Georgia
M. Dunston,
Ph.D.
Director
|
The
molecular
genetics
research
interests
are in
human
population
genetics,
anthropological
genetics,
immunogenetics,
and the
genetics
of complex
diseases.
Ultimate
goals
surround
elucidating
questions
of human
variation,
the evolutionary
history
of genes
within
populations
and how
these
gene histories
are involved
in the
etiology
of complex
diseases.
While
the laboratory's
research
goals
have shared
consequences
for all
humanity,
specific
interests
focus
on populations
of African
ancestry.
Operational
Objectives:
1.
Develop
a SNP
database
for mapping
functional
mutations
linked
to diseases
common
in African
peoples.
2.
Utilization
of evolutionary
history
of candidate
genes
to identify
polymorphisms
that are
associated
with diseases.
3.
Exploit
the linkage
disquilibrium
generated
by admixture
in the
African
American
population
for gene
mapping. |
|
CURRENT
RESEARCH PROJECTS
The
biological transition
of enslaved
Africans-to-African
Americans is
marked by the
transition of
environmental
stresses from
Africa to those
in the Americas,
and to a lesser
extent, by The
incorporation
of non-African
genes into the
African American
gene pool. The
transition from
the various
African environments
of origin to
the diverse
American environments
is far from
insignificant.
The American
environment
imposed new
selective pressures
on the Africans.
These selective
pressures may
have favored
certain genes
while eliminating
others. This
evolutionary
hypothesis has
been a controversial
explanation
for the high
incidence of
diseases such
as hypertension
in African Americans.
Thus, African
American biology
has been significantly
shaped by periods
of intermixture
creating high
heterogeneity,
and selective
pressures emanating
from the unique
and particularly
adverse social,
economic, and
political conditions
in the US. All
of these factors
might contribute
to the high
incidence of
diseases with
a significant
genetic component
such as type
2 diabetes,
asthma, hereditary
cancer (prostate,
breast and lung),
and hypertension
in African Americans.
Prostate
cancer is
the most common
solid malignancy
among men in
the United States.
African American
men have the
highest incidence
of prostate
cancer compared
to other ethnic
groups. This
cohort also
appears to present
more commonly
at an advanced
stage with aggressive
histology and
increased cancer-related
mortality. Thus,
there is a critical
need to explore
the etiologic
pathways (genetic
and environmental
factors) that
contribute to
this disparity.
In on of our
projects "Genes,
environment
and prostate
cancer in populations
of African descent"
we seek to understand
the relative
contribution
of allelic variations
of candidate
genes and environmental
factors to determine
an individuals
risk of prostate
cancer. The
work is geared
towards the
African American
population,
for whom genomic
studies are
limited. African
Americans share
a common genetic
background with
West Africans
yet vastly different
environments.
Comparative
genetic and
epidemiological
research on
the two populations
reveal potential
risk factors.
This project
will provide
a better understanding
of gene-gene
(epistasis),
and gene-environment
effects on prostate
cancer. At research
sites in Washington,
DC, Chicago,
Illinois, and
Benin City,
Nigeria the
goals of the
project are
to (1) recruit
a well characterized
cohort of 1200
cases and controls
and collect
blood for biochemical
and molecular
assays, along
with diet and
other environmental
information;
(2) use state
of the art DHPLC
technology to
provide a formal
evaluation of
single nucleotide
polymorphism
(SNP) variation
in 22 candidate
genes for prostate
cancer (androgen
associated genes,
apoptosis related
genes, and diet
related genes);
(3) construct
a web-based
database of
the SNPs discovered;
(4) determine
if haplotypic
variation in
candidate genes
accounts for
phenotypic variation
in prostate
cancer, prostate
specific antigen
(PSA) levels,
and disease
progression;
and (5) assess
whether gene-gene
and gene-environment
interactions
exist by examining
if prostate
cancer risk
is modified
after stratification
of genetic and/or
environmental
factors. This
is the first
study which
examines SNP
markers within
the proposed
candidate genes,
diet, and other
environmental
variables in
clinically evaluated
African and
African Americans
and which evaluates
their relative
interactions
and contribution,
if any, to prostate
cancer.
