Short introduction to Human Variation - CBS...2016/06/06 · Short introduction to Human Variation...

Short introduction to Human Variation

Lasse FolkersenCenter for Biological Sequence analysis

Technical University of Denmark

Human 1AGGAAAACACGGAGTTGATGCA G AAGCCCCAACATCCAACCTCGAAGGAAAACACGGAGTTGATGCA G AAGCCCCAACATCCAACCTCGA

Human 2ACGAAAACACGGAGTTGATGCA G AAGCCCCAACATCCAACCTCGAAGGAAAACACGGAGTTGATGCA C AAGCCCCAACATCCAACCTCGA

Human 3AGGAAAACACGGAGTTGATGCA G AAGCCCCAACATCCAACCTCGAAGGAAAACACGGAGTTGATGCA C AAGCCCCAACATCCAACCTCGA

Human 4AGGAAAACACGGAGTTGATGCA C AAGCCCCAACATCCAACCTCGAAGGAAAACACGGAGTTGATGCA C AAGCCCCAACATCCAACCTCGA

Human 5ACGAAAACACGGAGTTGATGCA G AAGCCCCAACATCCAACCTCGAAGGAAAACACGGAGTTGATGCA G AAGCCCCAACATCCAACCTTGA

33M letters

147M letters

33M letters

33M letters 147M letters

147M letters

33M letters

147M letters

33M letters

147M letters

SNP1 SNP2 SNP3?

33M letters

147M letters

33M letters

147M letters

SNP1 SNP2 SNP3?(50%) (0.1%)(1%)

33M letters

147M letters

SNP: One nucleotide difference occuring in at least 1% of a population

33M letters

147M letters

rs2278007 rs16891982 mutation

1.0.01% (eg. 300k)

2.0.1% (eg. 3 million)

3.1% (eg. 30 million)

4.10% (eg. 300 million)

Question: How many SNPs differ on average between two people?

Human: 3 billion base-pairs~ one base pair out of every 1,000 will be different between any two individuals

Another similar project?

Human 1: European ancestryAGGAAAACACGGAGTTGATGCA G AAGCCCCAACATCCAACCTCGAAGGAAAACACGGAGTTGATGCA G AAGCCCCAACATCCAACCTCGA

Human 2: Mixed ancestryAGGAAAACACGGAGTTGATGCA G AAGCCCCAACATCCAACCTCGAAGGAAAACACGGAGTTGATGCA C AAGCCCCAACATCCAACCTCGA

Human 3: Asian ancestryAGGAAAACACGGAGTTGATGCA C AAGCCCCAACATCCAACCTCGAAGGAAAACACGGAGTTGATGCA C AAGCCCCAACATCCAACCTCGA

33M letters

147M letters

SNP: rs16891982 – ethnicity dependent

C-frequency Scandinavia2%

C-frequency China:99.9%

Practically no Chinesehave GG

GorillaAGGAAAACACGGAGTTGATGCA C AAGCCCCAACATCCAACCTCGAAGGAAAACACGGAGTTGATGCA C AAGCCCCAACATCCAACCTCGA

DogAGGAAAACACGGAATTGATGCA G AAGCCCCAACATCCAACCTCGAAGGAAAACACGGAATTGATGCA G AAGCCCCAACATCCAACCTCGA

33M letters

147M letters

59M letters

73M letters

SNP: rs16891982 – ethnicity dependent

34M letters

14M letters

GorillaAGGAAAACACGGAGTTGATGCA C AAGCCCCAACATCCAACCTCGAAGGAAAACACGGAGTTGATGCA C AAGCCCCAACATCCAACCTCGA

DogAGGAAAACACGGAATTGATGCA G AAGCCCCAACATCCAACCTCGAAGGAAAACACGGAATTGATGCA G AAGCCCCAACATCCAACCTCGA

33M letters

147M letters

59M letters

73M letters

SNP: rs16891982 – non-synonymous coding

34M letters

14M letters

E V G C W G F/L C I N S V F SAmino acids:

33M letters

147M letters

SNP: rs16891982 – hair colour associated

Unravelling a hair-colour SNP

Hair colour and genome-wide association studies (GWAS)

Results from largest hair colour GWAS: there are many hair-colour SNPs

Hair colour and genome-wide association studies (GWAS)

Results and conclusions

Human 1 Phenotype: average scandinavianGenotype-rs16891982 : light homozygousGenotype-others: mixed

Human 3Phenotype: blackGenotype-rs16891982 : dark homozygousGenotype-others: almost all light colour

Human 2Phenotype: average scandinavianGenotype-rs16891982 : heterozygousGenotype-others: half mixed, half complete light

Short introduction to Human Variation - CBS...2016/06/06 · Short introduction to Human Variation...

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