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Penetrance and expressivity
“The terms penetrance and expressivity quantify the
modification of the influence on phenotype of a particular
genotype by varying environment and genetic background;
they measure respectively the percentage of cases in which
a particular phenotype is observed when the specific allele
of a gene of interest is present and the extent of that
phenotype.”
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“Cancer Free at 33, but
Weighing a Mastectomy”
Deborah Lindner, 33, did intensive research as she considered having a preventive mastectomy after a DNA test.
The New York Times, Sunday, Sep. 16, 2007
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The New York Times, Sunday, Sep. 16, 2007
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www.nytimes.com
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“Little gene cards” – what if it says,
BRCA1-mutant?!
“The Lindners share a defective copy of a
gene known as BRCA1 (for breast cancer
gene 1) that raises their risk of developing
breast cancer sometime in their lives to
between 60 and 90 percent. Only 30,000
of more than 250,000 American women
estimated to carry a mutation in BRCA1 or
a related gene, BRCA2, have so far been
tested.”
The New York Times, Sunday, Sep. 16, 2007
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“Never ask, for whom the bell tolls”
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Hanahan and Weinberg (2000) Cell 100: 57–70.
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Knudsen “two-hit” model
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“Malignancy of somatic cell hybrids”
B. Ephrussi et al., Nature (1969) 224:1314
The studies of Ephrussi et al. and Harris provided compelling evidence that
the ability of cells to form a tumor is a recessive trait. They observed that the
growth of murine tumor cells in syngeneic animals could be suppressed when
the malignant cells were fused to nonmalignant cells, although reversion to
tumorigenicity often occurred when the hybrids were propagated for extended
periods in culture. The reappearance of malignancy was found to be associated
with chromosome losses. Stanbridge and his colleagues studied hybrids made
by fusing human tumor cell lines to normal, diploid human fibroblasts. Their
analysis confirmed that hybrids retaining both sets of parental chromosomes
were suppressed, with tumorigenic variants arising only rarely after
chromosome losses in the hybrids. Moreover, it was demonstrated that the loss
of specific chromosomes, and not simply chromosome loss in general,
correlated with the reversion to tumorigenicity.
The observation that the loss of specific chromosomes was associated with
the reversion to malignancy suggested that a single chromosome (and perhaps
even a single gene) might be sufficient to suppress tumorigenicity. To directly
test this hypothesis, single chromosomes were transferred from normal cells to
tumor cells, using the technique of microcell-mediated chromosome transfer. It
was found that the transfer of a single chromosome 11 into the HeLa cervical
carcinoma cell line suppressed the tumorigenic phenotype of the cells. Many
studies have now demonstrated that transfer of even very small chromosome
fragments will specifically suppress the tumorigenic properties of certain cancer
cell lines.
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Ventura et al (T. Jacks) Nature 445: 661
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Beyond Mendel – interactions of
gene products in the formation of
traits as revealed by highly
modified progeny ratios in
crosses
EPISTASIS (“to stand on top of”)
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Epistasis
(or: an epistatic interaction between two loci)
1.
2.
3.
4.
Pick a trait.
Find a mutant  phenotype #1
Find a different mutant  different phenotype (#2)
Cross the two mutants: get not a mix of phenotypes,
but instead, either phenotype #1 or #2.
The term “epistasis” refers to a phenomenon in which an
allele of one gene masks (“stops”) the effects on the
phenotype of an allele of a different gene.
The discovery of epistatic interactions between gene
products is one of the most powerful tools in genetics –
it allows the assembly of individual genes into
pathways – and understanding of pathways leads to
an understanding of mechanism.
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“For difference determined by one
gene…”
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Fig. 3.7
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Fig. 3.6
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How can one tell, if two
organisms under study that
exhibit mutant phenotypes for a
particular trait have a mutation in
different genes
or in the same gene?
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Complementation test
“Complementation is the production of a
wild-type phenotype when two haploid
genomes bearing different recessive
mutations are united in the same cell.”
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The cis-trans test
(aka complementation test)
Edward Lewis
(NP 1995)
Are two different recessive mutations that appear to affect the same trait
in the SAME gene or in DIFFERENT genes?
