Eric D. Wieben, M.D. - Role of Polymorphisms in Human Diesease

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Role of Polymorphisms in Role of Polymorphisms in Human Disease Human Disease December 6, 2008 Eric Wieben, Ph.D.

Transcript of Eric D. Wieben, M.D. - Role of Polymorphisms in Human Diesease

Page 1: Eric D. Wieben, M.D. - Role of Polymorphisms in Human Diesease

Role of Polymorphisms in Human Role of Polymorphisms in Human DiseaseDisease

December 6, 2008

Eric Wieben, Ph.D.

Page 2: Eric D. Wieben, M.D. - Role of Polymorphisms in Human Diesease

We’re not all the same

Yao Ming (7 feet, 6 inches)Yao Ming (7 feet, 6 inches)

Page 3: Eric D. Wieben, M.D. - Role of Polymorphisms in Human Diesease

If you determine DNA sequence on 2 copies of each chromosome, you find that most of DNA

is identical between 2 copies

If you determine DNA sequence on 2 copies of each chromosome, you find that most of DNA

is identical between 2 copies

About once every 200 letters, there is a difference at 1 spotAbout once every 200 letters, there is a difference at 1 spot

Our DNA is Not the Same EitherOur DNA is Not the Same Either

CP1208758-4

CC TTattacaggcg tgagccactg cacctggcct gacattcttt atgaaattta gaattgttga agaactataa catttcagta gggttcaagg tggtcccaaa agttatataa aagattagtt tttactataa acccttgtct tttacccaga tcctagcatc ccttttcaca tggtttctcc atgtatataa cagaatcaag aaacaaattt taattaaaca atctgtaaca gaatcaagaa acaaatacat tttaattaaa caatctatat ggaacaaaca ttcccaaatt ctaagaataa

attacaggcg tgagccactg cacctggcct gacattcttt atgaaattta gaattgttga agaactataa catttcagta gggttcaagg tggtcccaaa agttatataa aagattagtt tttactataa acccttgtct tttacccaga tcctagcatc ccttttcaca tggtttctcc atgtatataa cagaatcaag aaacaaattt taattaaaca atctgtaaca gaatcaagaa acaaatacat tttaattaaa caatctatat ggaacaaaca ttcccaaatt ctaagaataa

CC

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attacaggcg tgagccactg cacctggcct gacattcttt atgaaattta gaattgttga agaactataa catttcagta gggttcaagg tggtcccaaa agttatataa aagattagtt tttactataa acccttgtct tttactcaga tcctagcatc ccttttcaca tggtttctcc atgtatataa cagaatcaag aaacaaattt taattaaaca atctgtaaca gaatcaagaa acaaatacat tttaattaaa caatctatat ggaacaaaca ttcccaaatt ctaagaataa

attacaggcg tgagccactg cacctggcct gacattcttt atgaaattta gaattgttga agaactataa catttcagta gggttcaagg tggtcccaaa agttatataa aagattagtt tttactataa acccttgtct tttactcaga tcctagcatc ccttttcaca tggtttctcc atgtatataa cagaatcaag aaacaaattt taattaaaca atctgtaaca gaatcaagaa acaaatacat tttaattaaa caatctatat ggaacaaaca ttcccaaatt ctaagaataa

If you determine DNA sequence on 2 copies of each chromosome, you find that most of DNA

is identical between 2 copies

If you determine DNA sequence on 2 copies of each chromosome, you find that most of DNA

is identical between 2 copies

Single nucleotide polymorphism--SNPSingle nucleotide polymorphism--SNP

Our DNA is Not the Same EitherOur DNA is Not the Same Either

CP1208758-4

TTCC TT

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PolymorphismsPolymorphisms

• “Strictly, the existence of two or more variants at significant frequencies in the population. Looser usages among molecular geneticists include:

• (1) any sequence variant present at a frequency >1% in a population

• (2) any nonpathogenic sequence variant, regardless of frequency”

