Our next series of podcasts are going to deal with some basic concepts in
genetics. This first one will deal with genetic variation. If you consider
genetic diseases in relation to single gene mutations, from the online Mendelian
inheritance in man, we know that there are something like 19,000 single gene
traits that are defined in humans. There are more than 18,000 of these single
gene traits on autosomes, perhaps a thousand or more on the X chromosome
with maybe only 60 or so on the Y chromosome. If we consider a single gene
trait, we're thinking of a monogenic trait or a Mendelian trait and the
behavior of these are exactly which you may have learned about in high school or
college biology classes. So, in this matrix or punnett square, we can say that
big A is dominant to little a which is recessive. If you work this punnett
square, you can see that there are three genotypes and two phenotypes. So, the
three genotypes would be big A-big A, big A- little a, and little a-little a. The two
phenotypes would be those phenotypes that are expressed by having the
dominant genes or the recessive genes. This is the easy part of genetics
because many, if not most, human diseases have genetic components that are not
related just to single gene traits and even those that are related to single
gene traits may have many different mutations associated with them. So, for
example, and I'll talk about this a little bit later, but cystic fibrosis is
an autosomal recessive condition, but there are more than 2,000 known
mutations associated with the gene that causes cystic fibrosis. If you look at
two genes the picture is much more complicated. You can see the table on the
left showing the genotype ratio with two genes there would be nine genotypes and
you can see the phenotype ratio of nine two three two three two one. Now, in this
course I'm not gonna ask you to calculate things like this but just it
gives you an idea of how complex things get when you talk about more than one
gene. For learning issues for this next series of podcasts you should be able to
recall some basics from biochemistry that relate to genetic variation and
mutations. You should be able to distinguish between gene frequencies and
genotype frequencies, you should be able to use the Hardy-Weinberg relationship
and/or punnett square analysis to solve basic genetic problems, you should be
able to determine recurrence risk from simple scenarios that you might be
presented with, you should be able to work simple pedigrees to make genetic
diagnosis, you should be able to distinguish between autosomal and
sex-linked inheritance, and you should be able to understand implications of
germline mosaicism, penetrants, variable expression, locus heterogeneity and
imprinting. Two principles from basic genetics that I hope you remember:
segregation genes occur in pairs and only one member of a gene pair is
transmitted to a gamete. Why do we say the genes occur in pairs? Well, we
understand that we have homologous chromosomes, one from mother, one from
father, and likewise, there are homologous genes. The gene that occurs for a given
trait would come from each parent. We also talked about independent assortment.
Genes at different loci are transmitted independently of each other and if the
genes reside on different chromosomes we know the chromosomes are sought
independently during meiosis one, and you remember the concept of two to the 23rd
for the number of possible gametes that can occur as a result of meiosis. Now,
just a thought question. Can we say that independent assortment does not occur?
Well, if you think about genes on different chromosomes then you know that
the chromosomes are sort of independently of each other, but
also know that if genes are linked very close together, they can't cross over and
therefore, those genes don't independently assort from each other if
they're linked together on a chromosome. These principles are key not only to
understanding heritability of single gene traits but they're basic to
understanding why meiosis works as it does and how one can use linkage
analysis to trace disease patterns within families or within larger groups
of people. Genotype is an individual's genetic constitution. At a locus, the
phenotype is what is physically observed or what is clinically observed. Genotypes
don't necessarily correspond to unique phenotypes and individuals with
different genotypes may have the same phenotype. So, for example, cystic fibrosis
is a single gene autosomal recessive condition. Only individuals who are
homozygous recessive: little a-little a would be affected by cystic fibrosis.
Individuals who have the homozygous dominant genotype, for example, big A-big
A, and those with the heterozygous genotype, big A-little a, would show the
same phenotype and they would be normal. Although individuals that a heterozygous
big A-little a would be considered carriers for a disease like cystic
fibrosis. Because there are almost 2,000 known mutations in the gene that causes
cystic fibrosis, the disease itself can manifest with very mild to very severe
symptoms. So, I'll have more to say about that later. The same genotype might also
produce different phenotypes within different environments. PKU, for example,
is another single gene autosomal recessive condition. It can lead to
severe mental retardation, but you can avoid all the adverse phenotypic effects
of PKU by placing babies on low phenylalanine diets within a month of birth.
We know that humans display fairly substantial genetic variation and this
is reflected in traits like height, blood pressure, skin color, or different disease
states. Genetic variation arises as a result of mutation. If the variation is
in the germline that variation can be transmitted from one generation to the
next, but if that variation occurs in somatic
cells that might lead to cancer. We also know that variation arises due to multi
factorial inheritance, and we'll have a lot to say about multifactorial
inheritance throughout our course, but that would relate to genes interacting
with the environment and especially when you can't attribute traits just to one
gene. This is just a diagrammatic example just to give you a sense of what a
single gene trait might look like and how you can easily see how it would be
expressed, how if you had a digenic trait how it would be expressed, and then
if you had multifactorial inheritance. So, for example, stature in humans is
determined by a number of different genes and environmental factors. And so,
if you look at stature from short to tall you can see how the population
frequency arrays itself almost on a normal distribution and this would
reflect the interactions of genes and environmental factors on a complex trait
like stature. These figures give you more of a pictorial view looking at genetic
variation and it's looking at genotype numbers versus the number of genes for
simple Mendelian crosses. These grids represent genotypes and they would
assume no variation within the genes. I don't expect you to make a big deal of
this, but it just gives you an idea of how complex things get. If you talk about
a single gene, we've already mentioned three genotypes, two phenotypes. If you
talk about two genes determining a trait then you know there are nine genotypes
with four phenotypes, but look at how complicated it
if you have something like five genes determining a trait, look at the number
of genotypes, look at the number of potential phenotypes, and this is not
even considering how the genes interact with each other or with the environment.
