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Clinical and Recreational Genomics. Personal experiences with direct-to-consumer genotyping. March 16, 2009. Mark Boguski, M.D., Ph.D. Department of Pathology Beth Israel Deaconess Medical Center. Outline of Presentation. A little history Personalized medicine/genomics

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Clinical and recreational genomics

Clinical and Recreational Genomics

Personal experiences with direct-to-consumer genotyping

March 16, 2009

Mark Boguski, M.D., Ph.D.

Department of Pathology

Beth Israel Deaconess Medical Center


Outline of presentation
Outline of Presentation

  • A little history

  • Personalized medicine/genomics

  • Two illustrative anecdotes

  • Compare and contrast three DTC genotyping companies

    • Products and services

    • Technologies and raw genotype data

    • Reports on genotype-phenotype associations

  • My “Health Compass”

  • Consumer genomics and the future



Victor mckusick m d 1921 2008
Victor McKusick, M.D. (1921-2008)

He founded

Mendelian

Inheritance in

Man in 1962…

Later MIM →

Online MIM

or OMIM

He founded

The journal

GENOMICS

In 1987

www.markboguski.net/

teaching.htm


The brave new world of personal genomes i personal stories
The Brave New World of Personal GenomesI.Personal Stories

  • A father uses commodity DNA sequencing technologies and publicly-available medical databases to investigate the elusive cause of his daughter’s genetic illness.

  • A controversial scientist publishes his autobiography which is partially based on the complete sequence of his own genome.

  • A Harvard geneticist launches a Personal Genome Projectto encourage medical altruism and self-knowledge and makes his own biological material available for study.


The brave new world of personal genomes ii demographics and commercial services
The Brave New World of Personal GenomesII.Demographics and Commercial Services

Several start-up companies (two of which are backed by Google) form to provide genotyping services as

direct-to-consumer businesses.



Clinical and recreational genomics

“It’s fun to learn about your genome.”

23andMe “Spit Party” in NYC

Fashion & Style section

September 12, 2008


Clinical and recreational genomics

“People think if you have money to spend on this, why not buy a test instead of a model train for Christmas.”

Dr. Alan Guttmacher, acting director of the National Human Genome Research Institute at NIH.


Home page comparisons links
Home Page Comparisons & Links buy a test instead of a model train for Christmas.”


Genotyping technologies
Genotyping Technologies buy a test instead of a model train for Christmas.”

23andMe and deCODE use

Illumina human1M duo DNA analysis beadchip

Navigenics uses

Affymetrix Genome-wide SNP array 6.0


Raw genotype data 23andme
Raw genotype data: 23andMe buy a test instead of a model train for Christmas.”

# This data file generated by 23andMe at: Tue Jul 1 19:13:29 2008

# Below is a text version of your data. Fields are TAB-separated

# Each line corresponds to a single SNP. For each SNP, we provide its

# identified (an rsid or an internal id), its location on the reference human

# genome, and the genotype call oriented with respect to the plus strand on the

# human reference sequence. We are using reference human assembly build 36.

# Note that it is possible that data downloaded at different times may be

# different due to ongoing improvements in our ability to call genotypes.

#

# More information on reference human assembly build 36:

# http://www.ncbi.nlm.nih.gov

#

# rsid chromosome position genotype

rs3094315 1 742429 AA

rs12562034 1 758311 GG

rs3934834 1 995669 CC

rs9442372 1 1008567 GG

rs3737728 1 1011278 GG

rs11260588 1 1011521 GG

rs6687776 1 1020428 CC

rs9651273 1 1021403 GG


Raw genotype data decodeme
Raw genotype data: buy a test instead of a model train for Christmas.”deCODEme

Name,Variation,Chromosome,Position,Strand,YourCode

rs4345758,C/T,1,28663,+,TT

rs4477212,A/G,1,72017,+,AA

rs1856862,A/T,1,110905,-,TT

rs4096703,C/G,1,160593,+,GG

rs2994597,A/T,1,593369,-,TT

rs3871859,G/T,1,640354,-,GG

rs4000335,A/G,1,679049,+,GG

rs28659788,C/G,1,713170,+,CC

rs3094315,C/T,1,742429,-,TT

rs3131972,C/T,1,742584,-,CC

rs3131969,C/T,1,744045,-,CC

rs1048488,C/T,1,750775,+,TT

rs2905046,A/G,1,752518,-,GG

rs12562034,A/G,1,758311,+,GG

rs4040617,A/G,1,769185,+,AA

rs2980314,A/C,1,771121,-,CC

rs2980300,C/T,1,775852,+,CC

rs2905036,A/G,1,782343,-,AA

rs11240777,A/G,1,788822,+,GG


Raw genotype data navigenics
Raw genotype data: buy a test instead of a model train for Christmas.”Navigenics

