The Boy Who Wasn't Short

by Kirk, Edwin;

  Lee-Ann’s CVS showed that, instead of the usual 46 chromosomes, there were 45; instead of XX or XY, there was just a single X. This was the point at which I was asked to see them, to talk about what this result might mean for their baby.

  In general — and there certainly are exceptions — if you have two X chromosomes, you’ll be a girl.13 In general — and there certainly are exceptions — if you have one X and one Y chromosome, you’ll be a boy. This is why the X and Y are called the ‘sex chromosomes’.

  [13 Here — and elsewhere in the book — when I refer to girls and boys, and male and female, I am referring to physiological sex rather than gender identity.]

  When its development begins, every embryo carries the potential to be either male or female. Early structures called the Wolffian duct, which has the ability to develop into male sex organs, and the Müllerian duct, which has the ability to develop into female sex organs, are present in every embryo. If, at around six weeks after conception, the SRY14 gene is activated, the Müllerian duct will wither and the Wolffian duct will develop. It’s a boy! As its name suggests, SRY is on the Y chromosome. If there is no SRY signal — for example, because there is no Y chromosome — a different set of signals kick in. The Wolffian duct withers, the Müllerian duct develops. It’s a girl!

  [14 SRY, for ‘Sex-determining Region on the Y chromosome’.]

  Except when it isn’t.

  This is a complex process, and, like all complex processes, it has vulnerabilities — ways that things can go wrong. The ‘disorders of sexual differentiation’ (DSD)15 include a spectrum of variations on a theme, ranging all the way from a boy with two X chromosomes to a girl with an X and a Y. Infertility is often part of the picture, and sometimes there are other medical complications, because some of the genes involved are important not just for sex development but for other parts of the body as well. Sometimes in these conditions, the baby’s genitalia can be ‘ambiguous’ — when the midwife checks the baby, the best answer to the question ‘Is it a boy or a girl?’ may be ‘I don’t know’.

  [15 Also known as ‘disorders of sex development’ and ‘differences of sex development’.]

  Perhaps surprisingly, abnormalities involving the sex chromosomes are only rarely a cause of any doubt about the sex of the baby,16 although they can and do cause problems, in ways that relate to the special status of the X and Y. As discussed in chapter 1, for all of your chromosomes but that one pair, you really, really need to have two copies, and only two.

  [16 The main scenario in which this sometimes happens is when the baby is a mosaic, with some cells having a Y and others not. Most commonly, this is a mixture of cells with 46 chromosomes, including X and Y, and other cells that have lost the Y and have 45 chromosomes with just the one X. Even in this situation, the most common outcome is a boy, although anything is possible — including a girl with Turner syndrome or a baby with ambiguous genitalia.]

  But the X and Y are special. Or, arguably, the X is special and the Y just basks in its glory. The X chromosome is large, and packed with important genes, including many that are essential for the way the brain develops, and thus for intelligence. The Y chromosome is mostly junk. Its genes include SRY, a handful of genes needed to grow testicles and make sperm … and not much else.

  Which leads to something of a mystery. Why is it okay for most men to have only a single copy of such a large, important chromosome — if having one copy of chromosome 21, a much smaller and less important chromosome, is uniformly lethal? Alternately, why is it okay for women to have two copies of the X chromosome if the single copy that men have is the correct number? Why isn’t the extra chromosome causing problems in women?

