Download Am J Hum Genet

positional cloning of human disease
genes: a reversal of scientific priorities
Prior To
1989
disease
phenotype
hypothesize
function
AFTER
1989
disease
phenotype
chromosomal
position
clone
the gene
clone
the gene
chromosomal
position
functional
cloning
hypothesize
function
positional
cloning
D Botstein, et al. 1980. Construction of a genetic linkage map in man using restriction
fragment length polymorphisms. Am J Hum Genet 32: 314-331.
JM Rommens, …, LC Tsui, FS Collins. 1989. Identification of the cystic fibrosis gene:
chromosome walking and jumping. Science 245: 1059-1065.
FS Collins. 1992. Positional cloning: let's not call it reverse anymore. Nat Genet 1: 3-6.
Botstein’s insight on human genetics
cause-and-effect
positionally close
gene
phenotype
statistical
correlation
marker
consider a mutagenesis and screening experiment that we might do in animals
genetic variations occur naturally and humans screen themselves for diseases
cause-and-effect is strongest when disease has Mendelian inheritance pattern
MARKER is any sequence that is variable and does not have to be in the gene
Q: why should there be a statistical correlation between the marker and gene?
genetic recombination is required to
localize Mendelian disease genes in a
family based positional cloning study
w/o genetic recombination linkage across chromosome would be complete
approximately one recombination per chromosome per meiosis
human mutation rate is known to be 10-8 per site per generation
there is no benefit to genotyping more markers than genetic recombinations
size of family analyzed determines number of genetic recombinations
additional experiments needed to identify gene once localized to Mb region
Online Mendelian Inheritance in
Man currently lists 2993 phenotypes
whose molecular basis is known
OMIM Statistics for 31 March 2011
* gene of known sequence
+ gene of known sequence and phenotype
# phenotype of known molecular basis
% phenotype of unknown molecular basis
phenotype suspected to be Mendelian
Autosomal
12,605
314
2,725
1,632
1,831
X-Linked
620
18
236
134
130
Y-Linked
48
0
4
5
2
Mitochondrial
35
2
28
0
0
Total
13,308
334
2,993
1,771
1,963
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
interesting traits tend to be less
genetic and more environmental
genetics is
important
Mendelian
diseases
interesting to
scientists
environment
is important
complex
diseases
psychiatric
disorders
human
behaviour
interesting to
the public
making positional cloning work on
diseases that the public cares about
despite the successes of positional cloning with Mendelian diseases analogous
procedures for complex diseases FAILED spectacularly
failure was attributed to inability to get large enough families to compensate for
weaker cause-and-effect in diseases that are not entirely genetic
sample sizes need not be a limitation if we do not restrict the studies to families
and instead use affected individuals from the population
human population originated from “family” of 15,000 individuals that survived a
near death experience 70,000 years ago (numbers controversial)
therefore, human variation occurs in haplotype blocks whereby polymorphisms
are statistically correlated on length scales of a few kb’s
novel mutations complicate the situation but to a first approximation the way to
find complex disease genes is to increase the number of makers
SNPs, haplotypes, and tag SNPs
(a) Chromosomal region with (three) sites of variation indicated. (b) A haplotype is a particular
combination of SNP alleles along the chromosome. Here we show all 4 observed haplotypes in
a surveyed population for a 6000 bp region with 20 SNPs. (c) Genotyping only 3 tag SNPs out
of the available 20 is sufficient to distinguish between all observed haplotypes.
RA Gibbs, et al. 2003. The International HapMap Project. Nature 426: 789-796.
genome wide association study (or
GWAS) to find complex disease genes in
population based positional cloning
simplifying assumptions were made about the nature of disease variants
GWAS
is easy
GWAS
is hard
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
one common variant has more public health impact than many rare ones
genetic loci found and heritability
explained for several complex traits
Manolio, et al. 2009. Nature 461: 747-753
feasibility of detecting genetic
variants by risk allele frequency
and strength of genetic effect
pharmacogenomics: genetic
variation in response to treatment
adverse drug reactions are a major cause of hospitalization and death; for USA
2.2 million serious cases and 100,000 deaths a year
human metabolism to detoxify drugs either makes them more water soluble for
excretion in urine or more fat soluble for excretion in stool
variability associated with cytochrome P450 enzyme detoxification is 1000-fold;
hence one person’s food is another person’s poison
Race in a Bottle
(Scientific American
August 2007)
BiDil is a patented (FDA in 2005) combination of two generic drugs specifically
indicated for African Americans with congestive heart failure
19q13.13 (IL28B gene) region
containing genome wide determinant
of response to hepC treatment
adapted from D Ge, et al. 2009. Genetic variation in IL28B predicts
hepatitis C treatment-induced viral clearance. Nature 461: 399-401
percent SVR by genotype and
C-allele frequencies by population
SVR (sustained virological response) refers to absence of detectable virus at end of follow
up evaluation, indicating successful response to treatment
individuals homozygous for C-allele respond better to treatment (regardless of population)
and C-allele is most often found in East Asian populations
an example of a flawed GWAS study
1 July 2010: this paper claimed to have identified genetic
factors for longevity; it was published with much fanfare
at Sciencexpress and got extensive media coverage; but
within days the result was challenged by sharper eyes
and a lesson on the power of blogs
which humbled that much-hyped paper in just a matter of days
7 July 2010: data of Sebastiani et al (right)
are unusual in that all of the highest-ranked
SNPs stand out by themselves and are not
flanked by a column of highly-ranked SNPs
as in other studies like the Wellcome Trust
Case Control Consortium (left)
http://www.wired.com/wiredscience/2010/07/Serious-flaws-revealed-in-longevity-genes-study