Decoding mutation nomenclature

-A curious adult from Oklahoma

April 18, 2017

It is a very specific way of saying that his person has a different gene from somebody else.

What it doesn’t tell us is which gene is affected. It also does not tell us if the difference has any effect on the person.

What it specifically means is that at position 113 of a protein (p.), there is an asparagine (Asn) instead of an aspartic acid (Asp). This is probably not very helpful yet!

A Simple Genetic Code

Our genes are made up of DNA which is made up of 4 nucleic acids represented by letters. We call these nucleic acids A, T, G, and C.                                    

These four letters are repeated many times and in different combinations in order to make up a gene. They form the “alphabet” of our instructions.

When your body reads a gene, it reads the nucleic acid letters in groups of three. These are the “words” in our genetic language (called codons). There are 64 possible “words” with 4 “letters.”

Finally, p.Asp113Asn

So now let’s put all of this information together to answer your question. As I mentioned earlier, “p.” means that we are talking about a protein. “113” means that we are talking about the 113th codon in this gene.

Asp stands for aspartic acid. Because Asp comes before 113, we know that in this gene, the three letters that make up this codon should lead to the amino acid Asp being added to the protein.

Gedmatch half vs full sibling

-A curious adult from Texas

April 13, 2017

From the ancestry data alone, you can’t really tell if the two of you are half or full siblings. As we talk about in our previous answer here, the two of you could have much more different ancestries than this and still be full siblings.

Full vs. Half Siblings

Here is part of a typical result for full siblings (from Kitty Cooper’s blog):

And here is part of a typical result from a half sibling (from the same blog):

Yellow vs. Green

OK so the key difference here is green vs. yellow. If you have lots of big blocks of green you are almost certainly full siblings.

To get into what these different colors mean, we need to take a step back and talk a little bit about your DNA.

DNA is stored in long stretches called chromosomes. People typically have 23 pairs of chromosomes for a total of 46.

We get one chromosome in each pair from mom and one from dad. That is why we are half related to mom and half related to dad.

Rh negative blood and sickle cell trait unlinked

-A curious adult from North Carolina

March 29, 2017

First, thank you for your question! I think what you might be really getting at is whether someone can inherit sickle cell trait from a white mother who has sickle cell trait and Rh- blood.

And the short answer to this question is yes they can! There are almost certainly people with sickle cell trait who inherited it from Caucasian mothers with Rh- blood and sickle cell trait.

Now this doesn’t mean it is necessarily common.

Now let’s say you want a lemon lollipop and blueberry bubblegum. And you have to either pick a piece of bubblegum and a lollipop from the first two bowls or a blowpop from the third. Blindfolded.

In this case your best bet is bowl 3. Because the two candies are linked in that bowl, you’ll get the right combination each time.

If you choose to pick from bowls 1 and 2 instead, then you have a 1 in 2 chance of getting the right lollipop and a 1 in 2 chance of getting the right bubblegum. Here, your chances of getting both drop to 1 in 4.

What Causes Sickle Cell Trait and Rh- Blood?

Earlier we said that sickle cell trait and Rh- blood are both traits, and that DNA is the molecule our bodies use to spell out the instructions needed to make each of these traits.

So, our bodies have a specific set of instructions that code for sickle cell trait and a specific set of instructions that code for Rh blood type. Spelling mistakes in these trait instructions are called mutations.

How GWAS works

-A curious student from California

March 21, 2017

I think this is a question that a lot of people have after doing tests like 23andMe. These markers are just places in the DNA that in some studies were found in more people with a particular illness.

Most of these markers in the “health” section—especially with 23andMe health results in the past—are not for sure things. Sometimes, they aren’t even found in people with the illness that much more often than in people without the illness.

For ALS and this SNP, the odds ratio looks at how often people with rs3849942 (A;A) (the specific SNP) get ALS. Then we compare that to the number of people with the same SNP who don’t get ALS.

Notice that there are people who have rs3849942 (A;A) who don’t have ALS. So we can say that having this SNP definitely does not mean someone will get ALS 100% of the time! That’s why the overall risk of someone who has this SNP having ALS is so low.

Lots of Limitations

Odds ratio like the one above for rs3849942 and ALS tell us that this SNP probably isn’t the best predictor of ALS. In fact, one might even ask if it is a SNP worth knowing: it only increases someone’s risk by a small amount. It could also cause someone to worry about getting the disease in the future.

The small odds ratio makes sense with what we know about the causes of ALS. Most cases aren’t inherited from our families.

Born lactose intolerant

-A high school student from Indiana

March 7, 2017

Yes, it is possible but it’s rare. Only something like 1 in 60,000 newborns are born lactose intolerant.

The most common situation for people (and most mammals) is that they are born able to digest lactose, a sugar in milk, and they lose the ability when they grow up. Pigs and people are pretty much the only mammals we know of where lots of adults can still drink milk.

Lactose is a Sugar Found in Milk

Did you know milk has sugar? Well it does, and it’s called lactose!