  The answer to this question was proposed by Mary F. Lyon, a mouse geneticist. Lyon had completed her PhD in the 1940s in Cambridge, under the supervision of R.A. Fisher, working on genetic mapping in mice.17 In the years following World War II, she went on to study the chromosomes of mice that had been exposed to radiation, in work funded because of concerns about the possible effects of nuclear weapons on chromosomes. In a letter to Nature published in 1961, Lyon put together several previous observations, including coat colour patterns in mice with mutations that had been linked to the X chromosome,18 and the fact that mice with only a single X chromosome were apparently normal females. She deduced that, early in embryonic life, one of the two copies of the X chromosome in each of the cells of a female mammal is switched off — inactivated — and the other is active. If a female mouse has a variation in a coat-colour gene on one of its two X chromosomes, and the normal,19 or ‘wild type’, version of the gene on the other copy of the X chromosome, you can expect exactly what had already been observed in at least six different types of mice: a patchy pattern, with a mix of normal and mutant coat colours. Hair roots with the normal gene active will produce fur of one colour, and those with the mutant gene active will produce fur of a different colour.

  [17 We’ll meet Fisher again in chapter 9. In an oral history interview recorded in 2004, Lyon made it clear that Fisher, a famous theoretician, was no great shakes as an experimental geneticist. All the same, supervising Mary Lyon’s PhD was arguably a major contribution to the field by Fisher, so his efforts in the lab were not wasted.]

  [18 Just as there are tortoiseshell cats, there are tortoiseshell mice — and the reason, Lyonisation, is exactly the same for both species. There don’t seem to be any tortoiseshell humans, which is a pity.]

  [19 Of course, you can’t really have an ‘abnormal’ coat colour, but the principle applies to X-linked genetic conditions.]

  Lyon’s proposal became known as the Lyon hypothesis, and the process was named Lyonisation20 (although it is now more commonly called, prosaically, X-inactivation). Every single prediction Lyon made about the underlying biology has since been proved correct. Lyon recognised that her hypothesis might have implications for human genetics, but, at the time, there wasn’t much known about human X-linked conditions. Now we know about lots of them. While males are often severely affected by such conditions, sometimes there are no effects in females at all; or effects can be patchy, whether in skin or in another tissue. At one extreme are conditions that are so severe that very few or even no males are ever seen — you need to have one functioning copy of the X chromosome to survive.

  [20 The word ‘lionised’, as in ‘lionised by the press’, isn’t so commonly used any more. But thanks to Mary Lyon, whenever I do come across it, I experience a moment of confusion, sometimes accompanied by an odd mental image of a tortoiseshell politician.]

  There are two parts of the X chromosome that are not affected by X-inactivation — they are switched on in both copies of a woman’s X chromosome, and they have exact copies in the Y chromosome. These pseudo-autosomal regions (so called because they behave as if they are on one of the non-sex chromosomes, the autosomes) are at the tips of the chromosomes and are necessary for the sex chromosomes to behave normally in cell division during sperm formation in males. They aren’t terribly large — PAR1, on the tip of the short arm of the X and Y chromosomes, contains just 16 genes, and PAR2,21 at the other end of the chromosomes, contains just three. But that doesn’t mean they aren’t important.

  [21 Some people reportedly have a PAR3 as well! But since most of us don’t, it probably isn’t very important.]

  If the PARs were just padding at the tips of the chromosomes, it probably wouldn’t much matter how many X chromosomes you had, because the extra ones would be switched off. It also wouldn’t matter if you had just a single X chromosome. And it probably wouldn’t matter a great deal if you had multiple copies of the Y chromosome.

  As it turns out, though, having an extra sex chromosome is not altogether harmless. Women with an extra X, so that they have 47 chromosomes with three Xs, tend to be tall for their families but otherwise are mostly just healthy people without particular medical problems. It’s entirely possible to live your w
hole life with XXX and never know about it, or need to know. On the other hand, it is pretty clear now that, compared with women with just two copies of the X, those with XXX have a tendency to learning difficulties, and may have behaviour problems in childhood, or even autism. Having an extra Y (XYY) seems to have quite similar effects: most such men lead normal lives and never find out about their extra chromosome. XXY is more likely to cause noticeable problems — boys and men with the associated condition, Klinefelter syndrome, don’t produce as much testosterone as usual, are more likely to struggle at school, and are infertile. Some of these problems are treatable with testosterone. Adding more chromosomes into the mix — 48,XXXY or 49,XXXXY for instance — does make things worse, as you might expect.

