Clever genetic tests, and mitigating the effects of Down Syndrome.

Down syndrome is a genetic disorder that presents itself right at the event of a child’s conception if said child has an excess amount of a particular portion of the genetic code embedded in its genetic makeup. Down syndrome occurs in about 0.13% of all live births and can manifest as physical growth defects, general mental slowness, and excessively impulsive behavior as the afflicted child matures. This genetic defect may also result in the loss of a pregnancy before birth as certain key developmental stages during pregnancy are perhaps significantly altered or hindered. Interestingly, this defect is more common with mothers that are of a relatively advanced age. Studies have shown that the frequency of down syndrome related pregnancies actually increases to ~1% in mothers that are 35 years of age or older. In our modern world where most women spend their 20s building careers, a lot of families now routinely have children while the childbearing mother is in her 30s and beyond. Thankfully, advances in modern medicine have yielded minimally invasive screening and diagnostic techniques that can tell a family with a high degree of certainty whether or not the current pregnancy is associated with a child afflicted by down syndrome. Such genetic screens and tests sound like sorcery at first… but the more I learn, the more I see that science at the highest level and sorcery are pretty much different sides of the same coin. At this point, the following questions have probably popped into your head: Is it really possible for medical professionals to tell that a baby has down syndrome without physically separating it from its perfectly healthy mother? How do such screens and tests work? Do these screens require drawing blood from the baby while it is still in the uterus? And if so, how do you draw blood from a baby in utero without killing it? These are all very good questions. Let’s now dissect the cause and effects of down syndrome in plain english from a genetic perspective, and hopefully get all your very astute questions answered in the process.

The human genome is a 3 billion nucleotide long set of instructions that codes for the physical and mental makeup of a human being. There are 4 unique nucleotides that serve as the building blocks of all human DNA sequences – Adenine (A), Guanine (G), Cytosine (C), and Thymine (T). The entirety of the human genome is contained within each of the trillion odd nucleated cells in our bodies. Yep… you read that correctly… all the genetic information that governs your form is contained in the epithelial cells in your mouth as well as in the Beta cells of your pancreas for example. It is all the more incridible that the entire genome can fit in each somatic cell because most somatic cells are so small that they cannot be seen without the aid a microscope. So how can something so large – 3 billion base pairs of the human genome – be contained in something so small – a single cell? The answer is that DNA doesn’t occur in our bodies in the plainly elegant “naked” double helix form that you have probably seen in textbooks or somewhere on the internet. Rather DNA is ingeniously packaged with special protein structures in a manner that facilitates a magnificent miniaturization of the genetic material to the point where it can fit into a cell. This DNA protein complex is often referred to as chromatin. A loose analogy to help you visualize the process of packaging DNA into a cell would be to consider how a really long string can be “miniaturized” into a ball of yarn by wrapping it around on itself multiple times. Now just magnify that miniaturization process about 10 million times and you’ll start to appreciate how awesome the process of fitting your genome into each one of your individual cells is.

The DNA protein complex known as chromatin doesn’t occur naturally as a single continuous entity, rather it is segmented into 46 parts in all healthy humans. These segmented portions of chromatin are called chromosomes. Healthy humans have 22 pairs of somatic chromosomes (numbered 1 through 22) and two sex chromosomes (X and Y if male, or X and X if female). Every so often though, a human is born with an extra copy of the 21st chromosome giving him or her 3 copies of chromosome 21 or what is technically called a trisomy (3 copies) at chromosome 21.

