Human fetal brain expression SNP-weights for use in TWAS

Single nucleotide polymorphism (SNP)-weights for Ensembl
gene and transcript-level expression were derived from genotyping and RNA
sequencing data from 120 human fetal brains aged 12 – 19 post-conception weeks.
Prior to deriving
SNP-weights, gene- and transcript-level expression data were normalized and
adjusted for sex, age, RIN, sequencing batch, 3 genotype principal components and
10 PEER factors. For a full description of the sample and data
generation, please see: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1567-1
Expression
weights for use in transcriptome-wide association studies (TWAS) were derived
using FUSION software (http://gusevlab.org/projects/fusion/#computing-your-own-functional-weights). SNP-weights were only generated for genes and transcripts with significant evidence of cis-heritable
expression at the default P-value (P < 0.01) in FUSION (1351
Ensembl genes and 3985 Ensembl transcripts). Note that the number of genes that will be testable by TWAS may differ as this will depend on the number of overlapping SNPs between the weights files and the GWAS summary statistics.

Expression
weights were derived using only SNPs available in the FUSION LD reference
(HapMap3 SNPs), in line with the FUSION protocol. Expression weights provided
here are in the same format as weights downloaded from the FUSION website.

Use of these expression weights to perform TWAS of attention
deficit hyperactivity disorder (ADHD), autism spectrum disorder, bipolar
disorder, major depressive disorder and schizophrenia are described in Hall et al. 'Cis-effects on gene
expression in the human prenatal brain associated with genetic risk for
neuropsychiatric disorders' Molecular Psychiatry (in press).

Files:
- Ensembl gene level weights:
op-fusion-fetal_brain-full_sample-gene_level.tar.gz

- Ensembl transcript level weights:
op-fusion-fetal_brain-full_sample-transcript_level.tar.gz