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Orgo
cis-2-butene
trans-2-butene
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The cis-trans test, 1949:
lozenge (M. Greene)
Two different recessive mutants, both with the same
phenotype (small eyes and fused facets).
Are they mutations in the same gene?
Make two different fly lines and compare their phenotypes.
Cis:
Trans:
wt
wt
wt
lz(g)
lz(BS)
lz(g)
lz(BS)
wt
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Cis:
Trans:
wt
wt
wt
lz(g)
lz(BS)
lz(g)
lz(BS)
wt
This is a control experiment.
The flies will be wild-type
regardless of whether
BS and g are in the
same gene or not.
If flies are normal, then
mutations are in different genes.
If the phenotype is still mutant,
then BS and g must be in the
same gene!!!
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Rine schematic
mate to a cells
Jasper Rine and Ira Herskowitz (1987) Genetics 116: 9-22.
Fig. 17.14
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The data
• Colonies screened: 675,000
• Colonies that mated to a: 295
• Major complementation groups: 4
silent information regulators:
SIR1, SIR2, SIR3, SIR4
Jasper Rine and Ira Herskowitz (1987) Genetics 116: 9-22.
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Baur et al. Nature 444: 337.
Lagouge et al. Cell 127: 1109.
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Xeroderma pigmentosum
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What was actually done
1.
By linkage analysis, it was discovered that the same
disease (XP) can be caused by mutations in 7 distinct
loci.
2. The cDNA from each gene was cloned.
3. An assay was developed to measure, how sensitive to
UV light cells are.
4. Experiment: take cells from patient type A, and
introduce each of the 7 cDNAs, one after another.
5. Whichever cDNA restores the wild-type phenotype
corresponds to the gene that is mutated in that cell.
 Bin XP mutations into “complementation groups”!
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Wait a minute
Ahem.
Fine. You take a cell that’s mutant, stick in a gene,
the cell is now wild-type, and you tell us this
means the gene you stuck in is the gene that is
mutated in the cell.
What if the cell has a mutation in a completely
different gene, and the gene you stuck in is just
epistatic to the first one?!
Good question. We’ll get to an answer shortly.
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http://www.gmi.oeaw.ac.at/
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For complete clarity
1. All genotypes – except in cases of
nondisjunction – follow Mendel’s first law, and
– except in cases of linked genes < 50 cM
away from each other – Mendel’s second law.
2. With the exception of human genetic disease,
which is, let’s face it, very rare, and things like
blood group inheritance, which belongs mostly
on the MCAT (note – its inheritance, not blood
groups themselves), the inheritance of
phenotype seldom follows Mendel’s laws.
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Complementary gene action (9:7)
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Recessive epistasis (9:3:4)
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Dominant epistasis (13:3)
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Future e-mail
Professor,
Thanks for nothing, BUSTER.
First you tell us that deviations from
Mendelian ratios can occur in monohybrid
crosses (e.g., in a dominance series), then
you tell us they occur in dihybrid crosses
and are, in fact, a hallmark of epistasis.
How can one tell the difference?
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Fig. 3.18
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“… the stadium capacity is now
officially listed as 75,662”
42:12 !!!
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Steinberg Curr Opin Hematol 13: 131
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“An SCN9A channelopathy causes
congenital inability to experience pain”
Nature Dec. 14, 2006
“The index case for the
present study was a tenyear-old child, well known to
the medical service after
regularly performing 'street
theatre'. He placed knives
through his arms and
walked on burning coals,
but experienced no pain. He
died before being seen on
his fourteenth birthday, after
jumping off a house roof.”
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So – let’s think about this
The small fraction of African-Americans who are
relatively pain-free …
… could they be heterozygous for a loss-offunction mutation in SCN9A?
In other words, could this be recessive epistasis?
If yes, could this suggest that a small-molecule
inhibitor of that specific pain receptor could be a
more effective analgesic for SCA patients than
God-awful parenteral morphine!
