population pathway ? genes snps analysis phenotypes haplotypes/coding snps snp discovery...

Population

Pathway

?

GenesSNPs

Analysis

Phenotypes

• Haplotypes/coding SNPs• SNP discovery• Sequencing/genotyping technology

• Polymorphism function• Replication

PolymorphismPolymorphism

Base pair substitutions

Synonymous - Do not result in a new amino acid in the protein

sequence.

GCA (Alanine) to GCG (Alanine) (Silent mutation)

Non-synonymous - Result in a new amino acid in the protein sequence.

GAG (Glutamate) to GTG (Valine) (Missense mutation)

- codon 6 substitution in the beta-globin protein chain causes sickle-cell

anemia

Nonsense mutations - Result in a termination codon.

CAG (Glutamine) to TAG (stop)

PolymorphismPolymorphism

Insertions - Deletions

GAG TTT TCT CGG AAT GGT GGT GCT AAT

GLU PHE SER ARG ASN GLY GLY ALA ASN

GAG TTT CGG AAT GGT GGT GCT AAT

GLU PHE ARG ASN GLY GLY ALA ASN

- Fragile X Syndrome (X-linked retardation)

Tandem CCG repeats - severity of disease depends on number of repeats

- Huntington’s Disease

Tandem CAG repeats adding Glutamine to encoded Huntingtin protein.

Increasing number of proteins destabilizes the protein and interferes with synaptic

transmission and leads to apoptosis of brain cells.

GAG TTT TCT CGG AAT GGT GGT GCT AAT

GLU PHE SER ARG ASN GLY GLY ALA ASN

GAG TTT TCG GAA TGG TGG TGC TAA

GLU PHE SER GLU TRP TRP CYS STOP

(Often result in new stop codons and truncated proteins)

O6-MGMTO6-MGMT

Ile143ValLeu84Phe

Lys178Arg

145Cys

DNA Repair

Metabolism

Inflammation

Immunity

Vitamin D MetabolismVitamin D Metabolism

• 25-Hydroxylase (P450C25): Hydroxylates Vitamin D3 producing 25(OH)D. • 1-a-Hydroxylase (CYP27B1): Activates 25(OH)D to 1,25(OH)2D.• 24-Hydroxylase (P450C24): Removes excess 25(OH)D from circulation and excess

1,25(OH)2D from the kidney.• VDR: Mediates effects of 1,25(OH)2D.

(1-a-Hydroxylase)

(24-Hydroxylase)

(24-Hydroxylase)

(25-Hydroxylase)

VDR

Ohmdahl et al. Ann. Rev. Nutr. 2002.

PathwaysPathways

‘Dynamic’ graphic models of molecular and biochemical pathways.

WARNING: THIS IS A COMMERCIAL SITE!

BioCartahttp://www.biocarta.com/index.asp

Calorie restriction

SIRTUIN

NAD+

Dependence

Glucose Homeostasis

G6Pase

PEPCK

PGC1 HNF4

LPK

GCKATP-synthase

Cyt-C

Glycolysis

Glugoneogenesis

Mitochondria

Fat Mobilization

NCOR1

SMRT RXR

PPARANT1

GDH

IDE

nDNA - Mitochondria

NMNAT1

PBEF1

NNMT

HaplotypesHaplotypes

7q21

Haplotype Blocks & Recombination HotspotsHaplotype Blocks & Recombination Hotspots

Tags:

SNP 1SNP 3SNP 6

3 in total

Test for association:

SNP 1SNP 3SNP 6

A/T1

G/A2

G/C3

T/C4

G/C5

A/C6

high r2 high r2 high r2

AATT

GC

CG

GC

CG

TCCC

ACCC

GC

CG

TCCC

GGAA

GGAA

Pairwise TaggingPairwise Tagging

Vitamin D ReceptorVitamin D Receptor

•Sequenced 94/164 kb.•245 SNPs discovered•916 GB individuals genotyped•68 SNPs > 10% MAF

Nejetsev et al. 2004. Human Molecular Genetics.

FokIApaI, TaqI, BsmI

Vitamin D ReceptorVitamin D Receptor

•55 SNPs common in Britons, Norwegians, Gambians, Finns, Romanians

•TagSNPs (r2 ≥ 0.8):

Europeans:26 TagSNPs

Gambians:42 TagSNPs

Nejetsev et al. 2004. Human Molecular Genetics.

HapMapHapMap

The International HapMap Project is analyzing DNA from a total of 270 people from populations with African, Asian, and European ancestry.

Nigeria - 30 trio samples (two parents and an adult child) from YorubaJapan - 45 unrelated individuals from TokyoChina - 45 unrelated individuals from Beijing U.S. – 30 trio samples with northern and western European ancestry.

Genotyping all individuals for a SNP ~ 1,000 – 2,000 base-pairs.

www.hapmap.org

http://www.broad.mit.edu/mpg/haploview/

ResequencingResequencing

Resequencing ResourcesResequencing Resources

Systematic identification and genotyping of single nucleotide polymorphisms (SNPs) in environmental response, inflammation, immunity genes.

Candidate genes are sequenced across a panel of individuals (~90) of known ethniticies to identify common sequence variation for functional analysis and population-based studies.

Websites provide tools for haplotype determination and TagSNP selection.

Environmental Genome Projecthttp://egp.gs.washington.edu/

Seattle SNPshttp://pga.gs.washington.edu/

Innate Immunityhttp://innateimmunity.net/

SNP databasesSNP databases

SNP DatabasesSNP Databases

Warehouses of SNP information.

WARNING: NOT ALL SNPs ARE VALIDATED!

NCBIhttp://www.ncbi.nlm.nih.gov/

Utah SNPshttp://www.genome.utah.edu/genesnps/

Children’s Hospital Informatics Programhttp://snpper.chip.org/

EvolutionEvolution

VISTA ToolsVISTA Tools

VISTA is a comprehensive suite of programs and databases for comparative analysis of genomic sequences.

VISTA Toolshttp://genome.lbl.gov/vista/index.shtml