985 de CODEme November 2007 399 Personal Genome

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

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

New sequencing Sequencing applications Increase in sequencing data output Demand for more sequencing Sequencing technology improvement CS 273 a Lecture 9, Aut 08, Batzoglou

Sequencing technology Sanger sequencing Cost per finished bp: $10. 00 $1. 00 $0. 10 $0. 01 1975 1980 1990 2008 Fred Sanger Read length: 15 – 200 bp Throughput: “grad-student years” CS 273 a Lecture 9, Aut 08, Batzoglou 500 – 1, 000 bp 2 ∙ 106 bp/day

Sequencing technology Sanger sequencing 3 ∙ 109 bp 1 x coverage 10 x coverage × 3 ∙ 109 bp 2∙ 106 bp/day = 40 years 10 x coverage × 3 ∙ 109 bp × $0. 001/bp = $30 million CS 273 a Lecture 9, Aut 08, Batzoglou

Pyrosequencing on a chip Mostafa Ronaghi, Stanford Genome Technologies Center CS 273 a Lecture 9, Fall 2008 CS 273 a Lecture 9, Aut 08, Batzoglou 454 Life Sciences

Sequencing technology Next-generation sequencing Read length: 250 bp “short reads” Throughput: 300 Mb/day Cost: ~ 10, 000 bp/$ De novo: yes Genome Sequencer / FLX CS 273 a Lecture 9, Aut 08, Batzoglou

Single Molecule Array for Genotyping—Solexa CS 273 a Lecture 9, Fall 2008 CS 273 a Lecture 9, Aut 08, Batzoglou

Polony Sequencing CS 273 a Lecture 9, Fall 2008 CS 273 a Lecture 9, Aut 08, Batzoglou

Sequencing technology Next-generation sequencing Genome Analyzer SOLi. D Analyzer Read length: ~ 35 bp “microreads” Throughput: 300 – 500 Mb/day Cost: ~ 100, 000 bp/$ De novo: yes CS 273 a Lecture 9, Aut 08, Batzoglou

Molecular Inversion Probes CS 273 a Lecture 9, Aut 08, Batzoglou

Illumina Genotype Arrays CS 273 a Lecture 9, Fall 2008 CS 273 a Lecture 9, Aut 08, Batzoglou

Sequencing technology Next-generation sequencing “SNP chips” Infinium Assay Gene. Chip Array Read length: 1 bp genotypes Throughput: 1 – 2 Mb/day Cost: 5, 000 bp/$ De novo: no CS 273 a Lecture 9, Aut 08, Batzoglou

Nanopore Sequencing CS 273 a Lecture 9, Fall 2008 CS 273 a Lecture 9, Aut 08, Batzoglou http: //www. mcb. harvard. edu/branton/index. htm

Sequencing technology Next-generation sequencing CS 273 a Lecture 9, Aut 08, Batzoglou

Sequencing technology Technology Read length (bp) Throughput (Mb/day) Cost (bp/$) De novo Sanger 1, 000 2 1, 000 454 250 300 10, 000 Solexa / ABI 35 500 100, 000 SNP chip 1 2 5, 000 Application Sanger 454 Bacterial sequencing $ sometimes Mammalian sequencing $$$ ? not likely today Mammalian resequencing $$$ $ sort of Metagenomics $ ? Genotyping $$$ $$$ CS 273 a Lecture 9, Aut 08, Batzoglou Solexa/ABI SNP chip

Multiple Sequence Alignment CS 273 a Lecture 9, Aut 08, Batzoglou

Evolution at the DNA level Deletion Mutation …ACGGTGCAGTTACCA… …AC----CAGTCCACCA… REARRANGEMENTS Inversion Translocation Duplication CS 273 a Lecture 9, Fall 2008 CS 273 a Lecture 9, Aut 08, Batzoglou SEQUENCE EDITS