• “Strictly, the existence of two or more variants at significant frequencies in the population. Looser usages among molecular geneticists include:

• (1) any sequence variant present at a frequency >1% in a population

• (2) any nonpathogenic sequence variant, regardless of frequency”

From Strachan and Read, Human Molecular Genetics 2

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Polymorphisms

I. Single Nucleotide--SNPs

G

A

II. “Indels” (insertion/deletion)

TGACG

TG

Variable Number of Tandem RepeatsShort Tandem Repeats

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C T

There are about 3 million single base differences in DNA sequence between any two

haploid genomes--SNPs

ataatacaca cagaaaaact ggcatttatt ttgttttatt tttttgagat ggagtttcgt 1201 tcttgttgcc caacctggag tgcagtggtg cggtctcggc tcactgcaac ctctgcctcc 1261 cgggttcggg tggttctcct gcctcggcct cctgagtggc tgggattgca ggtgtgcgcc 1321 accacgcccg gctagttttt tgtgttttta gtggagacgg ggtttcacca tgttggtcag 1381 gctgatctcg agctcctgac ctcaggtgat ctacccacct cggcctccca aagtgctggg 1441 attacaggcg tgagccactg cacctggcct gacattcttt atgaaattta gaattgttga 1501 agaactataa catttcagta gggttcaagg tggtcccaaa agttatataa aagattagtt 1561 tttactataa acccttgtct tttactcaga tcctagcatc ccttttcaca tggtttctcc 1621 atgtatataa cagaatcaag aaacaaattt taattaaaca atctgtaaca gaatcaagaa 1681

acaaatacat tttaattaaa caatccatat ggaacaaaca ttcccaaatt ctaagaataa 1741 atttttcttt aagttttctc tgagtttggc aattgttgtt ttttataatt taatctgttt 1801 aaatcatcag gtcttataaa atataatgta cttagagctg gattcatggc tgtttattat 1861 gaaaggttag atttctcagt tcttctttaa ccacattttg ttatatcaga cagtcctcta 1921 taactctgta ctacccaaca actaaatggt ttagattgtt tagctcatgt taataggatg 1981 gttgtgtatt ataaaaaacg agttacgtgt gtgtgtgcac gcatgcacgc acatgtgctg 2041 gcttaaaggt tgttaatgca aggtttgggg tcccctttaa cactggtgaa agctacggta 2101 ctctccccag agatatgtct tgtcagcctc tctagttccc cttggcctgc atgtacaaac 2161 ttctacccta gaagctctct gccatcgatg tattctaata gatttgtaag gctattaatt 2221 tgaagcaact ccttgctcac agtgattctt gcttctctga gacctgctcc cagtcgatac 2281

The assay of specific differences in DNA sequence is called “Genotyping”

Current technology allows for the measurement of all 3 million differences

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Why SNPs?Why SNPs?

• Account for a lot of the diversity in the population

• Easier and cheaper to assay than other polymorphisms-usually biallelic•Many competing technologies

•Take advantage of different size and sequence of variant sequences

•Costs are now less than $0.001/SNP

• Account for a lot of the diversity in the population

• Easier and cheaper to assay than other polymorphisms-usually biallelic•Many competing technologies

•Take advantage of different size and sequence of variant sequences

•Costs are now less than $0.001/SNP

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Illumina infinium

2008Adapted from Steve Channock, NCI

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SNPsSNPs

• Common sequence differences

• May have direct functional significance• Increase activity of product• Decrease activity of product

• May just be linked to sequence changes that have functional significance

• May be silent

• Common sequence differences

• May have direct functional significance• Increase activity of product• Decrease activity of product

• May just be linked to sequence changes that have functional significance

• May be silent

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DNA sequence differences have a major impact on Medicine

