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Basic biopharmaceutical genetics & genomics what's the difference?
      Evolving Terminology for Emerging Technologies
  Suggestions? Comments? Questions?  mchitty@healthtech.com
Last revised October 29, 2013

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Related glossaries include Ethics, Molecular Medicine, Genomics  See especially complex, Mendelian genetics, penetrance, polygenic and post- genomic, Technologies overview especially disruptive technologies, emerging technologies, enabling technologies, nonlinear.

How does genomics differ from genetics?
Genetics looks at single genes, one at a time, as a snapshot.  Genomics is trying to look at all the genes as a dynamic system, over time, to determine how they interact and influence biological pathways, networks and physiology, in a much more global sense. A dynamic process, 2D vs. 3D and 4D. 

Genetics is much more linear than genomics, complicated but not as complex as genomics.  There is a whole lot more we need to understand, some of  which we are only beginning to get glimpses of.  It is exciting, but humbling to realize how much remains to be learned.

Doing (a few of) the numbers: The scale of genomics and bioinformatics

Genomics: a quick tour

Current bioinformatics and chemoinformatics methods of analysis and interpretation are having difficulty keeping up with the rapid growth in sequencing data. New technologies such as microarrays (and advances in existing ones such as mass spectrometry) are leading to rapid growth in new terminology. An even bigger  challenge then new vocabulary is the conceptual shift from classical genetics to a more dynamic genomic “big picture” understanding of genomics, functional genomics, proteomics and structural genomics.

DNA sequences are essentially linear snapshots. In the human genome less than 2 % of  the DNA is genes. To understand genes' functions we need to look at 3D protein structures, and to begin to decipher physiological processes we need to examine changes in gene and protein expression over time (4D).  Our knowledge of genetic variations is still sketchy and crucial to an understanding of the role these differences play in pharmacogenomics.  Will genomic approaches lead to faster drug discovery and development? How can we sort out the incremental advances from the true paradigm shifts without experiencing information overload?

Biology for non-biologists, some particularly for students and teachers
Exploring Our Molecular Selves, National Human Genome Research Institute, NIH, US http://www.genome.gov/Pages/EducationKit/ Online, multi-media educational kit

Genome Glossary http://www.ornl.gov/sci/techresources/Human_Genome/glossary/ 

Intute: Bioresearch, University of Nottingham, UK  http://www.intute.ac.uk/healthandlifesciences/bioresearch/  Best of the web.

Particularly for students & teachers  - but potentially useful for anybody
Access Excellence, National Health Museum, US  http://www.accessexcellence.org/ Provides high school biology and life science teachers access to their colleagues, scientists, and critical sources of new scientific information. Originally developed and launched by Genentech Inc.

Bio-Interactive, Howard Hughes Medical Institute http://www.biointeractive.org/

DNA Learning Center, DNA Lab, Cold Spring Harbor Laboratory, US  http://vector.cshl.org/  A clearinghouse for information on DNA science, genetic medicine, and biotechnology, to provide an interactive learning environment for students, teachers, and nonscientists, extending the Laboratory's traditional research and postgraduate education mission to the college, precollege, and public levels.

Educational Outreach Program, Broad Institute, Cambridge MA, US http://www.broadinstitute.org/outreach/education 
   Quick Links for students & educators http://www.broadinstitute.org/quicklinks/quicklinks-students-and-educators 

Folding@home, Stanford Univ. http://www.stanford.edu/group/pandegroup/folding/education/index.html An opportunity for teachers and students to participate in scientific research. Organic chemistry, molecular modeling and distributed computing (and proteomics).

Genetics Education Center, Univ. of Kansas Medical Center, 2002  http://www.kumc.edu/gec/  For educators interested in human genetics and the human genome project.

