20  Applications of Genomics and Proteomics

20.1 Transforming the World

Genomics and proteomics aren’t just academic subjects—they’re changing our world in practical ways every day!

20.2 Medicine and Diagnostics

20.2.1 Personalized Medicine

Traditional medicine: One-size-fits-all approach Personalized medicine: Treatment tailored to YOUR genes!

How it works:

  • Sequence your genome

  • Identify genetic variants

  • Predict disease risks

  • Choose best treatments for YOU

Examples:

1. Cancer Treatment:

  • Sequence tumor DNA

  • Find specific mutations

  • Choose drugs targeting those exact mutations

  • Example: Herceptin for HER2-positive breast cancer

2. Pharmacogenomics:

  • Your genes affect how you process drugs

  • Some people metabolize drugs quickly, some slowly

  • Genetic testing chooses right dose for YOU

  • Avoid dangerous reactions!

Example - Warfarin dosing:

  • Blood thinner with narrow safe range

  • Genes affect proper dose (3-fold variation!)

  • Genetic test determines your safe dose

  • Prevents bleeding or clotting

3. Rare Disease Diagnosis:

  • Many rare diseases have genetic causes

  • Whole genome sequencing finds mutations

  • Often ends “diagnostic odyssey”

  • Enables treatment or management

Success story:

  • Child with mysterious illness

  • Years of tests, no diagnosis

  • Genome sequencing finds rare mutation

  • Diagnosis leads to treatment

  • Child improves!

20.2.2 Early Disease Detection

Finding diseases before symptoms appear:

1. Cancer Screening:

  • BRCA1/BRCA2 mutations → high breast/ovarian cancer risk

  • Early screening saves lives

  • Preventive surgery option

2. Liquid Biopsies:

  • Test blood for cancer DNA

  • Catch cancer very early

  • Monitor treatment response

  • Detect recurrence

3. Carrier Screening:

  • Before having children, test if you carry disease genes

  • Cystic fibrosis, sickle cell, Tay-Sachs, many others

  • Informed reproductive choices

4. Newborn Screening:

  • Test babies for genetic conditions

  • Early treatment prevents problems

  • Example: PKU (phenylketonuria) - special diet prevents brain damage

20.2.3 Understanding Disease Mechanisms

Genomics reveals HOW diseases work:

Alzheimer’s Disease:

  • Multiple genes involved

  • APP, PSEN1, PSEN2 cause early-onset forms

  • APOE4 increases late-onset risk

  • Understanding guides drug development

Diabetes:

  • Type 1: Autoimmune (some genetic risk factors)

  • Type 2: Complex, many genes involved

  • Monogenic diabetes: Single gene mutations (different treatment!)

Heart Disease:

  • Familial hypercholesterolemia: LDLR gene mutations

  • Very high cholesterol from birth

  • Gene therapy in development!

20.3 Biotechnology and Synthetic Biology

20.3.1 Making Useful Products

Using organisms as factories:

20.3.2 1. Therapeutic Proteins

Insulin for Diabetes:

  • Traditionally from pig/cow pancreases

  • Now made in bacteria with human insulin gene!

  • Cheaper, safer, unlimited supply

Other examples:

  • Growth hormone

  • Clotting factors for hemophilia

  • Antibodies for cancer/autoimmune diseases

  • Vaccines (hepatitis B, HPV)

How it’s done:

  1. Insert human gene into bacteria/yeast

  2. Bacteria make human protein

  3. Purify protein

  4. Give to patients!

20.3.3 2. Industrial Enzymes

Laundry Detergent:

  • Contains enzymes that break down stains

  • Engineered for better performance

  • Work in cold water (save energy!)

Food Processing:

  • Cheese making (rennet)

  • Brewing (specialized yeasts)

  • Sweeteners (high-fructose corn syrup)

Biofuels:

  • Engineer microbes to make ethanol, biodiesel

  • From agricultural waste

  • Renewable energy source!

20.3.4 3. Synthetic Biology

Designing organisms from scratch:

Craig Venter’s Synthetic Genome:

  • First synthetic self-replicating cell (2010)

  • Designed genome on computer

  • Built it from chemicals

  • Worked!

Applications:

  • Bacteria that produce biofuels

  • Organisms that clean up pollution

  • Microbes that make medicines

  • Programmable cells

Artemisinin production:

  • Anti-malaria drug

  • Traditionally from plant (expensive!)

  • Engineered yeast to produce it

  • Cheaper medicine saves lives!

20.4 Agriculture and Food

20.4.1 Feeding the World

Genomics improves crops and livestock:

20.4.2 Crop Improvement

1. Disease Resistance:

  • Identify resistance genes

  • Breed disease-resistant varieties

  • Reduces pesticide use

  • More sustainable

2. Drought Tolerance:

  • Find genes for drought resistance

  • Important for climate change

  • Crops survive with less water

3. Nutritional Enhancement:

  • Golden Rice: Engineered with vitamin A

  • Prevents blindness in developing countries

  • Biofortification: More iron, zinc, etc.

