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SHI Meng
Abstract
• The genetic basis of gene expression variation has long been
studied with the aim to understand the landscape of regulatory
variants, but also more recently to assist in the interpretation and
elucidation of disease signals. To date, many studies have looked in
specific tissues and population-based samples, but there has been
limited assessment of the degree of inter-population variability in
regulatory variation. We analyzed genome-wide gene expression in
lymphoblastoid cell lines from a total of 726 individuals from 8
global populations from the HapMap3 project and correlated gene
expression levels with HapMap3 SNPs located in cis to the genes.
We describe the influence of ancestry on gene expression levels
within and between these diverse human populations and uncover
a non-negligible impact on global patterns of gene expression. We
further dissect the specific functional pathways differentiated
between populations.
Abstract
•
We also identify 5,691 expression quantitative trait loci (eQTLs) after controlling
for both non-genetic factors and population admixture and observe that half of
the cis-eQTLs are replicated in one or more of the populations. We highlight
patterns of eQTL-sharing between populations, which are partially determined by
population genetic relatedness, and discover significant sharing of eQTL effects
between Asians, European-admixed, and African subpopulations. Specifically, we
observe that both the effect size and the direction of effect for eQTLs are highly
conserved across populations. We observe an increasing proximity of eQTLs
toward the transcription start site as sharing of eQTLs among populations
increases, highlighting that variants close to TSS have stronger effects and
therefore are more likely to be detected across a wider panel of populations.
Together these results offer a unique picture and resource of the degree of
differentiation among human populations in functional regulatory variation and
provide an estimate for the transferability of complex trait variants across
populations.
Background
• Human population differentiation
– Neutral DNA sequence
– functional variants
• non-synonymous variants
• eQTLs
• Previous eQTLs studies
– limited to only several well-defined populations
– have not contrasted geographically proximate populations
• first analysis of eQTL differentiation among eight
human population samples
Materials
• LCLs (lymphoblastoid cell lines)
• Samples:
– 726 individuals of 8 HapMap populations
CEU
CHB
GIH
JPT
LWK
MEX
MKK
YRI
109
80
82
82
82
45
138
108
• Expression data:
– Sentrix Human-6 Expression BeadChip version 2
– 47,294 transcripts, plus controls
– 21,800 probes: 18,226 unique autosomal Ensembl genes
• Genotype data:
– MAF > 0.05, < 20% missing data
– 1.1 million ~ 1.3 million per population
Methods
• Raw expression data normalization
– log2 scale
– quantile normalization across replicates of a single individual
– mean normaliztion across all individuals of the eight populations
• Population stratification correction of expression data
– Admixed populations: GIH, LWK, MEX, MKK
– EIGENSTRAT: princinple components based on genotype
– Expression values were adjusted for each population using ten primary
axes of variation form corresponding intra-population PCA
Methods
• Correction for known and unknown factors:
‘‘REDUCED’’ dataset generation
– probabilistic estimation of expression residuals (PEER)
framework
• Structure of gene expression variation among
populations
– Vst: (VT - VS)/VT;
VS =(V1*n1+V2*n2)/(n1+n2)
– top 5% probes: GO term enrichments
Methods
• Association and multiple-test correction (individual
populations)
– cis: <= 1Mb from TSS
– Association: Spearman Rank Correlation (SRC) model
– significance accessment
• 10,000 permutations of each phenotype (probe) relative to the
genotypes
• threshold: 0.01
– FDR:
• 1 - (the number of genes with replication/total number of
significant genes)
Methods
• Stepwise association model
– determine whether independent cis- regulatory signals
exist for a given gene
– Steps:
• regressed out of the expression levels the effect of the mostsignificant SNP
• re-ran the SRC analysis
• stored those SNPs with p-values more significant than the gene’s
permutation threshold
• repeated until there were no SNPs from the initial significant eQTL
list left to test
Results
• Structure of gene expression variation among populations
– expression- based PCA plot: not separate distinctly
– Vst:
• Vst values: heavily skewed toward values near 0
• the amount of VST between a pair of populations is correlated with the
degree of genetic distance
• the vast majority of genes do not exhibit highly differentiated expression
variation between populations
– probes exhbiting top 5% Vst scores: enriched in GO terms
• significant population-specific GO term enrichment
• GO terms corresponding to genes significantly diverged in expression in
one population are also diverged in expression in the other, closelyrelated populations
Results
• Cis associations of gene expression with SNPs
Results
• Multiple effects underlying cis-eQTLs
– at least two significant cis-eQTL SNPs at the 0.01
permutation threshold
– a total of 33 (0~2% for 8 populations) genes with
multiple eQTLs
– At most, a single gene had five independently
associated SNPs
Results
• Population sharing of cis-eQTLs
– 1,074 (34%) of 3130 genes had a significant cis-eQTL in at
least two populations
– more closely-related populations tend to share more cisassociated genes than more distantly-related populations
– 98.9–100% concordance of allelic direction
– effect size (fold difference between homozygotes of the
two different genotypic states of a SNP) is shared between
any two populations when the association is also shared
– the discovery of an eQTL mainly due to allele frequency
differences, not due to differences in absolute effect size
Results
• Genomic properties of eQTLS
– majority of association signals are approximately
symmetrically centered on the TSS
– the strongest statistical signals located directly at the TSS
– population sharing increases from in only one population
to all eight populations,s gradual tightening of the
distribution around the TSS
– SNPs associated with more than one gene
• 264 genes
• 52 clusters of 2 or more genes in at least two populations
• the distance to TSS: larger
Results
• eQTLs and disease
– 62 SNPs from GWAS catalog
• the most-significant SNP of a cis-eQTL in at least one
population
• 57 Ensembl genes, and 51 traits
– Alcohol dependence, Crohn’s disease, ...
• 15 (24%) were the most significant SNP of the same
gene in at least one additional population
– assist in fine-mapping causal variants for complex
traits
Disscussion
• extensive sharing of eQTLs across human populations
• effect size and the direction of effect for eQTLs: highly conserved
• symmetric distribution of eQTLs around the TSS
• additional cell types under a variety different cellular and developmental
conditions
• how the frequency spectrum of regulatory variants has been shaped by
selective and demographic processes
• how these functional variants contribute to higher order phenotypes
• methods to preprocess microarray data and detect eQTLs
• comprehensive analysis of eQTLs and functional association
Thank you!