Knowing the unborn

Knowing the unborn

S harachand

The trajectory to determine the risk of foetal abnormalities of genetic origin has been made a lot simpler and safer for clinicians today with the advent of non-invasive prenatal testing (NIPT).

Till a few years ago, the detection and diagnosis of autosomal aneuploidies involved a multi-step process. The combined first-trimester screening (FTS) to assess the risk comprises the analysis of the pregnancy-associated plasma protein A and the free beta-human chorionic gonadotropin in the maternal blood, plus an ultrasound measuring foetal nuchal translucency (NT) thickness. The detection rate of the two biochemical marker analysis, in combination with NT ultrasound, has only been around 75%, with 5% false positives.

A positive finding invariably led to invasive procedures like amniocentesis or chorionic villus sampling (CVS) to confirm the diagnosis. Extraction of foetal samples for genetic evaluation causes considerable distress to both the unborn foetus and the pregnant woman. Besides, the method itself carries a risk of miscarriage, especially when carried out in locations where expertise and facilities are inadequate.

Genomic abnormalities are the leading cause of birth defects, including foetal growth retardation and pregnancy complications. NIPT, in a technological breakthrough, now makes it possible to determine the genomic status of the foetus by analysing the circulating foetal DNA in the maternal blood.

NIPT has a sensitivity of 99% and a specificity of 99.92% for trisomy 21, which detects Down’s syndrome and nearly similar level of accuracy for trisomy 18 and trisomy 13 — the common autosomal aneuploidies.

Cell-free foetal DNA, or the DNA of placental origin, comprises less than 10% of the DNA in the blood of a pregnant woman. The ’foetal fraction’ analysis can be done earlier than any other pregnancy screening or diagnosis. It helps to complete testing formalities earlier in those receiving a negative result. As a sufficiently informative test with better accuracy, it obviates the need for other investigations.

The increased level of sensitivity and specificity in detecting aneuploidies makes NIPT a better option for patients and clinicians. Even though its use is currently limited to screening purposes and not for diagnosing, several countries, including the Netherlands, have already implemented NIPT as a part of their national prenatal screening programme.

Evidence from studies conducted in low-risk, general populations shows that NIPT can be considered an alternative to the current first-tier testing for first-semester prenatal screening in many healthcare settings. Also, there are indications that the number of invasive foetal tests has decreased considerably since the introduction of NIPT in many parts of the world, including in the US and Australia. Many women who previously would have had invasive testing are choosing NIPT because of the small risk of pregnancy loss.

”NIPT has seen unprecedented, rapid clinical adoption with studies showing a decrease in both the number of traditional screening tests and invasive diagnostic procedures,’’ says Maximilian Schmid, MD, Head of Medical Affairs, Roche Sequencing Solutions, California. Roche’s Harmony prenatal test to detect trisomy 21, 18 and 13 is currently available in more than 100 countries, with more than 1.4 million patient samples tested, he adds.

Expanding potential

Recent advances in genome sequencing have broadened the scope of NIPT further. Going by the trend, disorders of monogenic origin are logically the next in line. Hemoglobinopathies such as thalassaemia and sickle cell anaemia are already brought under its purview. Since the principle of cfDNA involves the analysis of the entire foetal genome in maternal plasma, NIPT can, technically, look beyond chromosomal abnormalities to Mendelian disorders and genetic risk profiles for multifactorial diseases, studies say. There is, virtually, no limit to the number of diseases and conditions that can be predicted through the technology.

Leading companies have already expanded their panel portfolio to include microdeletion syndromes like DiGeorge.

“Deletion of 22q11.2 is the second most common identifiable genetic cause of developmental delay and major congenital heart disease after Down syndrome. Occurring in as many as 1/1,000 pregnancies, it is the most common microdeletion syndrome,” according to Dr Schmid.

As demonstrated with 22q11.2 deletion, Roche will continue to focus on adding clinically meaningful content to its test offerings, he added.

NIPT is the best technology that is available today for screening chromosomal disorders in pregnancy, and it is being recommended by obstetric and gynaecological societies the world over, points out Dr. Priya Kadam, Programme Director – NIPT, MedGenome Labs, a genomics-based research and diagnostics company from Bengaluru.

According to Dr Kadam, it would be a better idea to have all pregnant women go through NIPT irrespective of their risk profile because genomic changes in the foetus can occur due to many factors. For instance, spontaneous chromosomal disorders, which is the most common type of chromosomal disorder, including Down’s syndrome, Edwards syndrome and 22q or DiGeorge syndrome, occurs during the pregnancy sans any previous family history. “In this case, not even the parents are carriers. The changes are spontaneous. It is important to note that in the case of family history or suspected genetic mutation in parents, one will be careful or cautious about the pregnancy. But, so far as spontaneous disorders are concerned, there is no alert factor, so it is recommended that every pregnancy should be screened for certain chromosomal disorders,” she explained

At present, India has several tests available for detecting almost all the disorders.

