Upload
malcolm-warner
View
231
Download
2
Tags:
Embed Size (px)
Citation preview
Overview
Introduction DNA Sequencing Circos Plot IDH1
Sequencing Genomes Examples of Sequenced Cancer Genomes Sequencing Disagreements Sequencing Proponents Small Scale Projects Impact Conclusions Future Research
Leading Causes of Death in US
Heart Disease: 631,636 Cancer: 559,888 Stroke (cerebrovascular diseases): 137,119 Chronic lower respiratory disease: 124,583 Accidents (unintentional injuries): 121,599 Diabetes: 72,449
Data for 2006 obtained from Centers for Disease Control and Prevention (CDC) (http://www.cdc.gov/nchs/fastats/lcod.htm)
Genetics and Genomics Timeline
http://www.nature.com/nature/journal/v422/n6934/full/nature01626.html
What is DNA Sequencing
DNA Made up of 3 billion chemical
building blocks (A, T, C, and G) DNA Sequencing
Process of determining the exact order of the building blocks that make up the DNA of the 24 different human chromosomes
Revealed the estimated 20,000-25,000 human genes within our DNA as well as the regions controlling them
http://www.scq.ubc.ca/a-monks-flourishing-garden-the-basics-of-molecular-biology-explained/
DNA Sequencing Process
http://www.ornl.gov/sci/techresources/Human_Genome/graphics/DNASeq.Process.pdf
Circos Plot
Circos is a software package for visualizing data and information
Used for identification and analysis of similarities and differences arising from comparisons of genomes
Ledford, Heidi. “The Cancer Genome Challenge”.
Previous Discovery
Mutation in the gene IDH1 found in 2006 study of 35 colorectal cancers
Not expected to be of importance
Changed only a lowly housekeeping enzyme involved in metabolism
13,000 other genes sequenced from each of 300 more samples
http://waynesword.palomar.edu/molecu1.htm
IDH1 Mutation Surfaced Again
12% of samples of glioblastoma multiforme (type of brain cancer)
8% of actue myeloid leukaemia samples
http://www.mir.wustl.edu/neurorad/internal.asp?NavID=92
http://www.cancerhelp.org.uk/type/aml/about/the-blood-and-acute-myeloid-leukaemia
Studying IDH1 Mutation
Studies showed the mutation changed the activity of isocirtrate dehydrogenase Caused a cancer-promoting
metabolite to accumulate in cells
Pharmaceutical companies hunting for a drug to stop the process
IDH1 mutation is the inconspicuous needle found in a veritable haystack of cancer-associated mutations thanks to high powered genome sequencing.
http://unitedcaremedical.com/services.shtml
Sequencing Genomes
Labs around the world are teaming up to sequence DNA from thousands of tumors as well as healthy cells from the same person
Nearly 75 cancer genomes have at least begun to be to sequenced and published
By the end of 2010 researchers expect to have over 100 cancer genomes fully sequenced
http://www.fhcrc.org/science/pacr/internships/index.html
Difficulties in Researching
Further the research goes the larger the “haystack”
Comparison of tumor cell to healthy cell reveals dozens of single-letter changes, or point mutations
Comparison also reveals repeated, deleted, swapped, or inverted sequences
http://nl.ijs.si/et/talks/esslli02/metadata.html
http://activerain.com/blogs/davidhitt
Difficulties
“The Difficulty is going to be figuring out hot to use the information to help people rather than to just catalogue lots and lots of mutations.” – Bert Voglestein, John Hopkins University
Clinically tumors can look the same but most differ genetically
http://archive.sciencewatch.com/sept-oct2003/sw_sept-oct2003_page1.htm
