Biology 116-Biotechnology
Ralph M. Sinibaldi, Ph.D..
Course Goals Technical training for research, development
or production positions in biotech Conceptual training in molecular biology and
biotechnology Biotech Industry overview Soft skill training
• Resumes• Interviews• Project teams and teamwork
Learning Outcomes Describe the science of biotechnology and identify its product and
company domains Give examples of careers and job responsibilities associated with
biotechnology Understand and apply safety considerations and lab etiquette Describe how scientific methodologies are used to conduct experiments
and develop products Understand and apply rules of documentation and intellectual property Describe what intellectual property is and why it is important in
biotechnology Understand regulatory compliance and what agencies are responsible for
it Describe the Human Genome project and be able to discuss its
implications
Vocabulary
• Insulin – a protein that facilitates the uptake of sugar into cells from the blood• DNA – abbreviation for deoxyribonucleic acid, a double-stranded helical
molecule that stores genetic information for the production of all of an organism’s proteins
• Recombinant DNA (rDNA) technology – cutting and recombining DNA molecules
• Polymerase chain reaction (PCR) – a technique that involves copying short pieces of DNA and then making millions of copies in a short time
• Cloning – method of asexual reproduction that produces identical organisms• Fermentation – a process by which, in an oxygen-deprived environment, a
cell converts sugar into lactic acid or ethanol to create energy• Diabetes – a disorder affecting the uptake of sugar by cells, due to
inadequate insulin production or ineffective use of insulin• Proteases – proteins whose function is to break down other proteins• Antibodies – proteins developed by the immune system that recognize
specific molecules (antigens)• Pharmaceutical – relating to drugs developed for medical use
Vocabulary• Research and development (R&D) – refers to the early stages in product
development that include discovery of the structure and function of a potential product and initial small-scale production
• Pure science – scientific research whose main purpose is to enrich the scientific knowledge base
• Virus – a particle containing a protein coat and genetic materials (either DNA or RNA) that is not living and requires a host to replicate
• Applied science – the practice of utilizing scientific knowledge for practical purposes, including the manufacture of a product
• NIH – abbreviation for National Institutes of Health; the federal agency that funds and conducts biomedical research
• CDC – abbreviation for Centers for Disease Control and Prevention; national research center for developing and applying disease prevention and control, environmental health, and health promotion and education activities to improve public health
• DNA fingerprinting – an experimental technique that is commonly used to identify individuals by distinguishing their unique DNA code
“New technology is neither inherently good or harmful, this is determined by how man chooses to use the technology”
What is Biotechnology?
Biology Technology
Defining Biotechnology
Biotechnology is defined as the study and manipulation of living things or their component molecules, cells, tissues, or organs.
Biotechnology Business and Business Strategy
Fact Most new Biotech
Companies Ultimately Fail
Domains of Biotechnology. The major domains of biotechnology include 1) industrial and environmental; 2) medical/pharmaceutical; 3) agricultural; and 4) diagnostic/research
Types of Companies Product Development
• Advantages– Therapeutic products with large markets– Patent protection– High gross margins
• Disadvantages– High risk– Long development times
Platform Technologies• Advantages
– Shorter development times– Lower risk
• Disadvantages– Highly competitive with ever changing technology
Reagent• Advantages
– Short development time– High profit margins
• Disadvantages– May not be proprietary– Manufacturing costs driven
Service• Advantages
– No manufacturing– Can be highly profitable
• Disadvantages– Can underestimate costs
Types of Companies
Type of companies Equipment or Instruments
• Advantages– Proprietary– Can bundle with associated reagents
• Disadvantages– Significant capital investment– Lower margins on instruments
Starting a Company An Idea or a
Technology Projected product(s)
or service(s) Market Analysis Business Plan
Funding • Seed round
– Friends & Family– Early Venture Capital Investor– Angel Investor(s)
• “A” round– Venture Capital– Angel Investors
• “B” Round– Venture Capital– Corporate Investors or
Partners• “C” Round• Exit Strategy
– IPO or Acquisition
Business Plan Summary-two pages Market Opportunity Company background- stage
& type Market
• Market analysis• Competitors
