positional cloning of human disease genes: a reversal of scientific priorities
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positional cloning of human disease genes: a reversal of scientific priorities. Prior To 1989. disease phenotype. hypothesize function. clone the gene. chromosomal position. functional cloning. AFTER 1989. disease phenotype. chromosomal position. clone the gene. hypothesize function. - PowerPoint PPT PresentationTRANSCRIPT
positional cloning of human diseasegenes: a reversal of scientific priorities
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.
functional cloning
disease phenotype
hypothesize function
chromosomal position
clonethe gene
Prior To 1989
positional cloning
disease phenotype
hypothesize function
chromosomal position
clonethe gene
AFTER 1989
Botstein’s insight on human genetics
gene
marker
phenotypecause-and-effect
statistical correlation
posi
tiona
lly c
lose
consider a mutagenesis and screening experiment that we might do in animalsgenetic variations occur naturally and humans screen themselves for diseases
cause-and-effect is strongest when disease has Mendelian inheritance patternMARKER 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 tolocalize Mendelian disease genes in afamily based positional cloning study
w/o genetic recombination linkage across chromosome would be completeapproximately one recombination per chromosome per meiosis human mutation rate is known to be 10-8 per site per generationthere is no benefit to genotyping more markers than genetic recombinationssize of family analyzed determines number of genetic recombinationsadditional experiments needed to identify gene once localized to Mb region
Online Mendelian Inheritance inMan currently lists 2993 phenotypes
whose molecular basis is known
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
OMIM Statistics for 31 March 2011 Autosomal X-Linked Y-Linked Mitochondrial Total
* gene of known sequence 12,605 620 48 35 13,308+ gene of known sequence and phenotype 314 18 0 2 334# phenotype of known molecular basis 2,725 236 4 28 2,993% phenotype of unknown molecular basis 1,632 134 5 0 1,771phenotype suspected to be Mendelian 1,831 130 2 0 1,963
interesting traits tend to be less genetic and more environmental
interesting to scientists
interesting to the public
genetics is important
environment is important
Mendelian diseases
psychiatric disorders
complex diseases
human behaviour
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
CDCV hypothesis: a few common allelic variants account for most of the genetic variance in disease susceptibilityReich 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 susceptibilityTerwilliger 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
GWAS is easy
GWAS is hard
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
BiDil is a patented (FDA in 2005) combination of two generic drugs specifically indicated for African Americans with congestive heart failure
Race in a Bottle (Scientific American August 2007)
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 andC-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 blogswhich humbled that much-hyped paper in just a matter of days
http://www.wired.com/wiredscience/2010/07/Serious-flaws-revealed-in-longevity-genes-study
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)