Download Chapter 1 A Perspective on Human Genetics

Chapter 15
The Human Genome Project and
Genomics
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Genomics
• Is the study of all genes in a genome
• Relies on interconnected databases and
software to analyze sequenced genomes
and to identify genes
• Impacts basic research in biology and
generates new methods of diagnosis and
treatment of disease
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Linkage refers to the transmission of two genes on
the same chromosome
How was linkage discovered?
Standard dihybrid cross
Find that observed ratios in the F2 progeny do not follow
mendelian ratios.
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Fig. 5.11
Dihybrid Cross:
purple flower
Fig. P:5.11
L: long pollen,
p: white flower
l: round pollen
P_L_: P_ll: ppL_ : ppll
9 : 3 : 3 :
1
Observed:
hi
low
low
Hypothesis: These two genes
are somehow linked, and do
not assort independently
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
hi
Fig. 5.11
Two extremes
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Crossing over Disrupts Linkage and creates new
combination of alleles (recombinants)
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Figure 5.10
Gene Linkage
• Two or more genes do not show
independent assortment
• They tend to be inherited together
• Located on the same chromosome
• A measure of the degree of
recombination gives relative distance
between them
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Recombination Frequency (RF)
= # of recombinant gametes/ total # of gametes
• RF for a set of genes is proportional to the distance between the
genes
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Figure 5.12
Linkage Maps.
Linear maps from RF data
RF of 1% between two genes:
= 1 map unit or 1 centiMorgan (cM) apart.
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Genetic Mapping
• Find linkages between genes
• Measuring the frequency of crossing over
to determine the relative distance between
the genes
• Linkage analysis is difficult to do in
humans: only 5 human linkage groups
were identified by 1969
• Unit of measure is a centimorgan (cM)
1cM = frequency of 1% recombination
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
General rules
Recombination frequency is constant between
two genes.
Recombination frequency varies between different genes.
NO Recombination = genes are very closely linked.
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Linked Genes
Fig. 15.3
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Positional Cloning
• Recombinant DNA-based method for
mapping and cloning genes
• No prior information about the gene
product or its function is required
• Maps cloned DNA sequences; most are
markers not genes
• 3,500 genes and markers identified in the
late 1980s
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Genes ID-ed by Positional Cloning
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Chromosome 1
Fig. 15.4
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Human Genome Project
• Arose from methods developed for
basic research recombinant DNA
technology and DNA sequencing
• It is an extension of genetic mapping
by recombination frequencies
• Took 13 years and $3 billion to
complete
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Goals of Genomics
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Timeline of HGP
Fig. 15.5
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Gene Sequencing Computers
Fig. 15.7
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Sequencing a Genome
Clone-by-Clone Method (used by public project)
• A genomic library (a collection of clones)
is developed
• Physical maps are prepared
• Clones are organized into overlapping
groups
• DNA cut with restriction enzymes
• Each clone is sequenced and software
assembles sequence from the libraries
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Clone-byClone Method
Fig. 15.9a
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
How We Sequence a Genome
Shear
add plasmid vector+
Subclone
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
How We Sequence a Genome
Transform
into bacteria
Grow bacteria
Purify DNA
Sequence DNA
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
How We Sequence a Genome
Sequence read
Feed all 30 M reads to assembly software
Software compares all reads
Assembles them together into consensus sequence
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
How to Do 30M Sequence Reads
30M reads, that’s a lot. Need robots...
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Sequencing a Genome
Shotgun Cloning (used by private project)
• Genomic library prepared
• No genetic or physical maps are created
• Restriction enzymes are used to cut DNA,
and overlapping fragments are created
• Clones selected at random from each
library and sequenced
• Assembler software programs organize
information into genomic sequences
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Sequence of Beta-Globin Gene
• Open reading
frames (ORFs)
are exons
labeled in blue
• Green
indicates
where
transcription
begins
Fig. 15.10
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Facts About the Human Genome
• Diploid, 23 chromosome pairs
• 3 x 109 bases
• ~30,000 genes
• Genes represent ~1.5-2% of genome sequence
• Non-genic functional sequences = ??
• Repetitive DNA = ~50%
• 8% present in large recent duplications
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Functions of Human Genes
Fig. 15.12
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Selected Genomes
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Genomics and Human Genetic
Disorders
Important questions that must be
answered include
• Where is the gene located?
• What is the normal function of the
protein encoded by this gene?
• How does the mutant gene or protein
produce the disease phenotype?
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Bioinformatics
• Comparative genomics
–Compares genomes
• Structural genomics
–Derives 3-D structures for proteins
• Pharmacogenomics
–Analyzes genes and proteins for
therapeutic use
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Comparative Genomics
*Using genomes of related species as keys to understanding
genome evolution and function
Key tools:
Conserved sequences (both genes and not)
Conserved order of sequences
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Evolution of Humans
Mammals
Increased
Genomic and
Developmental
Complexity
Chordate
Body Plan
Primates (Human)
Rodents (Mouse)
Reptiles
Birds
Amphibians
Bony fish (Tetraodon)
Cartilaginous fish
Jawless vertebrates
Cephalochordates
Urochordates (Ciona)
Hemichordates
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Mouse and Human Genomes
Very similar biology
Separated by ~75 million years of evolution
Similarity at nucleotide level
~83% in genes
~60% between genes
Shared gene content:
99% similar genes
96% similar genes in similar location
Synteny- regions of genomes that share order of
conserved features
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Syntenic Regions Between Human and Mouse
• Identify sequences that are highly similar
• Find their locations in each genome
• Syntenic blocks: conserved order over long stretches
• ~200 syntenic blocks between mouse and human
• Span 95% of genome
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Humans have low rate of genetic variation
~100,000 BC, 104 humans
3000 generations
Present day,
6 x109 humans
• Humans: small species that grew large rapidly
• Amount of variation implies 10,000 founders
• Current variation in population ~10,000 individuals
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Proteomics
Study of expressed proteins in a cell
• Important in
– Understanding gene function and its
changing role in development and aging
– Identifying proteins that are markers for
diseases
– Finding proteins that are targets for
drugs in order to treat diseases and
genetic disorders
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Studying
Proteins in a
Cell
Fig. 15.15
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Ethical, Legal, and Social Implications
(ELSI)
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Future Issues
• Resources
– Genome sequences
– Libraries of cloned DNA sequences
• Technology
– New sequencing methods
– Techniques of monitoring gene expression
– Links to disease
• Software for computational biology
– Reveal protein-protein interactions in disease
– Evaluate environmental factors on health
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Future Issues
• Training
– Scientists, physicians and scholars
• Ethical, Legal, and Social Implications
– Protection of human subjects and
genomic information
• Education
– Healthcare professionals
– Public
– Develop reliable resources
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning
Grading for Discussions
Background and Methods of topic
 History – place into context.
 Why is this being done



10
Discuss how it’s done
Discuss the problems (if any) with the methods
Applications
10
Issues and Prospects – Arguments for and against
40
Ethical
 Moral
 Social
 Legal
 Broader issues – eg. genetic diversity in the case of cloning


What can and sho uld be done to address these issues
Discuss conditions under which the issue could be justified
All members of a group get the same grade
Total of 60
Chapter 15 Human Heredity by Michael Cummings ©2006 Brooks/Cole-Thomson Learning