 

 

This anomalous genetic profile – 3 copies of chromosome 21 – is what is commonly known as down syndrome. Thinking deeper, one may start to wonder what causes an individual to be born with an extra copy of this chromosome. The simple answer to this question is usually that the ovum or egg cell in question brought an extra copy of chromosome 21 to its “fusion party” with its sperm cell counterpart during conception. During conception, a male sex cell (sperm) and a female sex cell (ovum or egg) fuse to form a fertilized egg which is technically known as a zygote. Nature in its infinite wisdom makes sperm and egg cells with only one copy of all chromosomes through a process called meiosis. Thus when sperm and egg cells fuse under normal circumstances, the resulting child should have two copies of each chromosome which is the normal state for a healthy human. In some rare cases however, the ovum may have an extra copy of Chromosome 21 due to a genetic/biological error. These types of genetic errors happen more frequently as we get older which is partly the reason why mothers over the age of 35 have an increased risk of bearing a child with down syndrome. If such an egg cell carrying 2 copies of chromosome 21 fuses with a sperm cell, the resultant child will end up with 3 copies of Chromosome 21 (2 copies from mom, one copy from dad) and the many life hindering qualities that come with down syndrome. Thankfully, we live in an age where modern science has come far enough to provide knowledge of a baby’s down syndrome status well before the pregnancy reaches term.

With the advent of genetic screening in modern science, we can now tell with a startling degree of accuracy if a pregnancy is associated with down syndrome by directly analyzing a sample of the mother’s blood at ten or more weeks into said pregnancy. If you’re like me, you’re probably wondering why we’d want to sample the mother’s blood when it is the genotype of the baby that should hold our interest. After all, if the mother were down syndrome positive, her physical symptoms would make it blatantly obvious. That is a fair point… but here’s why modern screening techniques sample mom’s blood when looking for down syndrome in her unborn child. Pregnant women are attached to their offspring as they develop in utero via an organ called the placenta. The placenta importantly allows for the exchange of gases (O₂ and CO₂), nutrients, and waste between mother and unborn child. It is important to note here that since the placenta develops from the same fertilized egg that yielded the baby, the placenta shares the same exact genetic makeup as the baby in most cases. With some non trivial level of frequency, some placental cells will break off from the organ itself and travel through the circulatory system into the mother’s blood. Like all things living, these placental cells will eventually “die” in the mother’s blood, releasing the DNA contained within them into the mother’s blood stream. This type of DNA is referred to as cfDNA (cell free DNA) because it is literally “free” of the confines of a cell. The presence of fetal/placental cfDNA in maternal blood is the main reason why a mother’s blood can be used as the input material for a screen that detects down syndrome in her unborn child. The explanation immediately above makes good sense at first glance. Upon deeper reflection though, you will notice another problem: even though there is some fetal/placental cfDNA in mom’s blood, it is only present in minute quantities relative to the mother’s genetic material… after all, it stands to reason that mom’s blood will be dominated by her own genetics. How do we prevent the dominant presence of the mother’s genetic material in her own blood from drowning out any signal from her unborn child’s cell free DNA?

 

 

The main source of mom’s DNA in her blood sample is from her blood cells, and finding a way to sequester these blood cells without disrupting them is key to protecting the information in her child’s cell free DNA which we are looking to analyze. Human blood contains mainly 3 cell types… red blood cells which carry oxygen around your body, platelets that act to clot wounds and prevent you from bleeding out when you get cut, and white blood cells which act as your immune system’s “special forces” specially designed to fight off infections like the common cold and other maladies when needed. These major cell types swim around in plasma which is the yellowish mostly-made-up-of-water fluid that serves as the liquid base of blood in our bodies. Our white blood cells are unique blood cells because they actually have a nucleus in which the mother’s entire genetic makeup is encoded. If too many of mom’s white blood cells are disrupted at any given time, the DNA released from them will completely dwarf the cfDNA from her unborn child. To prevent this from happening we must find a way to separate the cells in her blood from the plasma in which the child’s cfDNA lives.

We can actively separate the cellular components of maternal blood from plasma through density based centrifugation. To picture density based centrifugation, imagine a miniaturized merry go round that spins around really fast (about 1600 rotations per minute) and imagine upright tubes of blood steadily secured in place of the children that are usually fastened to the seats of this imaginary merry go around. If tubes of blood are subjected to these conditions for about 10 minutes, the cells will settle to the bottom because they are more dense, and the plasma (where the child’s cfDNA lives) will rise to the top because it is less dense. I should mention here that in the absence of a high speed centrifuge, you could just let the tubes of blood sit upright for a number of days and gravity will force the denser cells to sink to the bottom while the plasma rises to the top. The centrifuge just considerably speeds up the process. Having now eliminated any potential interference from maternal white blood cells, the plasma obtained from the mother’s blood is then used as the input to the genetic screen that is designed to detect down syndrome.

