MV Hejmadi (bssmvh)
BB30055: genes & genomes
2006-7
What are the potential applications of genome sequencing projects?
1) Molecular Medicine
2) Energy sources and environmental applications
3) Risk assessment
4) Bioarchaeology, anthropology, evolution, and human migration
5) DNA forensics (identification)
6) Agriculture, livestock breeding, and bioprocessing
Reference: http://www.ornl.gov/hgmis/project/benefits.html
1) Molecular medicine

improved diagnosis of disease

earlier detection of genetic predispositions to disease

rational drug design

gene therapy and control systems for drugs

pharmacogenomics "custom drugs"
DNA polymorphism: A DNA sequence that occurs in two or more variant forms
Alleles: any variations in genes at a particular location (locus)
Haplotype: combination of alleles at multiple, tightly-linked loci that are transmitted together over
many generations
Anonymous locus : position on genome with no known function
DNA marker: polymorphic locus useful for mapping studies
RFLP Variation in the length of a restriction fragment due to nucleotide changes at a restriction site,
detected by a particular probe / PCR.
SNP: presence of two different nucleotides at the same loci in genomic DNA from different individuals
DNA fingerprinting: Detection of genotype at a number of unlinked highly polymorphic loci using one
probe
Genetic testing: Testing for a pathogenic mutation in a certain gene in an individual that indicate a
person’s risk of developing or transmitting a disease
HOW TO IDENTIFY HUMAN DISEASE GENES
Various approaches have been used to identify the ‘candidate gene’which is tested by screening for
mutations in patients with the disease. 2 broad strategies used; either a) Position independent approachbased on knowledge of gene function (biochemical or animal model approach) or b) Position dependent
approach - based on mapped position)
Position independent approach
1) Biochemical approach
e.g FactorVIII in haemophiliacs
 Isolate enzyme
 Obtain amino acid sequence
 Design synthetic
oligonucleotides in all 6 ORF
 Hybridise to cDNA / genomic
library
 Isolate clone & map
2) Animal model approach: This
approach compares animal mutant models in a phenotypically similar human disease. One rare
success in this approach is the identification of the SOX10 gene in human Wardenburg syndrome4
(WS4). This gene was identified in Dom mutant mice, which shared phenotypic traits (Hirschsprung
disease, hearing loss and pigment abnormalities) similar to these human patients. Screening the few
WS4 patients for SOX10 mutations then confirmed the role of this gene in WS4.
Dr. MV Hejmadi
MV Hejmadi (bssmvh)
BB30055: genes & genomes
2006-7
A) Position dependent approach:
Positional cloning identifies a disease gene based
on only approximate chromosomal location. It is
used when nature of gene product / candidate genes
is unknown. Candidate genes can be identified by a
combination of their map position and expression,
function or homology
Strategies
Step 1 – Collect a large number of affected families
as possible
Step 2- Identify a candidate region based on genetic
mapping (~ 10Mb or more) using either
 Genetic markers: RFLPs, SSLPs, SNPs
 Linkage association:
 Chromosmal abnormalities
 Halpotype association
Step 3- Establish a transcript map, cataloguing all
the genes in the region using computational and/or
experimental approaches.
Step 4- Identify potential candidate genes (gene
expression, function, homology or animal models)
Step 5 – confirm a candidate gene screen for mutations among affected families
One of the major successes using the positional candidate approach was Duchenne Muscular Dystrophy
(DMD). Years of the biochemical approach had failed to identify the genetic determinant of this
condition. Several groups raced to clone the DMD gene and it provided the inspiration for all
subsequent positional cloning efforts.
DNA markers or polymorphisms
RFLPs (restriction fragment length polymorphisms)
- Size changes in fragments due to the loss or gain of a restriction site
SSLPs (simple sequence length polymorphisms) or microsatellite repeats. Copies of bi, tri or tetra
nucleotide repeats of differing lengths e.g. 25 copies of a CA repeat can be detected using PCR analysis.
SNPs (single nucleotide polymorphisms)- presence of two different nucleotides at the same loci in
genomic DNA from different individuals
Reading on mapping disease genes:
1) Human Molecular genetics 3 by T Strachan & AP Read : Chapter 14 AND/OR
2) Genetics by Hartwell (2e) chapter 11
Recommended Reading on Molecular medicine:
Nature (May2004) Vol 429 Insight series
1) human genomics and medicine pp439 (editorial)
2) predicting disease using medicine by John Bell pp 453-456.
Dr. MV Hejmadi