Distinguishing Mutation Data
Drivers – mutations that cause and accelerate cancers
Passengers – Accidental by-products and thwarted DNA-repair mechanisms
Distinguishing between the drivers and passengers is not always trivial
http://www.modified.com/motorsports/0203scc_subaru_us_rally_team_petter_solberg/photo_02.html
Finding Mutations
Mutations that pop up again and again
Identify key pathways that are mutated at different points
Finding more questions than answers
How do researchers decide which mutations are worthy of follow up and functional analysis? http://www.answersingenesis.org/home/area/
cfol/ch2-mutations.asp
World Collaboration
The International Cancer Genome Consortium Pilot Project 11 Countries to
sequence DNA 20 cancer types
500 tumor samples for each
Cost to sequence each cancer type = US$20 Million
http://www.jonessoda.com/wordpress/?m=200904
Contributing Countries
UNITED STATES OF AMERICA
BRITAIN
More than 6 types of cancer being sequenced
Ovarian Cancer Brain Cancer
Glioblastoma Multiforme (IDH1 Mutation found in 12%)
Lung Cancer Adenocarcinoma
Acute Myeloid Leukaemia (IDH1 Mutation found in 8%)
Colon Cancer Adenocarcinoma
Others
Breast Cancer ER-, PR-, HER-
Breast Cancer Lobular
Breast Cancer ER+, HER-
European Union Sponsored
http://www.state.gov/p/eur/ci/uk/
http://www.medicstravel.co.uk/countryhospitals/usacanada/usa_and_canada.htm
Contributing Countries
FRANCEAUSTRALIA
Breast Cancer HER2 overepxpressing
Liver Cancer Alcohol-associated
Renal-cell carcinoma European Union
Sponsored
Pancreatic Cancer Ductal
adenocarcinoma Ovarian Cancer
http://www.state.gov/p/eur/ci/fr/
http://www.state.gov/p/eap/ci/as/
Contributing Countries
CANADA CHINA Pancreatic Cancer
Ductal adenocarcinoma
Gastric Cancer
Germany• Pediatric Brain Cancer
– Medulloblastoma– Pilocytic Astrocytoma
• Oral Cancer– Gingivobuccal
India
http://www.thecommonwealth.org/YearbookHomeInternal/138389/
http://www.oiep.umd.edu/Training/chinaMap.html
http://geology.com/world/germany-satellite-image.shtml
http://www.state.gov/p/sca/ci/in/
Contributing Countries
ITALY JAPAN Rare Pancreatic
Cancers Enteropancreatic
endocrine Pancreatic exocrine
Liver Cancer Virus-
Associated
Spain• Chronic lymphocytic leukaemia
http://www.state.gov/p/eur/ci/it/ http://www.state.gov/p/eap/ci/ja/
http://www.state.gov/p/eur/ci/sp/
ICGC
The International Cancer Genome Consortium (ICGC), est. 2008, combined two older, large scale projects The Cancer Genome Project
Over 100 partial genomes and roughly 15 whole genomes. Tends to tackle over 2,000 more in the next 5-7 years
The US National Institutes of Health’s Cancer Genome Atlas (TCGA) Sequence up to 500 tumors for
each of 20 cancers over next 5 years
http://www.bfeedme.com/cancer-fighting-foods-spices/
http://www.icgc.org/
TCGA Pilot Project
The two groups in the TCGA are collaborating to sequence a subset of tumor samples (about 100) from each cancer type
The most promising areas of the genome will then be sequenced in the remaining 400 samples
From the Study
Larger sample numbers could provide driver mutations like the one in IDH1
Knowledge and study of these mutations could lead to developing new cancer therapies according to researchers
http://www.cancercompass.com/cancer-guide/complementary-therapies/complementary-therapies.html
“IF THERE ARE LOTS OF ABNORMALITIES OF A PARTICULAR
GENE, THE MOST LIKELY EXPLANATION IS OFTEN THAT THOSE MUTATIONS HAVE BEEN SELECTED FOR BY THE CANCERS
AND THEREFORE ARE CANCER-CAUSING.”
