presentation ppt

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Human non-synonymous SNP molecular function,
evolution and disease
Shamil Sunyaev Genetics Division, Brigham
Womens Hospital Harvard Medical
School Harvard-M.I.T. Division of HST
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Predicting the effect of mutations in proteins
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Why is this useful?

• Understanding variation in molecular function and
  structure
• Evolutionary genetics comparison of polymorphism
  and divergence rates between different functional
  categories is a robust way to detect selection

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Linkage analysis
Rare
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Classical association studies
Common
Control
Disease
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Why is this useful?

• Rare human developmental disorders / mouse
  mutagenesis screens linkage studies are
  impossible
• Genetics of complex disease SNP prioritization
• Genetics of complex disease Rare variants

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Technically, polymorphism should not exist!
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Mendelists Biometricians
Forces to maintain variation
Selection
Mutation
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Common disease / Common variant
Trade off (antagonistic pleiotropy) Balancing
selection Recent positive selection Reverse in
direction of selection
Examples
APOE Alzheimers disease AGT Hypertension C
YP3A Hypertension CAPN10 Type 2 diabetes
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Individual human genome is a target for
deleterious mutations !
Frequency of deleterious variants is directly
proportional to mutation rate (qm/s)
40 of human Mendelian diseases are due to
hypermutable sites
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Multiple mostly rare variants
Many deleterious alleles in mutation-selection
balance
Examples
Plasma level of HDL-C Plasma level of
LDL-C Colorectal adenomas
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What about late onset phenotypes?
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Harmful mutations

• Advantageous pseudogenization (Zhang et al. 2006)
• Gain of function disease mutations
• Sickle Cell Anemia

• Function damaging
• Evolution deleterious
• Phenotype detrimental

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protein
multiple alignment
profile
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PolyPhen
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Prediction rate of damaging substitutions
possibly probably
82 57
Disease mutations
9 3
Divergence
Polymorphism
27 15
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10 of PolyPhen false-positives are due to
compensatory substitutions
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Williamson et al., PNAS 2005
Estimate of selection coefficient
Phylogenetic measures
    PAM-120 -5.32   -8.35 -12.76
    BLOSUM-45 -8.41 -3.96 -13.39
    BLOSUM-62 -8.41 -4.09 -12.75
    BLOSUM-80 -8.46 -4.49 -13.52
Site-specific structural/phylogenetic measures
-23.602
-6.072
-11.732
    Polyphen
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de novo mutation effect spectrum
Effect of new mutation may range from lethal, to
neutral, to slightly beneficial
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Mutation effect spectrum
?
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Neutral mutation model
Human ACCTTGCAAAT Chimpanzee ACCTTACAAAT Baboon
ACCTTACAAAT
Prob(TAC-gtTGC) ? Prob(TGC-gtTAC)
Prob(XY1Z-gtXY2Z) 64x3 matrix
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Strongly detrimental mutations
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Effectively neutral mutations
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Mildly deleterious mutations
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Mildly deleterious mutations
54 genes, 757 individuals
inflammatory response 236 genes, 46-47 individuals
DNA repair and cell cycle pathways 518 genes,
90-95 individuals
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Frequency itself is a reliable predictor of
function!
The majority of missense mutations observed at
frequency below 1 are deleterious
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Fitness and selection coefficient
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Mildly deleterious mutations
54 genes, 757 individuals
inflammatory response 236 genes, 46-47 individuals
DNA repair and cell cycle pathways 518 genes,
90-95 individuals
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Fraction of detectable polymorphism
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Estimation of selection coefficient - simulation
present
Human effective population size
10010011001111010100100101110101000011110011000111
00010111001
past
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Estimation of selection coefficient - simulation
present
Human effective population size
Fsingl(s)
FMAFgt25(s)
SNP probability to be observed
past
Selection coefficient
-log(s)
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Classical association studies
Common
Control
Disease
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Mutation enrichment association studies
Rare
Control
Disease
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Mutation enrichment association studies
Rare
Control
Disease
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Mutation enrichment association studies
Rare missense variants in NPC1L1 gene contributes
to variability in cholesterol absorption and
plasma levels of low-density lipoproteins
(LDLs) Cohen J et al., PNAS 2006 in
press
Nonsynonymous sequence variants in ABCA1 gene
were significantly more common in individuals
with low HDL-C (ltfifth percentile) than in those
with high HDL-C (gt95th percentile). Coh
en J et al., Science 2004
Multiple rare variants in different genes account
for multifactorial inherited susceptibility to
colorectal adenomas Fearnhead NS et
al., PNAS 2004
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Cholesterol
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Adopted from Brewer et al., 2003
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Effect of rare nsSNPs on HDL-C
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What about common alleles of smaller effect?

• Population of 3500 individuals with known plasma
  levels of HDL-C
• Population includes both genders and three ethnic
  groups
• 839 SNPs genotyped
• Independent population of 800 individuals for
  validation

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What about common alleles of smaller effect?

• Introduce a linear model (ANCOVA)
• Subsequently add SNPs to the linear model
• Include SNPs based on the likelihood ratio test
• Prioritizing SNPs based on conservation did not
  help

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Effect of common SNPs on HDL-C
HDL
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And a different population
HDL
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Acknowledgements

• The lab
• Gregory Kryukov, Steffen Schmidt, Saurabh
  Asthana, Victor Spirin, Ivan Adzhubey
• Bioinformatics Human genetics
• Vasily Ramensky Jonathan Cohen