Download Human Genomics

CfE Higher Human Biology
Unit 1
Chapter 5 - Human Genomics
Human Genomics
• Human genomics is the study of the human
genome. It involves determining the sequence
of the nucleotide base molecules all the way
along the DNA and then relating this genetic
information about genes to their functions.
Human Genome Project
• Started in 1986 (USA and UK) but officially ‘started’ in 1990,
Europe and Japan joined in 1992
• Completed in 2003 – under budget and 2 years early
• The sequence is not that of one person, but is a composite
derived from several individuals. Therefore, it is a
"representative" or generic sequence. To ensure anonymity of
the DNA donors, more blood samples (nearly 100) were collected
from volunteers than were used, and no names were attached to
the samples that were analysed. Thus, not even the donors knew
whether their samples were actually used.
• Also sequenced yeast and animals used in medical research e.g.
zebra fish and rats.
What were the aims of the human genome project?
• To identify all the approximately 20,000-25,000 genes in human DNA.
• To find where each gene is located
• To determine the sequences of the 3 billion chemical base pairs that
make up human DNA.
• Store this information in databases.
• Estimated time 15 years. (started in 1980)
• Estimated cost US$3 billion
Human Genomics
• The sequence of bases can be determined for individual
genes and entire genomes
• This genetic information can be used to find the function of
different genes.
• Entire genomes can be compared using single nucleotide
polymorphisms (SNPs). (These are differences between
individuals due to base substitutions. )
SNPs
Sequencing DNA
A portion of DNA with an unknown base sequence is chosen to be sequenced. Many
copies of one of this DNA’s strands (the template) are synthesised. Then, in order
to make DNA that are complementary to these template strands, all the
ingredients needed for synthesis are added to the preparation. These include
DNA polymerase, primer and the four types of DNA nucleotide. In addition the
preparation receives a supply of modified nucleotides (ddA, ddT, ddG and ddC),
each tagged with a different fluorescent dye.
Every so often during the synthesis process, a molecule of modified nucleotide
just happens to be taken up instead of a normal one. However, when a modified
nucleotide is incorporated into the new DNA strand, it brings the synthesis of
that strand to a halt because a modified nucleotide does not allow any subsequent
nucleotide to become bonded to it. Provided that the process is carried out on a
large enough scale, the synthesis of a complementary strand will have been
stopped at every possible nucleotide position along the DNA template.
• The DNA Fragments of various lengths(each with its
modified nucleotide and its unique fluorescent tag) are
separated using electrophoresis. The order of the
nucleotides in the original DNA can then be worked out from
the fluorescent dye that is used.
• Usually a computer working as an automated sequence
analyser, detects the four fluorescent dyes processes this
information quickly and displays the sequence of bases in
the DNA sample.
genome sequencing animation
A variation in DNA sequence that affects a single base pair in a DNA chain is
called a single nucleotide polymorphism (SNP). SNPs are one of the ways in which
genomes are found to differ from one individual to another. For example, the
DNA of two people might differ by the SNP shown below. This difference has
arisen as a result of a point mutation where one base pair has been substituted
for another. Two out of every three SNPs involve the replacement of cytosine
(C) and with thymine (T). SNPs can occur in coding and non-coding regions of the
genome.
SNP maps
• Scientists have managed to catalogue more than a million
SNPs. They believe that an SNP map will help them identify
and understand the workings of genes associated with
disease.
• Some SNPs may indicate the likelihood of a person
developing a particular illness.
Alzheimer’s Disease
• One of the genes associated with this disease is called ApoE
(Apolipoprotein E)
• The gene is affected by two SNPs and different
combinations of these produce three different forms of the
gene (Apo E2, Apo E3 and Apo E4).
• Research has shown that inheritance of the ApoE4 allele
increases the chance of Alzheimer’s disease whilst
inheritance of the Apo E2 allele makes the person less likely
to develop the condition.
Bioinformatics is
the name given to
the fusion of
molecular biology,
statistical analysis
and computer
technology. It is an
ever-advancing area
that enables
scientists to carry
out rapid mapping
and analysis of DNA
sequences on a huge
scale and then
compare them.