# This data file was generated by Navigenics Fri Sep 5 09:17 2008

# The file contains genotype calls from the Affymetrix Genome-Wide

# Human SNP Array 6.0.

# The genotyping was performed on behalf of Navigenics, Inc. by the

# CLIA-certified Affymetrix Clinical Services Laboratory (ACSL).

# The data was securely transmitted from ACSL in .chp format.

SNP_A-2131660 rs2887286 TT chr1 1145994 C/T

SNP_A-1967418 rs1496555 GG chr1 2224111 A/G

SNP_A-1969580 --- GG chr1 2319424 A/G

SNP_A-4263484 rs3890745 TT chr1 2543484 C/T

SNP_A-1978185 rs10492936 GG chr1 2926730 G/A

SNP_A-4264431 rs10489588 GG chr1 2941694 G/A

SNP_A-1980898 rs2376495 GC chr1 3084986 G/C

SNP_A-1983139 rs4648462 AA chr1 3155127 A/C

SNP_A-4265735 rs10492939 GG chr1 3292731 G/A

SNP_A-1995832 rs9424283 CG chr1 3695086 C/G

SNP_A-1995893 rs2154068 AG chr1 3710825 A/G

SNP_A-1997689 rs12060299 GG chr1 3753024 A/G

SNP_A-1997709 rs10909802 TT chr1 3753427 T/C

SNP_A-2004249 rs676853 AC chr1 4461025 A/C


Reports on genotype phenotype associations
Reports on genotype-phenotype associations buy a test instead of a model train for Christmas.”


Comparison of covered diseases and conditions
Comparison of covered diseases and conditions buy a test instead of a model train for Christmas.”

23andMe

deCODEme

Navigenics


Home page comparisons links1
Home Page Comparisons & Links buy a test instead of a model train for Christmas.”


Consumer exploitation in the genome era

Consumer Exploitation in the Genome Era buy a test instead of a model train for Christmas.”


Clinical and recreational genomics

1/2 buy a test instead of a model train for Christmas.”


Clinical and recreational genomics

1/2 buy a test instead of a model train for Christmas.”


Clinical and recreational genomics

“Dr. Dave” writes: buy a test instead of a model train for Christmas.”

I am super busy and don't normally

write a review on anything! But this

book is sooooooooo baaaaaad that

I felt compelled. The author provides

almost no real information and

continuously berates the reader to

"start a consumer advocacy group" to

do this and that. For my $25 I would

have rather donated it to a consumer

advocacy group to prevent the

publication of awful books like this one!

And to think this lady has written

36 books! If Ms Hart's book were

required reading by criminals, we

wouldn't need the death penalty…

the prisoners would all commit suicide!


Clinical and recreational genomics

No reviews buy a test instead of a model train for Christmas.”


Clinical and recreational genomics

No reviews buy a test instead of a model train for Christmas.”


Clinical and recreational genomics

½* buy a test instead of a model train for Christmas.”

*Average of 38 reviews


The six primary genotypes

Hunter buy a test instead of a model train for Christmas.”

Gatherer

Warrior

Teacher

Explorer

Nomad

The Six Primary Genotypes


The six primary genotypes1

Hunter buy a test instead of a model train for Christmas.”

Gatherer

Warrior

Teacher

Explorer

Nomad

The Six Primary Genotypes

Formula for calculating the genotypes:

30,000 genes + prenatal experience + the last 100,000 years on earth

= 6 Genotypes


Clinical and recreational genomics

$2500 buy a test instead of a model train for Christmas.”

$ 985

$ 399


Clinical and recreational genomics

$2500 buy a test instead of a model train for Christmas.”

$ 985

$ 399


Clinical and recreational genomics

$2500 buy a test instead of a model train for Christmas.”

$ 985

$ 399


Clinical and recreational genomics

$2500 buy a test instead of a model train for Christmas.”

$ 985

$ 399

$14.95


Clinical and recreational genomics

“Be careful about reading health books.  You may die of a misprint.”

-Mark Twain

A copy of today’s presentation and related materials

can be found at

www.markboguski.net/presentations.htm


Clinical and recreational genomics

Leaping beyond the genome – what lies ahead? misprint.”

Dr. William B. Neaves

President & CEO, Stowers Institute for Medical Research

Kansas City, MO