Human Genetics

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Human Genetics
A field with enormous practical consequences.
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Human Genetics

• Provides insights into the cellular and
  molecular mechanisms underlying a variety of
  human diseases, including cancer.
• Provides tools for early diagnosis of inherited
  disorders.
• Suggests strategies for potential therapeutic
  manipulation.

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Human Genetics
One cannot do an experiment, in order to
understand the genetic mechanisms underlying a
biological process. One has to find the relevant
biological data.
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Human Genetics
Is like astronomy -- it is largely an
observational science rather than an
experimental science.
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How to find the data

• Need a well-characterized phenotype!!

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How to find the data

• Need a well-characterized phenotype!!

Why? You ultimately want to determine the
underlying genetic cause of the phenotype. If
you start with a poorly delineated phenotype,
which is made up of several distinct phenotypes,
then you will have too many unaccounted variables
in the data base and the subsequent analyses will
be rendered worthless.
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How to find the data

• Need a well-characterized phenotype!!

• Even in ideal circumstances
• Identical phenotypes can be caused by more than
  one gene (often in the same pathway).
• Defects in a single gene can cause what appear
  to be completely distinct phenotypes.

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How to Identify a Human Gene

• Functional cloning (pre-genome project)
• Candidate gene cloning
• Positional cloning (early genome project)

Positional candidate cloning (post-genome
project completion)
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How to Identify a Human Gene
Regardless of strategy, you first start with
large informative pedigrees.
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How to find the data

• Need a well-characterized phenotype!!

• Need families with well-characterized
  pedigrees!!

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Need well-characterized pedigrees!!
Human geneticists often begin a study with a
single affected individual, the proband. They
then expand their database to include all members
of his/her family.
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Need well-characterized pedigrees!!
Likely inheritance pattern
AD
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Need well-characterized pedigrees!!


Likely inheritance pattern AR
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Need well-characterized pedigrees!!
Likely inheritance pattern
XD
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Need well-characterized pedigrees!!
Likely inheritance pattern
XD
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Need well-characterized pedigrees!!


Likely inheritance pattern XR
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Need well-characterized pedigrees!!
What kind of families are the most useful for
such analyses?

• Large.
• Multi-generational.
• Well-defined (documented).

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Need well-characterized pedigrees!!
What kind of families are the most useful for
such analyses?

• Isolated.
• Geographically
• Culturally

• Why
• Founder effects (rare defects may be
  over-represented).
• Decreased variability of the genetic background.

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Need well-characterized pedigrees!!
Where do you look to find more families (more
data)?
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How to analyze the data

• Need well-characterized markers!!

• Need a well-characterized map!!

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4 Generation Pedigree
All affected individuals display a bleeding
disorder.
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How to Map a Gene

• Need to have a genetic marker that correlates
  with phenotypic or disease trait in multiple
  generations and/or families.
• Types of markers include cytogenetic markers
  and various molecular markers.
• A marker is not necessarily synomous with the
  gene that is responsible for the phenotypic or
  disease trait. It is simply close to the gene
  of interest.

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Types of Markers
Cytogenetic Markers
Human Haploid Genome 30,000 genes
Human Haploid Genome 30,000 genes
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Chromosomes segregate independently
Therefore, if two markers or traits are on two
different chromosomes, they will segregate
independently. If two markers or traits do not
segregate independently, then chromosomal linkage
is suggested.
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Scale of Human Genome Size
Haploid genome 3000 x 106 bp (35,000 genes)
Ave. chromosome 50-260 x 106 bp
1000-4000 genes
Ave. microband 3 x 106 bp
50-75 genes
Ave. YAC 750 x 103 bp
10-40 genes
Ave. BAC 40-200 x 103 bp
1-5 genes
Ave. gene 1.5-1000 x 103 bp
Mutation 1 bp
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Genetic Mapping within a Chromosomal Unit Depends
on
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Genetic mapping within a chromosomal unit depends
on the fact that Mendels second law is
frequently broken.
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3 Generation Pedigree
All affected individuals display a bleeding
disorder.
All affected individuals also have a white
forelock (known to map to chromosome 12).
No unaffected individuals have a white forelock.
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4 Generation Pedigree
All affected individuals display a bleeding
disorder.
All affected individuals also have a white
forelock, except the individual with the .
No unaffected individuals have a white forelock,
except the individual with a .


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Genetic Mapping within a Chromosomal Unit Depends
on Meiotic Recombination

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Impact of recombination on chromosome anatomy in
a 3 generation pedigree
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4 Generation Pedigree
All affected individuals display a bleeding
disorder.
All affected individuals also have a white
forelock, except the individual with the .
No unaffected individuals have a white forelock,
except the individual with a .


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4 Generation Pedigree
All affected individuals display a bleeding
disorder.
WF
B
All affected individuals also have a white
forelock, except the individual with the .
No unaffected individuals have a white forelock,
except the individual with a .
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Genetic Map Distance Measure of Recombination
Frequency
Based on the assumption that the more frequent
the recombination events between 2 loci, the
greater the distance between 2 loci. 1
centimorgan 1 chance of recombination between
2 loci On average, 1 cM 106 bp However, can
vary because of recombination hot or cold
spots.
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4 Generation Pedigree
All affected individuals display a bleeding
disorder.
All affected individuals also have a white
forelock, except the individual with the .
No unaffected individuals have a white forelock,
except the individual with a .


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4 Generation Pedigree
All affected individuals display a bleeding
disorder.
WF
B
All affected individuals also have a white
forelock, except the individual with the .
No unaffected individuals have a white forelock,
except the individual with a .
2/35 6
33/35
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Lod Scores
logarithm of the odds scores

• statistical calculation which determines the
  probability of linkage.
• determines the ratio (log10) of the likelihood
  that two loci are linked to the likelihood that
  the two loci are unlinked.
• in single gene disorders, want to have a lod
  score above 3.

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Types of Markers
Visible Markers Cytogenetic markers,
morphological markers, disease markers Molecular
Markers
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Molecular MarkersRestriction Fragment Length
Polymorphisms (RFLPs)
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Molecular MarkersVNTRs (variable number of
tandom repeats 9-64 bp repeats Southern
analysis)SSRs (simple sequence repeats 2-4 bp
repeats PCR analysis)
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Molecular Markers
STRs (sequence-tagged repeats) any of the
following markers that are defined by two primers.
RFLPs VNTRs (variable number of tandom repeats
9-64 bp repeats Southern analysis)SSRs (simple
sequence repeats 2-4 bp repeats PCR analysis)
SNPs (single nucleotide polymorphisms) spaced
every 1900 kb in a given population
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How to Map a Gene
Post-completion of the human genome project
Start with STRs (symbolized by ) scattered
evenly throughout the genome (approx 400) for an
initial genome wide scan.
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To be continued..