• Computer programs can
be used to identify
– Gene sequences by
looking for coding
sequences similar to
know genes
– Start sequences
(there is a good
chance that each of
these will be followed
by a coding sequence
– Sequences lacking
stop codons (a protein
coding sequence is
normally a very long
chain of base triplets
containing no stop
codon except the one
at its end
Videos
• BBC documentary (1 hour)
https://www.youtube.com/watch?v=Fgq-XoyorWY
• Ethics of genome project (5 mins)
http://www.bbc.co.uk/learningzone/clips/ethics-of-thehuman-genome-project/8732.html
• History of the world
• https://www.youtube.com/watch?v=q13WCTOFJvo
Learning Intentions
• Describe what is meant by systematics
• Explain the role of genomics in personalised medicine
• Explain what pharmacogenetics is and how it is used
Systematics
Video
This can be defined as the study of a group of living things with respect to their
diversity, relatedness and classification. Data obtained by comparing human
genome sequences are used in systematics to study the origins of modern humans
and their evolutionary relationships. Unlike other primates such as orangutans,
hose DNA differs among the members of the species by around 5%, the mean
difference in genomic sequence among the members of the human race is only
about 0.3%. This high degree of similarity indicates that all humans are more
closely related to one another than other types of primate.
Careful examination of the genetic differences that do exist between different
human populations shows that the greatest variation occurs among populations in
Africa rather than those on other continents. Furthermore, genetic evidence
indicates that all human populations outside Africa possess only a small part of
the total genetic diversity found among African populations. These findings
support the “out of Africa” theory. This propses that humans originated in Africa
and underwent early evolutionary divergence in that continent over a very long
period of time (e.g. mllions of years) to form a variety of genetically different
populations. Then small groups migrated out of Africa relatively recently (e.g.
100,000 yeards ago) and gave rise to all other human populations.
Personal Genome Sequence
Personalised Medicine
A complete sequencing of a person’s DNA bases is called a personal genome
sequence. The branch of genomics involved in sequencing the genomes of
individuals and analysing them using bioinformatics tools is called personal
genomics. As a result of advances in computer technology, the process of
sequencing DNA is rapidly becoming faster and cheaper. Sequencing an
individual’s DNA for medical reasons will soon become a real possibility. In
years to come, a person’s entire genome may be sequenced early in life and
stored as an electronic medical record available for future consultation by
doctors when required.
Harmful and Neutral Mutations
Having located the mutant variants present in the genome, it is important to
distinguish between those altered sequences that are genuinely harmful.
Pharmacogenetics
This can be defined as the study of the effects (therapeutic, neutral or adverse)
of pharmaceutical drugs on the genetically diverse members of the human
population. Already it is known that one in ten drugs (e.g. the blood thinner
warfarin) varies in effect depending on differences such as SNPs in the persons
DNA profile. In the future it may be possible to use genomic information and
Customise medical treatment to
suit an individuals exact metabolic
requirements. The most suitable
drug and the correct dosage
would be prescribed as indicated
by personal genomic sequencing.
Ideally
this
advance
would
increase drug efficacy while
reducing side effects and “onesize-fits-all” approach would be
consigned to history.
Amplification and Detection of DNA SequencesPolymerase Chain Reaction (PCR)
The polymerase chain reaction (PCR) is a technique that can be used
to create many copies of a piece of DNA in vitro (i.e. outside the
body of an organism). This amplification of DNA involves the use of
primers. In this case, each primer is a piece of single-stranded DNA
complementary to a specific target sequence at the 3’ end of the
DNA strand to be replicated.
Amplification and Detection
of DNA SequencesPolymerase Chain Reaction
(PCR)
The DNA is heated to break
the hydrogen bonds between
base pairs and separate the
two strands. Cooling allows
each primer to bind to its
target sequence. During the
next step, heat-tolerant
DNA polymerase adds
nucleotides to the primers at
the 3’ end of the original
DNA strands.