  Even though it’s decades since these conditions were first described, we don’t have rock-solid information about all this, because of the way that most people with these differences in their chromosomes are identified in the first place. If you are doing fine, nobody is going to bother counting your chromosomes. This means that the people who have a chromosome test are not representative of the group as a whole — they are skewed towards the more severe end of a spectrum. This is known as ascertainment bias and is the bugbear of researchers studying any condition that can be mild or severe.

  During the 1960s and 1970s, there were several studies of prison inmates that seemed to show that men with XYY were more likely to be incarcerated, and the idea that the extra chromosome made you more aggressive and thus more likely to be locked up persisted for decades. As recently as 2006, the question was still open enough that a group of Danish researchers conducted a large study that concluded that criminal convictions were indeed more likely in men with either XYY or XXY … but that this effect almost entirely went away when adjusted for poverty, which itself is linked to a higher likelihood of being convicted of a crime. Since they were studying only men who were known to have an extra sex chromosome, and since these people were tested for a reason, it seems very likely that ascertainment bias is enough to explain the increased chance of criminal conviction that still remained after adjusting for poverty.

  There have been a couple of studies in which large numbers of babies were screened for extra chromosomes and those with sex chromosome differences were then followed over time — a heroic effort, considering how many years you need to wait before you really know how things have turned out. As you might expect, the problems seen in those groups are generally much milder than those seen in people who were diagnosed because a doctor thought they had a problem that might be caused by a chromosomal condition.

  Lee-Ann and Derek didn’t need to know about the effects of an extra chromosome, because their baby was one short. In general, missing chromosome material is more of a problem than extra, and this situation was no exception. It’s thought that 99 per cent of all babies that are conceived with a single X chromosome are miscarried, often before a pregnancy is even recognised. A common problem in pregnancy is a build-up of fluid in the tissues of the developing fetus, and this can by itself be severe enough to cause a miscarriage. Girls with just one X chromosome who get to be born have a condition called Turner syndrome. The effects of this are very variable indeed. Girls with Turner are pretty much always short,22 and pretty much always infertile, but everything else about the condition is unpredictable.

  [22 Growth hormone can help with this.]

  Just how variable are we talking about? Well, a girl with Turner syndrome might be born with congenital heart disease and kidney malformations. Her neck might be webbed, and she may have a distinctive facial appearance. She might have significant difficulties at school — her intelligence would usually be normal, but there are some particular areas that she might struggle with, to the point of needing extra help. She might be shy, anxious, and reserved. Planning and decision-making might be particular weaknesses for her.

  Or she might have only some of those problems; or she could be completely fine, apart from being short. She might grow up not suspecting that she had any kind of medical problem at all, and the diagnosis might be made only when she is having tests to find out why she is infertile.

  When I met Lee-Ann and Derek, I explained all of this, including the statistics about the likelihood of different aspects of the condition affecting a baby diagnosed in this way, as well as the weaknesses in the way those statistics were collected. I also explained that the only parts of all this that we could give them extra confidence about were the heart and kidney abnormalities, which mostly should be detectable on ultrasound. The rest was unpredictable; they would be facing uncertainty, much of which would take years to resolve.

  For Lee-Ann and Derek, the decision about what to do with this information was relatively simple. They told me that if the baby had had a lethal problem, they would have requested a termination of pregnancy, and that if the baby had had a condition like Down syndrome, it would have been a challenging decision for them, and they weren’t sure what they would have done. For them, though, Turner syndrome — even at the end of the spectrum with the most problems — seemed like a milder issue. They were sad about the prospect that their daughter would face extra challenges in her life, and the infertility that is part of the condition was particularly a blow to Lee-Ann. But they definitely wanted to continue with the pregnancy.

