Last updated: 2022-07-09

Checks: 5 2

Knit directory: funcFinemapping/

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Backgrounds

Post-transcriptional regulatory (PTR) processes have been implicated in development and diseases, however, it is largely unknown how genetic variations are mediated through PTR processes. We propose to annotate GWAS variants using both experimental measurements and computational predictions. With this prior knowledge, we can further identify most likely causal variants through fine-mapping and then link them to genes.

Several post-transcriptonal features will be explored:

  • alternative splicing
  • RNA modification: m6A
  • RNA binding
  • Polyadenylation

Methods

SNP effect predictions
The predictions of variant effects on post-transcriptional regulation were performed on 10 million SNPs after some QC criteria, from 1000 genome phase 3 project.

Enrichment analysis
We first tested annotations one at a time using both TORUS and S-LDSC.Then we jointly assessed a set of annotations.

For the early attempts, I ran torus and S-LDSC on different numbers of test SNPs. As an example, there are 6M SNPs for SCZ, but 8M SNPs for aFIb after the same filtering steps. However, for S-LDSC analysis, around 1M hapmap3 SNPs were tested across all traits.

Results

Enrichment analysis on SCZ GWAS

To make it comparable, I ran LDSC and Torus on the same set of test SNPs, which are around 1 million SNPs from hapmap3.

Legends for the plots:

  • y-axis - annotations(% of SNPs within annotations)
  • x-axis - fold of enrichment
  • label on the plot - percent of SNP heritability explained by each annotation
  • dashed line - no enrichment

LDSC

modified baselines from m6A paper:
genic features (introns excluded), LD, MAF, background selection, nucleotide diversity, promoter, recombination rate.
annotations: spidex, spliceai, fetal brain m6a, neuronal OCR, differentially methylated regions in brains (DMR)

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Fig 1.1 Enrichment of SCZ risk variants in each annotation from S-LDSC. All the annotations were binary. For instance, spliceai_binary"X" represents if a GWAS SNP is predicted to have a spliceAI score equal or higher than X. Spidex_top"Y" means if a GWAS SNP is predicted to have a spidex score among the top Y percent. The rest of the annotations are bed files and each GWAS SNP was asked whether it lies in the peak regions.

Examine baseline annotations

  • baseline annotations from m6A paper: baseline_gene_MAF_LD
  • test annotation:spliceai score >=0.05

The intron region annotations explain ~50% of SNP heritability. To not interfere with our testing of splicing effects, I removed intron related annotations from baselines.

Version Author Date
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467bc60 Jing Gu 2022-07-03

Fig 1.2 Baseline enrichment of SCZ risk variants from LDSC. The baseline models used in this analysis was from the m6A science paper. We observed that coding and 3'UTR regions show significant enrichment, but the overall contribution to SNP h2g is small(<5%). While introns and their planking regions were slighty enriched, they contribute to ~50% of SNP heritability.

Torus

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Fig 1.3 Enrichment of SCZ risk variants in individual annotation from Torus. There is no baseline annotation jointly tested for each torus run. The first plot was generated using 1M hapmap SNPs, while the second one was from running torus over ~6M SNPs using our pipeline.

With the same set of test SNPs, the enrichment estimates are similarly low between torus and LDSC for SCZ. The enrichment signals seen in the previous runs for torus were gone, likely due to the background difference.

Enrichment analysis on AFib GWAS

Version Author Date
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Fig 2.1 Enrichment of aFib risk variants in individual annotation from Torus.

For aFib, we see significant enrichment of variants with spliceAI scores >=0.05. Approximately, they contribute to 2.4% of SNP heritability based on taking a product of percent of variants within annotation and enrichment estimate. However, we did not see such enrichment in LDSC results. The possible reason might be the signal was drowned out in the baseline annotations.

Comparing LDSC and Torus with the same baselines

Version Author Date
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Fig 2.2 Comparing enrichments results between LDSC and TORUS with the same baselines The spliceAI related annotations were jointly run with the same baseline annotations one at a time over aFib risk variants.

With the same baseline annotations, Torus produces lower but still significant enrichment estimates for the SNPs with spliceai >=0.05. However, we see no enrichment in LDSC results based on either enrichment estimates or p-values.

QQ plots for comparing p-values

Comparing p-values of SNPs with high spliceAI scores against genome-wide SNPs with spliceAI scores >=0.

black: 1M genome-wide SNPs with spliceAI scores >=0
blue: GWAS SNPs with spliceAI scores >=0.05

Schizophrenia

QQ plots

QQ plots

Afib

QQ plots

QQ plots

Allergy

QQ plots

QQ plots

  • For SCZ, the p-values of GWAS SNPs with spliceiAI scores above the threshold deviate from the null in a similar way as compared to genome-wide SNPs.

  • For AFib and allergy, we observed that p-values of SNPs with high spliceAI scores deviated more from the null compared to the genome-wide SNPs. However, this enrichemnt signal was gone after adjusting for baseline annotations with LDSC.

LDSC results across multiple traits

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Fig 3.1 LDSC Enrichment results across traits Enrichment estimates each with a 95% confidence interval for PTR annotations across various traits.


sessionInfo()
R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el7-x86_64/lib/libopenblas_haswellp-r0.3.13.so

locale:
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 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ggplot2_3.3.3

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8        pillar_1.5.0      compiler_4.0.4    bslib_0.2.4      
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[13] jsonlite_1.7.2    evaluate_0.14     lifecycle_1.0.0   tibble_3.0.6     
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[21] rstudioapi_0.13   yaml_2.2.1        xfun_0.21         withr_2.4.3      
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[29] fs_1.5.0          vctrs_0.3.8       sass_0.3.1        tidyselect_1.1.1 
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[49] httpuv_1.5.5      labeling_0.4.2    utf8_1.2.2        stringi_1.5.3    
[53] munsell_0.5.0     crayon_1.4.1