,chr19:34641744-48886315,chr19:40837074-55473296,chr19:43631573-57160893,chr19:46290022-58617616APOC1
$target_LD_ids
A matrix: 1 x 4 of type chr
chr19:41137068-42346101chr19:42346101-44935906chr19:44935906-46842901chr19:46842901-48590136
$target_sums_ids
A matrix: 1 x 4 of type chr
19_41137068-4234610119_42346101-4493590619_44935906-4684290119_46842901-48590136
$gene_region
'chr19:41840000-47960000'
$target_TAD_ids
A matrix: 1 x 2 of type chr
chr19_40837074_46645602chr19_43631573_48886315
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>
ENSG00000130208chr19418400004796000044914246chr19:41137068-42346101,chr19:42346101-44935906,chr19:44935906-46842901,chr19:46842901-4859013619_41137068-42346101,19_42346101-44935906,19_44935906-46842901,19_46842901-4859013619_41137068-42346101,19_42346101_44935906,19_44935906_46842901,19_46842901_48590136TADB_1261,TADB_1262chr19_40837074_46645602,chr19_43631573_488863154491424744919349chr19:29228289-44527222,chr19:31719752-46645602,chr19:34641744-48886315,chr19:40837074-55473296,chr19:43631573-57160893,chr19:46290022-58617616APOC1
$target_LD_ids
A matrix: 1 x 4 of type chr
chr19:41137068-42346101chr19:42346101-44935906chr19:44935906-46842901chr19:46842901-48590136
$target_sums_ids
A matrix: 1 x 4 of type chr
19_41137068-4234610119_42346101-4493590619_44935906-4684290119_46842901-48590136
$gene_region
'chr19:41840000-47960000'
$target_TAD_ids
A matrix: 1 x 2 of type chr
chr19_40837074_46645602chr19_43631573_48886315
In [3]:
gene_id = target_gene_info$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/APOC1/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: 1 x 8
colocalized phenotypespurity# variantshighest VCPcolocalized indexcolocalized variantsmax_abs_z_variantcset_id
<chr><dbl><dbl><dbl><chr><chr><chr><chr>
PCC; AC_unproductive0.919090820.51428315409; 15380chr19:44914939:C:G; chr19:44909484:C:Gchr19:44914939:C:Gcoloc_sets:Y5_Y8:CS1
In [12]:
# effect sign for each coloc sets
get_effect_sign_csets(cb_res)
$`coloc_sets:Y5_Y8:CS1` =
A data.frame: 2 x 3
variantsPCCAC_unproductive
<chr><dbl><dbl>
chr19:44914939:C:Gchr19:44914939:C:G-3.96623910.350213
chr19:44909484:C:Gchr19:44909484:C:G-4.535243 9.257702
In [13]:
# LD between coloc sets
get_between_purity_simple(cb_res, gene.name = gene_id, path = '/data/colocalization/QTL_data/eQTL/')

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/APOC1/sec3.colocboost_res_allad.pdf', width = 10, height = 5)
replayPlot(cb_ad$p)
dev.off()

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 = 'APOC1')

