Check Yourself for Genetic Abnormalities – Wired How-To Wiki

 

Check Yourself for Genetic Abnormalities

From Wired How-To Wiki

Jump to: navigation, search

Nearly every day, somebody in the research community claims to have found a genetic marker associated with some sort of health condition. If you are curious and want to check yourself for those inherited traits, there are several options at your disposal. Some are easy, others are quite hard, but none of them are cheap.

Contents

[hide]

Option 1: Visit a Genetic Counselor

The easiest, and most traditional, way to learn about your genetic makeup is by visiting a genetic counselor. To find a good one, visit the National Society of Genetic Counselors website.

If you are worried about having a genetic disease, or transmitting one to your children, they will know what to do. But if you just want to pick through your genome for the sake of curiosity, their services may be a bit too expensive and unsuitable for your needs.

For ethical reasons, they shy away from talking about genetic information that is not extremely well-understood. So, if you want to check yourself for a gene that was recently discovered, counseling may not be the best option.

Example: Mary gets sick whenever she eats wheat products. So does her son Jimmy and her aunt Ludmilla. She wants to know if they have Celiac Sprue, a disease that makes people terribly ill when they consume foods containing gluten. She would do well to visit a genetic counselor.

Option 2: Scan Your Whole Genome

Online genetic testing companies, like 23andMe and deCODEme, might be the most cost-effective and fun way to pick through boatloads of your own genetic information. Instead of checking you for a handful of genes, they analyze up to 1 million points, called SNPs, in your genome. These companies are gaining the ability to perform more thorough analyses all the time, so testing should only improve. Both companies allow you to download the raw data or peruse it in your browser at their websites.

23andMe's webapp

23andMe’s webapp

The keys to browsing your genome are tags called rsID or refSNP numbers. If you just read a report that a particular SNP has been linked to hating vegetables, and you want to know if your hatred of spinach has genetic roots, the first thing to do is look for the rsID number of that SNP. The best place to look for that information is in the original research paper, which was written by the scientists themselves. Once you have found the rsID, simply paste it into the search window of your genome browser and then take a look at your genotype.

DNA is made up of four building blocks called bases — G, A, T, and C. The original research paper will say which base is normal, and which is linked to an unusual condition or dangerous abnormality. For practice, you can browse through some sample data on the deCODEme website. You can do the same thing on the 23andMe website, but only after registering for a demo account.

Tip: One of the biggest sources of confusion when looking at microarray data is the so-called “stranding issue.” In other words, the microarray data might not perfectly match up with what you are looking for. Often, that is caused by a discrepancy between the tests done by researchers and the microarray company. DNA is double stranded. The researchers may have examined one strand, while the microarray company tests for the same marker, but on the opposite strand.

Option 3: Perform Lab Tests at Home

What You’ll Need
  • Cotton Swabs
  • Pipettes and Tips
  • Centrifuge Tubes
  • Latex Gloves
  • DNA Extraction Kit
  • PCR Mix
  • Thermocycler
  • PCR Tubes
  • PCR Cleanup Kit
  • Centrifuge
  • Cloning kit

Why do it the hard way?

The State of California is trying to shut down direct-to-consumer genetic testing services. If this trend spreads, the ad hoc approach may be your next best option. You also may have privacy concerns, or you want to check yourself for a rare genetic marker that is not covered by microarray tests.

Step 1: Swab some cells from your cheek

Just stick the cotton swab into your mouth and rub it up against the inside of your cheeks.

Step 2: Extract DNA from those cells

You can buy a kit that makes extracting DNA from the cells on your cotton swab easy, or you can use an improvised approach with household materials. Unfortunately, the MacGyver methods might not provide you with DNA that is suitable for copying.

Step 3: Design and Order PCR primers and controls

Primers are short DNA strands that serve as starting points for DNA copying reactions. They must match the first few bases of the sequence that you want to copy. Designing them may be the hardest step. Look up the DNA sequence flanking your genetic marker of interest in a database like dbSNP. Pick a segment that is about 20 bases long and slightly ahead of the marker. That is your forward primer. Pick another 20ish base sequence that is behind the region of DNA that you want to study. Use a web app of your choice to find its reverse complement.

Step 4: Copy the DNA with the PCR reaction

A DNA Engine Dyad thermocycler

A DNA Engine Dyad thermocycler

Mix the extracted DNA with some pre-made PCR mix and your primers. It contains an enzyme, polymerase, that copies DNA every time it is heated and cooled.

Fill a PCR tube with 100µL of the mixture. Put it in a thermocycler and program the machine to go through roughly 40 heating and cooling cycles.

Run a second and third PCR reaction with DNA samples that contain, or do not contain, the genetic marker of your choice. Those are the positive and negative controls.

Step 5: Sequence the amplified genetic material

You'll need a cloning kit

Check Yourself for Genetic Abnormalities – Wired How-To Wiki

Advertisements

Leave a Reply

Please log in using one of these methods to post your comment:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s

Blog at WordPress.com.

Up ↑

%d bloggers like this: