1. $399 Personal Genome Service $2,500 Health Compass service $985 deCODEme (November 2007) (April 2008) $350,000 Whole-genome sequencing (November 2007) Genetic Information Nondiscrimination Act (May 2008)

2. Whole-genome sequencing Comparative genomics Genome resequencing Structural variation analysis Polymorphism discovery Metagenomics Environmental sequencing Gene expression profiling Applications Genotyping Population genetics Migration studies Ancestry inference Relationship inference Genetic screening Drug targeting Forensics

3. CS273a Lecture 9, Aut08, Batzoglou Sequencing applications Demand for more sequencing Sequencing technology improvement Increase in sequencing data output New sequencing applications

4. CS273a Lecture 9, Aut08, Batzoglou Sequencing technology Sanger sequencing 19751980200819902000 $10.00 $1.00 $0.10 $0.01 Cost per finished bp: Read length:15 – 200 bp500 – 1,000 bp Throughput: “grad-student years”2 ∙ 10 6 bp/day Fred Sanger

5. CS273a Lecture 9, Aut08, Batzoglou Sequencing technology Sanger sequencing 3 ∙ 10 9 bp 1x coverage 10x coverage 2 ∙ 10 6 bp/day = 40 years × 3 ∙ 10 9 bp 10x coverage × 3 ∙ 10 9 bp × $0.001/bp = $30 million

6. CS273a Lecture 9, Aut08, Batzoglou CS273a Lecture 9, Fall 2008 Pyrosequencing on a chip Mostafa Ronaghi, Stanford Genome Technologies Center 454 Life Sciences

7. CS273a Lecture 9, Aut08, Batzoglou Sequencing technology Next-generation sequencing Read length:250 bp Throughput:300 Mb/day Cost: ~ 10,000 bp/$ De novo:yes Genome Sequencer / FLX “short reads”

8. CS273a Lecture 9, Aut08, Batzoglou CS273a Lecture 9, Fall 2008 Single Molecule Array for Genotyping—Solexa

9. CS273a Lecture 9, Aut08, Batzoglou CS273a Lecture 9, Fall 2008 Polony Sequencing

10. CS273a Lecture 9, Aut08, Batzoglou Sequencing technology Next-generation sequencing Read length: ~ 35 bp Throughput:300 – 500 Mb/day Cost: ~ 100,000 bp/$ De novo:yes Genome AnalyzerSOLiD Analyzer “microreads”

11. CS273a Lecture 9, Aut08, Batzoglou Molecular Inversion Probes

12. CS273a Lecture 9, Aut08, Batzoglou CS273a Lecture 9, Fall 2008 Illumina Genotype Arrays

13. CS273a Lecture 9, Aut08, Batzoglou Sequencing technology Next-generation sequencing Read length:1 bp Throughput:1 – 2 Mb/day Cost:5,000 bp/$ De novo:no Infinium AssayGeneChip Array genotypes “SNP chips”

14. CS273a Lecture 9, Aut08, Batzoglou CS273a Lecture 9, Fall 2008 Nanopore Sequencing http://www.mcb.harvard.edu/branton/index.htm

15. CS273a Lecture 9, Aut08, Batzoglou Sequencing technology Next-generation sequencing

16. CS273a Lecture 9, Aut08, Batzoglou Sequencing technology TechnologyRead length (bp) Throughput (Mb/day) Cost (bp/$) De novo Sanger1,0002 45425030010,000 Solexa / ABI35500100,000 SNP chip125,000 ApplicationSanger454Solexa/ABI SNP chip Bacterial sequencing$ sometimes Mammalian sequencing$$$? not likely today Mammalian resequencing$$$$sort of Metagenomics$ ? Genotyping$$$

17. CS273a Lecture 9, Aut08, Batzoglou Multiple Sequence Alignment

18. CS273a Lecture 9, Aut08, Batzoglou CS273a Lecture 9, Fall 2008 Evolution at the DNA level …ACGGTGCAGTTACCA… …AC----CAGTCCACCA… Mutation SEQUENCE EDITS REARRANGEMENTS Deletion Inversion Translocation Duplication

19. CS273a Lecture 9, Aut08, Batzoglou CS273a Lecture 9, Fall 2008 Evolutionary Rates OK X X Still OK? next generation

20. CS273a Lecture 9, Aut08, Batzoglou CS273a Lecture 9, Fall 2008 Orthology, Paralogy, Inparalogs, Outparalogs

21. CS273a Lecture 9, Aut08, Batzoglou CS273a Lecture 9, Fall 2008