latestdevelopments relevant for the Ag sector André Eggen Agriculture Segment Manager, Europe

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1 Overviewof Illumina s latestdevelopments relevant for the Ag sector André Eggen Agriculture Segment Manager, Europe Seminar der Studienrichtung Tierwissenschaften, TÜM, July 1, 2009

2 Overviewof Illumina slatestdevelopmentsrelevant for the Ag sector The current trends in the Agriculture sector Whole Genome Sequencing in Agriculture relevant species A new booster to the search for causal mutation A change of paradigm in breeding programmes Perspectives 2

3 Whole Genome Sequencing in Agriculture relevant species A reality and no more a dream 3

4 Human Genome Project (HUGO) A catalyser contributed to the improvement of technologies and strategies Awoke dreams for the study of livestock genomes 4

5 Limited Expectations! For livestock, one thought that only few «representative genomes» will be sequenced White papers to make the case Improving human health Informing human biology Example : Cattle Expand knowledge of basic biological process relevant to human health Provide surrogate systems fo human experimentation Facilitating the ability to do experiments (positional mapping) 5

6 Sequencing the Giant Panda using the Genome Analyzer (2008) Three Gigabases genomes can be sequenced and assembled using «short read» sequences 150 Gb of sequences (50x) 75 bp «Paired reads» 80 % of the genome 95 % of the genes covered Assembly in 2 days! 6

7 SNPs as added value from Whole Genome sequencing Reference sequence (6-12x Coverage) Several 100k sequences from several animals belonging to different breeds Align Sequences to identify several 100k SNPs SNP validation with a restricted number of animals from different breeds (optional) Build a whole genome SNP array (International Consortium) 7

8 A new booster to the search for mutations underlying variation in complex traits Availability of large panels of SNPs 8

9 Illumina whole genome beadchip for Ag species Species SNP Horse Cattle Sheep Dog Pig Chicken 60 K (NC) 9

10 iselect Custom Genotyping iselect & iselect HD BeadChips 3,000 to 200,000 attempted bead types on iselect / iselect HD Target any variant, any species 12 samples per chip on standard or HD BeadChip 288 samples per day Low DNA input (200ng) Minimum 80% Beadtype success rate Infinium II / Infinium HD assay High-plex custom genotyping arrays developed using the Infinium Assay to ensure high data quality and high sample throughput 10

11 Genome-wide SNP panels : bypassing the mapping step! Tens to hundreds of thousands of SNPs genotyped for a cheaper price than few hundreds of microsatellites Direct interrogation of Linkage Disequilibrium (LD)(relaxes the requirements for specific pedigree relationships) Drastically reduction of the localisation interval of the QTLs (< 500Kb) 11

12 Sampling size (estimation in Dog) Trait Case / Control Success Probabilityof the Study Monogenic recessiv Monogenic dominant % % Complex % 12

13 13 First results in Cattle

14 14 Regions of interest identified with a limited number of samples

15 5285 bulls as reference population SNPs with MAF >

16 16

17 Targeted Resequencing as logical follow up from association studies Illumina s BeadChips allow the identification of genomic region with relative high precision Through a genome scan, the critical interval is reduced to one or a few candidate region(s) less than 1 Mb in size The challenge is to identify the causal mutation 17

18 SureSelect Target Enrichment System Agilent Technologies Targeted resequencing of a limited number of samples with extreme phenotype is one of the key to identify the causal molecular mechanism Genomic regions of up to 5 Mb Region covered with 120mer (55k) Libraries available for Cattle, Chicken 18

19 SureSelect Workflow Probe design in earray Illumina library prep up front Capture oligos bind DNA regions Magnetic bead selection Illumina sequencing following capture 19

20 Excellent Coverage Uniformity ~80% targeted reads at >20X depth 20 20x coverage benchmark for accurate SNP detection <4% of targeted bases missed

21 iscan with Sequencing Module Key Features 21 iscan Scans HD BeadChips Multi-sample formats Infinium & Golden Gate assays Up to 4800 samples a day Seamless automation integration Available since April iscan Sequencing Module Scans flow cells Uses SBS reagents ~ 3 Gb per run, >0.3 Gb per day Paired end capability Up to 2 x 50bp > 32 M clusters per run

22 iscan with Sequencing Module - Applications iscan GWAS CNV Focused arrays for genotyping Gene expression + iscan Sequencing Module mirna ChiP-Seq DGE mrna-seq Targeted re-sequencing Small genome sequencing 22

23 A change of paradigm From finding the right Plant/Animal to finding the right Gene(s)/Genome 23

24 Science and Technology Have Changed the Paradigm from Finding Animals to Finding the right genomes OLD PARADIGM Finding the right Animals NEW PARADIGM Finding the right genomes 24