• Prevention• Predict susceptibility in time to

intervene

• Diagnosis• Improved sensitivity and precision

• Treatment• Right drug, at the right dose, for the

right patient

• Prevention• Predict susceptibility in time to

intervene

• Diagnosis• Improved sensitivity and precision

• Treatment• Right drug, at the right dose, for the

right patient

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Bipolar

Unaffected

Utility of “linked” SNPs—Association Studies

Take two groups of patients:

Genotype for two different SNPs from two different parts

of the genome

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SNP A

Bipolar

Unaffected

Association studies

Neither version of this SNP (green or black) is associated with disease

Each person in each group gets genotyped

A T

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SNP B

Bipolar

Unaffected

Association Studies

Red version of this SNP is associated with the disease

This suggests that some gene “near” this SNP is

associated with this disease

C T

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Nature 447, 661-678 (7 June 2007)

Statistically significant associations between regions of the genome and coronary atery disease

Most significant—9p21CDKN2A, CDKN2B??

But is this real? Or is it chance?

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What would Bonferroni say?

.05500,000

10-7

P = 0.05?

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Nature 447, 661-678 (7 June 2007)

2000 cases for each disease,

500,000 SNPs for each case=

1 billion SNPs

MHC

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Meta-analysis of 1 SNP from chromosome 6 and risk of lung cancer

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H Stefansson et al. Nature 000, 1-5 (2008) doi:10.1038/nature07229

Large recurrent microdeletions associated with schizophrenia

1q21.1

15q11.2

15q13.3

*none in Venter

Moving Beyond SNPs

10 genes

4 genes

6 genes

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Compared to the reference sequence, Venter has:

Time.com

•3,213,401 single nucleotide polymorphisms (SNPs)•53,823 block substitutions (2–206 bp) •559,473 homozygous indels (1–82,711 bp)•62 CNVs•292,102 heterozygous insertion/deletion events (indels)(1–571 bp) •90 inversions

•3,213,401 single nucleotide polymorphisms (SNPs)•53,823 block substitutions (2–206 bp) •559,473 homozygous indels (1–82,711 bp)•62 CNVs•292,102 heterozygous insertion/deletion events (indels)(1–571 bp) •90 inversions

•Non-SNP DNA variation accounts for 22% of all events identified in the donor, however they involve 74% of all variant bases.

•Non-SNP DNA variation accounts for 22% of all events identified in the donor, however they involve 74% of all variant bases.

Levy et al., PLoS Biol. 2007 October; 5(10): e254 Levy et al., PLoS Biol. 2007 October; 5(10): e254

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Prevention

• Risk Profile Analysis• We now have the capability to use DNA

information to help predict the relative risk of developing many diseases before symptoms occur

• Improvements in technology and bioinformatics are expanding the list to common multifactorial diseases• Heart disease, schizophrenia,

depression, bipolar

To do this, have to identify genes that influence characteristics of disease--

SNPs

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Chromosome

“Reference genome”

Deletion

Insertion

Copy number variant

Segmental duplication

Copy number variation is widespread in our genomes

Estimate is that typical people are hemizygous for 30-50 deletions larger than 5 kb (affecting the expression of hundreds of genes)Conrad et al., Nature Genetics 38, 75 - 81 (2006)

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Genotyping is a (temporary) substitute for complete genomic

analysis

Genotyping is a (temporary) substitute for complete genomic

analysis

•Recent advances have made large scale genotyping studies (association studies) commonplace

•Knowledge•HapMap project is defining common haplotypes•Reduces the need for so many data points

•Technology•Genotyping Technology is evolving rapidly

•Recent advances have made large scale genotyping studies (association studies) commonplace

•Knowledge•HapMap project is defining common haplotypes•Reduces the need for so many data points

•Technology•Genotyping Technology is evolving rapidly

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SNPs identify a specific location on a specific chromosome

250,000 bp from chromosome 16 contains 7 genes

PALB2—Partner and localizer of BRCA2

GWAS signal could be from any of themHaplotype—(from “haploid genotype”) a set of closely linked genetic markers along a single chromosome which tend to be inherited together (not easily separable by recombination).