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.APOC1.rds', sQTL = 'no_MSBB')
multigene_flat
A data.frame: 97 x 6
gene_id#chrstartendgene_namecontexts
<chr><chr><int><int><chr><chr>
ENSG00000007047chr194507928745079288MARK4 ROSMAP_AC_sQTL,ROSMAP_PCC_sQTL,ROSMAP_DLPFC_sQTL
ENSG00000008438chr194602305246023053PGLYRP1 MiGA_SVZ_eQTL
ENSG00000010310chr194566822045668221GIPR MiGA_SVZ_eQTL,ROSMAP_DLPFC_sQTL
ENSG00000011332chr193822971338229714DPF1 ROSMAP_DLPFC_sQTL
ENSG00000011478chr194569240245692403QPCTL ROSMAP_DLPFC_sQTL
ENSG00000011600chr193590829435908295TYROBP ROSMAP_DLPFC_sQTL
ENSG00000012061chr194547882745478828ERCC1 ROSMAP_DLPFC_sQTL
ENSG00000062370chr194436721644367217ZNF112 ROSMAP_AC_sQTL
ENSG00000069399chr194474783544747836BCL3 ROSMAP_AC_sQTL
ENSG00000073008chr194464379744643798PVR ROSMAP_AC_sQTL
ENSG00000073050chr194358047243580473XRCC1 ROSMAP_AC_sQTL,ROSMAP_PCC_sQTL
ENSG00000079432chr194226853642268537CIC ROSMAP_DLPFC_sQTL
ENSG00000079435chr194242738742427388LIPE ROSMAP_DLPFC_sQTL
ENSG00000104783chr194378125643781257KCNN4 MiGA_THA_eQTL
ENSG00000104814chr193861888138618882MAP4K1 MiGA_THA_eQTL,ROSMAP_AC_sQTL
ENSG00000104853chr194495459044954591CLPTM1 Knight_eQTL,PCC_DeJager_eQTL,ROSMAP_AC_sQTL,ROSMAP_PCC_sQTL,ROSMAP_DLPFC_sQTL
ENSG00000104856chr194500144845001449RELB ROSMAP_PCC_sQTL
ENSG00000104859chr194503904445039045CLASRP ROSMAP_AC_sQTL,ROSMAP_PCC_sQTL
ENSG00000104879chr194532287445322875CKM MiGA_THA_eQTL
ENSG00000104881chr194540634845406349PPP1R13LROSMAP_DLPFC_sQTL
ENSG00000104884chr194537091745370918ERCC2 AC_DeJager_eQTL,ROSMAP_AC_sQTL
ENSG00000104888chr194944235949442360SLC17A7 ROSMAP_AC_sQTL
ENSG00000104892chr194533343345333434KLC3 ROSMAP_AC_sQTL,ROSMAP_PCC_sQTL,ROSMAP_DLPFC_sQTL
ENSG00000104936chr194578255145782552DMPK MiGA_THA_eQTL
ENSG00000104983chr194599546045995461CCDC61 ROSMAP_DLPFC_sQTL
ENSG00000105197chr193948041139480412TIMM50 ROSMAP_PCC_sQTL
ENSG00000105204chr193983420039834201DYRK1B ROSMAP_DLPFC_sQTL
ENSG00000105221chr194028553540285536AKT2 ROSMAP_DLPFC_sQTL
ENSG00000105270chr193603334236033343CLIP3 ROSMAP_DLPFC_sQTL
ENSG00000105281chr194678859346788594SLC1A5 MiGA_THA_eQTL
..................
ENSG00000167601chr194121922241219223AXL ROSMAP_AC_sQTL,ROSMAP_DLPFC_sQTL
ENSG00000167645chr193831727238317273YIF1B MiGA_THA_eQTL
ENSG00000167754chr195095309250953093KLK5 ROSMAP_PCC_sQTL
ENSG00000167766chr195269049552690496ZNF83 ROSMAP_AC_sQTL,ROSMAP_DLPFC_sQTL
ENSG00000170949chr195310343553103436ZNF160 ROSMAP_PCC_sQTL
ENSG00000174951chr194875538948755390FUT1 ROSMAP_PCC_sQTL
ENSG00000176182chr194590261245902613MYPOP ROSMAP_AC_sQTL,ROSMAP_PCC_sQTL
ENSG00000178980chr194777858447778585SELENOW ROSMAP_AC_sQTL,ROSMAP_PCC_sQTL
ENSG00000179820chr195386476253864763MYADM ROSMAP_AC_sQTL
ENSG00000179846chr194516081445160815NKPD1 MiGA_THA_eQTL
ENSG00000182013chr194647156246471563PNMA8A MiGA_SVZ_eQTL,ROSMAP_DLPFC_sQTL
ENSG00000186567chr194466227744662278CEACAM19 DLPFC_DeJager_eQTL,Exc_mega_eQTL
ENSG00000187244chr194480907044809071BCAM DLPFC_Klein_gpQTL,ROSMAP_AC_sQTL,ROSMAP_DLPFC_sQTL
ENSG00000188227chr193750693837506939ZNF793 MiGA_GTS_eQTL
ENSG00000188368chr194230209742302098PRR19 MiGA_GTS_eQTL
ENSG00000188766chr193838842038388421SPRED3 ROSMAP_DLPFC_sQTL
ENSG00000196235chr193943615539436156SUPT5H ROSMAP_DLPFC_sQTL
ENSG00000196961chr194976700049767001AP2A1 ROSMAP_DLPFC_sQTL
ENSG00000204936chr194335368543353686CD177 MiGA_SVZ_eQTL
ENSG00000224916chr194494223744942238APOC4-APOC2DLPFC_DeJager_eQTL,STARNET_eQTL
ENSG00000234906chr194494603444946035APOC2 DLPFC_DeJager_eQTL,AC_DeJager_eQTL,ROSMAP_PCC_sQTL,STARNET_eQTL
ENSG00000254004chr193652827036528271ZNF260 ROSMAP_DLPFC_sQTL
ENSG00000263002chr194414155344141554ZNF234 ROSMAP_DLPFC_sQTL
ENSG00000267173chr194440160744401608AC245748.1 ROSMAP_AC_sQTL
ENSG00000267173chr194440160744401608ZNF285 ROSMAP_AC_sQTL
ENSG00000267467chr194494223644942237APOC4 BM_36_MSBB_eQTL,STARNET_eQTL
ENSG00000268083chr193884017738840178AC008982.1 ROSMAP_AC_sQTL
ENSG00000268434chr194578597245785973AC011530.1 ROSMAP_DLPFC_sQTL
ENSG00000272333chr193571797235717973KMT2B ROSMAP_AC_sQTL
ENSG00000278318chr194444857744448578ZNF229 ROSMAP_DLPFC_sQTL