-Michael Stratton(Co-Director of the
Cancer Genome Project)
http://www.icr.ac.uk/research/research_profiles/2750.shtml
Challenging
IDH1 was first overlooked on the basis of the colorectal cancer data alone Search expanded to other cancers before
importance was revealed Some drivers are mutated at very low
frequency (less than 1% of the cancers) heavy sampling is needed to find these low
frequency drivers Sequencing 500 samples per cancer reveal
mutations present in as few as 3% of the tumors, but may still have important biological lessons Need to know in order to understand the overall
genomic landscape of cancer
Another Popular Approach
Look for mutations that cluster in a pathway
In an analysis of 24 pancreatic cancers 12 identified signaling
pathways had been altered Very difficult approach
Pathways overlap and boundaries not clear
Many pathways that are obtained using data from different animals or cell types do not always match up with what’s found in human tissue
http://mkweb.bcgsc.ca/circos/
There is A Lot More to Do
Distinguishing between drivers and passengers gets increasingly harder as researchers are beginning to sequence entire tumor genomes
Only a fraction of the existing cancer genomes have been completely sequenced
http://www.lbl.gov/Science-Articles/Archive/sabl/2007/Jan/breast-cancer-genome.html
Protein and Non-Protein Coding Regions
Most cancer genome sequences are only covering the exome Keep costs low Directly codes for protein (easiest
to interpret) Importance of mutations found
in the non-protein coding depths More challenging Scientists don’t know what
function these regions usually serve
Majority of mutations
http://pandasthumb.org/archives/2005/12/another-example.html
Cancer Genomes Coming Fast
Some Full Genome have been Sequenced Small-cell lung carcinoma
(Type of Lung Cancer) Metastatic melanoma (Type
of Skin Cancer) Basal-like breast cancer
(Type of Breast Cancer) Only exome has been
sequenced Glioblastoma multiforme
(Type of Brain Cancer)http://www.mir.wustl.edu/neurorad/internal.asp?NavID=92
http://www.mydochub.com/skin-cancer.php
http://www.asa3.org/ASA/topics/Youth%20page/index.html
Lung CancerCancer: Small-Cell Lung Carcinoma
Sequenced: full genome Source: NCI-H209 cell line Point mutations: 22,910 Point mutations in gene regions: 134 Genomic rearrangements: 58 Copy-number changes: 334
Highlights:Duplication of the CHD7 gene confirmed in two other small-cell lung carcinoma cell lines
http://scienceblog.cancerresearchuk.org/2009/12/16/skin-and-lung-cancer-genomes-are-truly-groundbreaking/
Skin CancerCancer: Metastatic Melanoma
Sequenced: full genome Source: COLO-829 cell line Point mutations: 33,345 Point mutations in gene regions: 292 Genomic rearrangements: 51 Copy-number changes: 41
Highlights:Patterns of mutation reflect damage by ultraviolet light
Ledford, Heidi. “The Cancer Genome Challenge”.
Breast CancerCancer: Basal-Like Breast Cancer
Sequenced: full genome
Source: primary tumor brain metastasis tumors transplanted into
mice Point mutations:
27,173 in primary 51,710 in metastasis 109,078 in transplant
• Point mutations in gene regions:– 200– 225– 328
• Genomic rearrangements: 34
• Copy-number changes:– 155– 101– 97
• Highlights:Patterns of mutation reflect damage by ultraviolet light
Ledford, Heidi. “The Cancer Genome
Challenge”.
Brain CancerCancer: Glioblastoma Multiforme Sequenced: exome (no complete
Circos plot) Source:
7 patient tumors 15 tumors transplanted into mice
Genes containing at least one protein altering mutation: 685
Genes containing at least one protein altering point mutation: 644
Copy-number changes: 281
Highlights:Mutations in the active site of IDH1 have been found in 12% of patients
http://www.mir.wustl.edu/neurorad/internal.asp?NavID=92
Finding all mutations
Very important to find all, even in non-protein, regions Maybe none of these mutations could pertain
to the causation of cancer Some could Only way to find out is to systematically
investigate them
Researcher Disagreements
Some researchers Argue against fully sequencing genomes Cost of projects outweighs the
benefits Prices will drop due to technology
advances in next few years, why not wait?
