11

Please, screen me

E pluribus unum (out of many, one)

ORIGINS UNCERTAIN

When Rachael and Jonathan Casella decided it was time to try for a baby, Rachael went to see her doctor, to make sure she was well prepared. The advice her doctor gave her was good, as far as it went. Look after your health; take folic acid, which reduces the baby’s risk of having some serious malformations.114 Once you’re pregnant, you can choose to have a screening test to see if the baby is likely to have Down syndrome — something Rachael went on to do. Unfortunately, however, the advice didn’t go far enough. Not having heard about the option of genetic carrier screening, Rachael’s doctor didn’t tell her about it.

[1 These are called neural tube defects, and they can be very severe. Among others, these conditions include anencephaly, in which the brain, top of the skull, and scalp do not form; and spina bifida, in which the spinal cord is open to the outside, and the amniotic fluid damages the cord, paralysing the baby below the level of the opening. Taking folic acid before pregnancy and in the early weeks of pregnancy greatly reduces the likelihood of having a neural tube defect — it’s one of the great public health wins of the later 20th century.]

Mackenzie Casella was a beautiful baby. Alert and smiley, in photographs her eyes are bright with intelligence. In a better world, she would have grown up into a beautiful young woman, would have gone to school and to university, and would have lived the full life her parents dreamed of for her. In the world as it is, none of those things happened, because Mackenzie had spinal muscular atrophy, and her life was just seven months long.

SMA, as you’ll remember, is a progressive condition that affects the nerves in the spinal cord that control the muscles. In a person affected by SMA, those nerve cells wink out like stars in the dawn sky. Without them, messages from the brain can’t get to the muscles, and the effect is muscle weakness that relentlessly gets worse. When Mackenzie was diagnosed, gene therapy for SMA wasn’t yet an option. Rachael and Jonny were offered the option of taking part in a trial of treatment with another drug, Nusinersen, but they made the difficult decision that this was too uncertain a prospect, and was too likely to leave their daughter — who was already showing signs of weakness that had led to the diagnosis — living with a poor quality of life. So they launched into making their little girl’s short life as full as it could possibly be, giving her all the experiences they could. Snow, sun, sand; every day held something new. Mackenzie’s life was joyful — but from the time of the diagnosis, her parents lived with the knowledge that it would be very short, and so it proved.115

[2 Rachael has written a book about Mackenzie’s life and what happened next, called Mackenzie’s Mission. It’s a moving personal account and well worth a read.]

Mackenzie’s doctor was Michelle Farrar, who has been at the forefront of research into the treatment of SMA. When she first met the Casellas, they asked the questions all parents have when faced with news like this. Why did this happen? Then, when they learned that this was a genetic condition, and that they were almost certainly carriers, they asked — why didn’t we know? Gently, Michelle explained that almost all parents of children with SMA are in the same boat as the Casellas: they have no family history, and only find out they are carriers once the diagnosis is made in their child. There are screening tests available that can identify carriers, and which could have told them that this could happen — but you can only have screening if you know it is an option.

The news shocked and distressed Rachael and Jonny, as it must have shocked and distressed many others in recent years, since screening first became available. But right from the beginning, in the midst of their grief, there was something else: determination. This, they decided, was a situation that could not continue — something needed to be done.

So they set out to do it.

*

Screening for genetic conditions has a longer history than you might imagine, going back more than 60 years. Among the many who have contributed to the story of screening, there are two names of special note — Bob Guthrie and George Stamatoyannopoulos. Of the two, Guthrie is by far the more famous, but perhaps with time the name of Stamatoyannopoulos will become as well known.116

[3 In his later career, Stamatoyannopoulos was a pioneer of gene therapy; his long and illustrious career extended from before the sequence of the first gene was discovered, until a time when gene therapy became a reality.]

I have met perhaps a dozen people with phenylketonuria (PKU). Of those, only one has had the classical features of this rare condition. Frank was a man born in the 1930s, before newborn screening for PKU began. At the time I knew him, he was in his 60s and had never learned to speak. His head was very small, he had a history of seizures, and the staff at the institution where he lived reported that he was often aggressive.

By contrast, all of the other people with PKU that I have met have been well, healthy children or adults, with normal intelligence and no neurological problems. The contrast between them and Frank could not have been more stark, and the reason for it was that they had all been screened for PKU in the first week of their lives. The early diagnosis had made it possible to start treatment immediately, and completely prevent the damage to their brains that otherwise would have been inevitable.

PKU is another metabolic condition, a disorder of the body’s chemistry, and it has to do with how the body deals with an amino acid called phenylalanine. Our bodies use amino acids to build proteins, and, in turn, when we eat foods that contain protein, we are consuming amino acids. In most of us, an enzyme converts the phenylalanine we eat into another amino acid, tyrosine. In people with PKU, that enzyme doesn’t function properly and levels of phenylalanine soar.

Unfortunately, at high levels, it is toxic to the brain. During pregnancy, the placenta filters the baby’s blood and no harm is done, so that babies with PKU are born with perfectly normal brains. As soon as they start drinking milk, they are taking phenylalanine into their bodies and the damage starts.