In
another project,
"Haplotype
analyses of
X chromosome
variants: population
genetics and
implications
for prostate
cancer"
the goals are
to (1) provide
a formal evaluation
of X chromosome
variation and
linkage disequilibrium
in the African
American population,
(2) determine
the relationship
of microsatellite
alleles (CAG
and GGN repeats)
within the androgen
receptor with
the risk for
prostate cancer
and (3) exploit
the evolutionary
history of X
chromosome haplotypes
in order to
determine if
differences
in X chromosome
haplotypes account
for phenotypic
variation in
prostate cancer
and prostate
specific antigen
(PSA) levels.
While
the molecular
genetic research
has shared consequences
for all humanity,
our specific
interests focus
on populations
of African ancestry.
Other areas
of immediate
interest are
molecular evolutionary
genetics, and
biological anthropology.
In another project,
"the
genetics of
human pigmentation,"
we seek to understand
the relative
contribution
of allelic variations
of candidate
genes responsible
for variation
in human pigmentation.
Pigmentation
is a classic
anthropological
trait that has
been studied
objectively
using reflectance
spectroscopy
for over 50
years. Skin
pigmentation
is likely the
trait that shows
the largest
degree of variability
among human
populations.
That there are
such dramatic
differences
in the levels
of skin pigmentation
among human
populations
is almost definite
evidence for
the action of
natural selection.
The identification
of the genes
that determine
normal within-population
variation in
pigmentation
and differences
between populations
is the first
essential step
in the elucidation
of the molecular
history of human
pigmentation.
The goals of
this project
are to (1) develop
a database and
sample collection
that will allow
for the delineation
of the genes
that determine
pigmentation,
and (2) genotype
these individuals
for a number
of candidate
genes to identify
those which
determine natural
variation in
pigmentation.
Mutation
analyses of
BRCA1 and BRCA2.
We are analyzing
the breast cancer
predisposing
genes, BRCA1
and BRCA2, for
germline mutations
in African American
families at
high-risk for
hereditary breast
cancer. Patients
are considered
high-risk if
they have a
family history
of the disease,
early onset
breast cancer,
bilateral breast
cancer, breast
and ovarian
cancer, or a
male affected
with breast
cancer. The
entire BRCA1
and BRCA2 coding
and flanking
intron regions
are being examined
for mutation
detection. In
preliminary
studies of BRCA1
using the technique
of single strand
conformation
polymorphism,
we identified
11 different
germline mutations/
variations in
7 patients from
45 high-risk
families. Two
pathogenic,
protein-truncating
mutations were
detected in
exon 11. A ten
base pair tandem
duplication,
943ins10, was
present in a
woman with breast
and ovarian
cancer whose
first-degree
relatives had
prostate cancer.
A four base
pair deletion,
3450del4, was
detected in
a breast cancer
patient with
five cases of
breast cancer
in the family;
two of the proband's
sisters with
breast cancer
also carried
the same mutation.
Four amino acid
substitutions
(Lys1183Arg,
Leu1564Pro,
Gln1785His,
and Glu1794Asp)
and four nucleotide
substitutions
in intron 22
(IVS22+78 C/A,
IVS22+67 T/C,
IVS22+8 T/A
and IVS22+7
T/C) were observed
in patients
and not in control
subjects. One
early onset
breast cancer
patient carried
five distinct
BRCA1 variations,
two amino acid
substitutions
and three substitutions
in intron 22.
An amino acid
substitution
in exon 11,
Ser1140Gly,
was identified
in 3 different
unrelated patients
and in 6 of
92 control samples.
The latter probably
represents a
benign polymorphism.
BRCA1 and BRCA2
analyses for
the detection
of mutations
are ongoing.
Genetic
variation in
asthma.
Asthma families
collected by
HU investigators
were part of
the Collaborative
Study on the
Genetics of
Asthma (CSGA)
genome-wide
search for asthma
susceptibility
loci in ethnically
diverse populations.
Asthma is an
inflammatory
airways disease
associated with
intermittent
respiratory
symptoms, bronchial
hyper-responsiveness
(BHR) and reversible
airflow obstruction
and is phenotypically
heterogeneous.
Patterns of
clustering and
segregation
analyses in
asthma families
have suggested
a genetic component
to asthma. Previous
studies reported
linkage of BHR
and atopy to
chromosomes
5q, 6p, 11q,
14q, and 12q.
