Transcript Personal genomics

Maryam Nazir
Personal Genomics:
Branch of genomics
concerned with the
sequencing and analysis of
the genome of an individual
 Once sequenced, it can be
compared with published
literature to determine
likelihood of disease risk or
trait expression
 Main aim: to inform
preventative action

Techniques
SNP arrays
 Partial sequencing
 Whole genome sequencing

 Can be used to evaluate:
○ SNPs
○ Indels
○ Large SVs
○ New sequences
○ Haplotypes
Cost of Sequencing

Continual development of new sequencing
technologies, next-generation sequencing
 Increased speed
and reduced cost
of sequencing
 Now possible to
offer genetic
testing to
consumers
Personal Genome Project
Large, long-term study
 Aim: To sequence and publicize the
complete genomes and medical records
of 100,000 volunteers
 All data will be available in the public
domain
 Purpose: To enable research in personal
genomics and personalized medicine


Each participant:
 Full DNA sequence
 Extensive phenotype information
○ Medical records
○ MRI images
○ Other measurements

Volunteer criteria:




Permanent residents of the US, Canada, UK
Able to submit tissue and/or genetic samples
Informed consent
“no promise of anonymity and data return”
Personalized Medicine



A model of medicine which
proposes the customization of
healthcare with medical decisions
being tailored to the individual
patient
Goal: To individualize prevention,
diagnosis, and treatment--by use of
genetic differences as markers
Disease risk
 >2500 diseases have predictive
medical value
○ Can be recommended for genetic tests
for single genes or whole genome
sequencing

Gene signatures
 Gene expression pattern in a cell can be uniquely
characteristic of a condition
 Risk assessment, diagnostic & prognostic applications
 Match patients and treatments
Pharmacogenomics
Field that analyzes how
genetic makeup affects an
individual’s response to
drugs
 Want to tailor treatments for
patients based on their
genetics

Cancer genomics
Main goal: to identify genes, or gene
signatures, that may provide insights into
cancer diagnosis, predicting clinical
outcomes or targets for cancer therapies
 Tumour sequence is compared to a
matched normal tissue
 Personalized cancer treatments
 Genetic profiles of tumours part of
recommended evaluation for certain
cancers (colon, breast, lung...)

Nutrigenomics
Study of how individual
genetic variation affects a
person’s response to
nutrients and impacts their
risk of nutrition-related
chronic diseases
 People respond differently to
certain foods

Human Ancestry
Looks at a person’s DNA at
specific locations compares
results to defined groups
 Mitochondrial DNA

 Traces direct maternal line

Y-Chromosome DNA
 Traces a male’s direct paternal
line

Autosomal DNA
 Tests all ancestry, shows how
closely a person is related to
others
Commercial Services

Gentle
 most comprehensive genetic test currently
on the market
 screens for >1700 genetic conditions
 predicts response to certain medications

HelloGenome (Korea)
 genotyping (SNP chips) and full genome sequencing
(Solexa machines)

Illumina, Sequenom, Oxford Nanopore
Technologies, Pacific Biosciences, Complete
Genomics, 454 Life Sciences
 commercializing full genome sequencing
 do not provide any genetic analysis or counselling
component

Positive Bioscience
(Mumbai)
 Next-generation sequencing
 To determine most beneficial
cancer treatment for patients

Nutrigenomix
 SNP genotyping
 Each gene tested is involved in
the way the body processes a
certain dietary component
 With information obtained, can
tailor the diet to prevent
chronic diseases (cancer, heart
disease, type 2 diabetes)
-ex. Caffeine
 Only available through
registered dieticians
 $385
23andMe
Mail order “spit kits”
 SNP genotyping (DNA array)
 Assessment of:

 inherited traits
 ancestry
 genetic risk for >240 diseases and common
conditions
Information presented in user profile
 $99

Ethical Issues

Personal privacy & misuse of information
 Whose responsibility?
 Who owns the genomic info?

Genetic discrimination
 Discrimination based on information obtained
from an individual’s genome
 Genetic Information Nondiscrimination Act
(U.S.)
○ Prevents discrimination by health insurers and
employers, but does not apply to life insurance
or long-term care insurance

Psychosocial stress
 Consequence of knowing one’s predisposition
to disease
 Know risk, have no cure
Other Issues
How relevant are the
results of commercial
services? Clinical utility?
 Education needed in
interpreting results and
communicating genetic
information

 For the average
person/patient
 For doctors
 For the public & media
 genetic counselling
Conclusions

A fairly large number of loci that are known to
be predictive of disease have been identified
 Many of these can be clinically targeted
Immediate applications are limited at present
 The promise of personal genomics lies in the
future

 Must first build a database of personal genomes

Many people envision a future where personal
genomic information is one of the essential
tools used to tailor one’s medical care
References

Offit, Kenneth. "Personalized medicine: new genomics, old
lessons." Hum Genet. 130. (2011): 3-14.

Snyder, Michael, Jiang Du, and Mark Gerstein. "Personal
genome sequencing: current approaches and
challenges." Genes Dev. 24. (2010): 423-431.

Werner, Thomas. "Next generation sequencing in functional
genomics." Briefings in Bioinformatics. 2.5 (2010): 499-511.

Cooper, David N., et al. "Genes, Mutations, and Human
Inherited Disease at the Dawn of the Age of Personalized
Genomics." Human Mutation. 31.6 (2010): 631–655.

Chin, Lynda, Jannick N Andersen1, and P Andrew Futreal.
"Cancer genomics: from discovery science to personalized
medicine." Nature Medicine. 17.3 (2011): 297-303.