In the 1950s, a German doctor, Horst Bickel,117 showed that a diet very low in protein could lower levels of phenylalanine in the blood, with some benefits for people with PKU. Bickel and two colleagues published a paper describing the first successful treatment of a child with PKU.118 The paper, published in the journal Lancet in 1953, makes for somewhat confronting reading by today’s standards. Part of that is the bluntness of the language, which to be fair was usual for the time. ‘She was an idiot and unable to stand, walk, or talk: she showed no interest in her food or surroundings, and spent her time groaning crying, and banging her head’. The paper describes a series of experiments to modify the food the girl was given, ending up with a diet containing almost no natural protein, tiny supplements of phenylalanine to supply the body’s essential needs, and the addition of a special formula that contained all of the other amino acids, except phenylalanine. The effects were dramatic: the child learned to crawl, then to stand; ‘her eyes became brighter, her hair grew darker; and she no longer banged her head or cried continuously’.

[4 By a nice coincidence, Bickel and Guthrie shared a birthday, 28 June, which is now international PKU day.]

[5 Unusually, we know the girl’s name: Sheila. She was diagnosed aged 17 months and, reportedly, her mother begged Bickel to try to find a treatment for her. Against enormous odds, Bickel and his colleagues succeeded.]

So far, so good. But how to be sure it was the treatment that was doing this? Even in 1953, it’s clear that Bickel and his colleagues were aware of the risks of introducing a treatment that only seemed to work. To make sure, they decided to add a large amount of phenylalanine back into the formula. This is scientifically sound: try a treatment, see what happens, withdraw it, see what happens, start it up again. The part that is shocking to a modern reader is that they deliberately concealed this plan from the child’s mother. They wanted her to be an unbiased observer of what happened after the phenylalanine was re-introduced. What happened was instant regression: within a day, the girl had lost nearly all the gains of the preceding ten months. Remarkably, the child’s mother then agreed (perhaps in reality she was given no choice) to a repeat of the experiment. Again the girl was given the phenylalanine-free formula and learned new skills, again (this time during a hospital admission) the toxic (to her) amino acid was added in, again the skills were lost. The treatment worked. Although Sheila undoubtedly had some permanent brain damage, in the long run, she must have been far better off with the treatment than she would have been without it.

Within a short time, this new way of treating PKU was being widely adopted. Treated children made significant gains, and the younger they were when the treatment was started, the better the outcome. This was because there was always some damage that could not be reversed, and the older the child, the further the damage had progressed. A grim clock was ticking from the moment of birth, counting out the time before it was too late to start treatment. Decades later, in the 1990s, I met Frank soon after his diagnosis was made, and we started treatment. There was some improvement in his behaviour, but that was all: the chance for meaningful benefit had long passed.

Back in the 1950s, the best results of all were in babies diagnosed soon after birth not because of symptoms in themselves but because they had an affected older sibling. From those early trials, the early indication — since proved correct — was that the fate of an affected baby could be utterly changed, with a devastating neurological injury completely avoided.

PKU had become a treatable disease,119 and the stage was set for Bob Guthrie’s rise to greatness.

[6 The treatment is very effective, but can be a real challenge for families to manage. The diet is extremely strict, the essential supplements are becoming more palatable but still have a very distinctive taste, and regular blood tests are needed. Especially strict management is needed when a woman with PKU has a pregnancy, because even moderately raised levels can be very harmful to the developing baby. As a side note, if you drink diet soft drinks, have a look at your next can: it may well say ‘Phenylketonurics — contains phenylalanine’ on the side. The artificial sweetener aspartame contains phenylalanine; even the small amount in a can of Diet Coke could be a problem for someone with PKU.]

Guthrie seems to have been something of a difficult character. The tributes written by colleagues after his death are carefully worded, in a way that tells its own story. I asked Bridget Wilcken about Guthrie. Bridget herself is something of a legend in the world of screening — she steered newborn screening in New South Wales through its first 50 years, and has been a world leader in the field for decades. She spoke of Guthrie’s great contributions to medicine, but she also told me that, many years ago, Guthrie was a guest at her house. He omitted to tell her, until dinner was already served on the first night, that he was a vegetarian. It just hadn’t occurred to him to mention it. This was at a time when it was uncommon to be vegetarian, and as a host you wouldn’t think to ask. Others speak of Guthrie calling collaborators at all hours of the night to discuss some new idea, or the details of an ongoing project. Later in the story of screening, he apparently resisted the addition of some other conditions to newborn screening, perhaps because they didn’t form part of his vision for the test.