One genome-wide
search in atopic
sib pairs had
been reported,
however, only
12% of their
subjects had
asthma. The
CSGA conducted
a genome-wide
search in 140
families with
> or = 2
asthmatic sibs,
from three different
populations
and reported
evidence for
linkage to six
novel regions:
5p15 (P = 0.0008)
and 17p11.1-q11.2
(P = 0.0015)
in African Americans;
11p15 (P = 0.0089)
and 19q13 (P
= 0.0013) in
Caucasians;
2q33 (P = 0.0005)
and 21q21 (P
= 0.0040) in
Hispanics. Evidence
for linkage
was also detected
in five regions
previously reported
to be linked
to asthma-associated
phenotypes:
5q23-31 (P =
0.0187), 6p21.3-23
(P = 0.0129),
12q14-24.2 (P
= 0.0042), 13q21.3-qter
(P = 0.0014),
and 14q11.2-13
(P = 0.0062)
in Caucasians
and 12q14-24.2
(P = 0.0260)
in Hispanics.
Dermatophagoides
pteronyssinus
(Der p) is one
of the most
frequently implicated
allergens in
atopic diseases.
Although HLA
could play an
important role
in the development
of the IgE response
to the Der p
allergens, genetic
regulation by
non-HLA genes
influences certain
HLA-associated
IgE responses
to complex allergens.
To clarify genetic
control for
the expression
of Der p-specific
IgE responsiveness,
a genome-wide
search was conducted
for genes influencing
Der p-specific
IgE antibody
levels by using
45 Caucasian
and 53 African
American families
ascertained
as part of the
Collaborative
Study on the
Genetics of
Asthma (CSGA).
Specific IgE
antibody levels
to the Der p
crude allergen
and to the purified
allergens Der
p 1 and Der
p 2 were measured.
Multipoint,
nonparametric
linkage analysis
of 370 polymorphic
markers was
performed with
the GENEHUNTER
program. The
best evidence
of genes controlling
specific IgE
response to
Der p was obtained
in 2 novel regions:
chromosomes
2q21-q23 (P
= .0033 for
Caucasian subjects)
and 8p23-p21
(P = .0011 for
African American
subjects). Three
regions previously
proposed as
candidate regions
for atopy, total
IgE, or asthma
also showed
evidence for
linkage to Der
p- specific
IgE responsiveness:
6p21 (P = .0064)
and 13q32-q34
(P = 0.0064)
in Caucasian
subjects and
5q23-q33 (P
= 0.0071) in
African American
subjects. No
single locus
generated overwhelming
evidence for
linkage in terms
of established
criteria and
guidelines for
a genome-wide
screening, which
supports previous
assertions of
a heterogeneous
etiology for
Der p-specific
IgE responsiveness.
Two novel regions,
2q21-q23 and
8p23-p21, that
were identified
in this study
merit additional
study. In addition
genome-wide
screening was
conducted for
genes influencing
Dermatophagoides
pteronyssinus-specific
IgE responsiveness
as a part of
the Collaborative
Study on the
Genetics of
Asthma (CSGA).
Evidence for
linkage was
found in some
regions, including
chromosomes
5131-q33 and
11q13 in African
American families.
Plans are underway
to initiate
an international
study of the
genetics of
asthma in collaboration
with medical
scientists in
Ghana and investigators
at the NHGC.
These investigations
will target
regions where
associations
with specific
IgE responses
have been indicated
in African Americans.
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DEVELOPING
PROJECTS
Characterization
of African American
Ancestral HLA
Haplotypes in
West Africa.
An important
area of investigation
at the NHGC
is the inclusion
of evolutionary
history of genes
as a diagnostic
probe in tracing
the history
of disease in
a population.
This
project builds
upon the foundation
of research
on the genetics
of complex diseases
common in African
Americans already
established
with the NHGRI
in partnership
with the NIH
Office of Research
on Minority
Health. More
specifically,
it would build
upon African
American Diabetes
mellitus (AADM)
an international
human gnome
research initiative
to map genes
for type 2 diabetes
in ancestral
populations
of African Americans.
Because of the
overlap in clinical
phenotype of
some subsets
of types 1 and
2 diabetes,
the rationale
for this study
is that characterization
of HLA class
II haplotypes
in the west
African study
population may
assist in refining
the clinical
phenotype of
a subset of
type 2 diabetes
patients.
