Genetic Analysis of Genomewide Variation in Human Gene Expression Morley M' et al' Nature 2004,430:

1
Genetic Analysis of Genome-wide Variation in
Human Gene ExpressionMorley M. et al. Nature
2004,430 743-747.
Yen-Yi Ho
2
Outline

• Introduction
• Data
• Method Linkage analysis
• Results
• Discussion
• Comments

3
Introduction
4
Goal Identify loci associated with variation in
expression levels
Nucleus
regulators
Genomic DNA
mRNA
mRNA
Target
5
Cis and Trans regulation
Target gene expression phenotype
6
Data

• Centre d'Etude du Polymorphisme Humain (CEPH)
  families are Utah residents with ancestry from
  northern and western Europe.
• 14 families with genotype and expression data
  available for all parents and a mean of eight
  offspring (range 7-9)

7

• 2,756 autosomal SNP genetic loci (100kb within
  cluster, 3 Mb between cluster).
• Gene expression phenotypes
• 8,500 gene expression phenotypes in immortalized
  B cells using Affymetrix Genome Focus Array.
• Expression intensity was scaled to 500 and
  transformed by log2.

8

• 3,554 most variable expression phenotypes are
  selected (between gt within variation).
• Using CEPH unrelated individuals (94
  grandparents), two array replicates per
  individual was performed. The within individual
  variation was indicated by the mean of variance
  of array replicates.

9
Method Linkage analysis

IBD1
IBD0
IBD identical-by-descent
10
(No Transcript)
11
For a particular target gene expression
t-statistics
SNP1 2 3 4 5 Genetic
Locus
12
Results
Criteria 1 t gt 5 (P-value lt 4.3 , LOD
gt 5.3) 142 expression phenotypes have at least
one significant regulator.
Criteria 2 t gt 4 (P-value lt 3.7 ,
LOD gt 3.4) 984 expression phenotypes have at
least one significant regulator.
13
Cis and trans- regulation

• Under criteria 1,
• 27/142 (19) expression phenotype have only a
  single cis-regulator.
• 110/142 (77.5) expression phenotype have only a
  single trans-regulator.
• 2 /142 have a cis and a trans-acting regulator
• 3 /142 gene expression have two trans-acting
  regulator
• Under criteria 2,
• 164 / 984 (16) has multiple regulators

14
T-statistic
1 2 3 . . . 3554
Gene expression Target
Criteria 2 t gt 3.4
SNP 1 2 3 ..2756
SNP 1 2 3 ..2756
Genetic Locus regulator
15
Master regulator
31 25
14q32 20q13
Divide the autosomal genome into 491 windows of 5
Mb, and count the number of regulators in the
regions under criteria 2 (total 984 phenotypes
with significant linkages).
16
Co-regulation

• Use the gene expression levels of 94 CEPH
  grandparents
• Hierarchical clustering was performed and group
  genes by the correlation of the 31 target gene
  expression levels
• Permutation test was used to determine the
  significant level of pair-wise correlation.

17
14 / 31
18
Population-based association analysis for
cis-regulators
(SNP regulator)
19
(No Transcript)
20
Discussion

• The study applied genome-wide mapping method to
  identify the chromosomal regions regulate to the
  gene expression phenotypes.
• This type of study has the potential to uncover
  complicated transcriptional control.
• Cis-, trans-acting and master regulators were
  discovered.
• The linkage results are reliable as verified by
  association study and qRT-PCR.

21
Comments

• In this study, gene expression measured in
  immortalized B cells may be very different from
  the expression of human B cells in the blood.
• Co-regulated genes and the pathways that connect
  genes are identified.
• We would be even more interested in utilizing the
  data to improve our understanding of human
  disease.
• Genotype Gene expression Phenotype
  

22

• Candidate regions have cis-effects.
• Different phenotype / expression signatures
  associated with different regulators.

23
Statistical design and analysis issues

• Design
• Choice of relative type or pedigree in humans.
• Choice of tissue and timing of mRNA sampling.
• Analysis
• Multiple testing linkage location, transcripts.
• Regulatory hotspots methods to find master
  regulatory loci.
• Regulatory networks searching for small sets of
• Co-regulated transcripts.

24
Reference

• Genetic analysis of genome-wide variation in
  human gene expression. Moley M., Molony C.M,
  Teresa M. Weber T.M. et al. Nature 430743-747
  (2004).
• Genetics of gene expression surveyed in maize,
  mouse, and man. Schadt E.E., Monks S.A., Drake
  T.A. et al. Nature 422 297-302 (2003).
• Mapping expression in randomized rodent genomes.
  Broman K.W. Nature Genetics 37 209-210 (2005).
• Natural variation in human gene expression
  assessed in lymphoblastoid cells. Cheung V.G.,
  Conlin L.K., Weber T.M. et al. Nature Genetics
  33 422-425 (2003).
• Mapping determinants of human gene expression by
  regional and genome-wide association. Cheung
  V.G., Spielman R.S., Ewens K.G. et al. Nature
  437 1365-1369 (2005).

25
Question?