Perhaps, though, that one-eyed focus on the task at hand was the secret of his success. Guthrie was a father of six; his second child, John, had intellectual disability and as a result, Guthrie and his wife became very active in the Buffalo Chapter of the New York State Association for Retarded Children. Through meetings of this group, Guthrie became aware of the existence of PKU and its treatment. One of the difficulties of managing PKU was measuring the levels of phenylalanine in the blood. Guthrie had been working in cancer research for over a decade and realised that it would be possible to adapt a simple test he had been using in his work to do this.120 He moved to the Buffalo children’s hospital and began developing the test. One of his greatest achievements, and one of which he was most proud, was the development of filter-paper cards onto which blood from the baby’s heel is dropped. Once the blood has dried, the cards can easily be mailed back to the laboratory that does the testing. If you’ve had a baby, it’s almost certain that he or she was screened, using tests that are only possible because of the existence of these cards, which are still known as Guthrie cards.

[7 The test is simple but elegant. Bacteria are grown on agar jelly that contains a substance that stops the bacteria from using phenylalanine. This inability to use the amino acid prevents them from growing — effectively they are being starved. A circle of filter paper soaked with the baby’s blood is placed on the agar. If there is a lot of phenylalanine in the blood, it overcomes the effect of the blocking substance, and the bacteria can grow. The more phenylalanine, the better the growth. You put spots of blood from lots of children onto a tray of the jelly, keeping track of which spot came from which baby, of course; incubate; then see which spots (if any) have made the bacteria grow.]

Once the test had been developed, it became possible to diagnose babies with PKU in the first weeks of life, before irreversible damage had been done to their brains, and get treatment started. Guthrie made it his mission to promote screening and to make it possible for others to get started. The first trials of screening using this method121 began in 1960, and, by 1963, 400,000 babies from 29 US states had been screened, with 39 babies with PKU identified — and saved.

[8 A less effective urine-based test had already been introduced in some areas.]

One reason for the rapid early progress of screening was that US president John F. Kennedy had a sister with intellectual disability, and had ensured that the Children’s Bureau, which had oversight of this kind of program, was well funded. There are other examples of politicians with a connection to an issue making a difference of this kind; particularly relevant for our purposes is former British prime minister David Cameron, whose son had a rare, severe form of epilepsy, Ohtahara syndrome. Cameron’s interest in genetic conditions had a great deal to do with the subsequent developments in genomic medicine in the United Kingdom, which has a world-leading diagnostic and research program.

Over more than half a century, newborn screening has improved and prospered. Most services in developed countries screen for 40 or more different conditions. Not all have such clear-cut benefits from early diagnosis as PKU, but there is no doubt that many tens of thousands of children have had their lives saved, or profoundly improved, by that simple heel prick. Because it seems like such a simple thing, it’s easy to take newborn screening for granted. Unless someone in your family is affected by one of the conditions, it’s something that barely touches your life. A few minutes of time lost in the flood of events and emotions soon after the birth of a new baby — many people quickly forget the test was even done. But make no mistake, this is one of the great triumphs of medicine.

Newborn screening, wonderful though it is, has the disadvantage that it can only ever be done on a child who has already been born. For many conditions, however, there are no effective treatments yet, and many parents would prefer to have a choice about whether they will have a child with a significant genetic condition. For this reason, screening for genetic conditions during and even before pregnancy has been developed.

Screening for genetic conditions during pregnancy also goes back a long way. As early as 1955, a method had been developed for collecting a sample of amniotic fluid during pregnancy (amniocentesis), and this was initially used for determining the sex of the fetus by examining the cells found in the amniotic fluid. By 1966, the technique had been improved to the point that cells from the amniotic fluid could be grown in the laboratory and their chromosomes analysed. In 1968, a 29-year-old woman who was known to have an inherited rearrangement of her chromosomes122 that gave her a high chance of having children with Down syndrome attended the Downstate Hospital in Brooklyn, New York. She was 16 weeks into her third pregnancy, having already had a healthy daughter and a son with Down syndrome. An amniocentesis was done and showed that this fetus was also affected, and the woman chose to have a termination of pregnancy. At this time, amniocentesis had already been used to diagnose several different conditions in the fetus with biochemical tests. Now, for the first time, a genetic test had been used to make a diagnosis during pregnancy. The next few years saw rapid development in the field of prenatal diagnosis. Once the technical skills to perform the procedure and the laboratory capacity to do the analysis became widely available, screening of large numbers of pregnant women also became a possibility.

[9 A Robertsonian translocation, to be exact.]

Over the decades that followed, screening for Down syndrome (and, later, other chromosomal conditions) has been performed using ever more sophisticated methods. The goal is to identify pregnancies with a higher chance of being affected, so that an invasive test such as amniocentesis123 need only be offered to a subset of women to definitively answer the question as to whether the baby is affected. The first screening test was simply to ask the woman her date of birth. The chance of having a baby with Down syndrome, and some other chromosomal conditions, rises with the mother’s age.124 Women are born with all the eggs they will ever have, held in a kind of suspended animation just short of maturity. If you have just turned 35, your eggs are a little older than that … and their capacity to complete that last step in their development without errors has been declining slowly for years. There’s no hard age cut-off at which the chance of having an affected baby suddenly jumps up; the probability rises slowly and smoothly, although the curve does steepen in the mid-30s. For a 20-year-old mother, the chance of having a baby with Down syndrome is about 1 in 1,500; for a 35-year-old, it’s 1 in 340; and for a 45-year-old, it’s 1 in 32. When I started in genetics, one of the main reasons for having a prenatal test for chromosomal conditions was still ‘AMA’ — advanced maternal age.125

[10 Chorionic villus sampling (CVS) is the other main method in use.]

