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Personal Genetics

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Sal Cyranowski

on 28 October 2015

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Transcript of Personal Genetics

Salwador Cyranowski / Łukasz Szymański
Human Genetics, University of Warsaw 2014

Background
Application
Market overview
Gen-ethics
Human genome complexity
3 billion base pairs
your sequence of interest
~1,5%
coding
~98%
noncoding
vs.
proteins
ncRNAs (tRNA, rRNA,
miRNA, siRNA, piRNA)
still very
important
gene-flanking sequences
short/long repeats
pseudogenes

when looking for a specific gene, you must be ready to go really deep
substantial regulatory function
UCRs - ultra conserved regions across species - must mean something
much to be discovered in this area
A haystack of sequences
An iceberg of processing
Expressinome
genome
(record of DNA)
transcriptome
(record of mRNA)
proteome
(record of proteins)
metabolome
(interaction of many)
epigenome
(record of chemical changes
in DNA and histones)
regulatorome
(record of genes silenced
and enhaced)
exonome
(record of spliced mRNA)
Trait of interest
A decade (and more) of human genetics
1977
1986/7
1995
1990
1970s
1953
2000
2006
DNA structure
discovered
major improvements
in DNA sequencing techniques
first whole genome sequenced
bacteriophage phi X174
first fully automated
DNA sequencing machines
Human Genome Project
launch
first free living organism genome sequenced
bacterium
Haemophilus influenzae
first draft of human genome
published
last chromosome sequence published in Science
99 to 20
DNA vs. proteins
in humans and chimpanzees
up to 99% corresponding DNA
only 20% corresponding proteins
HGP, 2010
"the material costs of sequencing at the time were "getting down to around about
10 cents a base
", says Michael Morgan"
Today, 2014
this trend would've followed,
3 billion base pairs genome would cost
US$ 300 millions today
— if —
(Knoppers, 2010)
no longer thinking of "per base" cost
— instead —
we're rather thinking big,
mega
big
Today, 2014
actually, no longer talking base pairs
— in fact —
we're talking
whole genomes
,
and this costs ca.
US$ 10 000
and less
Future
as for now, whole genome
testing is unaffordable
for many people
— but —
DNA sequencing cost
drops faster than Moore's law predicts
targets are set for
$1000 per genome

for the most forseeable future
Cost of DNA sequencing
DNA sequencing: know-how
Testing for diseases
Analytical validity
the results of the test
are acurate and reliable
Clinical validity
the results are of clinical significance
The three criteria of useful medical tests
Clinical utility
the results are ready to be utalised with clear benefit
to patient's health
Testing for diseases
Types of screening
Diagnosis
patient shows symptoms
Presymptomatic
tests
patient is asymptomatic and seems healthy, but there's a disease in the family
— or —
genetic test to diagnose the predicted disease
screening
for SNPs
checking
for CNVs
deletions and chromosome aberrations
uniparental
disomy
loss of
heterozygosity
(Li, 2011)
Voluntary genetic
sequencing programs
1000 Genomes
Personal Genome Project
Overview of

genetic

companies
deCODEme
23andMe
Genomed
Illumina
Pills with your initials
Bespoke medication to maximise the treatment
"Bring your ancestry to life."
Human Whole-Genome sequencing - $4000
Other services
Next-generation Sequencing Technology provider
Polish company founded in 2007
Wide range of services. 150 - 5000 PLN
don't forget the environment
Design and commercialisation
Websites about personal sequencing
SNPedia is a wiki investigating human genetics.
The Ethical, Legal and Social Implications (ELSI) Research Program
was established in 1990 as an integral part of the Human Genome Project
program funds and manages studies, and supports workshops, research consortia and policy conferences related to ethical, legal and social implications of genetic and genomic research
National Human Genome Research Institute
Privacy
genetic information storage
the rights to have an insight into genetic information
scientific usage of personal genetic information
Unwanted awareness
the right not to know
applied also to family members who might be in the risk group
Discrimination
family
school
society
employment
Up to 30 percent of people prescribed the medication do not activate the drug, and may as well take sugar pills
— Michael Christman, Coriell Institute for Medical Research, on clapidogrel - a heart attack medication
(Mullich, 2012)
Aims
Application
maximising treatment outcomes
diminishing adverse effects of drugs
saving money and time
The two main fields are
Pharmacogenomics
Cancer treatment
pharmaceutical companies designing drugs based on population genetics - releasing several variants of the drug to meet the most common patterns of metabolism
clinics having an insight into patient's genetics prior to, often speculative, cancer treatment -
e.g. saving patiens from ineffective chemotherapy
Is a division of the National Institutes of Health
Was established in 1989 to carry out the role of the NIH in the International Human Genome Project

Back in the 90s
Present
lots of bacteria-based replication, purification, running gels, etc. = tedious and time-consuming
only relatively small sequences (can't do the whole genome - to much work)
nowadays quite obsolete
'next generation sequencing'
high throughput + high procedure
global aproach
computer-based data analysis
several different technologies (pretty sophisticated)
Gene by gene, gel by gel
The procedure got global
Under development
Giga precision at nano scale
"FDA is concerned about the public health consequences of inaccurate results from the PGS device - the main purpose of compliance with FDA's regulatory requirements is to ensure that the tests work,"
-Alberto Gutierrez, director of the FDA's centre for devices and radiological health
using nanopores in graphene (carbon single-molecule-thick membrane) or polymer membranes
basically getting it down to a single molecule being sequenced
very precise, very sophisticated
Science, afterall
A plethora of study information
every human on Earth having his or her genome sequenced
the sequences properly stored and available for scientists worldwide
IMAGINE
that's a lot of information to work with - perhaps resulting in better understanding of human biology
watch the videos!
(Li, 2011)
Cordero, P., and Ashley, E.A. (2012). Whole-genome sequencing in personalized therapeutics. Clin. Pharmacol. Ther. 91, 1001–1009.

Knoppers, B.M. 2010. Consent to ‘personal’ genomics and privacy. European Molecular Biology Organisation Reports. 11(6), 416–419.

Li, C. (2011). Personalized medicine - the promised land: are we there yet? Clin. Genet. 79, 403–412.

Maher, B. (2011). Genomes on prescription. Nature. 478, 22–24

Mullich, J. (2012). Tailored treatment. The Wall Street Journal. Available: http://online.wsj.com/ad/article/lifesciences-treatment (accessed 16/01/2014)

McGuire, A.L., Caulfield, T., and Cho, M.K. (2008). Research ethics and the challenge of whole-genome sequencing. Nat. Rev. Genet. 9, 152–156.

Tabor, H.K., Berkman, B.E., Hull, S.C., and Bamshad, M.J. (2011). Genomics really gets personal: how exome and whole genome sequencing challenge the ethical framework of human genetics research. Am. J.
Med. Genet. A. 155A, 2916–2924.

Williams, R. (2010). Genomics in our own hands. The Lancet. 9, 656–657.

Author Unknown (2013). FDA bans personal genetic test kit. BBC.
Avaiable: http://www.bbc.co.uk/news/technology-25100878 (accessed 16/01/2014)
Sources
Where it all began
medium.com
Roughly speaking ~700 megabytes
2007
NGS hits
Google's efforts to bring big data genomics to reality
With big data come big partners
Genomics and personal genetics demand constant cooperation with bioinformatics and data analysis experts
Still a bit mysterious
wikimedia.org
as an indicator of improvement of DNA sequencing techniques
Full transcript