Milk is made up of water (mostly) and has a small amount of lactose. Milk also has other stuff like proteins, fat, vitamins, and minerals.

Because a lot of food items contain milk, lactose is found in many different foods like ice cream, cheese, and creamy soups and sauces, just to name a few.

Developing Lactose Intolerance Over Time

While lactose intolerant babies are rare, lactose intolerant adults are pretty common. Around 65% of the human population loses the ability to digest lactose as they grow and develop.

It’s actually the “normal” trait. When you can drink milk as an adult, you have a condition called lactase persistence.

GenFun

Click on the picture below to launch an app where you can see a bit about what you can and can't learn from your DNA, And if you have results from 23andMe or Ancestry.com, you can upload them and learn a bit about your DNA.

ALS genetics SNP

-A curious adult from the UK

February 27, 2017

The answer to your question is: no. The DNA change you are asking about is found more often in people with ALS, but not by much. In other words, having this bit of DNA does not mean you will for sure end up with ALS.

ALS stands for amyotrophic lateral sclerosis. It is a neurodegenerative disease of the neurons that control the movement of our muscles.

What is rs3849942(A;A)?

Our DNA is basically a long string of letters that our body reads to build and run each one of us. There are only four letters in that string: A, T, G, and C.

More than 99% of the time, we have the same sequence of letters as any other person on Earth. But since we’re all a little bit different from each other, we all have some changes in our DNA that are different from the next person.

Why would rs3849942 be linked to ALS?

Scientists aren’t really sure why this SNP is linked with ALS. It might just be close to a gene that plays a role in developing ALS. If the SNP is close enough to a gene like this, it shows up as linked to ALS.

The bottom line is: having the SNP doesn’t cause ALS. Many other factors play a role in who gets ALS. Not smoking, for example, could theoretically offset someone’s chance of getting ALS, even if they had the rs3849942 SNP.

Bioengineering immortality

-A curious adult from Ivory Coast

February 15, 2017

That’s a very interesting question! The short answer is no, probably not for humans.

The most likely reason we get old and die is that living takes a lot out of us. The buildup of damage over time causes us to break down and eventually die.

When I say “mistakes” I mean damage done to the instructions that let a cell do its job. These instructions are in a cell’s DNA.

DNA damage can happen when a cell makes a copy of itself. DNA damage can also happen when we come into contact with something called a mutagen.

Mutagens cause mutations, or changes, in our DNA. The longer we live, the more time we have to be exposed to mutagens.

Not Worth the Energy

It takes energy to stay alive. It also takes energy to fix DNA damage.

Sometimes our cells don’t have enough energy to do both. So like someone on a budget, a cell has to “decide” where to spend its energy.

Inheriting Kabuki syndrome

-A graduate student from the UK

February 7, 2017

Odds are that your husband isn’t a carrier for Kabuki syndrome because of how it is passed on. It tends to follow one of three patterns.

The most common way for people to end up with Kabuki syndrome is that it literally appears of out nowhere. Basically, the person’s DNA ends up with a new mistake in it that did not come from either parent. This kind of new mistake is called a de novo mutation. 

Most People Do Not Inherit Kabuki Syndrome

Kabuki syndrome is pretty rare. Only something like 1 in 32,000 newborns are born with it each year.

People with this condition can have a wide variety of symptoms in many parts of the body. They often have arched eyebrows or larger ears. Some will also have trouble with thinking and understanding, so special education can be helpful.  Click here to learn more about the symptoms associated with this condition.

Autosomal Dominant Kabuki syndrome

Mutations in the KMT2D gene cause around 75% of Kabuki syndrome cases that have symptoms. So this is the most common cause.

Like the majority of our genes, most everyone has two copies of KMT2D. We get one copy from mom and one copy from dad.

There only needs to be a problem or mutation in one copy of the KMT2D gene to cause Kabuki syndrome. This is called autosomal dominant inheritance.

Ethnicity DNA Percentages Not Solid

-A curious adult from Florida

January 31, 2017

If the 51% were a rock solid number then yes, both parents would have to have some Italian in their DNA. After all, you only get 50% of your DNA from one parent! At least 1% of your Italian heritage would have had to come from the other parent.

But in the real world of DNA ancestry testing, that percentage is a bit more wishy washy. I think of them as telling you that a sizeable part of your heritage looks Italian in the DNA test. Could be lower, could be higher.  

Parent and Child with 40% Italian

To understand how a parent whose DNA looks to be 40% Italian might have a child with the same percentage, we need to take a step back and review how DNA is stored in our cells. And how it is passed on.

DNA is stored in something called chromosomes. People usually have 46 of these.

These chromosomes come in nearly identical pairs. One from each pair comes from mom and one from dad.

Imagine these are the 23 pairs:

Ancestry.com

Ancestry.com has a very useful resource that gives you the likely range of your percent ancestry. In other words, it lets you know how reliable that 51% is and what its upper and lower limits are.

Let’s use my results as an example. If I click on a particular ancestry, the following image comes up:

This is a little hard to see so I will break it up into two separate images:

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