Comparison of quantitative trait loci methods: Total expression and allelic imbalance method in brain RNA-seq

TY - JOUR

T1 - Comparison of quantitative trait loci methods

T2 - Total expression and allelic imbalance method in brain RNA-seq

AU - Gådin, Jesper R

AU - Buil, Alfonso

AU - Colantuoni, Carlo

AU - Jaffe, Andrew E

AU - Nielsen, Jacob

AU - Shin, Joo-Heon

AU - Hyde, Thomas M

AU - Kleinman, Joel E

AU - Plath, Niels

AU - Eriksson, Per

AU - Brunak, Søren

AU - Didriksen, Michael

AU - Weinberger, Daniel R

AU - Folkersen, Lasse

AU - BrainSeq Consortium

PY - 2019/6

Y1 - 2019/6

N2 - BACKGROUND: Of the 108 Schizophrenia (SZ) risk-loci discovered through genome-wide association studies (GWAS), 96 are not altering the sequence of any protein. Evidence linking non-coding risk-SNPs and genes may be established using expression quantitative trait loci (eQTL). However, other approaches such allelic expression quantitative trait loci (aeQTL) also may be of use.METHODS: We applied both the eQTL and aeQTL analysis to a biobank of deeply sequenced RNA from 680 dorso-lateral pre-frontal cortex (DLPFC) samples. For each of 340 genes proximal to the SZ risk-SNPs, we asked how much SNP-genotype affected total expression (eQTL), as well as how much the expression ratio between the two alleles differed from 1:1 as a consequence of the risk-SNP genotype (aeQTL).RESULTS: We analyzed overlap with comparable eQTL-findings: 16 of the 30 risk-SNPs known to have gene-level eQTL also had gene-level aeQTL effects. 6 of 21 risk-SNPs with known splice-eQTL had exon-aeQTL effects. 12 novel potential risk genes were identified with the aeQTL approach, while 55 tested SNP-pairs were found as eQTL but not aeQTL. Of the tested 108 loci we could find at least one gene to be associated with 21 of the risk-SNPs using gene-level aeQTL, and with an additional 18 risk-SNPs using exon-level aeQTL.CONCLUSION: Our results suggest that the aeQTL strategy complements the eQTL approach to susceptibility gene identification.

AB - BACKGROUND: Of the 108 Schizophrenia (SZ) risk-loci discovered through genome-wide association studies (GWAS), 96 are not altering the sequence of any protein. Evidence linking non-coding risk-SNPs and genes may be established using expression quantitative trait loci (eQTL). However, other approaches such allelic expression quantitative trait loci (aeQTL) also may be of use.METHODS: We applied both the eQTL and aeQTL analysis to a biobank of deeply sequenced RNA from 680 dorso-lateral pre-frontal cortex (DLPFC) samples. For each of 340 genes proximal to the SZ risk-SNPs, we asked how much SNP-genotype affected total expression (eQTL), as well as how much the expression ratio between the two alleles differed from 1:1 as a consequence of the risk-SNP genotype (aeQTL).RESULTS: We analyzed overlap with comparable eQTL-findings: 16 of the 30 risk-SNPs known to have gene-level eQTL also had gene-level aeQTL effects. 6 of 21 risk-SNPs with known splice-eQTL had exon-aeQTL effects. 12 novel potential risk genes were identified with the aeQTL approach, while 55 tested SNP-pairs were found as eQTL but not aeQTL. Of the tested 108 loci we could find at least one gene to be associated with 21 of the risk-SNPs using gene-level aeQTL, and with an additional 18 risk-SNPs using exon-level aeQTL.CONCLUSION: Our results suggest that the aeQTL strategy complements the eQTL approach to susceptibility gene identification.

U2 - 10.1371/journal.pone.0217765

DO - 10.1371/journal.pone.0217765

M3 - Journal article

C2 - 31206532

SN - 1932-6203

VL - 14

JO - PLoS Computational Biology

JF - PLoS Computational Biology

IS - 6

M1 - e0217765

ER -