Technology• Proof of concept• Similar technologies• Expert opinions
Intellectual property• Patent applications• Potential conflicts
Development Plan Marketing Plan
• Distribution Management
• Org chart• Bios of Principals
Appendices
Role of People Corporate structure Skill base of employees Building the right team Human resources system
Technology Publications Patents Proof of concept for components Breadboard Full Working prototype
Types of Finance Debt Financing
• Loans • Credit
Equity Financing• Private stock
– Friends & family– Private investors– Angel Investors– Venture Capital funds– Corporate partners
Other Sources of Funding Grants
• SBIR– NIH, NSF, USDA, NASA, NIST
• Stage I- $100,000.00• Stage II- $750,000.00 to 1 million
– ATP- 2 million up to 32 million– DARPA- national defense applications
Corporate partnerships• Marketing & Distribution relationship• Equity
What appeals to investors Technology Business Plan Management Team Multiple Products
Compensation Salary Bonus -10 to 30 % of salary
• Must achieve aggressive goals Stock options
• Founder’s• Employee
Corporate Structure Hierarchical
Manager Manager
CCost accountant
Comptroller
XCFO
Supervvisor
Manager
DDirector of Genomics
Manager
FDirector of Mol Biol
Manager
GDirector of Chemistry
BVP of Life Science
YCSO
Supervisor
Manager
VDirector of Optics
Manager Manager
Director of Sotware
Manager
Director of Materials
AVP of Engineering
ZCTO
CEO
Corporate Structure-Matrix
Type Name HereCFO
Project ManagerProject Team A
Project ManagerProject Team B
Project ManagerProject team C
Type Name HereCSO
CEO
Corporate Structure-Hybrid Hierarchical & Matrix Combined
• Departmental Organization• Multidisciplinary Project Teams
Decision Making Technology-based
• Research• Manufacturing
Resource-based Marketing-based
Sustainable Business Reducing Chances
• Large and Unpredictable Capital Requirements
• Long Product Development Cycles
• Regulatory Issues with Product
• Rapidly Changing Market Forces
• High Probability of Late Stage Product Failure
• Rare Instances of Sustained Profits
Increasing Chances• Capital Requirements Kept
Low• Well-Defined, Predictable
Business Milestones • Clear, Market-Oriented
Business Plan• Critical Mass to
Successfully Compete• Experienced Management
Relevant to Strategy Being Pursued
Evolution of Company Production-based Technology-based Market-based
Marketing SWOT analysis Strengths Weaknesses Opportunities Threats
Safety
Safety Values Safety is not just a priority but a value Safety is an unwritten rule, a special
norm, the workers should follow in all circumstances
It is a value that is never questioned or compromised
Safety Habits Safe for you and me Prevent accidents by noticing at-risk
situations and behaviors Live safely at home, at work, and
everywhere you go Teach an attitude, promoting safety
Personal Safety Right to work in a safe workplace Responsibility
• Protect your circle of safety and know how it may influence others
• Illness and Injury prevention program
Work Environment Organize safety for everyone Remove tripping hazards Do not store heavy items up high where
they may fall Do not rush or run in the workplace Cleanup any liquid spills immediately Report any potential hazards
Stress can lead to accidents Recognize personal burn-out Get enough sleep Get professional help Respect emotions of coworkers Develop active listening skills Develop positive, healthy relationships
with coworkers
Emergencies Medical response Earthquake Fire Chemical spills Regional disasters
What to do Know emergency numbers-911 etc. Be prepared and have a plan Follow plan Stay calm Consider immediate need and response Communicate with others Know safety procedures, tools & escape
routes
Neighborhood or regional disaster Home communication plan Know alternative routes Know who are your neighbors Be a good citizen You may have to stay where you are
Emergency Evacuation Plan Assist those who need help to get to the
protected area Know who is present and absent Communicate with other tenants Be prepared for first aid and medical
responses
Medical responses Immediate first aid Notify response teams, call 911 Provide assistance and comfort Transport to trauma or urgent care
facility
Earthquake Safety Stay calm, shield yourself from falling
objects Prevent falling objects by storing heavy
objects low and tie down equipment Keep aisles and routes clear Follow evacuation plan
Fire Safety Report fires immediately-response time is
critical Know locations of fire fighting equipment
• Extinguishers• Fire blankets• Fire alarm
Know when to evacuate & get everyone out If smoke is present stay low, crawl if necessary Know evacuation route
Fire Extinguishers Classification
• A- Ordinary combustible• B- Flammable Liquid• C- Electrical• D- Combustible metal
P-A-S-S• Pull-Aim-Squeeze-Sweep• Aim at the base of the fire and sweep• Limited time and quantity of extinguishing material