Of late, companies have even started marketing tests that track down single point mutation disorders in India.

According to Dr Shailesh Pande, Consultant-HOD, Dept. of Medical Genetics, Metropolis Healthcare Ltd, a wide range of maternal serum screening test from dual marker to NIPS are available. Proper genetic counselling and appropriate test selection can really help to identify at risk population for foetal chromosomal abnormalities.

Addressing awareness gap

Even as genomic advances have significantly improved screening and diagnosis of chromosomal conditions prenatally, they have also created new challenges for health professionals and families.

The growing number of available tests are likely to have positive effects on prenatal care. However, the level of awareness about them among patients and providers continues to impede their uptake.

“Obstetricians have poor awareness of foetal therapy conditions and tend not to advise patients correctly,’’ says Dr Anita Kaul, Clinical Director, Apollo Centre for Fetal Medicine, New Delhi. The ever-increasing possibilities of genetic screening also make doctors a bit uncertain.

“As doctors, we are not reassuring the patients in the way we used to, because we always keep saying that you haven’t done all the possible tests that can be run on this foetus, so we cannot allay your anxiety completely.’’

Earlier, the obstetrician could order for a karyotyping and inform the patient that “we’ve done the only genetic test available and as that is fine, the baby should be ok,’’ beams Dr Kaul. The scenario has changed completely, now.

“There are so many tests available, so naturally there is confusion in the market,’’says Dr Sheetal Sharda, Consultant Clinical Geneticist, MedGenome.

The bigger challenge, as far as the genetic tests are concerned in India, avers Dr Sharda, is the lack of awareness about which tests are already available in the country.

To address this issue, MedGenome has developed certain modules to help doctors choose the most appropriate test, as they often put forward their queries based on patient observation and suspected indications.

If there is a differential diagnosis, the scientists in the company can identify the main etiology or the main genetic components that cause a particular kind of disorder and suggest the right kind of tests for the patients instantly. There could be a number of variations or large chromosomal abnormalities.

Quite often, Dr Sharda continues, MedGenome gets requests for spinal muscular atrophy screening after sending the sample for exome sequencing. Since this disorder is a common case of exome 7 and 8 gene deletions, it can be initially tested in a PCR based small lab. If found positive for the said gene deletions, the samples can be sent to an academic lab for confirmation. “But, later, if they come to know that there are other genes such as SMN2, which is a pseudogene, also involved and that such information is important for the prognosis and to know the phenotype, then the sample needs to be tested with an MLPA (Multiple Ligation-Dependent Probe Amplification) test, where we get the ratio of how many genes are deleted and how many are duplicated. This is important for the correct prognosis.” This approach helps the patient to actually save cost by avoiding unnecessary tests or methods.

Obviously, a large section of the obstetricians in India is lacking the latest advances in the field. This is partly because genomics is, comparatively, a new discipline. It is yet to be made part of the medical curriculum. The super-specialty DM curriculum has already incorporated genetic studies and the methods quite elaborately. But the graduation level courses are yet to get updated with this emerging, but crucial area of medicine. Nevertheless, we are moving fast into the era of personalised medicine, potentially the most accurate disease detection and treatment management approach. Here again, genetic tests play the most critical role, she comments.

Educating care pathways

In fact, clinicians have a more active role to play in helping pregnant women with meaningful options of reproductive choice in a milieu of overwhelming genomic information.

“Obstetrical healthcare providers will need to incorporate more education into their care pathways,’’says Kimberly Martin, M.D., Senior Global Medical Director, Women’s Health at Natera Inc, a leading global player in cell-free DNA testing based in San Carlos, California.

Delving into its practicality, Dr Martin observes that it is unlikely that this can be achieved using the traditional face-to-face encounters alone. There are many opportunities for “tech” based learning that are currently available and/or in development, including web-based videos, apps for phone/computer and even telemedicine with online genetic counsellors.

Constrained by time, providers are now receiving assistance from both the industry and professional societies to meet the growing educational needs. “This should translate into them having time to actually counsel regarding the decision making about testing, which is consonant with the goals and values of the family,’’ she recommends.

Counselling is the most important aspect of NIPT, underscore all the guidelines. The objective of any prenatal screening activity should be made explicit. In a country like India, where the awareness level is rather low and familial, social and ethical considerations galore, this poses an additional challenge.

“Doctors, of course, are very open, but we have been confronted by situations where the parents hide the fact that their daughter is a carrier as it may affect her likelihood of marriage,’’says Dr Kaul. This sort of issue can present a significant challenge while implementing routine prenatal screening to detect hemoglobinopathies as proposed by India.

All this points to the necessity of social change and the need to impart the correct knowledge of such conditions amongst the public, she adds.

