Understanding GWAS Chip Design – Linkage Disequilibrium a - PowerPoint Presentation

Slide1

Understanding GWAS Chip Design – Linkage Disequilibrium and HapMap

Peter Castaldi

January 29, 2013Slide2

Objectives

Introduce the concept of linkage disequilibrium (LD)

Describe how the

HapMap

project provides publically available information on genetic variation and LD structure

Review how LD enables genome-wide screens with only a subset of genome-wide SNP markers

Describe the design of chip-based genotype assaysSlide3

Human Genome

3 billion base pairs, 23 paired chromosomes

99.9% sequence similarity between individuals

~12 million variant sitesSlide4

What are the Different Types of Genetic Variation?

Single base pair change (A

C

GT

 A

T

GT), aka

S

ingle

N

ucleotide

P

olymorphism

~12 million across the genome

Insertions/Deletions (TGGT

TTC

TA  TGGT---TA)

Can be of variable size

Trinucelotide

repeats (microsatellites)

Highly polymorphic, less common than SNPs

Responsible for certain clinic disorders (Huntington’s, Fragile X,

myotonic

dystrophy)Slide5

SNPs in detail

SNPs can have up to four possible alleles (A,C,G,

T

), most have only two alleles present in human populations

Each person has two SNP alleles (one for each copy of the chromosome)

when both copies are the same, you’re homozygous (i.e. AA, CC, GG, TT). When they’re different (AT), your heterozygous.

Each allele has a frequency in which it appears in a given population

major allele (more common), minor allele (less common)

they sum to 1 (or 100%)Slide6

SNPs are Used as Genetic Markers for GWAS Chips

Properties of SNPs that make them good markers for GWAS

densely spaced across the genome

usually bi-allelic (only 2 alleles in the population, simplifies statistical tests)

GWAS chips can effectively represent most common variation with just a subset of SNPs

with ~500,000 SNPs, most common variation can be captured

this is because there is significant correlation between neighboring SNPs Slide7

Linkage Disequilibrium Causes Correlation Between Neighboring SNPs

Mendel’s laws state that genes (alleles) are independently transferred across generations (random assortment – linkage equilibrium).

This is not the case when two genetic loci are physically close to each other.

When two physically close genetic loci are not randomly assorted, this is called linkage disequilibrium.Slide8

Linkage Equilibrium Arises Because of Meiotic Recombination

http://kenpitts.net/hbio/8cell_repro/meiosis_pics.htmSlide9

Linkage and Recombination

X

Y

Z

x

y

z

X

y

z

X

y

z

y

X

z

X

Y

z

Gametogenesis

Paternal DNA

Maternal DNA

From Paternal grandfather

From Paternal grandmotherSlide10

Recombination Breaks Up Chromosomal Segments Over Generations

recombination is not uniform across the genome (

recombination hotspots

).

SNPs within the yellow region are correlated with each other and form

haplotypes

.

Because of this correlation, one can often use a single SNP from a haplotype to represent all the SNP variation within a haplotype.Slide11

Haplotype Structure Reflects Evolutionary History

The structure of haplotype blocks varies across racial groups

African populations have short LD blocks, reflecting the longer evolutionary history of those populationsSlide12

~500,000 SNP Markers Can Reasonably Represent Most

of the Common Genetic Variation in European Genomes

GWAS relies upon linkage disequilibrium and the ubiquitous nature of SNP markers to enable genome-wide surveys of the impact of

common variation

on disease susceptibility

Pe’er

et al. Nat Gen. 2006Slide13

The HapMap Project is a catalog of human variation across populations

The Human Genome project provided the complete human sequence for a small number of individuals

To get an accurate sense of variable sites, data from many individuals is needed

HapMap

has three iterations

(

http://

hapmap.ncbi.nlm.nih.gov

/)

dense genotype data from multiple populations groups

CEU – individuals of Northern and Western European ancestry from Utah

YRI –

Yorubans

from Nigeria

JPT – Japanese from Tokyo

CHB – Han

Chinese

from BeijingSlide14

Data from the HapMap Project Enabled GWAS Chip Design

Information from

HapMap

Used in chip design

panel of potential SNPs to use in a genotype

chip

population specific LD structure to allow the identification of

tag SNPs

that effectively tag haplotypesSlide15

Using Linkage Disequilibrium to find Genes

Linkage disequilibrium (LD) means that sites of genetic variation can serve as “markers” for larger chromosomal segments.

Correlation between markers is quantified with r-squared and D’.Slide16

GWAS identify novel disease loci, but additional localization is often necessarySlide17

Genotype Chip Technology

http://science-education.nih.gov/newsnapshots/TOC_Chips/Chips_RITN/How_Chips_Work_1/how_chips_work_1.htmlSlide18

Kang et al. The

American Journal of Human Genetics Volume 74, Issue 3 2004 495 - 510Slide19

Summary

Genetic material is transmitted across generations in blocks called

haplotypes

.

Linkage disequilibrium and haplotype blocks allow for

SNP tagging approaches that enable GWAS chips to capture common genetic variation with a subset of genetic markers.

Haplotype structure varies across ancestral groups.

The

HapMap

project catalogs human genetic variation and LD structure

across populations.