Personal Protection Actively work to prevent & avoid
accidents Protect working space Protect coworkers Secondary containment- create
boundaries & layers of safety appropriate for conditions and scale of work
Working with hazards Create a safety zone, CONTAIN Know the hazard, PROTECT
• Protect yourself• Protect those around you• Protect environment around you
Safe to touch, DECONTAMINATE Secondary & tertiary zones reduce the
chances of injury or disaster
Personal safety attire Lab coat Safety glasses Closed-toed shoes Gloves when appropriate
Chemical safety Know the hazards-MSDS sheets Specialized training may be necessary Proper storage of chemicals Use proven well thought-out protocols Additional personal protection attire may be required
• Face shield• Chemical goggles• Latex gloves and aprons• Additional shielding
Adequate ventilation Proper disposal of chemicals
Radiation safety Proper training Shielding Monitoring equipment
• Geiger counter• Wipe tests
Proper storage and disposal of radioactive materials
Radiation Safety Commonly used isotopes
• 14C, 35S, 32P, 3H, 125I, 131I Geiger counters
• Different probes Scintillation Counters Radiation exposure badges
Lab Etiquette & Lab Operation
Common Courtesy Do not use the last of a reagent and not replace it Do not use other people’s equipment and
reagents without asking Keep your work area and common work areas
clean and orderly Do not play the radio/music without consulting
others in the work area Be willing to work as a team on all projects Dress appropriately including avoiding excess
perfume/cologne
Levels of Operation Sterile reagents
• Liquids autoclave at 121º C for 15-20 minutes using slow exhaust. Alternatively, reagents can be filter-sterilized using a 45 or 22 micron filter
• Glassware autoclaved and cover with aluminum foil. • Plastic ware is sterile• Bottles/reagents may be needed to be flamed when opened or opened in a
sterile environment (laminar flow hood) RNase-free
• Liquids sterilized for 1 hour or made with Rnase-free reagents and solvents.
• Glassware treated in an oven for several hours and covered with foil• Reagents must be RNase-free
Clean room conditions• Dress and garb appropriately for the level of clean room• May include no makeup and cologne
Documentation
Documentation System Corporate Policy & Procedures Department Policy & Procedures Quality System Requirements Management Control Traceability, Records & Archival
Quality System Each manufacturer shall establish and
maintain a quality system that is appropriate for the specific medical device(s) designed or manufactured, and that meets the requirements of this part
Quality System Requirements Management responsibility
• Quality Policy- commitment to quality that is understood, implemented and maintained at all levels
• Organization- assigned responsibility and independent authority, adequate resources, effectively establish, effectively maintain, review, quality plan, quality procedures
Quality Audit- independent & documented Personal- qualifications & training
• Made aware of device defects which may occur from improper performance of theirs specific jobs
• Made aware of defects & errors in verification & validation
Quality System Subparts Subpart B- Quality system requirements Subpart C- Design controls Subpart D- Document controls Subpart E- Purchasing controls Subpart F- Identification & traceability Subpart G- Production & process controls Subpart H- Acceptance activities
Quality System Subparts Subpart I- Nonconforming product Subpart J- Corrective & preventive action Subpart K- Labeling & packaging control Subpart L- Handling, storage,distribution and
installation Subpart M- Records Subpart N- Servicing Subpart O- Statistical techniques
Subpart D- Document Controls Each manufacturer shall establish and maintain
procedures to control all the documents required. The procedures shall provide for the following• Shall designate an individual(s) to review for
adequacy and approve prior to issuance• Date and signatures of approval• Available where needed and obsolete documents
removed• Changes reviewed, approve, documented, described,
recorded, identity documents affected,communicated and effective date noted
What is a Document? Legal perspective- any scrap of paper that has
written information A memo, email,letter, note, meeting minutes Notebook entry, patent application, report Plan, protocol, written instruction, procedure, policy
statement Label, tag, placard, sign, flowchart, blueprint,design
description Formal documentation, contracts, licenses,
publications, marketing ads, regulatory submissions
Document Chain Quality requirement, quality procedure,
corporate policy, Mfg process, records of work, history files, legal contracts, Dept specific procedures, communication, personnel, training, reports, etc.