[11 Men aren’t completely off the hook here, because some other types of genetic condition become more likely as fathers age.]

[12 I once put my foot in it very badly by wishing one of our genetic counsellors ‘happy AMA day’ on her 35th birthday. The term ‘advanced maternal age’ is unfortunate, considering that 35 years is not really an advanced age in most other contexts. There’s an even worse term in obstetrics — an ‘elderly primigravida’ is a woman who becomes pregnant for the first time at 35 or older. ‘Elderly’? What were they thinking?]

This approach reduces the number of women who might receive more-invasive screening, but the problem remains that, if there is a 1 in 200 chance that an older woman is carrying a baby with a chromosome condition of some kind, the follow-up invasive testing will return 199 negative results for every one affected pregnancy that you identify. When you consider that amniocentesis carries a roughly 1 in 200 chance of causing a miscarriage, you can see that there’s a trade-off happening. Are those 199 tests, with their costs and the anxiety they cause, plus one miscarriage, worth identifying one affected pregnancy?

On top of that, screening only women aged 35 and above will miss most affected pregnancies, because, even today, the great majority of babies are born to younger women.

There have been various efforts to address these problems. The first worked by measuring combinations of several substances in the mother’s blood that change during pregnancy, with levels that tend to be higher or lower if the baby has a chromosomal problem. The results of these tests, combined with the mother’s age, were used to refine the risk assessment. Later, measurement of the thickness of skin at the back of the neck was added into the calculation. Many different medical conditions, including Down syndrome, can lead to a build-up of fluid in this area early in pregnancy, so the measurement improved the accuracy of the screen.

Every version of these tests still suffered from the same basic problem. Even as they became more sensitive, with lower false-positive rates, that trade-off remained; for most women who were flagged as being at higher risk, it was still much more likely that, if they chose to have an amniocentesis, the result would be normal — yet they still were exposed to the risk of miscarriage from the procedure. In that sense, having a screening test carries risks — the risk that you might have an invasive test you don’t need, and possibly even lose the pregnancy.

Recently, a far better screen has become available.126 Non-invasive prenatal screening (NIPS) uses the new genetic sequencing technology in a nifty way: it treats DNA simply as something to be counted. Usually, when we extract DNA from a blood sample, we take it from the white blood cells, each of which has a nucleus (red blood cells have lost theirs, and their mitochondria, so they don’t contain DNA). However, there is a small amount of DNA in the plasma, the fluid that makes up the half or so of your blood that isn’t blood cells. In the late 1990s, it was discovered that, if you take blood from a pregnant woman, discard the cells, and extract DNA from the plasma, some of that DNA will come from the placenta. It’s often called the fetal fraction, but the fact that the DNA is from the placenta, not directly from the fetus, is important. We’ll see why shortly.

[13 It’s a bit harder to pin down who the key people were for some of the prenatal screening methods, because of contributions from many different people over a long period of time. But Dennis Lo from Hong Kong was the first to develop NIPS, and Kypros Nicolaides from London led the use of ultrasound for Down syndrome screening.]

There are different ways that NIPS can be done, with several companies having come up with their own approaches. The most common approach involves sequencing DNA using one of the new sequencers that reads many individual strands of DNA at once (the same ones discussed in chapter 5). Sequences are read from regions spread across the genome. Each continuous stretch of sequence, representing one molecule of DNA, is a ‘read’. The fetal fraction varies between blood samples, but suppose for example that it is 9 per cent. On average, you expect that, at any one place, there will be 100 reads from the mother’s DNA and ten from the placenta (representing the fetus); ten out of 110 is 9 per cent. You don’t necessarily even have to distinguish which are which: all you need to do is count. If you have, on average, 110 reads for every chromosome except 21, but 115 reads127 across chromosome 21 — then there are half again as many from the placenta as you expect: there must be three copies of that chromosome instead of two. The baby has Down syndrome.

[14 You’ll likely need to do more sequencing than 110 reads for the statistics to work, but the principle remains the same.]

Except if it doesn’t.

There are various ways you can be fooled into thinking the baby has a chromosome abnormality when really it doesn’t. One of the most important reasons128 this can happen is that, sometimes, there are chromosomal changes in the placenta that are not in the fetus. The early embryo is a ball of cells that splits into two: part of it goes on to become the fetus, and eventually the baby, and the rest becomes the placenta, membranes, and so on. If a mistake in cell division happens after that split, the placenta can have a chromosome change it doesn’t share with the fetus … and since the fetal fraction is really a placental fraction, the test can be fooled. It really is correctly counting an extra copy of chromosome 21 — it’s just that the extra copy is in a tissue where it doesn’t matter.

