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Basic  genetics & genomics what's the difference? 
      Evolving Terminology for Emerging Technologies
  Suggestions? Comments? Questions? 
Mary Chitty MSLS  mchitty@healthtech.com
Last revised July 09, 2019

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

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.

Broad Institute, Cambridge MA, US  for students https://www.broadinstitute.org/for-students  for Educators https://www.broadinstitute.org/for-educators  For the Public  https://www.broadinstitute.org/community/public
For Scientists  https://www.broadinstitute.org/for-scientists
  
Folding@home, Stanford Univ. https://foldingathome.org/  a distributed computing project for disease research that simulates protein folding, computational drug design, and other types of molecular dynamics. As of today, the project is using the idle resources of personal computers owned by volunteers from all over the world. Thousands of people contribute to the success of this project.

Genetics and Rare Diseases Information Center, NIH  Teaching Resources https://rarediseases.info.nih.gov/guides/pages/128/teaching-resources

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.

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 

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, Sanger Centre  https://www.yourgenome.org/   Topics include In the Cell, Methods & Technology, Targeting disease, Society & Behaviour, Animals & Plants

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/ 

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.

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. ...Though 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, https://publications.nigms.nih.gov/structlife/ reveals how structural biology provides insight into health and disease and is useful in developing new medications.  PDF, video

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 https://www.genome.gov/genetics-glossary

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.  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 4th ed, 2000 https://www.ncbi.nlm.nih.gov/books/NBK21475/   The more we learn about the structure, function, and development of different organisms, the more we recognize that all life processes exhibit remarkable similarities. Molecular Cell Biology concentrates on the macromolecules and reactions studied by biochemists, the processes described by cell biologists, and the gene control pathways identified by molecular biologists and geneticists. In this millennium, two gathering forces will reshape molecular cell biology: genomics, the complete DNA sequence of many organisms, and proteomics, a knowledge of all the possible shapes and functions that proteins employ.

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

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 Also appeared in Trends in Plant Science, 6(5): 195- 196, 2001.

GenBank grows at an exponential rate, From 1982 to the present, the number of bases in GenBank has doubled approximately every 18 months.
NCBI Databases, National Center for Biotechnology Information, US   Dec 2017 https://www.ncbi.nlm.nih.gov/genbank/statistics/

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

What does a microarray look like?  https://commons.wikimedia.org/wiki/File:DNA_microarray.svg

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:   Newly created information is stored in four physical media � print, film, magnetic and optical � and seen or heard in four information flows through electronic channels � telephone, radio and TV, and the Internet. This study of information storage and flows analyzes the year 2002 in order to estimate the annual size of the stock of new information recorded in storage media, and heard or seen each year in information flows. Where reliable data was available we have compared the 2002 findings to those of our 2000 study (which used 1999 data) in order to describe a few trends in the growth rate of information.  Lyman, Peter and Hal R. Varian, "How Much Information", 2003 http://groups.ischool.berkeley.edu/archive/how-much-info-2003/  

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 drug discovery and diagnostics
Developing a drug is a risky and hugely expensive undertaking. Some 90% of publicly traded biopharmaceutical companies are not expected to make a profit this year, and, profitable or not, such companies require massive investments in research and development. How massive? The most thorough study of what it costs to a develop single new drug was conducted by three PhD economists: Joseph A. DiMasi, director of economic analysis at the Tufts Center for the Study of Drug Development, Henry G. Grabowski of Duke, and Ronald W. Hansen of the University of Rochester. Their papers on the subject go back to 1979 and have been cited by other researchers, including those of the U.S. government, to analyze policy questions. DiMasi and Grabowski wrote the chapter, “R&D Costs and Returns to New Drug Development: A Review of the Evidence,” in The Oxford Handbook of the Economics of the Biopharmaceutical Industry.  Tufts Research, Published in 2016, Examined 106 Drugs at Random  The most recent estimates of the three researchers were published in the May 2016 issue of the Journal of Health Economics. They looked at the research and development costs of 106 randomly selected drugs from a survey of 10 pharmaceutical firms. These data were used to estimate the average pre-tax cost of new drug and biologics development. The costs of compounds abandoned during testing were linked to the costs of compounds that obtained marketing approval.  The researchers determined that the average out-of-pocket cost per new compound approved by the Food & Drug Administration was $1.4 billion. http://www.cost-of-health-carenews.com/our-blog/issue-no-21-what-it-costs-to-make-a-pill

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

Cost per raw megabase of DNA Sequence, NIH NHGRI 2001-2017

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

How to look for other unfamiliar  terms