This is just simple Mendelian traits. Things to recall from your studies of
biochemistry: there are molecular consequences to mutation. You've talked
about gain or loss of function mutations. You've talked about haploinsufficiency,
you usually see this in autosomal dominance like in familial
hypercholesterolemia, where maybe 50% of the gene product is not enough for
normal function. You've also talked about clinical consequences of mutations, for
example, with respect to hemoglobin disorders. You've talked about causes of
mutations and mechanisms for repair. And you've talked about various molecular
biology methods. So, these are all things you should keep in mind as you approach
your study of genetics. Now, types of mutations with respect to translation or
protein synthesis that might lead to genetic variation. We can talk about base
pair substitution or point mutations. These can be missense mutations where
there's a change in amino acid sequence. There can be nonsense mutations with this
premature chain termination. Or, there may be silent mutations where you see no
effect because of the mutation, perhaps, because the genetic code is
redundant. We can talk about deletions and insertions that can lead to frame
shift where there may be a change of amino acid sequence where you may add or
lose an amino acid. You talk about duplications of entire genes and that
might lead to dosage effect. You've of course talked about insertion of mobile
genetic elements and you've also talked about mutations that might occur in non
translated sequences. So, perhaps, those mutations in promoter or enhancer
sequences that relate to how genes are expressed. You've talked about splice
site mutations, especially in donor or acceptor junctions, and you may talk about
mutations and ribosomal DNA sequences. These are usually non-consequential
because the ribosomal genes are middle repetitive genes, in other words, they're
redundant. Now, a gene is the fundamental unit of heredity, you already know this.
DNA sequence, which is associated with regulatory regions, transcribed regions
or other functional sequence regions. All of those DNA sequences would be part of
a gene. Now, as a result of mutations a gene can differ among different
individuals with respect to DNA sequence. The differences in DNA sequence
represent the alleles and so the alleles are alternative forms of genes and
you'll find alleles on a maternal chromosome and a paternal chromosome. The
locus is actually the genes location on a chromosome. This is just an example. I
think you may have talked about this in you studies of biochemistry, but you know
that patients have different alleles at the beta globin gene locus and chromosome
11. So, a homozygous individual the patient would have the same allele at
the beta globin locus on both members of chromosome pair 11, whereas if the person
was heterozygous, the patient would have different alleles at the beta globin
locus on the maternal versus the paternal chromosome. The alleles that are
present at a given locus would be the patient's genotype. Now, we talked about
cystic fibrosis, that's an autosomal recessive condition. So here, I'll just
assume that big A is the wild-type version of the allele, little a is the
mutant version of the allele. The gene responsible for cystic fibrosis it codes
for the cystic fibrosis transmembrane conductance regulator. This is a
transmembrane protein that regulates movement of chloride and hence water
across cell membranes. If you look at the relationship between genotype and
phenotype with expect to disease outcome three factors
might contribute to severity and variability of a disease like cystic
fibrosis. First would be the patient's genotype, in other words, the patient's
specific pair of cystic fibrosis mutations. There may be other genetic
factors like whether there are cysts or trans variants that might affect intron
splicing and, of course, there may be environmental factors that might
include diet and/or therapy. And as we said, there are almost 2,000 known
mutations for cystic fibrosis. An individual that's wild-type
or homozygous would not be affected obviously. Here's an individual that's
heterozygous but this person is a carrier, because one of the alleles is
the wild-type, the other allele is this mutation. So, the so called Delta F-508,
this happens to be a phenylalanine deletion at position 508. You don't have
to know that, but this person is a carrier, they're not affected. Here's another
carrier, again, not effective because the one of the alleles is a mutated allele
but the other allele is the wild-type allele. On the other hand, here is a
patient that has two mutant alleles.This would be a homozygous patient. This
patient it would happen to have severe lung disease and pancreatic
insufficiency. Is another homozygous individual this individual has a
bilateral absence of the vas deferens but otherwise might not have as many
severe conditions. These are homozygous recessive mutations. But, we can also talk
about individuals that a compound heterozygous that, in other words, they
have two different mutations in the CF gene and compound heterozygous reflect
diversity of mutations in an autosomal recessive disorder, and knowing the
different recessive mutations might be useful in relating to clinical
management of people with cystic fibrosis. I'm not going to ask you at
this point in the to know what these different mutations
stand for or even know what the symptoms are. Now, we can talk about polymorphisms
and mutations and in human genetics mutations are usually defined as changes
in DNA sequence that result in genetic diseases. These generally occur at
relatively infrequent rates in a population, so mutations are considered
to be rare. In human genetics, polymorphisms are recognized when two or
more clearly different phenotypes would exist in the same population.
Polymorphisms are common in nature and these would relate to biodiversity to
genetic variation into things like adaptation. And polymorphisms would be
driven by evolution to retain variability in populations that live in
varied environments. So, for example, sexual dimorphism, mimicry in insects,
we talked about the various human blood types, these are all polymorphisms. You
can see, polymorphisms and, for example, in male versus female birds but we know
about sexual dimorphism they even in humans. I don't need to go over these for
you, but you can also see polymorphisms and cardiac enzymes. And I'm not making a
big deal here I just want you to be aware that we know that polymorphisms
exists in all kinds of different human traits. Now, when two or more alleles at a
given locus have frequencies that exceed one percent in a population they're said
to be polymorphic. Polymorphisms can be recognized at
frequencies of less than 1%, so polymorphisms are known to influence the
risks for contracting complex diseases like diabetes or heart disease and the
distinction between mutations and polymorphisms in human genetics is
becoming more and more blurred.