Request forms, Drafts, revision control, Identification, approval process, signatures,dates, archival, accessibility
Material Chain Acceptable design and supply, vendor,
identity, purchasing, receiving, inspection, acceptance, raw material, storage inventory, use, in-process, finished good, labeling, packaging, qualification, storage, distribution, customer, non-conformance, complaint,retention practices, disqualification, disposition, records
Subpart M- Records All records required by this part shall be maintained at
the manufacturing establishment or other location that is reasonably accessible to responsible officials of the manufacturer and to employees of FDA designated to perform inspections
Such records, including those not stored at the inspected establishment, shall be made readily available for review and copying by FDA employees
Such records shall be legible and shall be stored to minimize deterioration and to prevent loss
Those records stored in automated data processing systems shall be backed up
Confidentiality & Retention The firm should be encouraged to mark records they
feel are confidential to assist the FDA in determining what information may be disclosed under the freedom of Information Act (FOIA)
Impress upon the manufacturers that marking all copies of records and documents confidential does not aid the FDA in making its FOIA determination
Records required by the QS/GMP must be retained by the manufacturer for a period of time equivalent to the design and expected life of the device, but in no case less than 2 years from the date of release for commercial distribution by the manufacturer
Records and Reports Final report
• Name & address of facility performing study• Objective and procedures in approved protocol• Statistical methods, transformation of data, calculations• Test articles & control articles (include stability), test system, dosage• Describe circumstances that may affect quality & integrity of data• Name study director, other professionals, scientists• Signed and dated reports of each individual• Location of data & records, specimens, final report• QA statement of completion• Signature of study director• Amendments to report, signed
Storage, retention, retrieval, of records & data, specimens
Notebook Entry Title, date, who, witness (legal, patent) Purpose, materials & methods TRACEABILITY- Identify equipment, and
source of materials & protocols used Factual Statements for observations and
conclusions Avoid unsupportable claims or leading
suggestions for follow-up
Development Report Title, project identity, investigators, date,
distribution Summarize, show linkage to records Objective and outcome Protocol & test methods The facts- results and conclusions The importance (simple and realistic)
Validation Report Title and identity, controlled document Reference approved validation protocol Object and outcome, clear conclusion
• Was the method, process, product validated?
• How? Results vs acceptance parameters Archive record, design history file
How to use documents Use approved, effective documents, or
documents identified for approved protocols Follow the procedure Indelible ink (black), legible, in designated
fields for entering information No extraneous entries!! Record deviations from
procedure by creating separate document Sign and date The job is not finished until documented!
Technical Writing DELIVER THE MESSAGE- communicate the
objective, scope and outcome DELIVER THE HOW- communicate the
means, source of records, raw data and conclusions
DELIVER THE SO WHAT- communicate the importance of the findings, the relevance to the business, project, process or system
Intellectual Property and Compliance
Intellectual Property Laboratory notebooks
• Content & Witnessing Disclosures of invention
• Priority dates Confidential Information
• Trade secret vs Patent• Patents
– Compositions of matter, Process or procedure, Articles of Manufacture, Machines and Improvements
• Types of Patents– Utility, Design and Plant
• Patent Criteria– Conception, Reduction to practice, Utility, Novelty, & Obviousness
Proper Research Notebooks Physical requirements
• Bound notebook ( no removable pages)• Permanent ink ( Blue or Black)
Content• Purpose of experiment• Materials and Methods• Results
– Pictures and graphs pasted in have to be signed across• Discussion and Conclusions• New inventions are recorded
Witnessing• Who should witness and how often?
Witnessing Lab Notebooks Who ?
• Someone familiar with the research– It should not be a colleague working on the
same project– Why not? They may be an inventor if they have
contributed know how How often?
• Every week or two weeks
Disclosure of Invention Some companies require as the second step in
pursuing a patent Refers to initial notebook entry Can include a brief mention of related technology and
prior art Who is the inventor or inventors?
