Presentation by Dan Koboldt dkoboldtgenetics'wustl'edu April 19, 2006

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Presentation by Dan Koboldt dkoboldt_at_genetics.wus
tl.edu April 19, 2006
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Presentation Outline

• Background
• Experimental Design
• Key Findings
• Summary and Implications

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The HapMap Project
The International HapMap Project is a
multi-country effort to identify and characterize
the genetic differences in humans. In the first
phase of the HapMap, over one million SNPs were
genotyped in 269 samples from four populations.
Information from the HapMap will help
researchers find genes that affect health,
disease risk, and response to pharmaceuticals.
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The CEPH Cell Lines

• In 1980, CEPH collected samples from 90 U.S.
  residents (30 trios) with northern and western
  European ancestry.
• Blood samples were converted to immortalized cell
  lines which are available from Coriell.

Professor Jean Dausset (winner of the 1980 Nobel
Prize in Medicine and Physiology) founded Centre
d'Etude du Polymorphisme Humain, a research
laboratory, in 1984.
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About ENCODE

• A research consortium formed in 2003 by NHGRI
  ENCyclopedia Of DNA Elements
• Goal To identify all functional elements in the
  human genome sequence.
• Rigorous study of defined regions of the genome
  totaling around 30 Mb (1 of total genome).
• 10 ENCODE regions comprehensively genotyped by
  the HapMap Project.

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Non-coding Functional Elements

• Genomic regions that do not encode proteins, but
  can have a functional role.
• Examples
• Genes encoding functional RNAs
• Sequences that affect the stability or splicing
  of pre-mRNA transcripts.
• Regulatory elements that enhance or suppress the
  transcription of genes.

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Experimental Design
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Selection of Genes to Include
Supplementary Figure S1

• All RefSeq genes in ENCODE regions (321 genes)
• All RefSeq genes on human chromosome 21 (191
  genes)
• All RefSeq and manually curated genes in region
  at 20q12-13.2 (118 genes)

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Overlap of Correction Methods
Table 1

• All analyses in cis showed that 10 associated
  genes were significant.
• Biggest discordance was between Bonferroni
  genome-wide (Bonf-wg) and Permutation genome-wide
  (Perm-wg) methods.
• Overall, a very good concordance between
  multiple-test correction methods

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Associations cis versus trans
Figure 1

• The majority of detectable signals were caused
  by SNPs located cis- to the gene in question.
• Signal decayed rapidly with distance from the
  gene.

Figure 2
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cis- Association Relative to Gene
Figure 3 excerpt 1
The majority of significantly associated SNPs are
located immediately upstream of the transcription
start site.
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cis- Association and Conservation
Figure 3 excerpt 2
Many associated SNPs lie in regions of
conservation, including conserved transcription
factor binding sites
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Shared cis- Associations
Figure 3 excerpt 3
TMEM8 Association
MRPL28 Association
Two biologically unrelated genes shared the same
associated SNPs. Transcripts spanning both genes
are driven by the same promoter.
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Inevitable Caveats

• SNP-in-probe SNPs located at the probe binding
  sequence may lead to spurious cis- associations.
• CNPs Some of the significant regions indicate
  the presence of copy-number polymorphisms.

copy
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Take-home Messages

• Theres a lot of common genetic variation that
  can explain gene expression differences.
• Far more cis- regulatory regions were found than
  trans- regulatory regions.
• The HapMap resource has sufficient density for LD
  mapping.
• Direct links between regulatory regions and genes
  can help interpret genotype-phenotype
  associations in the study of complex disease.