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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


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


Exome Sequencing in Prostate Cancer

Barbieri et al. Nature Genetics 2012


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


Outliers after adjusting for tas2r38 diplotype
Outliers After Adjusting for TAS2R38 Diplotype

Number of Subjects

PTC Score






Quality control 99 8 concordance
Quality Control:99.8% Concordance




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





Huntington’s Disease Testing

Almqvist AJHG 1999


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



Families can reduce error rates

Roach et al. Science 2010


Families can reduce error rates

Roach et al. Science 2010


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