Geospiza Education section http://www.geospiza.com/education/  Interactive learning tools for students

Exploring the Nanoworld, University of Wisconsin,  http://www.mrsec.wisc.edu/edetc/index.html 2004.

myDNA Teacher Guide http://www.dnai.org/teacherguide/guide.html 

Neuroscience for Kids, Eric H. Chudler, Univ. of Washington, US 2001 http://faculty.washington.edu/chudler/neurok.html

Understanding the Human Genome Project, NHGRI, 2008 http://www.genome.gov/25019879 
All about the Human Genome Project, NHGRI, 2008  http://www.genome.gov/10001772 

User's guide to the Human Genome, Nature Genetics, 32 (1): supp 2002 http://www.nature.com/cgi-taf/DynaPage.taf?file=/ng/journal/v32/n1s/index.html 

Virtual Cell Webpage http://www.ibiblio.org/virtualcell/ 

Whitehead Institute Teacher Program, MIT, US http://www.wi.mit.edu/programs/teacher/index.html 
   

Your Genome.org
- Beginner, Sanger Centre, UK http://www.yourgenome.org/dgg/ 

Science literacy: Project 2061, American Association for the Advancement of Science http://www.project2061.org/  A long- term initiative working to reform K-12 science, mathematics, and technology education nationwide.

Good starting points for almost anyone wanting to know more about genomics
American Institute of Biological Sciences, Genomics What potential does understanding our genetic playbook hold?  http://www.actionbioscience.org/genomics/ 

Beginner's guide to molecular biology, Molecular Biology Notebook, Rothamstead Research, UK, 2004 http://www.rothamsted.ac.uk/notebook/courses/guide/ 

Biointeractive, Howard Hughes Medical Institute http://www.biointeractive.org/ Virtual labs, animations, virtual museums, web videos, click and learn tutorials.

BBC News In-depth Human Genome, UK http://newsvote.bbc.co.uk/low/english/in_depth/sci_tech/2000/human_genome/default.stm Current news from the UK, articles on what the genome can do for you, and archives on completed genomes.

European Initiative for Biotechnology Education,  EIBE, European Commission http://www.rdg.ac.uk/EIBE/home.html Lesson units and teaching approaches.

Human Genome Project Information Archive 1990-2003, Oak Ridge National Laboratory, DOE, US  http://web.ornl.gov/sci/techresources/Human_Genome/index.shtml Completed in 2003, the Human Genome Project (HGP) was a 13-year project coordinated by the U.S. Department of Energy (DOE) and the National Institutes of Health. During the early years of the HGP, the Wellcome Trust (U.K.) became a major partner; additional contributions came from Japan, France, Germany, China, and others. ...hough the HGP is finished, analyses of the data will continue for many years.

Meet the Decoders, Nova, PBS, US. http://www.pbs.org/wgbh/nova/genome/decoders.html Interviews with Francis Collins (NHGRI), Craig Venter, Eric Lander (Whitehead Institute)

Genome News Network, Center for the Advancement of Genomics (TCAG)    http://www.genomenewsnetwork.org/   Online news, 2000 - present.

Structures of Life, National Institute of General Medical Sciences, 2000- 2001.  http://www.nigms.nih.gov/news/science_ed/structlife.pdf.

Welcome to the NCBE, National Centre for Biotechnology Education (NCBE), UK http://www.ncbe.reading.ac.uk/ Listservs and other teacher resources, protocols for classrooms and school labs, GM food, lab safety, links. 

What's it going to mean to me? 
Our Molecular Selves, National Human Genome Research Institute, US http://www.genome.gov/25520211   
NHGRI Glossary of genetic terms http://www.genome.gov/glossary/index.cfm

Genomes to Life, US Department of Energy http://doegenomestolife.org/

Your genes, your choices: Exploring the choices raised by genetic research Catherine Baker, part of the AAAS Science + Literacy for Health Project http://ehrweb.aaas.org/ehr/books/index.html

Patient resources links to websites for general patient and disease related information.

Sources for more information
A useful accessible guide to technology is William Bains' Biotechnology A-Z, Oxford University Press, 2003. About 400 entries/ definitions.  To order: http://www.oup.co.uk/isbn/0-19-852498-6  Particularly strong in bioprocessing and manufacturing technologies, and environmental applications, which are not areas of major emphasis in these glossaries.

Lodish, Harvey, Molecular Cell Biology 4e, WH Freeman & Co.,1999 and website. http://www.whfreeman.com/lodish/

 Doing (a few of) the numbers: Genomics and bioinformatics

Drug discovery 
There isn’t enough matter in the universe to make all the possible combinatorial chemistry compounds. Combinatorial  libraries & synthesis glossary

Useful metaphor? Grain of rice on a chessboard, doubles each square.