• Inventors must contribute to the conception of the idea• People or staff who perform the experiments are not
inventors unless they contribute intellectually
Trade Secret or Patent Trade secret
• When the process or formulation is not novel• When it can be easily used by competitors without the
knowledge of inventor• Can last indefinitely
Patenting is publishing exactly how something is made or produced• Patent to protect the inventor from others using his invention
or idea• Patents can be licensed to others for a fee and/or royalty• Patents are not intended to create a monopoly• Patents last 20 years
What can be patented Compositions of matter
• A new chemical entity produced from a combination of two or more compounds
– Common in agricultural & pharmaceutical research Process or procedures
• A series of steps that are followed to synthesize a new compound or make a new product
Articles of manufacture• Nearly every man-made object
Machines• Any mechanical or electrical apparatus/device
Improvements on any of the previous
Types of Patents Utility Patent
• Most common and most difficult• Functional characteristics of machines, devices, compounds• Exhaustive description of how to make and use the invention
including drawings• Duration is 20 years
Design Patent• Protects the shape and ornamental design of an article• 14 year duration
Plant Patent• New plant variety awarded for 20 years
Patent Criteria Conception
• Formulation of the invention detailed enough to allow a person knowledgeable in the field to make and use the invention
Reduction to practice• Inventor makes or constructs the invention to demonstrate its
usefullness Utility
• Invention must be useful or have utility Novelty or prior art
• Must not be a copy or a repetition of an existing invention Obviousness
• The invention should not be obvious to some one well-practiced in the field
Filing a Patent Filing fee
• The applicant is required to pay a fee for the processing of the application
Search & examination• The examiner will conduct a prior art search to ascertain
novelty and evaluate the claims to establish the scope of the invention
Publication• Sucessful applications will be published
Maintenance fees• Applicant must pay periodic maintenance fees
Parts of a Patent Title Inventors Assignee- the company or entity who is assigned
ownership of the patent Abstract Summary of invention Detailed description of invention Figures and drawings Claims
• Establish scope of the invention
Patent Strategy Patenting life forms and genes
• Easier following 1980 US Supreme court ruling, Diamond vs Chankrabarty
Reach-through patents• Patenting of genes based on their sequence but
having no idea about their function Patent stacking
• Situation where more than one scientist has filed a patent on a gene
Making Money on Patents Assignment- patent or patent application of invention
can be sold or assigned to another party License- the patent may be licensed to another party.
This may include a licensing fee and royalties Cross licensing- a situation where multiple patents
cover the same or similar areas exist and the owners of such patents may have to cross license each other’s patents to exploit the invention
Regulatory Compliance
Regulatory Compliance US agencies & their roles
• Food and Drug Agency (FDA)– GLP and GMP– Standard Operating Procedures (SOPs)
• United States Dept of Agriculture (USDA-APHIS)• Environmental Protection Agency (EPA)• National Institutes of Health (NIH)
– Office of Recombinant DNA Drug Development GLP
GMP ISO 9000
US Regulatory Oversight in Biotech
Agency Products RegulatedUS Dept of Agriculture Plant pests, plants and
veterinary biologics
Environmental Protection Agency
Microbial/plant pesticides,new uses of existing pesticides, novel microorganisms
Food and Drug Administration
Food, feed, food additives, veterinary drugs, human drugs, medical devices, diagnostics
USDA and APHIS APHIS is authorized to regulate the interstate
movement importation and field testing of organisms and products altered or produceds through biotech processes that are plant pests or suspected of being so.• Permit for movement and importation
– Organism, origin and its intended use• Permit for release into environment
– Oversight of field testing of biotech products• Genes and gene products, origin, purpose of test, experimental
design,and precautions to prevent escape• Courtesy permits
– Involves non regulated plants – Can involve intrastate movement
FDA Unexpected effects- unexpected genetic effects
Known toxicants Nutrient level Allergenicity New Substances Antibiotic resistance selectable marker Plants developed to make specialty nonfood
substances Issue specific to animal feed
Research and DevelopmentVocabulary
• Reagent – chemical used in an experiment• Efficacy – the ability to yield a desired result or demonstrate that a product does what it
claims to do• Large-scale production – the manufacture of large volumes of a product• Clinical trials – a strict series of tests that evaluates the effectiveness and safety of a
medical treatment in humans• FDA – abbreviation for the Food and Drug Administration; the federal agency that
regulates the use and production of food, feed, food additives, veterinary drugs, human drugs, and medical devices