The
association
of HLA class
II genes with
susceptibility
to type 1 diabetes
is well documented
in many populations.
In African Americans
type 1 diabetes
patients, unique
HLA class II
polymorphisms
have been instructive
in determining
risk assessment
of closely linked
HLA loci. We
have reported
the association
of a unique
HLA-DR3 haplotype
in African Americans
that appears
to be associated
with resistance
to type 1 diabetes.
The higher frequency
of this haplotype
among controls
raises questions
about the frequency
of this haplotype
in west African
ancestral populations
of African Americans.
The long range
goal of research
at the NHGC
is to improve
the health status
of African Americans
through research
on human DNA
sequence variation
and to apply
the knowledge
gained to better
understand the
biomedical significance
of gene-based
differences
already known
to exist among
populations
in the immune
response to
organ transplants;
sensitivity
to drugs; influence
of environment
on health, and
susceptibility
to complex diseases,
such as cancer
and diabetes.
The research
goals of the
molecular genetics
component are
predicated upon
the two broad
hypotheses of
population variation
in DNA polymorphic
markers used
to map genes
and the correlation
of population-based
variation in
DNA polymorphic
markers with
disease. Studies
of human leukocyte
antigen (HLA)
polymorphisms
and other genetic
polymorphic
systems have
consistently
shown greater
genetic variability
in African populations.
The biomedical
implications
of population-based
variation in
HLA genes are
seen in association
in the arena
of clinical
transplantation,
where decisions
regarding the
distribution
of limited donor
organs must
be informed
by science and
balanced by
the ethical
concerns of
the larger society.
The goal of
this study is
to define HLA
alleles and
haplotypes in
the study population
and determine
whether allele
and haplotype
frequencies
in diabetics
differ from
controls. If
a difference
is found, the
implication
of HLA associations
with the clinical
phenotype of
type 2 diabetes
will be investigated.
The study of
HLA haplotypes
in west African
ancestral populations
of African Americans
will help identify
HLA polymorphisms
that are common
in this population. Since
HLA has been
associated with
a variety of
autoimmune diseases,
the results
of this study
should not only
be useful in
the analysis
of HLA haplotypes
in type 2 diabetes,
but also informative
for population-based
HLA evolutionary
studies.
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Linkage
disequilibrium
(LD) in African
Americans.
Linkage
disequilibrium
is a population
genetic phenomenon
that has been
useful for gene
mapping efforts.
LD can usually
be found in
populations
for genes that
are tightly
(close genetic
distance) linked,
and can be generated
by mutation,
selection, or
admixture of
populations
with different
allele frequencies.
Generally, disequilibrium
is dependent
on population
size, time (generations),
and distance
between genetic
markers. Normally,
the greater
the distance
between markers,
the faster the
decay of disequilibrium.
The nonrandom
association
of alleles at
different genetic
loci can be
measured by
a variety of
linkage disequilibrium
measures.
Within
the African
American population
one would expect
to find short
genomic areas
of tight LD,
a legacy of
this population's
roots in the
antiquity of
African human
history, together
with large areas
of LD, a legacy
of more recent
admixture with
Europeans and
Native Americans.
Assessment of
the level of
genetic variation
and LD in the
African American
population is
important for
several reasons.
It will allow
us to better
understand the
mechanisms responsible
for the creation
and maintenance
of LD over genomic
regions.
This
better understanding
will aid in
the mapping
of genes responsible
for complex
diseases. We
expect to observe
a diverse pattern
of LD among
the African
American chromosomes
when compared
to other populations.
While the pattern
observed among
African Americans
is not restricted
to the population,
it is observed
at higher frequency
than others
with diffferent
populatioin
histories. African
American chromosomes
with ancestry
in West Africa
should exhibit
closely linked
disequilibrium
while chromosomes
with ultimate
ancestry from
Europe will
reveal broader
regions of disequilibrium.
What this study
will do is assess
patterns and
level of LD
among chromosomal
regions within
the African
American population.
Significance
of the African
American population
for gene mapping
As
stated above,
LD can be generated
by admixture
between divergent
populations.
Thus, a genetic
consequence
of the unique
population history
of African Americans
is increased
LD. We caution
that much of
the disequilibrium
may not actually
be due to genetic
linkage, but
are artifacts
of divergent
allele frequencies
in the parental
populations.