[15 Most of the other reasons are technical, but a rare cause is that the mother has cancer, the cancer cells have abnormal chromosomes, and they in turn are spilling DNA into her blood that has abnormal chromosomes. There have been a number of women around the world who have unexpectedly had a cancer diagnosis made this way.]

This means that this truly is a screen. It’s often called ‘non-invasive prenatal testing’ (NIPT), but I strongly prefer ‘non-invasive prenatal screening’ for this reason. There is good reason to believe that some obstetricians have misunderstood NIPS reports and acted on that result alone, without doing a confirmatory test.129 If so, there would certainly have been some terminations of pregnancy that were done based on a mistake, with the baby not having had any chromosomal abnormality at all — a disturbing thought.

[16 Ideally the confirmatory test would be an amniocentesis, because chorionic villus sampling also looks at the placenta rather than directly at the baby.]

Don’t get me wrong — NIPS is very good at what it does. It misses far fewer affected pregnancies than the other screening options, and a positive result is much less likely to be wrong. In the time since NIPS first became available, we’ve seen a sharp fall in the number of prenatal tests being done, thanks to this better performance. Recently, however, the trend has been reversing, because of mission creep.

Most NIPS is provided by private companies, and there are limited ways that they can compete with each other. Price is one option, obviously, but making the case that their test is better in some way is another. One way to do that is to test for more conditions than the competition. NIPS started out looking for extra copies of chromosomes 13, 18, and 21 as well as extra or missing copies of the sex chromosomes. As we’ve seen (in chapter 4), testing for sex chromosomes has the potential to produce results that are not straightforward. Still, overall, this approach produced a relatively small number of false-positive results — more for chromosomes 13 and 18 than for 21, but, even so, a NIPS result that says there is a high chance that the fetus has an extra copy of chromosome 13 has a reasonable chance of being correct.

Adding in extra targets has been … problematic. Some companies have added in screening for relatively common, but still rare, abnormalities, such as the deletion on chromosome 22 that causes velocardiofacial syndrome (or Sedláčková syndrome if you prefer). Others have taken to reporting differences affecting other chromosomes if they happen to show up in the data, such as an extra copy of chromosome 10.

One of my jobs in the lab is to issue reports about prenatal diagnostic tests. So far, I have only seen one ‘extra target’ NIPS result turn out to be a true positive that we confirmed at amniocentesis, a large chunk missing from one chromosome. All of the follow-up tests for smaller deletions that I’ve reported on so far have been negative, although presumably at some point that will change.

The reason for all these false positives is mainly a simple quirk of statistics. It’s one that can affect all sorts of laboratory tests, and it can be summed up like this: the rarer the condition, the more likely a positive test result for that condition will be wrong. Unintuitively, the exact same test can give you different results, depending on whom you are testing.

NIPS test reports often include a statement similar to: ‘this test is 99.9 per cent sensitive and 99.9 per cent specific for the detection of Down syndrome’. That sounds very impressive, and it is: 99.9 per cent sensitive means that if 1,000 women who were carrying a baby with Down syndrome had the test, 999 would have a positive result, and only one would be missed. That’s really good, way better than the best of the previous options, which would detect 900 and miss 100, rather than just one. The problem lies in the other number, the specificity: 99.9 per cent specific means that if 1,000 women carrying a baby without Down syndrome had the test, one would have a false positive.

One out of a thousand doesn’t seem so bad, does it? To see why this isn’t as good as it sounds, here are some simple numbers that are made-up but make the point. Let’s say you have two groups of women. Group A have a 1 in 100 chance of having a baby with Down syndrome, because of their age. Group B are younger and only have a 1 in 1,000 chance. A thousand women from both groups have NIPS done, using a test like the one described above.

In the 1,000 women from Group A, with a 1 in 100 chance, there are 10 affected pregnancies. The test is so sensitive that all of them are detected. There is also one false positive (the 1 in 1,000 chance comes up). That means there are 11 positive results, of which 10 are correct. For these women, a positive result has a 10 out of 11 chance (91 per cent) of being correct.130

[17 This is called the positive predictive value (PPV) of the test.]

Now we test 1,000 women from Group B. There is one affected pregnancy, with a (correct) positive result. There is also one false positive. For these women, a positive result has only a 1 in 2 chance (50 per cent) of being correct. A positive result from exactly the same test has a different meaning in the two groups.

As you can see, the rarer a condition is in the population that’s being tested, the lower the chance that a positive result will be correct. If the specificity is a bit lower (because you are looking for a smaller target than a whole chromosome, for instance) things will get worse. Because the tests were originally designed to look for the most common problems, each extra condition you add is going to be rarer than the last, and the test will perform worse as a result. In the last couple of years, we’ve started to see the number of invasive tests in pregnancy rise again. Is more better? Is it a good idea to extend these tests out to look for rarer conditions? If you get a true positive for a rare condition, giving you options you wouldn’t otherwise have had, you might think it is. If you have a miscarriage due to an invasive test that was done because of a result that then turned out to be a false positive, you may think otherwise.