 

The genetic screen that is used to detect down syndrome is based on a method called DNA sequencing. DNA sequencing is an ingenious method that gives us the power to literally read off the sequence of nucleotides (A’s, C’s, G’s and T’s) that make up a section of DNA in the order in which they appear. cfDNA molecules are relatively small, ranging in size between 160 – 180 base pairs long so even though we can read off the sequence of nucleotides that make up a given cfDNA fragment, it is still a challenge to figure out where in the genome each cfDNA strand came from. Thankfully, some very intelligent scientists have designed computer programs that can take the sequence of each cfDNA strand (as determined by DNA sequencing) and map it back to the genome provided the strand is sufficiently long and unique. You may be wondering how long is sufficiently long and the answer to that is approximately 30 base pairs long or longer. Such computer programs are called “genetic sequence alignment tools”.

Let’s now use a practical example to show how the combination of DNA sequencing and genetic sequence alignment tools can be used in tandem to detect the presence of down syndrome. Imagine that we have three expectant mothers that have each given a blood sample to us and our task is to detect the absence or presence of down syndrome in their respective children. We will refer to these mothers as Patient A, Patient B, and Patient C. Here are the steps we would take to provide answers to these requests from our imaginary expectant mothers:

1. We’d use high speed centrifugation to separate plasma from the blood of each patient.
2. We’d use molecular biology techniques to extract cell free DNA from each patient’s plasma
3. We’d then DNA sequence the cfDNA extracted from each patient’s plasma
4. We’d align the cfDNA sequences we learned from DNA sequencing the samples to the reference human genome using genetic sequence alignment tools

At the end of the listed exercise above, we’d have some cfDNA sequences from all three patients that align specifically to chromosome 21 as depicted in the figure below.

 

 

If you look closely at the figure above, you’ll notice that Patient C has a lot more sequence reads that align to chromosome 21 relative to the other patients in the group. The only way this can be explained is that Patient C’s baby must have had an extra copy of chromosome 21 in its genetic makeup, contributing an excess number of Chromosome 21 sequences because the mother is normal. This is roughly how we’d conclude that the unborn child has a trisomy or three copies of chromosome 21. Note that I’m taking liberties to simplify here so that we can all understand. The actual process is much more intricate and complex than discussed above, but this conveys the general idea so that most all of us can understand.  

The technical name for the genetic screen designed to detect down syndrome is “Non Invasive Prenatal Screen” and it is available to most people in the developed world. As I type this, many companies are working very hard to make sure that more people across the globe can gain access to such vital information that implicates the well being of their children regardless of where they live on our planet. The advent of genetic screening has been met with a lot of skepticism and controversy because of some of the ethical issues that surround such sensitive information. The aim of this article isn’t to scare people with the effects and downsides of down syndrome, or the ethical implications of genetic screening. Rather, it is to get the word out to as many people as possible that the miracle of science actually now means that you can control more of your reproductive destiny. The knowledge of your unborn child’s down syndrome status only 10 weeks into a pregnancy gives you options. You can still choose to carry the baby to term, or choose to terminate it and try again. There are many ethical implications that come along with choosing to terminate a baby, but I don’t think it is my business or anyone else’s for that matter to tell people how to plan their families. After all, if a family has a child with down syndrome, it’s not like anyone is going to show up pro bono to help them care for that child for the rest of its natural life.

To conclude, you now know that valuable genetic information like the down syndrome status of your unborn child is available to you for a price (which is steadily dropping by the way). I hope you choose to use this information for the continued betterment of your life and of the lives of those closest to you. 
 
 
Without Wax
Oyolu B.C. Ph.D.
chubaoyolu.org
Visit our ETSY store!