Transcript lecture27WHITE_Hapma.. - University of Alberta

rare Mendelian diseases versus
common multi-factorial diseases
people affected
hereditability
genes involved
environment
cases mapped
Mendelian diseases
young children
run in families
one major gene
less important
2284 (in OMIM)
Complex diseases
older adults
some to none
10's to 100's
very important
small handful
e.g., cystic fibrosis is one of the most common life-shortening childhood-onset
inherited diseases in the United States, affecting 1 in 3900 births; one of every
31 individuals is a carrier of the recessive disease allele
e.g., in the United States, the lifetime risk for developing cancer is slightly less
than 1 in 2 for men and slightly more than 1 in 3 for women; although there are
subclasses of cancer like early onset breast cancer that obey Mendelian rules,
they make up a negligible fraction of the overall disease
1980: DNA markers are the key to
identifying Mendelian disease genes
(a)
(b)
(a) disease cosegregates
with marker A; (b) disease
cosegregates with marker
B prior to a recombination
event, and marker C after
power to localize genes is
reliant on having sufficient
number of recombinations
Botstein D, White RL, Skolnick M, Davis RW. 1980. Am J Hum Genet 32: 314-331
the fact we cannot experiment on people does not preclude us from doing genetics; all we
need are more DNA markers to differentiate individuals; the markers themselves need not
cause the disease; they need only be sufficiently close to the gene that does; markers can
take many forms including RFLPs, microsatellites, SNPs, etc.
1989: successful cloning of CFTR
gene responsible for cystic fibrosis
Mutation
DF508
G551D
R117H
621+1 (G>T)
G542X
N1303K
1717-1 (G>T)
R1162X
R553X
3849+10KB (G>T)
R334W
W1282X
Prevalence (%)
79
2.17
0.70
0.50
0.50
0.35
0.28
0.14
0.14
0.07
0.07
0.07
Rommens JM, …, Tsui LC, Collins FS.1989. Science 245: 1059-1065
the DF508 mutation is one of over 1500 eventually found in this gene but it is still the
most important; this was the first disease gene identified by its chromosomal position
instead of by its hypothesized function; Huntington’s was mapped before CF but the
unexpected nature of that mutation (triplet repeat) took longer to solve
Online Mendelian Inheritance in
Man currently lists 2284 phenotypes
whose molecular basis is known
OMIM Statistics for April 6, 2008
Autosomal
* gene of known sequence
11,577
+ gene of known sequence and phenotype
358
# phenotype of known molecular basis
2,065
% phenotype of unknown molecular basis
1,471
phenotype suspected to be Mendelian
1,954
X-Linked
538
30
191
129
140
Y-Linked
48
0
2
5
2
Mitochondrial
37
0
26
0
0
Total
12,200
388
2,284
1,605
2,096
the success of what came to be known as positional cloning was a tribute to an
admission of ignorance; we did not know enough human biology to guess the
likely gene for a disease so we focused instead on determining where the gene
was on the chromosome; for the overwhelming majority of cases, the answer
turned out to be a completely unknown gene that no scientist had hypothesized
1990-6: birth and death of sib pair
analysis for linkage based studies of
common multi-factorial diseases
Risch N, Merikangas K. 1996. The future of genetic studies of complex
human diseases. Science 273: 1516-1517
linkage analysis had been successfully used to find genes for Mendelian
diseases; in 1990, Risch popularized a method (sib pairs) to find genes
for complex multi-factorial diseases; that method failed and they wanted
to propose a different method that would be more powerful
association studies were to be performed on functional polymorphisms
for as many candidate genes as technically feasible, the entire genome if
need be, regardless of how impractical that was; at least the number of
patients would no longer be a limiting factor
past, present, and (near) future
genetic studies of human diseases
samples used
methodology
DNA markers
Past
rare families
linkage (pedigrees)
microsatellites
applicable to
causality link
Mendelian diseases
definitely yes
Present
populations
linkage disequilibrium
HapMap SNPs
common diseases
w/common variants
probably not
Future
populations
direct association
1000 genomes
common diseases
w/moderate variants
probably not
the biggest change from before is we are now doing these studies on the
general population instead of rare families
we must study common diseases in the general population because rare
mutations that cause Mendelian subcategories of disease are not typically
responsible for those diseases in the general population
the problem however is that without families we lose statistical power and
must compensate by gathering more data
population bottleneck, subsequent
recombination, linkage disequilibrium
mutation is the red ;
chromosomal stretches
derived from common
ancestor are yellow; the
new stretches due to
recombination are blue
although the parameters and details of the human population bottleneck are still not
settled, the order of magnitude estimates are that our species collapsed to 15,000
individuals 70,000 years ago; assuming few new mutations the only thing that would
have happened since that time is recombination, and we can model any particular
individual’s genome as a mosaic of segments from these 15,000 ancestral genomes
we need not test all the functional
