$399 Personal Genome Service $2,500 Health Compass service $985 deCODEme (November 2007) (April...

$399 Personal Genome Service

$2,500 Health Compass service

$985 deCODEme(November 2007)

(November 2007)

(April 2008)

$350,000 Whole-genome sequencing(November 2007)

Genetic Information Nondiscrimination Act(May 2008)

Whole-genome sequencing

Comparative genomicsGenome resequencing

Structural variation analysis

Polymorphism discoveryMetagenomicsEnvironmental

sequencingGene expression profiling

Applications

GenotypingPopulation genetics

Migration studiesAncestry inference

Relationship inferenceGenetic screening

Drug targetingForensics

CS273a Lecture 9, Aut08, Batzoglou

Sequencing applications

Demand for more sequencing

Sequencing technology improvement

Increase in sequencing data output

New sequencing applications

CS273a Lecture 9, Aut08, Batzoglou

Sequencing technologySequencing technologySanger sequencing

1975 1980 20081990 2000

$10.00

$1.00

$0.10

$0.01

Cost per finished bp:

Read length: 15 – 200 bp 500 – 1,000 bp

Throughput: “grad-student years” 2 ∙ 106 bp/day

Fred Sanger

CS273a Lecture 9, Aut08, Batzoglou

Sequencing technologySequencing technologySanger sequencing

3 ∙ 109 bp

1x coverage

10x coverage

2 ∙ 106 bp/day= 40 years

× 3 ∙ 109 bp

10x coverage × 3 ∙ 109 bp × $0.001/bp = $30 million

CS273a Lecture 9, Aut08, BatzoglouCS273a Lecture 9, Fall 2008

Pyrosequencing on a chip

Mostafa Ronaghi, Stanford Genome Technologies Center

454 Life Sciences

CS273a Lecture 9, Aut08, Batzoglou

Sequencing technologySequencing technologyNext-generation sequencing

Read length: 250 bp

Throughput: 300 Mb/day

Cost: ~ 10,000 bp/$

De novo: yes

Genome Sequencer / FLX

“short reads”

CS273a Lecture 9, Aut08, BatzoglouCS273a Lecture 9, Fall 2008

Single Molecule Array for Genotyping—Solexa

CS273a Lecture 9, Aut08, BatzoglouCS273a Lecture 9, Fall 2008

Polony Sequencing

CS273a Lecture 9, Aut08, Batzoglou

Sequencing technologySequencing technologyNext-generation sequencing

Read length: ~ 35 bp

Throughput: 300 – 500 Mb/day

Cost: ~ 100,000 bp/$

De novo: yes

Genome Analyzer SOLiD Analyzer

“microreads”

CS273a Lecture 9, Aut08, Batzoglou

Molecular Inversion Probes

CS273a Lecture 9, Aut08, BatzoglouCS273a Lecture 9, Fall 2008

Illumina Genotype Arrays

CS273a Lecture 9, Aut08, Batzoglou

Sequencing technologySequencing technology

Next-generation sequencing

Read length: 1 bp

Throughput: 1 – 2 Mb/day

Cost: 5,000 bp/$

De novo: no

Infinium Assay GeneChip Array

genotypes

“SNP chips”

CS273a Lecture 9, Aut08, BatzoglouCS273a Lecture 9, Fall 2008

Nanopore Sequencing

http://www.mcb.harvard.edu/branton/index.htm

CS273a Lecture 9, Aut08, Batzoglou

Sequencing technologySequencing technologyNext-generation sequencing

CS273a Lecture 9, Aut08, Batzoglou

Sequencing technologySequencing 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 Solexa/ABISNP chip

Bacterial sequencing $ sometimes

Mammalian sequencing $$$ ?not likely

today

Mammalian resequencing $$$ $ sort of

Metagenomics $ ?

Genotyping $$$ $$$ $$$

CS273a Lecture 9, Aut08, Batzoglou

Multiple Sequence Alignment

CS273a Lecture 9, Aut08, BatzoglouCS273a Lecture 9, Fall 2008

Evolution at the DNA level

…ACGGTGCAGTTACCA…

…AC----CAGTCCACCA…

Mutation

SEQUENCE EDITS

REARRANGEMENTS

Deletion

InversionTranslocationDuplication

CS273a Lecture 9, Aut08, BatzoglouCS273a Lecture 9, Fall 2008

Evolutionary Rates

OK

OK

OK

X

X

Still OK?

next generation

CS273a Lecture 9, Aut08, BatzoglouCS273a Lecture 9, Fall 2008

Orthology, Paralogy, Inparalogs, Outparalogs

CS273a Lecture 9, Aut08, BatzoglouCS273a Lecture 9, Fall 2008