25 The big promises of genomic selection General idea With enough markers one can follow the transmission (segregation) of the entire genome and not only a set of specific regions of interest Parental relationship is no more used to explain similar performances in animal Similar performances are explain by the fact that animals are sharing identical chromosome fragments 25

26 Advanced Animal Breeding Where to go Breeding objectives Trait measurement How to get there Score animals for desirable traits Repeat until original goal is met 26 Mate sires and dams with high scores Reproductive technologies Genomic breeding value!! Estimation of breeding value Phenotype Pedigree BLUP Genetic Markers

27 GENOMIC ANIMAL PASSPORT International DNA- Based Identity Card N :? Animal Phenotype ACGTTTGCTGCATGCATGCATGCTGAATAGCTTAGATTCGATACACCATGGC Phenotype ATGACTAGCATCGACTAGCTACGACTGACTAGCATCGACTAGCATTCTTAGC of Ancestor TTCTAGCTATTACGACTCGATCGACTAGCTACGAGCTACGACTACACGTTTG CTGCATGCATG CTGCATGC ATGCATGCTGAA CATGCTGAATAGCTT TAGCTTAGATTCGATACACCATGGCATGACT AGATTCGATACACCATGGCATGACT GACTGACTAGCATCGACTAGCATTCTTAGCTTCTAG CTTAGCTTCTAG AGCATCGACTAGCTACGACTGACTAGCATCGACTAGCATT AGCATCGACTAGCTAC CTATTACGACTCGATCGACTAGCTACGAGCTACGACTACACGTTTGCTGCAT GCATGCATGCTGA GCATGCAT GCTGAATAGCTTA ATAGCTTAGATT GATTCGATACACCATGGCATGACTAGCATC CGATACACCATGGCATGACTAGCATC GACTAGCTACGACTGACTAGCATCGACTAGCATTCTTAGCTTCTAG GACTA GCTACGACTGACTAGCATCGACTAGCATTCTTAGCTTCTAGCTATTA CTATTA CGACTCGATCGACTAGCTACGAGCTACGACTACACGTTTGCTGCATGCATGC ATGCTGAATAGCTTAGATTCGA ATGCTGAATAGCTTAG ATTCGATACAC TACACCATGGCATGACTAGCATCGACTAG CATGGCATGACTAGCATCGACTAG CTACGACTGACTAGCATCGACTAGCATTCTTAGCTTCTAGCTATTACGACTC CTACGACTGACTAGCATCGACTAGCAT TCTTAGCTTCTAGCTATTACGACTC Phenotype Breeding GATCGACTAGC GATCGAC TAGCTACGAGCTACGACTACACGTTTGCTGCATGCATGCATGCTG TACGAGCTACGACTACACGTTTGCTGCATGCATGCATGCTG value TCGATACACCATGGCATGACTAGCATCGACTAGCTACGA of Fullsibs AATAGCTTAGATTCGATACACCATGGCATGACTAGCATCGACTA AATAGCTTAGAT GCTACGA CTGACTAGCATCGACTAGCATTCTTAGCTTCTAGCTATTACGACTCGATCGA CTAGCTA CTAG CTACGAGCTACGACTACGGCACGTTTGCTGCATGCATGCATGCTGAAT CGAGCTACGACTACGGCACGTTTGCTGCATGCATGCATGCTGAAT AGCTTAGATTCGATACACC AGCTTAGATTCGAT ACACCATGGCATGA ATGGCATGACTAGCATCGA CTAGCATCGAC CTAG TAGCT CTACGAC ACGACTG TG ACTAGCATCG ACTAGC ATCGACTAGCATTCTTA ACTAGCATTCTTAGCACG GCACGTTTGCTGCATGCATGCATGCTGAA TTTGCTGCATGCATGCATGCTGAA TAGCTTAGATTCGATACACCATG TAGCTTA GATTCGATACACCATGGCATGACTAGCATCGACTAGCTACGACTG GCATGACTAGCATCGACTAGCTACGACTG Phenotype of Offspring

28 Complete Platform Solutions for Agrigenomics The technology of the new paradigm Discover Interrogate Validate/Screen Platform Genome Analyzer II iscan + Sequencing module BeadXpress Applications Non-Human Genome Sequencing Digital Gene Expression SNP Discovery Genome-wide marker / phenotype association Focused marker / phenotype association Genetic Identity Confirmation Genetic Purity Screening Parentage / Lineage Marker Assisted Selection DNA Methylation, Targeted Resequencing Genomic Selection Disease Screening Illumina will drive the use of genetic variation-based approaches to crop and livestock markets. 28

29 29 Custom solutions for specific needs

30 Sequence/Genotype Gene Expression Phenotype Methylation/Epigenetics CNV 30

31 Discover. Validate. Screen Dankefürihre Aufmerksamkeit! 31 A new evolution in agriculture genetic analysis.