Back
to BiopharmaceuticalGlossaries.com
You are here Biopharmaceutical/
Genomic
glossary
homepage > Biology > Basic genetics & genomics
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
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
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
Particularly for students & teachers
- but potentially useful
for anybody
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
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 Understanding the Human
Genome Project, NHGRI, 2008 http://www.genome.gov/25019879 Virtual Cell
Webpage
http://www.ibiblio.org/virtualcell/
Whitehead Institute
Teacher Program, MIT, US http://www.wi.mit.edu/programs/teacher/index.html 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 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?
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
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 Useful metaphor? Grain of rice on a chessboard, doubles
each square. Genome sizes – how many 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.
Gene expression informatics
What does a microarray look like?
https://commons.wikimedia.org/wiki/File:DNA_microarray.svg
True microarray story 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
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
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
<%end if%>
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.
Exploring Our Molecular Selves, National Human
Genome Research Institute, NIH, US http://www.genome.gov/Pages/EducationKit/
Online, multi-media educational kit
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.
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.
Neuroscience
for Kids, Eric H. Chudler, Univ. of Washington, US 2001 http://faculty.washington.edu/chudler/neurok.html
All about the Human Genome Project, NHGRI, 2008 http://www.genome.gov/10001772
Your Genome.org,
Sanger Centre
https://www.yourgenome.org/
Topics include In the Cell, Methods &
Technology, Targeting disease, Society & Behaviour, Animals & Plants
American Institute of Biological Sciences, Genomics
What potential does understanding our genetic playbook hold? http://www.actionbioscience.org/genomics/
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
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.
There isn’t enough matter in the universe to make all the
possible combinatorial chemistry compounds.
Combinatorial
libraries & synthesis
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."
NCBI Databases, National Center for Biotechnology Information, US
Dec 2017
https://www.ncbi.nlm.nih.gov/genbank/statistics/
Microarrays of 7,000 genes = 24 million pairwise
comparisons.
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."
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
Back to GenomicGlossaries.com