Genome sizes – how many genes?
Oxford English Dictionary quotation in the entry for "genome" Scientific American Oct. 1970 "The human genome consists of perhaps as many as 10 million genes."

Feb. 2001 Science and Nature working drafts t Human genome issues estimated 30K- 40K human genes (much lower than expected), but alternative splicing (in genes) is much higher, producing more variant proteins. Compared to proteins, genes were easy.  Proteomics is the next step. 

The barley and wheat genomes have more genes than the human genome. Joachim Messing, "Do Plants have more genes than people?" HMS Beagle, June 21, 2001 http://news.bmn.com/hmsbeagle/105/viewpts/op_ed  Also appeared in Trends in Plant Science, 6(5): 195- 196, 2001.

GenBank grows at an exponential rate, with the number of nucleotide bases doubling approximately every 14 months. Currently, GenBank contains more than 17 billion bases from over 100,000 species. [NCBI Databases, National Center for Biotechnology Information, US " Revised March 22, 2002] http://www.ncbi.nlm.nih.gov/Database/index.html See chart of growth 1982- 2000.

Gene expression informatics
Microarrays of 7,000 genes = 24 million pairwise comparisons.

What does a microarray look like?  http://mathforum.org/mam/02/images/Microarray.jpg

True microarray story
Bioinformatician/statistician "For statistical significance you should replicate this microarray experiment 100 times. What were you planning on?"
Research biologist: "Once."
Bioinformatician/statistician: "So we compromised on twice." 

informatics:  The world produces between 1 and 2 exabytes of unique information per year, which is roughly 250 megabytes for every man, woman, and child on earth. An exabyte is a billion gigabytes, or 1018 bytes. Printed documents of all kinds comprise only .003% of the total. Magnetic storage is by far the largest medium for storing information and is the most rapidly growing, with shipped hard drive capacity doubling every year. [Lyman, Peter and Hal R. Varian, "How Much Information", 2000. Retrieved from http://www.sims.berkeley.edu/how-much-info on [May 19, 2002] Executive summary 

1 Megabyte: A small novel OR a 3.5 inch floppy disk; 2 Megabytes: A high resolution photograph;  5 Megabytes: The complete works of Shakespeare OR 30 seconds of TV- quality video;  {Powers of ten, How much information, UC- Berkeley, US, 2000 [retrieved May 19, 2002] http://www.sims.berkeley.edu/research/projects/how-much-info/datapowers.html

Really big numbers  Computers & computing peta (exa, zetta, yotta), petaflop, teraflop 

Really small numbers  Ultrasensitivity glossary atto, femto, micro, nano, pico, yocto, zepto 

Perspectives: Powers of Ten National High Field Magnetic Lab, Florida State Univ. US  http://micro.magnet.fsu.edu/optics/activities/students/perspectives.html

Economics of genomics
Human genome sequencing
  When the HGP was initiated [1990], vital automation tools and high-throughput sequencing technologies had to be developed or improved. The cost of sequencing a single DNA base was about $10 then; today, sequencing costs have fallen about 100-fold to $.10 to $.20 a base and still are dropping rapidly. [DOE, Human Genome Project and the Private Sector, 2002]  http://www.ornl.gov/hgmis/project/privatesector.html

1990@ $10/base = $3 billion.  2002 @ $.10/base = $3 million 

Nov. 30, 2001 – The Tufts Center for the Study of Drug Development today announced that the average cost to develop a new prescription drug is $802 million. Joseph DiMasi, Center for the Study of Drug Development, Tufts Univ. http://csdd.tufts.edu/NewsEvents/RecentNews.asp?newsid=6 

During the entire decade of the 90s, drugs that accounted for about $17 billion in sales went off patent. The next five years will see drugs with sales of $19 billion lose their patents, according to data from brokerage UBS PaineWebber.  Sam Jaffe "Biotech- Big Pharma Betrothals Declining" Scientist 16 (14): 57 July 8, 2002

Useful metaphor Sailing and tacking - getting there as quickly as possible: Straight ahead stops dead, tacking from side to side is the fastest way to get where you’re going 

Bibliography

Alpha glossary index

How to look for other unfamiliar  terms


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