Deciphering the Human Genome Production of Human …

Two discoveries that will shape the 21st century

Deciphering the Human Genome

Lifebook.dat – the database required to make a human being

Production of Human Embryonic Stem Cell Lines

Formlife.exe – the executable program to make a human being

Cloning of Human Beings (a negative utopia)

Copy.exe – a possibility of pertuating ourselves?

Cell

Nucleus

Chromosom

Gene

Gene-product: Protein

DNA

Blueprint of LifeDiakoniePublik 3/2001

Informationsübertragung bei der zellteilung

Cell division: Transfer of Information!

C in phosphate ester chain

C and N in bases

Base pairs

Sugar phosphatebackbone

Minorgroove

Majorgroove

H

O

P

5‘ 3‘

DNA as carrier of Information

Human ß-Globin, Segment ... TAAGCCAGTG CCAGAAGAGC CAAGGACAGG TACGGCTGTC ATCACTTAGA CCTCACCCTG TGGAGCCACA CCCTAGGGTT GGCCAATCTA CTCCCAGGAG CAGGGAGGGC AGGAGCCAGG GCTGGGCATA AAAGTCAGGG CAGAGCCATC TATTGCTTAC ATTTGCTTCT GACACAACTG TGTTCACTAG CAACCTCAAA CAGACACCAT GGTGCACCTG ACTCCTGAGG AGAAGTCTGC CGTTACTGCC CTGTGGGGCA AGGTGAACGT GGATGAAGTT GGTGGTGAGG CCCTGGGCAG GTTGGTATCA AGGTTACAAG ACAGGTTTAA GGAGACCAAT AGAAACTGGG CATGTGGAGA CAGAGAAGAC TCTTGGGTTT CTGATAGGCA CTGACTCTCT CTGCCTATTG GTCTATTTTC CCACCCTTAG GCTGCTGGTG GTCTACCCTT GGACCCAGAG GTTCTTTGAG TCCTTTGGGG ATCTGTCCAC TCCTGATGCT GTTATGGGCA ACCCTAAGGT GAAGGCTCAT GGCAAGAAAG ...

Human ß-Globin, Exon1, Segment ...GTG CAC CTG ACT CCT GAG GAG Val His Leu Thr Pro Glu Glu

AAG TCT GCC GTT ACT GCC CTG Lys Ser Ala Val Thr Ala Leu

TGG GGC AAG GTG AAC GTG ... Trp Gly Lys Val Asn Val + 126 further AS !

TGA Stop !!!

Genomic Library of Mankind

• 46 Chromosomes 2 * 3,2 billion letters• 30 000 – 40 000 Genes• ca. 99 % not protein-coding (excess of void information)• Man/Chimpanzee 1-2% global text difference

(ca. 120 Mio Letters)

i.e. in every line of the lifebook about 1-2 „misprints“• enormous repetitive segments • Retroviral traces (hundreds of thousand items) –

the human genome is a museum of virus infections !

Genomic Library of Individual Person

• ca. 2 Mio differences (SNPs)(between non-related persons)

• ca. 60 000 of them in coding regions• ca. 10 000 genetic defects

(each individual carries disposition for about 5 defects)

• every 500 -2000 letters a variation • (i.e. on every page of the life book a few „misprints“

Evolutionary Traces in the Genome

• 25 % of the human genome are „deserts"

• ca. 50 % are repetitions

• among them ca. 45 % „jumping copies",

(silent since millions of years)

Genomic Non-sensebut important identification tag!

Person 1 : CA CA CA CA CA CA CA 7 repeats no!!(Father ?) CA CA CA CA 4 repeats

Person 2: CA CA CA CA CA CA CA CA 8 repeats(Father ?) CA CA CA 3 repeats

Person 3: CA CA CA CA CA CA CA CA 8 repeats(Father ?) CA CA 2 repeats !!

Person 4: CA CA CA CA CA CA CA CA 8 repeats(Mother) CA CA CA CA CA CA CA 7 repeats !!

Person 5: CA CA CA CA CA CA CA 7 repeats (Child) CA CA 2 repeats

Genetic prediction: Scope

It can establish a diagnosis

It can predict the future

It provides implied information on related individuals

Genetic Diagnosis and Prediction: Scale

„Within the next decade genetic testing will be used widely for predictive testing in healthy people and for diagnosis and management of patients.“

Bell J (1998) „New Genetics in Clinical Practice“, Brit. Med. J. 316, 618-620

Genetic Prediction: Upper Limit of Determination

Concordance of traits in monozygotic twins:

Rare mendelian diseases: up to 100%

Frequent complex diseases: 30 – 70%

Relevant prediction is in terms of probabilityrather than of certainty (maybe useful for the insurance company, but of limited use for the individual)

There is always considerable non-genetic variability!