• Cystic fibrosis (CF) – genetic disorder that clogs the respiratory and digestive systems with mucus
• Therapeutic – an agent that is used to treat diseases or disorders• EPA – abbreviation for the Environmental Protection Agency; the federal agency that
enforces environmental laws including the use and production of microorganisms, herbicides, pesticides, and genetically modified microorganisms
• USDA – abbreviation for United States Department of Agriculture; the federal agency that regulates the use and production of plants, plant products, plant tests, veterinary supplies and medications, and genetically modified plants and animals
Good Laboratory Practice (GLP) A very consistent way of performing and
documenting research & development work All documented experiments are performed in a
consistent fashion and are witnessed in a timely and consistent fashion
Procedures are validated Reagents are validated and listed Instruments and equipment that are utilized in
experiments are routinely calibrated and validated FDA monitored
Good Manufacturing Practice (GMP)
All procedures used in manufacturing are consistent, fully validated and witnessed
Use Standard Operating Procedures (SOPs) Reagents, chemicals and equipment are specified,
validated and calibrated Testing equipment specified and routinely calibrated Some drugs need to be produced in a sterile
environment• The sterility of the manufacturing environment needs to be
monitored and documented FDA monitored
Standard Operating Procedure Detailed specific protocol
• Steps may be monitored or witnessed Reagents specified
• Grade• Source or manufacturer
Equipment specified• Manufacturer• Model number
Equipment calibration• Calibration method• Calibration frequency• Calibration log
Calibrations are witnessed
Iso 9000 or above Standard ways of doing business and documenting it In addition to manufacturing practices it can include
• Shipping• Maintenance of plant and equipment• Order taking• Customer and technical service• Handling of complaints• Communications
Needed for world marketing and distribution
Scientific Method Codefined and promoted in 17th century by
Rene Decartes and Francis Bacon Steps involved in scientific method
• Make observations• Ask questions• Make educated guesses about possible answers• Base predictions on the guesses• Devise ways to test predictions• Draw conclusions
Scientific Method Hypothesis – “educated guess” based
on observations and questioning Predicted result occurs – hypothesis is
most likely correct Individuals using scientific method
should be objective and unbiased
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The Scientific Method
Scientific MethodOriginal Hypothesis Devise method to
test hypothesisAnalyze results
Results support
hypothesis
Results support
hypothesis but suggest minor refinements
Results are so unexpected that
they do not support original hypothesis and require a new
hypothesis
Results do not support original
hypothesis but fall within range that
could be expected if original
hypothesis is slightly modified
Retest using minor
refinements of process
Test using slightly modified
hypothesis
Test new hypotheses
ObserveObserve
Ask QuestionsAsk Questions
Formulate HypothesisFormulate Hypothesis
Derive PredictionsDerive Predictions
Test HypothesisTest Hypothesis
Perform ExperimentsPerform Experiments
Analyze DataAnalyze Data
Evaluate outcomeEvaluate outcome
Hypothesis supportedHypothesis supported
Curiosity satisfiedCuriosity satisfied
Move onto another topicMove onto another topic
No
No New Hypothesis New Hypothesis
Scientific Method & Experimental Design
Testable hypothesis One variable at a time Positive controls Negative controls Background determinations Data Normalization
Human Genome Project
The Human Genome Project• Determining the human DNA sequence• Understanding the function of the human genetic code• Identifying all of the genes• Determining their functions• Understanding how and when genes are turned on and off
throughout the lifetime of an individual
HGP (1990 – 2003 ) Participants
US DOE
NIH
UK Medical Research Council and Wellcome Trust, UK
18 countries including France, Japan, Germany and China
Goals of HGP
1. Identify all the approximate 25,000 genes in human DNA.
2. Determine the sequences of the 3 billion chemical base pairs that make up human DNA.
3. Store this information in databases
4. Improve tools for data analysis,
5. Transfer related technologies to the private sector and
6. Address the ethical, legal, and social issues (ELSI) that may arise from the project.
Methodology
DNA Source
Mapping • Genetic Linkage Map• Physical Map
DNA sequencing• Clone by clone sequencing• Whole Genome Shotgun
sequencing
Assembling
Genetic Linkage Map
Distance between markers (genes) are determined by meiotic recombinational frequencies between the markers (or genes).
Gives only an estimate of the distance between markers or genes
Unit of measurement – cM (centiMorgans)
Construction of Genetic Linkage Map
Physical Map
Constructed from information obtained from the chemical characteristics of the DNA itself and not from the genetic recombination analysis.
Unit of Measurement – bp (basepair). Hence, more precise and exact in pinpointing the location and distance of the genes.
