A survey of proteomic variation across two ethnic groups in Nigeria and its relationship to obesity risk
- Resource Type
- Authors
- Biddanda, Arjun; O'Dushlaine, Colm
- Source
- Subject
- Proteomics
Quantitative Trait Loci
Genomics
- Language
- English
Data Resources for Biddanda et al (A survey of proteomic variation across two ethnic groups in Nigeria and its relationship to obesity risk) These are the assorted data resources necessary for reproducing and validating analyses from our manuscript on proteomic variation. ## Genotype and Imputed Data This dataset consists of all individuals with intersecting genotype data from this study that were subsequently imputed using the TopMed imputation server on hg38. Data is provided as binary PLINK files for association testing using [tensorQTL](https://github.com/broadinstitute/tensorqtl). ## Phenotypic Data Raw and cleaned phenotypic data (`*.metadata.tsv.gz`) which contains all information for association testing. Olink-proteomics derived PCs are also available for usage as covariates in analysis. ## Proteomic Data Raw and cleaned proteomic data from Olink Proteomics for 176 subjects. Cleaning was performed using the [Olink quality control pipeline developed by 54gene](https://54gene-olink-qc.readthedocs.io/en/latest/). Note that appropriate linker files and ignore files are also provided under `raw_data`. We recommend using post-qc data when performing analyses. ## Intermediate Results & Configurations The directory `intermediate_data` contains both configuration data for (1) running linear models for differential expression and (2) running `tensorQTL`. We have also separated intermediate results for these two specific analyses within this directory as appropriately named. These represent intermediate data sources for both differential expression and cis-pQTL discovery. ## Resources This directory includes additional resources used while processing this data for analysis. Specifically this includes the definition of protein-coding genes from Gencode v41. # Relevant Links [Olink Processing & QC pipeline](https://54gene-olink-qc.readthedocs.io/en/latest/)
For users of this dataset, please attribute 54gene, Inc for data access and cite the appropriate primary preprint and manuscript.