polymorphisms, just enough markers
to be within linkage disequilibrium
linkage disequilibrium (LD) is the non-random association of two alleles on adjacent loci;
there are many reasons why this might happen, but for the HapMap, the assumption is that
human variation is intrinsically limited because of the recent population bottleneck
common-disease-common-variant
versus common-disease-rare-variant
CDCV hypothesis: a few common allelic variants account for most of the
genetic variance in disease susceptibility
Reich DE, Lander ES. 2001. On the allelic spectrum of human disease. Trends
Genet 17: 502-510
CDRV hypothesis: a large number of rare allelic variants account for the
genetic variance in disease susceptibility
Terwilliger JD, Weiss KM. 1998. Linkage disequilibrium mapping of complex disease:
fantasy or reality? Curr Opin Biotechnol 9: 578-594
for complex reasons having to do with human population history, linkage
disequilibrium would only work in diseases where the CDCV hypothesis is
valid; the best justification for the HapMap was that one common variant
has more public health impact than many rare variants, so it makes sense
to find these first
multiple rare alleles contribute to
low plasma HDL cholesterol levels
candidate genes ABCA1, APOA1, LCAT
15 non-synonymous
variants in 21 out of
128 outlier samples
3 non-synonymous
variants in 3 out of
128 outlier samples
HDL-C levels
for 128 individuals with low plasma HDL-C, 21 (16%) had variants not present in the
high HDL-C group; conversely, only 3 (2%) of individuals with high plasma HDL-C
had variants not present in the low HDL-C group (P < 0.0001); Cohen JC, …, Hobbs
HH. 2004. Science 305: 869-872
International HapMap Consortium
http://www.hapmap.org/thehapmap.html.en
International HapMap Consortium. 2005. Nature 437: 1299-1320
phase I genotyped common SNPs of frequency greater than 0.05 in every 5-kb interval for 269
individuals from 3 populations in Africa (YRI), Europe (CEU), and Asia (CHB+JPT)
solid line represents ENCODE region data, dashed line represents neutral model with constant
population size and random mating and no ascertainment biases
7 tag SNPs capture all the common
variation in a locus on chromosome 2
left plot shows the 7 haplotypes and their respective counts, with colored circles indicating SNP
positions where a haplotype has the less common allele; groups of SNPs captured by a single
tag SNP (r2  0.8) using a pairwise tagging algorithm have the same color; right plot shows the
SNPs mapped to a genealogical tree relating the seven haplotypes for this region
Wellcome Trust Case Control
genome wide association studies
Wellcome Trust Case Control Consortium. 2007. Nature 447: 661-678
genotype 500,000 SNPs from HapMap in a British population of 2,000 affected individuals
for each of 7 major diseases, with another 3,000 shared individuals for control
of the 14 variants for which there was a strong prior evidence of association to the studied
diseases all but two (APOE and INS) were reproduced by this analysis
genome wide scan in
seven diseases; y-axis
represents statistical
significance using -log10
of a p-value
the chromosomes are
shown in alternating
colors; significant SNPs
with p-value <110-5 are
in green
a doubling in relative risk for a
disease is not as bad as it sounds
Disease
Sample
2005
1,700
1 new gene 400% to 600%
2006
4,500
1 new gene
120%
Prostate cancer
2007
17,500
2 variants
(just 1 new)
123%
Obesity
2007
38,700
1 new gene
67%
Type 2 diabetes
2007
32,500
9 variants
(just 3 new)
80%
Heart disease
2007
41,600
1 variants
25% to 40%
Macular
degeneration
Inflammatory
bowel disease
Identified
Increased
relative risk
Year
Couzin J, Kaiser J. 2007. Science 316: 820-822
with the notable exception of macular degeneration there is only a doubling in
relative risk; the 120% increase in relative risk for inflammatory bowel disease
only bumps the absolute risk from 0.5% to 1.1%
but gene therapy remains elusive
19 years after the cystic fibrosis gene
Jesse Gelsinger (June 18, 1981 to September 17, 1999) was the first person identified as
having died in a clinical trial for gene therapy. He was only 18 years old. Gelsinger suffered
from ornithine transcarbamylase OTC deficiency, a disease of the liver whose victims are
unable to metabolize ammonia, a byproduct of protein breakdown.
Gelsinger was injected with adenoviruses containing the corrected gene in the hope that it
would manufacture the much needed enzyme. He died four days later, having suffered a
massive immune response, triggered by the viral vector used to transport the gene into his
cells. This led to multiple organ failure and brain death.
Food and Drug Administration investigators concluded that scientists involved in the trial,
including lead researcher Dr. James M. Wilson (University of Pennsylvania), broke several
rules of conduct: (a) Inclusion of Gelsinger as a substitute for another volunteer who had
dropped out, despite his having high ammonia levels that should have led to his exclusion
from the trial, (2) Failure by the university to report that 2 other patients had experienced
serious side effects from the therapy, (3) Failure to mention the deaths of monkeys given a
similar treatment, as should be been done for the informed consent.
The university paid the parents an undisclosed amount.