The awareness level, however, has gone up considerably since 2011, when NIPT was introduced, according to Dr Kadam. A lot of awareness programmes and direct education workshops among the doctors and diagnostics players were conducted. Of course, awareness about technology has been growing all over the world as well.It supported a positive response in the Indian market along with exposure to new technologies. The level of awareness among the parents and pregnant women is also high nowadays. “In fact, we and our hospital partners have started getting direct inquiries from pregnant women asking about the availability of NIPT tests,’’ says Dr Sharda. “But still, I would emphasise the need for more coordinated efforts from the industry, the government and the medical community to maximise the utility of such technology breakthroughs in India,” she adds.

Some clinicians too seem to corroborate the view that the awareness among the public is growing pretty fast. “Many patients now come asking for the test (NIPT). Sometimes they insist on doing it,’’says Dr Ajay Kumar, Additional Professor, Department of Obstetrics & Gyenaecology, Government Medical College, Kottayam. Most of the time, patients come well-prepared and are thoroughly informed about genetic tests.

Higher costs: Impeding factor?

Another big barrier that comes in the way is the exorbitant cost of genetic tests. Advances in NIPT is better, from the provider standpoint, because they can give answers to more conditions now. However, for the patient, the costs are getting enormous. In the earlier days, a karyotyping was good enough and that did not cost much. But now a prenatal microarray as the first-line test itself is hugely expensive compared with earlier tests. And if the test proves non-informative, then going into the option of sequencing increases the cost manyfold, says Dr Kaul.

Many clinicians are yet to adopt the screening test as part of their routine practice, though they are aware of NIPT.

“We don’t generally ask patients to do NIPT unless we find a higher risk in an anomaly scan or the patient is afraid of invasive procedures. This is because the cost of the test is too high. Most of the patients can’t afford it,’’ says an obstetrician practising in KIMS Hospital, Thiruvananthapuram, preferring anonymity.

Apprehension about the cost remains the key factor that makes many refrain from genetic tests. As a matter of fact, the availability of a large number of tests which help pick up a variety of genetic disorders has helped costs to come down drastically in the last few years, bringing the tests within the affordable range of the majority of patients, notes Dr Kadam.

Yet, many women throughout the world do not have access to such tests because of a lack of funds, either the result of restrictive terms and conditions of their health insurance or due to a total lack of coverage for such procedures. Often, these women do not have the financial resources required to pay for these tests out of pocket, observes Dr Martin of Natera.

Tech know-how vis-a-vis clinical ability

NIPT, as mentioned, is recommended only as a screening test and not as a diagnostic procedure, despite the huge potential of the technology. The ability of cfDNA analysis to detect autosomal aneuploidies is far superior to any other available tests and the results are nearly comparable with those of invasive analysis such as amniocentesis or CVS. Nonetheless, the results of NIPT must be confirmed through an invasive diagnosis before considering medical termination of pregnancy, mandate the guidelines. This is because NIPT is less than fully accurate.

The failure, however, to touch 100% mark is purely technical. Most of the current NIPTs employ whole genome massive parallel sequencing (MPS) technology and use counting of cfDNA fragments to detect autosomal aneuploidies. The DNA sequenced comprise DNA of both maternal and placental origin. So, factors other than aneuploid foetal karyotype. including placental mosaicism, vanishing twin, maternal tumour etc., could inevitably signal false positives, studies say.

To tide over this problem and minimise false positives, some commercial companies use another approach based on single nucleotide polymorphisms.

Targeted sequencing that maps only the chromosome region of interest is yet another technology approach to NIPT.

Though these tests can give more accurate results, only diagnostic techniques like amniocentesis or CVS can say with 100% accuracy whether the DNA has a chromosomal abnormality. No irreversible decisions should be made based upon a high-risk NIPT result in isolation.

Similarly, these tests only measure the probability for a limited number of conditions, while amniocentesis and CVS can be used to test for a much broader number of genetic abnormalities, emphasises Nateram, which makes SNP-based Panorama NIPT.

Clearly, the technical ability to test for a condition does not necessarily correspond with a clinical benefit. Hence it is important for the companies to be certain about the benefit of every new addition.

“Test results must aid clinical decision-making and should be beneficial to patients. Each condition added to a screening panel adds to the overall false positive rate of the test and decreases the positive predictive value,’’ says Dr Schmid of Roche Sequencing Solutions, which recently included 22q11.2 microdeletion testing as part of its prenatal test portfolio. Therefore, additional cfDNA test menu options must focus on clinically relevant conditions and require comprehensive validation studies to demonstrate clinical utility in the population to be tested.

Furthermore, counselling becomes more challenging with an increase in the complexity of testing options and the potential of identifying conditions with an uncertain prognosis, according to Dr Schmid.

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