Applied Genomics
What is Genetics?
Genetics is the connection between phenotype and genotype.
- Genotype: The gene content—what's written in your DNA
- Phenotype: What we actually see—the observable traits
Two Approaches to Understanding Genetics
Forward Genetics: Moving from phenotype to genotype
→ "Why do I sneeze in sunlight?" → Find the responsible gene through mapping
Reverse Genetics: Moving from genotype to phenotype
→ "What happens if I break this gene?" → Create mutations and observe the effects
Real Examples of Phenotypes
Examples of how genetics shapes our everyday experiences:
Cilantro Taste: Some people think cilantro tastes like soap. This isn't about preference—it's genetics. Variations in the OR6A2 gene literally change how cilantro tastes to you.
ACHOO Syndrome: Ever sneeze when you look at bright sunlight? That's not random. It's linked to a genetic polymorphism near the Zeb2 gene. (ACHOO stands for Autosomal Dominant Compelling Helio-Ophthalmic Outburst—yes, someone really wanted that acronym to work.)
These examples show that genetic differences create genuinely different experiences of the world, not just different disease risks.
What is a Gene?
This seems like a simple question, but it has multiple valid answers depending on your perspective:
1. DNA Sequence Definition
A gene is simply a stretch of DNA—a sequence of nucleic acids.
2. Functional Definition
A gene corresponds to a phenotype. It's associated with specific traits or conditions (like ACHOO syndrome).
3. Mendelian Definition
A gene is an independently segregating unit in inheritance—the discrete units Mendel discovered with his peas.
4. Genomic Definition
A gene is a specific physical location in the genome. This matters for mapping studies and understanding genomic architecture.
The Structure-Function Connection
DNA's double helix isn't just beautiful—it's functional. The structure provides a mechanism for copying and transmitting genetic information from one generation to the next. Form follows function, and function requires form.
Key Terminology
Let's define the language we'll use throughout this course:
Alleles
Different versions of a gene. Since humans are diploid (two copies of most chromosomes), we have two alleles for most genes. They can be:
- Homozygous: Both alleles are identical
- Heterozygous: The two alleles are different
Mutants
An altered version of a gene that has been observed to change. Important: we only call something a "mutant" when we witness the mutation for the first time—like seeing a new change in a child that isn't present in either parent.
Genotype
The complete set of alleles in an individual. Your genetic makeup.
Wildtype
A standard reference genome used as a baseline for comparison. Important points:
- Often highly inbred (identical alleles)
- Used to identify mutations
- Does NOT mean "healthy" or "normal"
- NOT applicable to humans—there is no single "normal" human genotype
Why "Wildtype" Doesn't Work for Humans
There is no universal standard for what is "normal" in human genetics. We have incredible natural variation. What's common in one population might be rare in another. What works well in one environment might be disadvantageous in another.
The idea of a single reference "wildtype" human is both scientifically inaccurate and philosophically problematic. Human genetic diversity is a feature, not a bug.
Pedigrees
Pedigrees are family trees that track the inheritance of traits across generations. They're one of our most powerful tools for understanding genetic inheritance patterns in humans, where we can't do controlled breeding experiments (for obvious ethical reasons).
How These Notes Are Organized
I'm not following a strict linear order because genetics doesn't work linearly. Genes interact. Pathways overlap. Everything connects to everything else.
These notes will grow recursively—starting with foundations, then branching out as connections become clear. Some sections will reference concepts we haven't covered yet. That's fine. Learning genetics is like assembling a puzzle where you can't see the final picture until enough pieces are in place.
My approach:
- Start with fundamentals (this page)
- Build out core concepts as we cover them in lectures
- Connect ideas across topics as patterns emerge
- Revisit and refine as understanding deepens
About Course Materials
These notes contain NO copied course materials. Everything here is my personal understanding and recitation of concepts, synthesized from publicly available resources (online courses, YouTube, documentation, textbooks).
This is my academic work, how I've processed and reorganized information from legitimate sources. I take full responsibility for any errors in my understanding.
If you believe any content violates copyright, contact me at mahmoudahmedxyz@gmail.com and I'll remove it immediately.