2 Types of Physical Maps
Low resolution• Chromosomal
(Cytogenetic) map• cDNA map
High resolution• Top-Down Mapping• Bottom-up Mapping
Top Down Bottom Up
Genetic Map VS. Physical Map
Automated sequencers: ABI 3700 and MegaBACE
96–well plate
robotic arm and syringe
96 glass capillaries
load bar
AUTOMATED SEQUENCE GEL
AUTOMATED DNA SEQUENCE
Methodology DNA Source
Mapping • Genetic Linkage Map• Physical Map
DNA sequencing• Clone by clone sequencing• Whole Genome Shotgun
sequencing
Assembling• GigAssembler
Result by the numbers The human genome contains 3164.7 million chemical nucleotide
bases (A, C, T, and G).
The average gene consists of 3000 bases, but sizes vary greatly, with the largest known human gene being dystrophin at 2.4 million bases.
The total number of genes is estimated at 20,000 to 25,000—much lower than previous estimates of 80,000 to 140,000.
Almost all (99.9%) nucleotide bases are exactly the same in all people.
The functions are unknown for over 30% of discovered genes.
Results Contd. Less than 2% of the genome codes for proteins.
Repeated sequences that do not code for proteins ("junk DNA") make up at least 50% of the human genome.
Repetitive sequences are thought to have no direct functions, but they shed light on chromosome structure and dynamics.
During the past 50 million years, a dramatic decrease seems to have occurred in the rate of accumulation of repeats in the human genome.
Genome Facts
The human genome's gene-dense "urban centers" are predominantly composed of the DNA building blocks G and C.
In contrast, the gene-poor "deserts" are rich in the DNA building blocks A and T.
Genes appear to be concentrated in random areas along the genome, with vast expanses of non-coding DNA between.
Stretches of up to 30,000 C and G bases repeating over and over often occur adjacent to gene-rich areas, forming a barrier between the genes and the "junk DNA.“
Chromosome 1 has the most genes (2968), and the Y chromosome has the fewest (231).
Area Goal Achieved Date AchievedGenetic Map 2- to 5-cM resolution map
(600 – 1,500 markers)1-cM resolution map (3,000
markers) September 1994
Physical Map 30,000 STSs 52,000 STSs October 1998
DNA Sequence 95% of gene-containing part of human sequence finished to 99.99% accuracy
99% of gene-containing part of human sequence finished to 99.99% accuracy
April 2003
Capacity and Cost of Finished Sequence
Sequence 500 Mb/year at < $0.25 per finished base
Sequence >1,400Mb/year at <$0.09 per finished base
November 2002
Human Sequence Variation
100,000 mapped human SNPs
3.7 million mapped human SNPs
February 2003
Gene Identification Full-length human cDNAs 15,000 full-length human cDNAs
March 2003
Model Organisms Complete genome sequences of E. coli, S. cerevisiae, C. elegans, D. melanogaster
Finished genome sequences of E. coli, S. cerevisiae, C. elegans, D. melanogaster, plus whole-genome drafts of several others, including C. briggsae, D. pseudoobscura, mouse and rat
April 2003
Endeavors after HGP
Transcriptomics - involves large-scale analysis of messenger RNAs transcribed from active genes to follow when, where, and under what conditions genes are expressed.
Proteomics - can bring researchers closer to what's actually happening in the cell than gene-expression studies.
Structural genomics - initiatives are being launched worldwide to generate the 3-D structures of one or more proteins from each protein family, thus offering clues to function and biological targets for drug design.
Comparative genomics - analyzing DNA sequence patterns of humans and well-studied model organisms side-by-side—has become one of the most powerful strategies for identifying human genes and interpreting their function.
Summary of Human Genome Project
Introduction: Background and History of HGP (1990-2003) Methodology: DNA source Genome Map
Genetic Linkage Map Physical Map – Low Resolution and High Resolution
DNA sequencing Clone-by-clone sequencing Whole Genome shotgun sequencing
Assembling GigAssembler
Results: Completed Human Genome Sequencing Identified 15,000 genesFuture: Applications in the field of Medicine, Forensics, Environment etc., Further research in the fields of Transcriptomics, Proteomics, Structural and
Comparative Genomics
Resourceful information available at: DOE website – www.doegenomics.org
National Human Genome Research Institute – www.genome.gov
Joint Genome Institute – www.jgi.doe.gov
National Center for Biotechnology Institute – www.ncbi.nlm.nih.gov