*

At about the time Rachael and Jonny Casella were learning the terrible news about their daughter Mackenzie’s diagnosis, the parents of two other children who were patients of Sydney Children’s Hospital were hearing similar news, and they were hearing it from me. Twice in the space of ten days, I had much the same conversation, gave the same stark message. We know now why your child has been having these symptoms. This condition is not curable, it will steadily get worse, and within a few years it will be fatal.

No matter how carefully or kindly, no matter how well you deliver news like this, you know that it is a hammer blow. For the parents, this will forever be remembered as one of the worst days of their lives.

At some point — often in the very hour that they learn the diagnosis — parents who receive news like this will ask the same question that Rachael and Jonny asked. Why did this happen to our child, to us? Wasn’t there something that could have been done? These days, they have often had screening for chromosomal disorders during the pregnancy, and it’s common that they mistakenly think that this was a test for all genetic conditions. So there’s another question — we had all the tests, why wasn’t this picked up?

For almost everyone who has a child affected by an autosomal recessive condition, there is no family history, no prior warning of the risk. For X-linked conditions, there may be a family history, but often there isn’t. This means that the only way to find out if you’re a carrier before having an affected child would be to have a carrier screening test. For most of my career, there simply haven’t been such tests available for most conditions, for most people. When I gave parents this type of bad news, I could at least look them in the eye and tell them there was no way they could have known in advance that this could happen to their child.

Now, though … things are changing.

Several years ago, when it first became evident that massively parallel sequencing was going to become available for reasonable prices, I started to think about carrier screening in earnest. In that, I was well behind the times.

Usually, being a carrier for a recessive condition is neither here nor there. It does you no harm, but it also does you no good. There are exceptions, however, and the best known of these has to do with malaria and a group of conditions that affect red blood cells. The various forms of the malaria parasite (species from the genus Plasmodium) have a life cycle that shuttles back and forth between humans and mosquitoes. In humans, the parasite spends part of its life living inside red blood cells (which are consumed by mosquitoes, which subsequently infect other humans, and so on). There is a group of blood conditions, the thalassaemias, in which the oxygen-carrying protein, haemoglobin, is abnormal, and in turn the red blood cells that contain haemoglobin are abnormal. They are fragile and don’t last very long in the bloodstream after they form; at worst, affected children would be lucky to make it to their third birthdays unless they have regular blood transfusions.

For carriers, though, the news is rather better. Their mildly fragile red cells do a good-enough job of carrying oxygen through the body, and usually this causes no health problems at all. But from the point of view of a Plasmodium,131 those mildly abnormal cells are an uncomfortable place to be. This gives partial protection against the effects of malaria, and especially against its most severe forms. Malaria remains a serious killer: according to the ongoing Global Burden of Disease study, 619,827 people132 died of malaria in 2017, out of 56 million deaths in total. Reduce your risk of death from malaria, and you increase your chances of living long enough to have children, and pass on your genes to the next generation. That’s called a selective pressure — if people with a particular type of genetic variation are more likely to successfully reproduce, that variation will become increasingly common in the population.

[18 To the extent that a Plasmodium has a point of view.]

[19 Yes, this is a suspiciously precise number. In case you’re interested, the top three killers were cardiovascular diseases with 17.8 million, cancers with 9.6 million, and respiratory diseases with 3.9 million. Malaria killed more people than many other causes, including murder (405,346), drowning (295,210), terrorism (26,445), and disasters (9,603). Malaria killed 23 people, mostly small children, for every one who died due to terrorism in that year. This is why the front page of your newspaper is forever running banner headlines about the ongoing malaria disaster. It isn’t? … nor mine, for some reason.]

The mosquitoes that can carry malaria like it hot, or at least warm: before people started trying to do something about it, malaria was found as far south as 32° of latitude, and as far north as 64° (!) … but it was always most concentrated in a belt around the equator, and has largely remained so. Where malaria is or was, you can expect to find thalassaemia and related conditions, and carrier frequencies can be very high indeed.133 This includes most of the countries around the Mediterranean — which brings us to Italy, to Greece, and then to Cyprus.

[20 You might think that a condition that is fatal when you have two copies of a faulty gene would be prevented by that from becoming common in the population. Consider though, that if 1 in 10 people is a carrier for a condition, in only 1 in 100 couples are both partners carriers (1/10 times 1/10), and therefore only 1 in 400 children are affected (1 in 100 times the 1 in 4 chance for each baby born to a carrier couple of being affected). If there is a benefit to carriers, 1 in 10 people benefits, but only 1 in 400 suffers negative consequences.]