Other genes implicated are PROC and HS6ST1 in MiGA cohort which may share causal eQTL with APOC1. Further look into the data-set --- using these genes as targets and repeating what we did above for APOC1 --- might be needed to establish a more certain conclusion.

Alternatively, we may be able to apply a multi-gene statistical fine-mapping test on APOC1 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. 'chr19:29228289-44527222'
  2. 'chr19:31719752-46645602'
  3. 'chr19:34641744-48886315'
  4. 'chr19:40837074-55473296'
  5. 'chr19:43631573-57160893'
  6. 'chr19:46290022-58617616'

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 APOC1:

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))
    }
}

$pip_plot

$effect_plot
No description has been provided for this image 
$z_plot
NULL

$effects
                L1 L2 L3
ENSG00000178982  0  0  0
ENSG00000275395  0  0  0
ENSG00000130203  0  0  0
ENSG00000130208  0  0  0
ENSG00000125755  0  0  0

$pip_plot
No description has been provided for this image 
$effect_plot
No description has been provided for this image 
$z_plot
NULL

$effects
                          L3           L1           L2          L5
ENSG00000130203 5.720778e-13 3.629693e-14 2.979669e-13 4.55119e-12
ENSG00000130208 5.720778e-13 3.629693e-14 2.979669e-13 4.55119e-12
ENSG00000182013 5.720778e-13 3.629693e-14 2.979669e-13 4.55119e-12
ENSG00000130748 5.720778e-13 3.629693e-14 2.979669e-13 4.55119e-12
ENSG00000105483 5.720778e-13 3.629693e-14 2.979669e-13 4.55119e-12
ENSG00000104894 5.720778e-13 3.629693e-14 2.979669e-13 4.55119e-12
ENSG00000104872 5.720778e-13 3.629693e-14 2.979669e-13 4.55119e-12
ENSG00000126464 5.720778e-13 3.629693e-14 2.979669e-13 4.55119e-12
ENSG00000126457 5.720778e-13 3.629693e-14 2.979669e-13 4.55119e-12
ENSG00000131398 5.720778e-13 3.629693e-14 2.979669e-13 4.55119e-12
ENSG00000129450 5.720778e-13 3.629693e-14 2.979669e-13 4.55119e-12
ENSG00000187474 5.720778e-13 3.629693e-14 2.979669e-13 4.55119e-12
ENSG00000171051 5.720778e-13 3.629693e-14 2.979669e-13 4.55119e-12
ENSG00000167766 5.720778e-13 3.629693e-14 2.979669e-13 4.55119e-12
ENSG00000130844 5.720778e-13 3.629693e-14 2.979669e-13 4.55119e-12
No description has been provided for this image

In this case, there is no statistical evidence for APOC1 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) )
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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 pvalue cutoff. Extract all variants names.No pvalue cutoff. Extract all variants names.
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Section 9: Non-linear effects of xQTL¶

see notebook

APOE interaction¶

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

ggplot(APOC1_int_res, aes(x = variant_id, y = qvalue_interaction)) +
  geom_point(alpha = 0.7, size = 6) +
  labs(title = "qvalue for APOC1 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/APOC1/sec11.interaction_association_APOC1_lessPIP25.pdf', height = 5, width = 8)
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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/APOC1/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.