Amplification and Detection of DNA SequencesPolymerase Chain Reaction (PCR)
The first cycle of
replication produces two
identical molecules of DNA
Amplification and Detection of DNA
Sequences- Polymerase Chain Reaction (PCR)
During the second cycle, the two DNA
molecules from the first cycle split
and then nucleotides are added. By
the end of the second cycle, four
identical molecules are produced.. This
will continue and the population of
DNA molecules will grow exponentially.
By this means a tiny quantity of DNA
can be greatly amplified and provide
sufficient material for forensic and
medical purposes.
Amplification and Detection of DNA SequencesPolymerase Chain Reaction (PCR)
By the end of the second
cycle four identical DNA
molecules are made.
DNA Probes
and Arrays
One of the meanings of the word array is an
orderly arrangement of many items. A DNA
microarray is an orderly arrangement of
thousands of different DNA probes as tiny
spots attached to a glass slide. A DNA
probe is a short, single stranded fragment
of DNA. It is used to detect the presence
of a specific sequence of nucleotide bases in
a sample of DNA. The DNA under
investigation is called the target DNA.
A probe is able to carry out its function
because its sequence of bases is
complementary to the specific base
sequence to be detected in the target DNA.
Fluorescent labelling indicates those spots
where a probe has successfully detected
and combined with its complementary
sequence on the target DNA.
Medical and Forensic Applications of Amplified
DNA- Genetic testing for Cystic Fibrosis
In the UK, it is estimated that 1 in 25 people
carries a recessive mutant allele for cystic
fibrosis. Carriers do not suffer the disease but
if two carriers produce a child, they risk a 1 in 4
chance of the child suffering cystic fibrosis.
Therefore couples planning a family may decide
to be tested for the presence of a mutant allele
for cystic fibrosis in their genome. This can be
done by genetic testing using blood cells. DNA is
amplified and tested for the presence of a
mutant allele using genetic probes.
Genetic testing for cystic fibrosis
Forensics
Each human genome possesses many non-coding regions of DNA composed of a
number of repetitive sequences
Each repetitive sequence is unique to an individual
These regions can be used to construct a person’s DNA profile, ‘genetic
fingerprint’
Forensic scientists amplify DNA samples from a crime scene as well as DNA
from the victim and suspects
The components of the samples are compared
Crime Scenes
Forensic Scientists make use
of the PCR reaction to
amplify DNA samples at a
crime scene. DNA samples
are taken from the victim
and the suspects are also
amplified. Next components
of the samples are separated
using gel electrophoresis and
then compared.
Paternity Disputes
PCR followed by gel electrophoresis can also be
employed to generate genetic profiles from DNA
samples and confirm genetic relationships
between individuals. Each person inherits 50% of
their DNA from each parent therefore every
band in their DNA profile (genetic fingerprint)
must match one in that of their father or their
mother. The fact that each person has 50% of
their bands in common with each of their parents
allows paternity disputes to be settled.
Evidence based on DNA amplified by PCR has
also been used to identify missing people from
human remains left at the site of a disaster and
to secure the release of innocent people who
have been wrongly imprisoned.
Is he the father?
Every band in a
person’s ‘genetic
fingerprint’ must
match one in that of
their father or mother!
Mother
Child
Father
Now answer the following questions
1. In PCR, what is a primer
2. Why is DNA heated during PCR process?
3. What is the purpose of cooling the DNA samples?
4. What is a genetic probe used for?
5. What feature of the human genome makes each individual unique and
allows genetic profiles to be constructed?
1. In PCR, what is a primer
A piece of single-stranded DNA complementary to a target sequence at the end of
the DNA strand to be replicated
2. Why is DNA heated during PCR process?
To break the H bonds to separate strands
3. What is the purpose of cooling the DNA samples?
To allow primer to bind to its target
4. What is a genetic probe used for?
To detect for the presence of a specific sequence of nucleotide bases in a sample
of DNA
5. What feature of the human genome makes each individual unique and allows
genetic profiles to be constructed?
Each human genome possesses many non-coding regions of DNA composed of a
number of repetitive sequences, each repetitive sequence is unique to an individual