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SNPsAndChips.com


What's a SNP, what's a chip,
and why does all this matter?

This is part ONE of a TWO-PART tutorial.
For the other part please select the link below.

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Enjoy learning about genomics !
Nearly every cell in your body has a nucleus that holds the genetic programming that determines most of your physical characteristics. This information is stored in chromosomes.

Each cell nucleus contains a complete set of chromosomes. Thus, your body contains billions of identical copies of your genetic program: one complete copy stored in each cell nucleus.

Cells with nucleii
man reading book
Chromosomes are very long molecules of a double-stranded chemical known as DNA. In this video, DNA is shown as a long twisted ladder-like molecule. Each "rung" consists of two chemical units that hook together in the middle.
These units are known as nucleotides, and each rung of the ladder is referred to as a nucleotide pair, or base pair.
(Double click on the video to start or stop it.)
DNA has two strands (shown here as red and green), and four nucleotides (A T G C) that pair: A-T, and G-C. Genetic information is stored in the exact list, or sequence of nucleotides.
Just as a computer stores data as a long but precise list of 1's and 0's, cells store genetic information as a precise sequence of A, T, G, and C in the chromosomes.
(Note: we just track the sequence of one strand. The other is determined by the A-T / G-C pairing rule.)
double helix
If we spill out the DNA from a cell nucleus, we see that it can be arranged in an ordered array of 23 pairs of chromosomes. All but the last pair in the array have been assigned numbers (1 to 22). The members of each pair are nearly (but not exactly) identical to each other.
(Point to the image to show the complete figure.)
(This DNA is from a woman. In men, the final pair, named "X", is replaced by a single X together with a single copy of another chromosome named "Y".)
We can determine the DNA sequence of entire chromosomes. The complete, ordered sequence of all 24 chromosomes is called the human genome.
The genome is very long (3 billion letters in all), but it is precise. It is accurately maintained in nearly all cells in the body.
(Chromosomes are much longer than they look; the DNA is tightly coiled and compacted.)
genome view
chromos from nucleus
Surprisingly, the human genome sequence is 99.6% identical in all people. This is true of everyone, regardless of race or heritage.

However, there are certain positions where some people have one nucleotide pair, while others have another. These positions are known as SNPs (pronounced "snips").
(Point to the image to show the complete figure.)
("SNP" stands for "Single Nucleotide Polymorphism".)
SNPs make up only 0.4% of the genome. But since the genome is so big, 0.4% equals 12 million places. Our differences at these places make each of us unique.

A SNP may be thought of as an address. It is a physical location on a particular chromosome. Like the address of a house on your street, a SNP may have various "occupants". The possible "occupants" are the four nucleotides, A, T, G, & C.
genome view with SNPs
two chromos with SNP
We use the term allele (pronounced ull-leel') to identify which nucleotide is present at a SNP.
For example, here is a segment of sequence from chromosome 1 that has a SNP. Paul and Julia have the G allele on both of their copies of this chromosome. However, Jose has one G and one A allele, and Roger has two C alleles.
(The SNPsAndChips logo (see top of this page) is an artistic rendition of SNPS on a pair of chromosomes.)
alleles table
Very efficient methods have been developed for determining SNP alleles. For example, this slide, which is less than 3 square inches in size, has 20 DNA chips that each have thousands of microscopic reaction sites.

The slide can test over a million SNPs for one person in one step. It is simply soaked in a chemically treated sample of saliva or blood, then placed in a machine that collects the data and sends it to a computer.
DNA chip

Summary of key concepts

  • Our genetic information is stored in the sequence of DNA in our chromosomes.
  • There are 24 chromosome pairs in the human genome. Men and women have slightly different sets of chromosomes.
  • SNPs are chromosome addresses. They are spots where some people have one nucleotide, while others have another.
  • SNPs have four possible alleles: A, T, G, and C.
  • Our collection of SNP alleles is what makes each of us unique.
  • Modern techniques make it possible to determine the status of large numbers of SNPs very efficiently.
  • These methods utilize DNA chip technology.