In 1955, the Italians Ida Bianco and Enzo Silvestroni suggested the possibility of preventive counselling: if you identify couples who are carriers, you could counsel them against having children. George Stamatoyannopoulos, fresh out of medical school, took on the challenge. In 1966, he went to Orchomenos, a village in Greece with a population of 5,000, and started screening for sickle cell disease (a variant of thalassaemia that is common in Africa but also crops up in some other places, including parts of Greece). There were a lot of carriers: nearly a quarter of the population. About 1 in 100 babies born in the village was affected. Stamatoyannopoulos advised unmarried carriers to steer clear of each other and choose non-carriers to marry, but, when he returned to the village, he found that his advice had been ignored. In that sense, the effort had not been a success — but the first attempt at carrier screening for reproductive purposes had been made, and a great deal had been learned. In 1971, when the World Health Organization called on Stamatoyannopoulos to visit Cyprus and advise about the problem of thalassaemia on that island, he was well prepared.

The situation in Cyprus was not unlike that of Orchomenos, although it was at the scale of an entire country rather than a single village. The carrier frequency for thalassaemia and the frequency of affected babies were just a little lower than for sickle cell disease in Orchomenos, but the impact on peoples’ lives and on the health system was considerable. Nearly half of the output of the blood bank in the capital, Nicosia, was being used for keeping people with thalassaemia alive, and, at the end of that decade, 6 per cent of the entire budget of the Ministry of Health was being spent on a single drug, desferrioxamine, which is needed to treat people for the dangerous overload of iron that comes with frequent blood transfusions.

It took much of the 1970s to figure out how best to do carrier screening and get it working effectively. An early effort to persuade carrier couples not to marry each other was just as unsuccessful in Cyprus as it had been in Greece. By 1977, it had become possible to do prenatal diagnosis, and attention was focused on screening people of reproductive age in order to give them information on which they could consider acting. This won strong support from the Church of Cyprus, because of the realisation that there were fewer terminations of pregnancy as a result of prenatal testing. Up to that point, many people who knew they had a 1 in 4 chance of having an affected baby were choosing termination of pregnancy rather than take that chance. For those couples, prenatal diagnosis meant that three out of four pregnancies could be shown to be unaffected, and thus would continue.

In 1979, the expected number of affected babies born in Cyprus (based on historical figures) was 77, and the actual number was only 18. Given a choice, couples were choosing to take steps not to have affected children.

The story of carrier screening in the decades since then has been one of mixed successes and mostly slow progress, until a recent boom. Carrier screening for the thalassaemias and related conditions, targeted at people from populations where these are common, is cheap and generally quite effective in many countries around the world. There are targeted screens for some other conditions, too.

In this regard, Israel is the undisputed world leader. There are a number of recessive conditions that are more common in people of Jewish ancestry, especially the Ashkenazi Jews (those who trace their ancestry to Central Europe). Most infamous of these is Tay-Sachs disease, another lysosomal storage disease that affects the brain. In the classical form of Tay-Sachs, most affected children do not reach their fourth birthday. There are community-led screening programs for Jewish people in various parts of the world, but in Israel the Ministry of Health offers free screening to everyone who is planning a pregnancy or is early in a pregnancy. It’s all targeted, to a very fine level of detail. There’s a list of genes recommended for most of the population, then different sets depending on ancestry — for Ashkenazi Jews, for Jews of North African origin (except Morocco), for Jews of Moroccan origin, and so on; and also for those from other populations: there’s a specific list just for Bedouins in the Negev region, for instance.

In much of the rest of the world, in order to access carrier screening, you need two things that not everyone has: information and money. You need to know that the tests exist, and you need to be able to afford to pay for them (or have health insurance that will pay for them).

Currently available tests range from covering as few as three conditions to as many as hundreds. ‘Three conditions’ in this case usually means SMA, which we’ve encountered already, cystic fibrosis (CF), and fragile X syndrome. CF is a complex condition in which the body’s secretions are thicker than they should be. That might not sound so bad, but it really is — untreated, this causes children to have progressive, serious lung infections and severe nutritional deficiencies due to failure of the pancreas; in the past, most affected children did not make it to adulthood. Modern treatment makes a lot of difference to the condition, with greatly improved life expectancy, but is burdensome on child and family. Fragile X syndrome is a common cause of intellectual disability. If someone is offering a screen for hundreds of conditions, they will almost always include these three.

This was the news that shocked Rachael and Jonny Casella. Had they known about SMA carrier testing, they could easily have found out that they were carriers before having a pregnancy — opening up choices, including PGT and prenatal diagnosis.

They became powerful advocates for screening, starting by writing to every member of the Australian Federal Parliament, as well as to New South Wales state politicians. They met with the state health minister, with the federal deputy health minister, and finally with the federal minister for health, Greg Hunt.

By a remarkable and fortunate coincidence, at much the same time that the Casellas began their advocacy, a group of researchers were talking to the government about the same topic. Nigel Laing, an internationally renowned expert on the genetics of muscle diseases who had advocated for carrier screening for many years, had convened a meeting of interested Australian doctors and scientists in late 2016. I attended the meeting and spoke about some research I had led, studying screening in couples who were related to one another. Because we share genes with our relatives, such couples have a much higher chance of having children affected by recessive conditions than those who are unrelated. We showed that screening using a very large panel of genes, about a quarter of the exome, worked well in such couples and was acceptable to them.

