Genomics and Diseases

Genetic vs Genomic Disease

 Single gene and multiple gene diseases

 Single gene
 sequence variant causes disease
 e.g., Huntington’s disease, cystic fibrosis
 Of great importance to individuals and families with
them
 Even when added together, are relatively rare

 Thus, most people are not directly affected

 Thus, genetic diseases play small role in health care
(and in society)
 Huntington’s disease

 This disorder characterized by abnormal body

movements, and loss of cognitive ability (thinking, speaking).

 The disease starts in the 30s and 40s in most cases.

 It usually takes between 10-25 years for the disease to

kill someone, and it is invariably fatal.

 It contributes to a chemical imbalance that leads many

victims to commit suicide.

 This is a autosomal dominant genetic disorder : Each

child of an affected parent has a 50% chance of having the
disease.
 Huntington’s disease

What is the cause of this disease?

 Mutation in the “huntingtin” gene (located in the Chromosome 4) that
codes for a 350 kDa cytoplasmic protein.

 Huntingtin has a characteristic sequence of 9- to 35 glutamine (CAG)

residues (trinucleotide repeats) in the normal form; the mutated huntingtin
causing the disease has more than 35 residues.

The severity of the disease is proportional to the number of extra glutamine residues..
 Genetic vs Genomic Disease

 Multiple gene
 variant predisposes to disease (∆ risk 5-50%)
 ‘polygenic’, ‘common’, ‘complex’, ‘genomic’ diseases
 e.g., hypertension, obesity, cancer, schizophrenia
 ApoE (Alzheimer’s disease)
 BRCA1 & 2 (breast & ovarian Cancer)
 CCR5 (HIV/AIDS resistance)

 Most common diseases have heritable component

 Other component is environmental (e.g., diet, smoking)
 Thus, most people directly affected
 Thus, genomics will play a large role in health care
How to find the genes involved in a specific
disease?

One approach (Candidate

Gene Analysis):

 Start with a gene whose

function is known and that is
suspected of playing a role
in the disease.

 Compare the DNA of

people who have the
disease with those who do
not to see if that gene is
associated with the disease.
 How to find the genes involved in a
specific disease?

Another approach (Genome-wide analysis):

To examine the DNA of large numbers of people with

and without the disease and search the whole genome
for areas that differ between the two groups.
 How to find the genes involved in a
specific disease?

Another approach (Genome-wide analysis):

To examine the DNA of large numbers of people with and

without the disease and search the whole genome for areas
that differ between the two groups.

Searching randomly through three billion base pairs of

DNA for tiny changes that may be linked to disease is very
difficult, time-consuming and expensive.
How to find the genes involved in a specific disease?

A new kind of genetic map, called a high-density

(SNP) map, has the potential to speed up this
research.

SNPs are single-base differences in the DNA

sequence that can be observed between different
individuals in the population. They are the simplest
and most common form of DNA polymorphism.

SNPs are present throughout the human genome

with an average frequency of 1 per 1,000 base
pairs. The frequency, stability and relatively even
distribution of SNPs in the Genome make them
particularly valuable as genetic markers.

SNPs may provide useful information to predict

our genetic risk of developing a certain disease, to
diagnose a disease more accurately, or to predict
how you most likely will respond to a medicine.
SNP Genotyping in a population

(i) Discovery of SNPs

(ii) Identification of SNPs

SNP genotyping (Discovery)
SNP genotyping (Identification of known SNPs)

RFLP
Identification of known SNPs
Genome-Wide Human SNP Array 6.0 (Affymetrix)

More than 906,600 SNPs:

Unbiased selection of 482,000 SNPs; historical SNPs
from the SNP Array 5.0

Selection of additional 424,000 SNPs

Tag SNPs
SNPs from chromosomes X and Y
Mitochondrial SNPs
New SNPs added to the dbSNP database
SNPs in recombination hotspots
 Genome-Wide SNP Microarray Experiment
• Genomic DNA is digested with REs (e.g. Nsp I or Sty I).

•The DNA fragments are ligated with Nsp I or Sty I adaptor

DNA fragments (that recognize the cohesive overhangs)
using T4 DNA ligase.

• Primers specific to the Nsp I or Sty I adaptor sequence are

used to PCR-amplify adaptor ligated DNA fragments.

• Purified PCR product is fragmented using appropriate

amount DNase I. An aliquot of the fragmented DNA is
separated and visualized on a 4% agarode gel to ensure that
bulk of the PCR product has been fragmented to an average
size <180 bp.
 Genome-Wide SNP Microarray Experiment

•The fragmented samples are then end-labeled with biotin

and hybridized to the GeneChip arrays for 16-18 hours at
49°C.

• Following hybridization, the arrays will be washed and

stained using Streptavidin Phycoerythrin stain solution.

• The arrays are scanned by a GeneChip high resolution

Scanner.

• Data analysis is done using GeneChip Genotyping Analysis

Software (GTYPE).
Validation of GWAS data
 Genotyping of individual SNPs

 Association analysis in independent

populations