GenomicsGenomicsGenomicsGenomics

• Mapping and sequencing genomes– Why and how ?

• Functional genomics– Basic understanding of genome function

– Study how genes affect economically important traits

Sigbjørn LienCentre for Integrative Genetics / Department of Animal and Aquacultural Sciences

Agricultural University of Norway

Sigbjørn LienCentre for Integrative Genetics / Department of Animal and Aquacultural Sciences

Agricultural University of Norway

Why Sequence the Bovine Genome?Why Sequence the Bovine Genome?Why Sequence the Bovine Genome?Why Sequence the Bovine Genome?

• National Human Genome Research Institute (NHGRI) ranks cow as high priority: – Physical map well advanced – Need 3rd equidistant mammal from rodents and humans– Preferably an animal model

• Comparative genomics– Genome dynamics– Human health

• Need a RUMINANT genome– Detailed gene order and organisation– Detailed structure of gene and control regions

• Step change in progress/cost of QTL/gene discovery (up to 10X)

NIH pays half of the sequencing!NIH pays half of the sequencing!

BOVINE GENOME SEQUENCINGBOVINE GENOME SEQUENCINGBOVINE GENOME SEQUENCINGBOVINE GENOME SEQUENCING

• 6-8X coverage 1.5-2.5X coverage ordered path of BAC clones + BAC end sequences 4-5X (2 kb), 1-2X (10 kb) and 0.4X (50 kb) coverage shotgun library sequencing

Sequencing for genetic variation -> SNPs ~ 40 million sequence reads ~ US$1.27 each (20% of current commercial rate!)

Assembly of 6X provides ~ 80% sequence coverage

• Total costs: ~US$51M, where NHGRI pays ~50% (~US$25M)

• Sequencing at Baylor College of Medicine (Houston, Texas)

• Start Dec 2003 and complete within 18 months

• Provide tools for functional genomics!!!

Holstein, Norwegian Cattle, Jersey, Angus, Limousin, Brahman

Hereford

Functional genomics

Genome sequencing

Technologies in functional genomicsTechnologies in functional genomicsTechnologies in functional genomicsTechnologies in functional genomics

• Gene expression– DNA-microarrays

• Genetic variation– Single Nucleotide Polymorphisms (SNPs)

DNA-microarrays

Spot (Gene)

1 2 3 ARRAY

cDNA cDNA

Mix and hybridize

1 1

1

3 3 3

2

3 1

2 2 2

TREATEDCONTROL

3 2 1

Detection

Genomic response:• Breed• Age• Nutrition• Environment • Disease

Genomic response:• Breed• Age• Nutrition• Environment • Disease

DNA-microarrays

• Meat quality• Meat quality• Gene expression• Gene expression

DNA SNPsSingle Nucleotide Polymorphisms

• Frequent• Well distributed • Stable• Functional?• High-throughput genotyping

• Frequent• Well distributed • Stable• Functional?• High-throughput genotyping

Genetic variation: 0.3 %

(~10 mill SNPs)

International Consortium Launches Genetic Variation Mapping Project

HapMap Will Help Identify Genetic Contributions to Common Diseases

WASHINGTON, October 29, 2002.An international research consortium today launched an approximately $100 million public-private effort to create the next generation map of the human genome. Called the International HapMap Project, this new venture is aimed at speeding the discovery of genes related to common illnesses such as asthma, cancer, diabetes and heart disease.Expected to take three years to complete…..

haplotypes/haplotype tagshaplotypes/haplotype tagsSNPsSNPs

Study genome function: Biological samples

Phenotypes

Pedigree

Control environment/nutrition

Genotypes

Gene expression data

Proteome data

Biological knowledge

…..

BIO

INF

OR

MA

TIC

S!!

!

BiobankBiobank

Agricultural University of Norway Agricultural University of Norway Norwegian School of Veterinary Science Norwegian School of Veterinary Science

Institute of Aquaculture Research Institute of Aquaculture Research University of Oslo University of Oslo

University of BergenUniversity of BergenNorwegian Computing CentreNorwegian Computing CentreNorwegian Radium Hospital Norwegian Radium Hospital

Norwegian University of Science and TechnologyNorwegian University of Science and Technology

Agricultural University of Norway Agricultural University of Norway Norwegian School of Veterinary Science Norwegian School of Veterinary Science

Institute of Aquaculture Research Institute of Aquaculture Research University of Oslo University of Oslo

University of BergenUniversity of BergenNorwegian Computing CentreNorwegian Computing CentreNorwegian Radium Hospital Norwegian Radium Hospital

Norwegian University of Science and TechnologyNorwegian University of Science and Technology

National platform for detection, typing and interpretation of SNPsNational platform for detection, typing and interpretation of SNPsNational platform for detection, typing and interpretation of SNPsNational platform for detection, typing and interpretation of SNPs

www.cigene.nowww.cigene.no

A. Establish and maintain a national core facility providing:

(i) a high-throughput SNP-typing service of human, animal, plant and microbial materials.

(ii) key competence concerning identification and methodological integration of experimental and theoretical approaches for making a causal connection between genomic and phenotypic data on complex traits in fish, mammals, plants and micro-organisms.

B. Use this core facility within livestock and marine functional genomics to promote a deep mechanistic understanding of commercially important traits

National platform for detection, typing and interpretation of SNPsNational platform for detection, typing and interpretation of SNPsNational platform for detection, typing and interpretation of SNPsNational platform for detection, typing and interpretation of SNPs

DNA/RNA-extractionBioRobot M48

Normalization of DNAVictor3 (PerkinElmer)

Workstation 1BiomekFX (Beckman)

Sequencing & SNPlex (ABI3730)MassARRAY (Sequenom)

PCRMJR-tetrads

Workstation 2Multimek96 (Beckman)

DATABASELIMS

High-througput technology - CIGENEHigh-througput technology - CIGENE

• Norway was the first country to establish a nation-wide health card recording system in cattle

• Each cow has an individual health card, drugs and antibiotics can only be prescribed by vets -> very reliable recording

10 traits ...........46 traits...........64 traits (1975) (1978) (1989) 10 traits ...........46 traits...........64 traits (1975) (1978) (1989)

• Also intensive recording of milk, beef and reproduction traits

• 90% of all cows have been registered since 1978 -> ~ 4 mill cows

• Complete listing of pedigree structure -> ~ 7,5 mill individuals

• Progeny testing of 250-300 daughters per sire

• Paternity testing of bulls

• Systematic storage of semen from all bulls since 1982 DNA

• Choose among ~280.000 cows/bulls for in vivo experiments

Norwegian Biobank CattleNorwegian Biobank CattleNorwegian Biobank CattleNorwegian Biobank Cattle

Norway’s participation in the sequencing consortium

Norway’s participation in the sequencing consortium

FOCUS ON OUR STRENGTHS:

Unique biobank material Competence and technology to “BRIDGE THE

GENOTYPE-PHENOTYPE GAP” Sequencing for genetic variation!!!

SNP-detectionValidation of

SNPsGenotype biobank

Phase 2

Phase 1Sequencing effortSequencing effort

Other projectsOther projects

Gene expression Proteomics