Thanks to Nigel’s leadership, the nucleus of an Australian team of carrier screening researchers was already in place in 2017, when I had to give terrible news to parents twice in ten days. That experience prompted me to reach out to the group, and together we decided to write to the federal health department to suggest that this was an area which needed attention.

A series of meetings in Canberra followed. There was support in principle within the health department for a pilot project, but nothing concrete was on the table. Unknown to us, however, we had a secret weapon: the Casellas. Michelle Farrar, Mackenzie’s neurologist, introduced me to Rachael and Jonny, and they arranged for us to be in the room when they met with Minister Hunt. The Casellas spoke about Mackenzie’s life and about their loss. They urged action on carrier screening. It was obvious that the minister was deeply moved by their story, as was everyone in the room. Hunt, already a strong supporter of research into genomic medicine, promised that he would take action, and he has been as good as his word. The government committed $20 million to a research project aimed at determining how best to introduce carrier screening to Australia, with the goal that screening should be available free of charge to any couples who wish to access it. The project was christened Mackenzie’s Mission by Hunt.

I am co-leading the study with Nigel Laing and Martin Delatycki,134 an eminent geneticist from Victoria who is a long-time advocate for screening for genetic conditions. We plan to screen 10,000 couples over the course of the study, with research into every aspect of carrier screening. You might think there are few questions left to answer about such a simple concept, but it’s surprising how many details remain to be worked out about how best to deliver screening.

[21 Working with Martin and Nigel, and with the many, many others involved in the project, has been a wonderful experience. It seems like nobody ever says no to helping with Mackenzie’s Mission.]

A major task in the first year of the project was to work out what, exactly, we should be screening for. This might seem easy enough — it’s a matter of choosing severe genetic conditions and screening for those, right? But straightaway that introduces difficulties. What do you mean by ‘severe’? There are plenty of conditions for which this is easy. Uncombable hair is an autosomal recessive condition;135 few people would consider that severe enough to screen for. The information just wouldn’t be useful to most people — certainly it’s unlikely that many people would change their reproductive decisions on that basis. At the other end of the spectrum, a lethal condition like Tay-Sachs disease is also straightforward; almost everyone who thinks screening is a good idea would include that. But there are many conditions that sit in a grey zone, where some might think them sufficiently severe but others do not. Take deafness, for instance. Most if not all of the commercial screening tests include at least one form of deafness. But how severe a condition is it, really? Some think that it should not be considered a ‘condition’ at all — it has been argued that treating deafness is a form of cultural genocide, because it may eliminate the Deaf community and its languages.

[22 While not affected by this condition, I am nonetheless undergoing the cure — like many men my age.]

For Mackenzie’s Mission, we decided that we would include genes if the associated condition caused a medical problem that started in childhood, that was severe, disabling and/or life-shortening without effective treatment (or where treatment is very burdensome), and for which an average Australian couple would take steps to avoid having a child affected by that condition. After much debate, we concluded that deafness does not meet those criteria, and we have not included any genes for isolated deafness.136 However, we think the questions of what to include in a screening program and where the boundaries should be drawn deserve further work, and one of the questions we aim to answer during the course of the project is whether Australians as a group agree that we have this right.

[23 In other words, deafness where that is the entirety of the condition. Deafness can be part of syndromes, too, in combination with a variety of other medical problems.]

Our final gene list wound up being much longer than we had expected — 1,300 genes associated with more than 700 conditions. There are more genes than conditions because there are plenty of conditions that can be caused by variants in multiple different genes. Of course, many of these are very rare, and for the majority there will be no couples among the 10,000 we screen who are found to have a 1 in 4 chance of having an affected child.

Other research questions we need to answer include some quite simple ones — for instance, how many of the 10,000 couples will be identified as carriers for one of the conditions? That one is simple, but important — if you want to plan a population-wide screening program, you need to know what resources will be needed, and this is a key piece of information. A similarly pragmatic question is: will screening be cost-effective? This may seem callous given the human impact of genetic conditions, but, if a government is going to pay for screening, it needs to know if it can afford it, so health economists are a key part of our team. Other questions are more complex: What are the ethical implications of doing this type of screening? How can we design a program that does the most good and the least harm? How do we translate the research evidence we generate into medical practice as efficiently and effectively as possible?137 And so on.

[24 This is a whole field of academic effort, called implementation science.]

There’s no such thing as a perfect screening program. There will always be gaps in our knowledge and limits to our ability to identify those who are affected by, or carriers for, genetic conditions. I’m hopeful, though. I hope that within a few years, we will be able to offer the option to be screened to all who wish it. I hope that many will choose to be screened, and that, while most will receive reassuring information, for those who are found to have a high chance of having an affected child, the information will be helpful.

Most of all, I hope that, over time, I will need to have fewer meetings with young couples to give them bad news about their children.

There is a great deal to be optimistic and excited about in genetics. This book has been about the past and present of genetics, and how it affects peoples’ lives. But what about the future?