In the mean time Mutations that affect how many
copies of a gene are found in a genome Cheaper to assess Provide more intuitive insight into
biological processes http://www.shutterstock.com/pic-2585059/stock-photo-costs-outweigh-benefits.html
Sequencing Proponents
Changes in genome copy number detection Array-based technology
Fast and relatively inexpensive Sequencing
Higher-resolution snapshot of regions The higher resolution can provide
More precision in mapping boundaries Ability to catch tiny duplications or deletions
that an array may not detect
Array-Based Process
http://www.nature.com/scitable/content/diagram-of-the-microarray-based-comparative-genomic-41020
Don’t Wait to Sequence
A lot of small scale hospitals are investing millions of dollars into cancer sequencing projects (e.g.) St. Jude Children’s Research
Hospital Proponents don’t want to wait
The real work starts after the sequencing is over
Determining what these mutations are doing Old-fashioned biology and
experimental analysis
http://www.stjude.org/stjude/v/index.jsp?vgnextoid=f2bfab46cb118010VgnVCM1000000e2015acRCRD
http://www.the-aps.org/education/k-12misc/careers.htm
US National Cancer Institute
Two 2-year projects Develop high-throughput methods
Test how the mutations identified by the TCGA pilot project affect cell function
Aim to pull needles from the haystack and make since of them (like the IDH1 mutation)
http://www.bfeedme.com/cancer-fighting-foods-spices/
US National Cancer Institute Projects
Dana-Farber Cancer Center (Boston) Systematically amplify
and reduce the expression of genes of interest in cell cultures
Cold Spring Harbor Laboratory (New York) Study cancer-associated
mutations using tumors transplanted into mice
http://www.gbaohn.org/files_for_update/Dana%20Farber-job.htm
http://www.scivee.tv/user/7054
Other Large Scale Projects
Asses effects of deleting each gene in the mouse genome Learn more about the
normal function of genes that are mutated in cancer
http://thecoloringspot.com/animals/animals-set-7.html
Impact
Global Cancer is a world-wide disease
Cancer Patients New Technology New Treatment Processes
Researchers More grants to make new advances
Conclusions
Sequencing tumor DNA genomes can lead to finding cancer-causing gene mutations
Very challenging to pinpoint gene mutations that are cancer-causing Very high sample numbers
Sampling and sequencing full cancer genomes is extremely expensive Some opponents think the cost outweighs the
benefits right now A lot of people think the cost is worth it, because
there is a lot more work to do after sequencing, so we should not wait for prices to come down
Future Research
Better technology for making the sequencing equipment to bring costs down
New technology to detect mutations Complete Full genome sequences for all
cancers Developing ways to stop or kill these
mutations but leave the healthy cells unharmed Nanotechnology (nanopharmaceuticals could
have an impact here)
References
Ledford, Heidi. “The Cancer Genome Challenge”. Nature Journal. Vol 464. 15 April 2010. p. 972-974. Macmillan Publishers Limited. 2010
Human Genome Project Information. Facts About Genome Sequencing. Accessed: April 29, 2010. Last modified: September 19, 2008. http://www.ornl.gov/sci/techresources/Human_Genome/faq/seqfacts.shtml.
Krzywinski, M. et al. Circos: an Information Aesthetic for Comparative Genomics. Genome Res (2009) 19:1639-1645
Francis S. Collins1, et al. “A vision for the future of genomics research”. Nature Publishing Group. 2010. Accessed April 30, 2010. http://www.nature.com/nature/journal/v422/n6934/full/nature01626.html
Circos Website. Acessed April 30, 2010. http://mkweb.bcgsc.ca/circos/