ARIC PWAS models

Author

Sabrina Mi

Published

September 8, 2021

The ARIC model for MetaXcan is in Box: https://uchicago.box.com/s/3sf4y4gv6c7zam0l5fxicpcd3zji5wzc

ARIC PWAS

The Atherosclerosis Risk in Communities Study (ARIC) generated genotype and proteomic data from a total of 9,084 participants (7,213 European Americans and 1,871 African Americans). The relative conectrations of plasma proteins or protein complexes was measured from blood samples using an aptamer-based approach. Genotyping of blood samples was imputed to the TOPMed reference panel (GRCh38).

Nilan Chatterjee et al analyzed cis-genetic regulation of the plasma proteome, generating PWAS through TWAS/Fusion pipeline. They study involved 4,665 SOMAmers measuring 4,491 unique plasma proteins or protein complexes encoded by 4,445 autosomal genes.

For details on the paper: https://www.biorxiv.org/content/10.1101/2021.03.15.435533v1.full

Generating the model

We created a prediction model compatible with MetaXcan software from the weights generated by Nilan Chatterjee et al’s PWAS study. The steps are documented below:

Validation

We validated the model by running SPrediXcan on height and coronary artery disease GWAS, then comparing the results to association found from Whole Blood mashr models.

---
title: ARIC PWAS models
author: Sabrina Mi
date: '2021-09-08'
slug: generating-metaxcan-prediction-model-from-aric-pwas
categories: []
tags: []
---

The ARIC model for MetaXcan is in Box:
<https://uchicago.box.com/s/3sf4y4gv6c7zam0l5fxicpcd3zji5wzc>

::: {#aric-pwas .section .level2}
## ARIC PWAS

The Atherosclerosis Risk in Communities Study (ARIC) generated genotype
and proteomic data from a total of 9,084 participants (7,213 European
Americans and 1,871 African Americans). The relative conectrations of
plasma proteins or protein complexes was measured from blood samples
using an aptamer-based approach. Genotyping of blood samples was imputed
to the TOPMed reference panel (GRCh38).

Nilan Chatterjee et al analyzed cis-genetic regulation of the plasma
proteome, generating PWAS through TWAS/Fusion pipeline. They study
involved 4,665 SOMAmers measuring 4,491 unique plasma proteins or
protein complexes encoded by 4,445 autosomal genes.

For details on the paper:
<https://www.biorxiv.org/content/10.1101/2021.03.15.435533v1.full>
:::

::: {#generating-the-model .section .level2}
## Generating the model

We created a prediction model compatible with MetaXcan software from the
weights generated by Nilan Chatterjee et al's PWAS study. The steps are
documented below:

1.  [Create prediction weights file](weights_EA.html)
2.  [Calculate covariances](covariances_EA_hg38.html)
:::

::: {#validation .section .level2}
## Validation

We validated the model by running SPrediXcan on height and coronary
artery disease GWAS, then comparing the results to association found
from Whole Blood mashr models.

1.  [GIANT height](ARIC_EA_hg38_validation_height.html)
2.  [CARDIoGRAM+C4D CAD](ARIC_EA_hg38_validation.html)
:::