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Next-Generation Sequencing. Eric Jorgenson Epidemiology 217 3/5/13. Outline. Overview Examples of Next Generation Sequencing Studies: Whole Genome, Exome, Families (IBD), Cancer PTC Taste Sensitivity Implications. Sequencing costs have fallen.

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next generation sequencing

Next-Generation Sequencing

Eric Jorgenson

Epidemiology 217

3/5/13

outline
Outline

Overview

Examples of Next Generation Sequencing Studies: Whole Genome, Exome, Families (IBD), Cancer

PTC Taste Sensitivity

Implications

number of genetic markers for genetic studies
Number of Genetic Markers for Genetic Studies

Genome-wide Linkage Studies

300-400 Microsatellite Markers

Genome-wide Association Studies

100,000-2,500,000 SNPs

Exome Sequencing Studies

30,000,000 Basepairs

Exome Array Studies

>240,000 exonic variants

Whole Genome Sequencing Studies

3,200,000,000 Basepairs

slide5

Links to Sequencing Projects

1000 Genomes:

http://browser.1000genomes.org/Homo_sapiens/Info/Index

Exome Sequencing Project:

https://esp.gs.washington.edu/drupal/

Exome Array Design:

http://genome.sph.umich.edu/wiki/Exome_Chip_Design#Second_Generation_Arrays

outline1
Outline

Overview

Examples of Next Generation Sequencing Studies: Whole Genome, Exome, Families (IBD), Cancer

PTC Taste Sensitivity

Implications

family sequencing for rare diseases
Family Sequencing for Rare Diseases

Roach et al. Science 2010

cancer tumor vs normal
Cancer: Tumor vs. Normal

Lee et al. Nature 2010

slide21

Exome Sequencing in Prostate Cancer

Barbieri et al. Nature Genetics 2012

slide22

Exome Sequencing in Prostate Cancer

Barbieri et al. Nature Genetics 2012

outline2
Outline

Overview

Examples of Next Generation Sequencing Studies: Whole Genome, Exome, Families (IBD), Cancer

PTC Taste Sensitivity

Implications

distribution of ptc phenotype
Distribution of PTC Phenotype

Number of Subjects

PTC Score

tas2r38 receptor structure
TAS2R38 Receptor Structure

rs1726866

rs10246939

rs713598

Kim et al. J Dent Res 2004

3 snps form 3 haplotypes
3 SNPs Form 3 Haplotypes

P A V

Taster

Non-taster

A V I

Rare

A A V

ptc phenotype by tas2r38 diplotype
PTC Phenotype by TAS2R38 Diplotype

Number of Subjects

PTC Score

using relatedness
Using Relatedness

11

8

9

3

8

10

12

9

9

9

outline3
Outline

Overview

Examples of Next Generation Sequencing Studies: Whole Genome, Exome, Families (IBD), Cancer

PTC Taste Sensitivity

Implications

how can whole genome sequence influence treatment
How can whole genome sequence influence treatment?
  • Identify Genes with Protein Altering Mutations
  • Determine Variation in Specific Genes
slide48

Links to videos and articles

http://www.bloomberg.com/video/84364498/

http://www.bloomberg.com/video/84364540/

http://www.businessweek.com/videos/2012-11-06/bloomberg-reporter-gets-second-opinion-on-dna-test

http://www.bloomberg.com/news/2012-01-17/search-genome-as-tennis-thrice-weekly-no-barrier-to-decoded-dna.html

http://www.bloomberg.com/news/2012-02-15/harvard-mapping-my-dna-turns-scary-as-threatening-gene-emerges.html

http://www.businessweek.com/news/2012-11-06/my-dna-results-spur-alzheimer-s-anxiety-at-12-000-cost#p1

slide50

Families can reduce error rates

Roach et al. Science 2010

slide51

Families can reduce error rates

Roach et al. Science 2010

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