Genetic Diagnosis and Prediction: Tests of What ?

Non-inherited genetic traits: Chromosomal Aneuploidy e.g. Down syndroma, Klinefelter syndroma

Mendelian diseases: about 1500 out of 5000 may be diagnoseddominant mode of inheritance: in every generation of familyrecessive mode of inheritance: in one family “out of the blue“

Complex (multifactorial) diseases: about 40 genes may contribute (example of cardiovascular disease)

Genetic Diagnosis and Prediction: Tests on Whom ?

• Partners• Embryo in vitro• Embryo in utero• Fetus before birth• Newborn• Child• Adult

Purposes (with example):

Prediction of disorder: HuntingtonSelection between alternatives: immunePrevention of disease: PKU

Examples of Mendelian Diseases

Huntington (D)BRCA (breast cancer, D)Cystic fibrosisThrombophiliaPorphyriaHaemochromatosisMyotonic dystrophyDuchenne muscular dystrophy (sex-linked)PhenylketonuriaGalactosemiaThalassemiaCongenital hypothyrioidism

Examples of Complex Diseases with Genetic Contribution

Diabetes type 1Diabetes type 2Breat cancerColon cancerProstate cancerAlzheimer´s dementia (early onset form)Multiple sclerosisBipolar disorderSchizophreniaAutismFamilial Parkinson disease

Risk prediction of Complex Disease:GRR

Genotype Relative Risk (GRR) =

Frequency of disease in carriers of variant alleleFrequency of disease in carriers of normal allele

GRR> 50 single gene disorder with high penetrance

4-50 oligogenic disorder<4 polygenic factors (complex disease)

Risk prediction of Complex Disease: Bad Test

Not even a high GRR guarantees a good test ifFrequency (of risk allele) > frequency (disease in population)

HLA-B27 other allele Sum

Healthy persons 985 8 898 9 983

Spondylitis ankylosans (Mb. Bekhterev) 15 2 17

All persons 1 000 9 000 10 000

Frequency of disease: 17 / 10 000 = 0.17%Frequency of gene variant: 1000 / 10 000 = 10%

GRR = 15/17 divided by 985/9983 = 8.9 Frequency of gene variant in disease: 15/17 = 88%Frequency of gene variant in healthy: 9845 / 9983 = 10%

Test prediction on risky gene : 15/1000 diseased persons = 1.5%Rate of false positives: 98.5% Rate of false negatives: 0.02%

Is genetic prediction of disease possible?

Monogenic case , rare, high GRR, high penetrance: yes, if genotype is moderately specific

Polygenic case and multifactorial causation, low GRR: only statistical prediction in large populations samples

Population screening instead of individual diagnosis:

• Screening for heterozygotes for recessive disorder• Screening of fetuses or newborns for necessary therapy• Screening for predictive genotype in frequent disease (breast cancer)

• Any screening runs the following risks:

False positives, if genotype is not the specific causative factorFalse negatives, if genotype is not the only causative factor

HDL2

IDL LDL

Chylo Chylo remnants

VLDL

HDL3

LDLRec

CETP/HL

CETP/HL

scavenger

SRB1 LCAT (LPL)

LPL

LPL

liver

intestine

periph. cholesterol

HL

discLCAT

nasc

surface remnants

surface remnants

HDLreccubulin

LRPHL

scavenger(on LPL def.)

(LRP&HSPG)

HLLDLRec

-

15/03/01

A C H B 48

A C E A C E

A C E A C E

E

B 100

B 48

B 100B 100

periph. cholesterol

Metabolic Network of Lipoproteins

Cholesterol as risk factor

Heritability is 50% - even the best prediction can reduce the variation of individual values by 50%

Variation in more than 20 genes are responsible for the normal statusof cholesterol (clinical LDL/HDL ratio). Each can contribute around 2%

Individual prediction will be useless

Statistical prediction for groups will be possible provided that the complexity of genetic causation is not too high

Test makes sense only if there are genotypes with normal cholesterol levelsin young, but high levels at advanced age

Risk and individual disease

Only part of all individuals with risk status will actually become ill

Every person belongs to several risk groups for a chronic disease with genetic component.

Thus in principle everybody should pay a risk surchargeFor all persons this will cancel

Provided that equity of information is established between insuranceand client!