4. Better Yields:

  • Genomics accelerates breeding

  • Select best plants faster

  • Feed growing population

5. Longer Shelf Life:

  • Tomatoes that don’t spoil quickly

  • Reduces food waste

20.4.3 Livestock Genomics

Breeding better animals:

  • Disease resistance

  • Better meat/milk production

  • Animal welfare

  • Efficiency (less environmental impact)

Example - Dairy Cows:

  • Genomic selection for milk production

  • Healthier cows

  • Higher efficiency

20.4.4 Precision Agriculture

Using genomics with technology:

  • Sequence soil microbes

  • Understand plant-microbe interactions

  • Optimize conditions for each field

  • Sustainable farming

20.5 Evolutionary Studies

20.5.1 Understanding Our Past

Genomics revolutionized evolutionary biology:

20.5.2 Comparing Genomes Across Species

What we’ve learned:

  • All life shares common ancestor

  • Humans share 96% DNA with chimpanzees

  • Even share 50% with bananas!

  • Shows unity of life

Molecular Clocks:

  • Mutations accumulate over time

  • Compare genomes to estimate when species diverged

  • Reconstruct tree of life!

20.5.3 Ancient DNA

Sequencing extinct species:

Neanderthals:

  • Sequenced Neanderthal genome

  • Found they interbred with humans

  • Most people have 1-4% Neanderthal DNA!

  • Tells us about our ancestors

Woolly Mammoths:

  • Sequenced from frozen remains

  • Understand what made them different from elephants

  • De-extinction projects in progress!

Ancient Humans:

  • Trace human migration out of Africa

  • Understand population history

  • See how humans adapted to environments

20.5.4 Conservation

Saving endangered species:

Genetic Diversity:

  • Sequence endangered species

  • Measure genetic diversity

  • Plan breeding to maintain diversity

  • Prevent inbreeding

Example - Cheetahs:

  • Very low genetic diversity

  • Genomics helps manage breeding programs

  • Preserve species

Forensics:

  • Catch wildlife poachers

  • Identify illegally traded animals

  • Track ivory sources

20.6 Personalized Medicine - The Future

20.6.1 Your Genome, Your Health

What’s possible now:

  • Whole genome sequencing: <$1,000

  • Identify disease risks

  • Pharmacogenomic testing

  • Carrier screening

What’s coming:

1. Preventive Medicine:

  • Know your risks early

  • Lifestyle changes prevent disease

  • Targeted screening

  • Earlier interventions

2. Gene Therapy:

  • Fix disease-causing mutations

  • Already working for some diseases!

  • Sickle cell disease cured in trials

  • Inherited blindness treated

3. Cancer Vaccines:

  • Personalized cancer vaccines

  • Based on YOUR tumor mutations

  • Teach immune system to attack cancer

4. Microbiome Medicine:

  • Sequence gut bacteria

  • Understand how microbiome affects health

  • Personalized probiotics

  • Treat diseases by modifying microbiome

5. Precision Public Health:

  • Track disease outbreaks (COVID-19!)

  • Understand antibiotic resistance

  • Predict epidemics

  • Targeted interventions

20.7 Forensics and Ancestry

20.7.1 DNA in the Courtroom

Criminal Justice:

  • DNA fingerprinting identifies suspects

  • Exonerates the innocent

  • Solves cold cases

  • Identify disaster victims

How it works:

  • Compare DNA from crime scene to suspect

  • Look at specific variable regions (STRs)

  • Match = very strong evidence

Paternity Testing:

  • Determine biological relationships

  • 99.9% accuracy

  • Child inherits half DNA from each parent

20.7.2 Ancestry Testing

Consumer Genomics (23andMe, Ancestry.com):

What you learn:

  • Ethnic background

  • Geographic origins

  • Find relatives

  • Trait predictions

  • Some health information

How it works:

  • Genotype ~1 million SNPs

  • Compare to reference populations

  • Statistical analysis

Cautions:

  • Estimates, not certainties

  • Privacy concerns

  • Surprising findings possible

  • Not comprehensive medical test

20.8 Ethical Considerations

20.8.1 With Great Power…

Important questions:

Privacy:

  • Who owns your genetic data?

  • Can insurance companies use it?

  • Employment discrimination?

  • Data security?

Equity:

  • Will benefits reach everyone?

  • Or only wealthy people/countries?

  • Access to treatments?

Gene Editing:

  • Should we edit human embryos?

  • Enhancement vs. treatment?

  • Unintended consequences?

  • Playing God?

Consent:

  • Who can consent for children?

  • Incidental findings (finding unexpected diseases)?

  • Right not to know?

These questions don’t have easy answers, but we must consider them!

20.9 Key Takeaways

  • Medicine: Personalized treatment, early detection, understanding diseases

  • Biotechnology: Making therapeutic proteins, industrial enzymes, synthetic organisms

  • Agriculture: Better crops (disease-resistant, drought-tolerant, nutritious), improved livestock

  • Evolution: Understanding our past, comparing species, ancient DNA

  • Conservation: Saving endangered species, maintaining genetic diversity

  • Personalized medicine: Prevention, gene therapy, cancer vaccines

  • Forensics: Criminal justice, paternity testing, ancestry

  • Ethical considerations: Privacy, equity, gene editing, consent

  • Genomics and proteomics touch nearly every aspect of modern life!

  • These fields continue to expand and create new applications

Sources: Information adapted from medical genomics literature, biotechnology applications, agricultural genomics, and ethical discussions in genetics.