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.
Prior To 1989
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.
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?
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
genetics is important
environment is important
interesting to scientists
interesting to the public
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
(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.
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 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
GWAS is easy
GWAS is hard
Manolio, et al. 2009. Nature 461: 747-753
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)
adapted from D Ge, et al. 2009. Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance. Nature 461: 399-401
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
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
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)