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Prophylactic bilateral mastectomy (and/or
oopherectomy) for BRCA1/2 mutation carriers
“A study of 139 women with deleterious BRCA1 or BRCA2 mutations who were
followed at the Rotterdam Family Cancer Clinic. To reduce their risk of breast
cancer, 76 of these women chose to undergo prophylactic bilateral mastectomy,
whereas the remaining 63 were followed according to a surveillance protocol
consisting of a monthly breast self-examination, a semiannual breast examination
by a health care professional, and annual mammography. … No breast cancers
were observed in the 76 women who underwent prophylactic bilateral mastectomy,
whereas eight were detected in the surveillance group. This study … supports the
report by Hartmann et al. that prophylactic bilateral mastectomy has an efficacy of
at least 90 percent in women classified as at high risk on the basis of a family
history of breast cancer. Together [these studies] suggest that of the strategies to
reduce the risk of breast cancer in high-risk women, prophylactic bilateral
mastectomy is the most effective.
Two decades of research have convincingly shown that most women with breast
cancer can safely be treated with breast-conserving surgery instead of
mastectomy. Thus, it is difficult to accept that prevention should be more extreme
than the cure. In this era of molecular medicine, we strive for cancer-prevention
options that are more targeted and less invasive than surgical extirpation.
Chemoprevention for breast cancer that is as effective and safe as prophylactic
bilateral mastectomy is a hope for the future.
Andrea Eisen and Barbara Weber (2001) NEJM 345: 208
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“Physical exercise and lack of
obesity in adolescence were
associated with significantly
delayed breast cancer onset.”
M.-C. King et al. Science 2003
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A Russian proverb that aptly describes most
current cancer treatment modalities
«Лучшее средство от кровотечения из носа –
жгут на шею».
“The best cure for a nosebleed is a torniquet on
the neck.”
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“Chemo” drugs
Depolymerization of microtubules
Intrastrand DNA crosslinking
Cell cycle arrest
Apoptosis (programmed cell death)
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Wilson and Elledge (2002) Science 297: 1822.
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Penetrance, expressivity, genetic
background, and the environment
“No gene is an island”
1. The effect of a given mutation in a given gene
can be modified by that particular individual’s
genotype at other loci (SCA). This will lead to
variable expressivity – perhaps even
incomplete penetrance!
2. Furthermore, the effect of a given mutation in a
given gene can be modified by the
environment (BRCA) – this will lead to
incomplete penetrance (for binary traits, such
as cancer), and variable expressivity (heart
disease).
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Genetics of continuous
variation
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Yao Ming, 7’6’’
Michael Jordan, 6’6’’
Muggsy Bogues,
5’3’’
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In a population, phenotypes of
individuals for a quantitative trait
tend to be normally distributed
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The Great Schism (1901-1935)
“Naturalists”
• the origin and
meaning of diversity
• populations, groups,
higher taxa
• gradualism
• ultimate causation
“The Mendelians”
• transformation of
genes
• individual genes/loci
• saltationism
• no “why” questions
“Only the experimental method would permit an objective discussion of
the theory of evolution, in striking contrast to the older speculative
method of treating evolution as a problem of history.” (T.H. Morgan)
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Synthesis: Population Genetics
•
•
H. Nilsson-Ehle, R.A. Fisher, J.B.S.
Haldane, S. Wright: continuous
phenotypic variation is not at odds with
particulate inheritance:
multiple loci + epistasis
S.S. Chetverikov: naturally occurring
recessives as food for natural selection.
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Morgan, ch. 8
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Hermann Nilsson-Ehle
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Central limit theorem
Carl Friedrich Gauss 
If a variable is the sum of many independent
variables, then its distribution will be normal:
e
x
2
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Fig. 3.17
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“Additive effects of genes”
Fig. 3.22
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Talking to laypeople
(and biochemistry majors)
1.
2.
3.
Technology and science have advanced to the point
where “DNA research” is materially affecting public
health – both at an individual level, and at a societal
one.
Our ability to interpret genetic data lags behind our
ability to act intelligently on those data.
While this gap is being worked on, and with the critical
exceptions of carrier (or prenatal) testing for inherited
human disease such as Tay-Sachs, and cystic fibrosis,
and also of breast, colon, thyroid, stomach, and skin
cancer for individuals with strong family histories of the
above – “the DNA stuff” is best left alone (for now) –
from an action perspective – but not from that of
knowledge!
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