  This decision is not as straightforward for most of the people I meet in similar situations. Many really struggle with the information, and, in the end, a majority of couples request termination of pregnancy after learning their baby has Turner or Klinefelter syndrome. Even when the finding is XXX or XYY, it’s not uncommon to choose termination.

  In dealing with this kind of finding, the uncertainty about what will happen is often one of the hardest parts.

  All of us have to make decisions in situations where the outcome is unknown — decisions about relationships, about education and careers. There’s a whole genre of self-help books about dealing with uncertainty, which speaks to how hard it can be. It’s true that every prospective parent faces uncertainties about what the child will be like, and how they will cope with parenthood. But few are presented with such a specific range of possibilities and asked to make a tough choice, knowing that either decision will have a huge impact on their lives. To make things harder, from the time of the result, there is pressure to decide soon, because, if you don’t, the pregnancy will be too far along and the choice will be out of your hands.

  Uncertainty is a constant in clinical genetics, and it comes in various forms. Our stock in trade is situations like Jason’s, in which the possible outcomes are clear, and the uncertainty is about whether to have a test; or like Lee-Ann and Derek’s, in which the test has already been done, and the diagnosis is clear, but exactly what it will mean remains uncertain.

  Increasingly, we find ourselves having to cope with another type of uncertainty. All too often, we do a test and find ourselves uncertain about whether the result means anything at all.

  5

  Needles in stacks of needles

  … as we know, there are known knowns; there are things we know we know. We also know there are known unknowns; that is to say we know there are some things we do not know. But there are also unknown unknowns — the ones we don’t know we don’t know.

  DONALD RUMSFELD

  I’ve always felt Donald Rumsfeld was unfairly pilloried for the comment above, because it seems like a pretty fair summary of the way the world works, particularly the world of medicine. I might further divide Rumsfeld’s last category, the ‘unknown unknowns’ into two: things we do not know about at all, and things we think we know, but are wrong about. Worrying about that last category is one of the many things that keep me up at night.

  *

  In 2011, when I had already been working for more than a decade as a clinical geneticist, a casual conversation with my friend and mentor Michael Buckley turned unexpectedly into one of those forks in the road w
e sometimes encounter in life. Michael is one of Australia’s leading genetic pathologists — a doctor whose specialty is the oversight of the laboratory aspects of genetic testing. His lab, in which I now work, is an important centre for the diagnosis of rare genetic conditions. I mentioned to Michael that I sometimes wished that I, too, was a genetic pathologist; and he said, not really expecting me to take it seriously, that there was no reason I should not become one. The idea caught hold, and I wound up spending several years training part-time in laboratory medicine and sitting a series of exams to qualify as a pathologist. Now, I divide my time between the clinic and the lab, both ordering genetic tests on patients I have seen and writing reports on tests ordered by others and performed in our lab.1

  [1 It’s considered unwise to report on complex tests that you’ve ordered yourself, on the grounds that you may bring biases to the task that could cause you to miss unexpected findings, or over-emphasize results that fit with your preconceptions about the case.]

  Chance event though this was, the timing could not possibly have been better. When I started training, it was already apparent that a new type of genetic testing was on its way. Over the course of the next few years, that promise became a reality, leading to a transformation in the specialty. By sheer good luck, I’ve found myself in the thick of it.

  You’ll remember the extraordinary fall in the costs of sequencing an entire human genome, from billions of dollars to a thousand or so. There were some noteworthy waypoints on that journey from moonshot to utility. Craig Venter and James Watson were the first two named human beings to have their whole genomes sequenced. The third was a businessman, Dan Stoicescu. Dr Stoicescu, who made his money in biotechnology, spent some of it to have his whole genome sequenced by a company called Knome. They charged him US$350,000 for the privilege, which must have seemed like a bargain, considering that, just the previous year, it had cost three times as much to sequence Watson’s. By the following year, Knome were charging just US$100,000 for the service: at that point, you would have needed to be very brave or very unconcerned about your money to shell out so much, for a product that was getting cheaper so very quickly.