However, it
is expected
that linked
loci will also
show significant
disequilibrium
in the African
American population.
The analysis
of LD between
marker and disease
loci has proven
to be a powerful
tool for positional
cloning of disease
genes.
When
a disease or
trait manifests
variation between
populations,
admixed populations
provide a population
based approach
to evaluate
the relative
importance of
genetic factors.
A variety of
statistical
genetic methods
for disease
studies exploit
the LD created
by admixture.
These include
the Transmission
Disequilibrium
Test (TDT) and
Mapping by Admixture
Linkage Disequilibrium
(MALD). An important
assumption of
many of these
methods is that
the ancestry
of alleles at
each locus be
assigned to
one of the two
founding populations.
The assignment
of alleles to
parent populations
is problematic
at times, however
as more informative
genetic markers
are found and
more individuals
and populations
sampled, the
statistical
power to assign
alleles increases.
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RESOURCES
The
Molecular Genetics
Laboratory in
the National
Human Genome
Center is newly
renovated and
is located on
the 6th floor
of the Howard
University Cancer
Center. This
facility is
approximately
7,500 square
feet. There
are two large
laboratories
(~1500 sq. ft.
each), a DNA
sequencing and
genotyping room
(~800 sq. ft.),
two cold rooms,
dark room, and
a walk-in freezer.
The laboratory
space is equipped
with benches,
tables, sinks,
distilled water,
fume hoods and
separate areas
for tissue culture,
PCR, and radioisotope
use.
Four
Pentium III
NT Workstations
(400-500 mHz)
and four Power
Macintosh G4's
provide the
computational
hardware for
the Molecular
Genetics laboratory.
The eight computers
are networked
together via
the Genome Center
NT server with
the 5 computers
operating three
ABI 377 DNA
sequencers and
two DNA Wave
Machines in
addition to
the computers
used by the
Genetic Epidemiology
and Statistical
Genetics units.
The molecular
genetics laboratory
contains all
the standard
equipment necessary
for large-scale,
high throughput
molecular analysis
of DNA variation.
These items
include centrifuges,
waterbaths,
gel electrophoresis
apparatus, pipettes,
glassware, balances,
etc. The laboratory
also has two
Transgenomics
DNA Wave machines
for SNP detection
using dHPLC.
The genotyping
room contains
three ABI 377
automated sequencers,
ten Perkin Elmer
9700 thermocyclers,
and the PSQ
96 Pyrosequencing
platform for
SNP genotyping.
Molecular
genetics laboratory
space on the
5th floor of
the cancer center,
contains two
ABI 373 automated
sequencers.
The immunogenetics
core research
laboratory,
also on the
5th floor
of the cancer
center, provides
approximately
800 sq ft of
additional laboratory
space for molecular
genetics work.
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CORE
SERVICES
The
Molecular Genetics
Laboratory will
utilize current
SNP technologies
to:
1)
identify and
characterize
DNA sequence
variation in
the NHGC African
American population
resource,
2)
generate databases
for locating
functional mutations
in candidate
genes involved
in the biology
and pathophysiology
of complex diseases
common in African
Americans and
other populations
in the African
Diaspora,
3)
develop a database
of allele and
haplotype frequencies
for a reference
panel of SNP
variants in
the NHGC population
resource. This
will include
a set of candidate
genes for complex
diseases common
in African Americans,
-
Prostate
Cancer
-
Breast
cancer
-
Asthma
-
Type
2 diabetes
-
Hypertension
-
HIV
aids
4)
Use coalescence
models to construct
phylogenies
of the candidate
genes in order
to evaluate
the evolutionary
history of the
genes in various
populations.
Construct haplotype
phylogenies
for a reference
set of DNA loci/markers
representative
of various types
of polymorphic
systems found
in the genome.
This will include
but is not limited
to the following:
-
Single
nucleotide
polymorphisms
(SNPs)
-
Microsatellites
(mono, di,
tri, and
tetra nucleotide
repeats)
-
Minisatellites
(variable
number of
tandem repeats/VNTRs)
-
Nucleotide
insertions
and deletions
-
Alu
repeats
MOLECULAR
GENETICS
UNIT
GROUP
PICTURE |
|
06-Jan-2008 |
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|
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