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Genetic Counselor
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If one or more embryos are identified as free of the familial genetic change, one is typically transferred into the uterus in a subsequent cycle, often using a frozen embryo while the results were pending. From that point, the pregnancy is monitored in the usual way, and confirmatory prenatal testing is still offered, since testing a full pregnancy sample is more reliable than testing a few embryonic cells. If no embryo turns out to be unaffected in a given cycle, which is more likely when few eggs are retrieved, couples may consider a further round of egg retrieval and testing, or discuss alternatives such as donor eggs or sperm, embryo donation, or prenatal diagnosis in a future pregnancy. Genetic counseling before and after testing is intended to be non-directive, meaning the counselor lays out the medical facts and options without steering the family toward a particular choice; the decision remains personal to each couple.
In India, this technology is permitted and specifically addressed under the Assisted Reproductive Technology (Regulation) Act, 2021, which allows testing of embryos “to screen the human embryo for known, pre-existing, heritable, or genetic diseases only.” The law explicitly rules out its use for selecting non-medical traits or for sex selection, in line with the long-standing Pre-Conception and Pre-Natal Diagnostic Techniques Act, 1994, except where sex-linked testing is medically necessary to avoid a serious X-linked disorder. Clinics offering this testing in India must be registered as genetic clinics under that same 1994 Act, and comprehensive genetic counseling is a mandatory step before proceeding, both to support informed decision-making and to safeguard against discrimination on the basis of genetic or disability status.
Modern techniques have made misdiagnosis uncommon, and data from a large European consortium tracking outcomes over many years has reported no confirmed cases of misdiagnosis when linkage-based testing is used correctly. That said, no laboratory test on a handful of cells is ever presented as absolutely perfect, and every reputable program discusses a small, quoted margin of error before testing begins.
Several factors can reduce the reliability of an individual result. Allele dropout, where one copy of a gene fails to be detected during the laboratory amplification process, is the most significant technical risk; combining direct variant testing with linkage analysis substantially lowers this risk compared with either method alone. Recombination, a natural process in which chromosome segments swap between generations, can occasionally interfere with the genetic markers being tracked. Poor-quality DNA from the biopsy sample, laboratory contamination, and certain difficult categories of genetic change, including repeat-expansion disorders such as fragile X syndrome, large deletions, and changes affecting genes with similar-looking backup copies elsewhere in the genome, also pose extra technical challenges. A variant that arose new in a family member, rather than being inherited from a parent, can be harder to track with certainty because there is no established family pattern of markers to follow.
Because of these limitations, every major professional body, including the American College of Obstetricians and Gynecologists, recommends that a pregnancy resulting from an embryo identified as unaffected still be offered confirmatory testing, through chorionic villus sampling or amniocentesis, once the pregnancy is established. This step provides a far higher level of diagnostic certainty than testing a few cells from an early embryo ever can, and it remains the safety net that makes the overall approach dependable.
A good candidate is someone, or a couple, who already knows the exact genetic change responsible for a condition in their family, confirmed through prior genetic testing of an affected family member or through carrier screening of both partners. The test cannot be used as an open-ended search for unknown problems; it is only as specific as the variant it was designed to detect.
The conditions considered for testing are severe, well-characterized disorders that cause serious illness, disability, or shortened life expectancy from infancy or early childhood.
Examples include:
• Severe blood and metabolic disorders: such as thalassemia major, sickle cell disease, and Tay-Sachs disease, where a child’s health is significantly affected from very early in life.
• Severe neuromuscular and multisystem conditions: such as spinal muscular atrophy and classic cystic fibrosis, both of which substantially limit a child’s health, development, and life expectancy without ongoing, intensive care.Testing here is reserved for conditions that are severe and certain from infancy or early childhood, where the diagnosis, its course, and its impact on the child are already well established. Conditions that first appear later in adulthood, such as certain hereditary cancers or degenerative neurological disorders, behave differently: the age of onset is often unpredictable and can vary widely even within the same family, and by the time symptoms might eventually appear, medical surveillance, preventive measures, or treatment options are frequently already available to manage the condition, for cancer syndromes there’s a chance the disease might not manifest at all. Because the timing is uncertain and effective management already exists for many of these later-onset conditions, embryo testing is not used for this purpose here; the clinical case for it is far less clear-cut than it is for a severe condition already causing illness in early childhood.
Professional guidelines also generally do not support using this technology for variants of uncertain significance, for carrier status alone without symptoms, or for selecting non-medical traits. In India, the law is explicit on this point: testing may be used only to screen for known, pre-existing, heritable, or genetic diseases, and sex selection is prohibited except when it is medically necessary to avoid a serious X-linked disorder.
As this test is built around one family’s specific genetic change, it cannot simply be ordered off a shelf. A custom test has to be designed first, and this groundwork typically takes a few weeks to a few months before in vitro fertilization even begins. The laboratory usually needs a blood or saliva sample not only from both partners but often from other relatives as well, such as an affected child or parent. This is because the most reliable approach, called linkage or haplotype analysis, does not just look for the variant itself but it tracks a pattern of genetic markers running alongside the variant on the same chromosome, inherited together as a set. Tracking this surrounding pattern, alongside direct testing for the variant, helps the laboratory avoid a technical error called allele dropout, in which a single cell’s DNA fails to amplify properly and produces a misleading result.
Once the custom test is ready, the couple proceeds through a standard in vitro fertilization cycle:
• Ovarian stimulation and egg retrieval: hormone medications are used to help the ovaries produce multiple eggs, which are then collected in a minor procedure.
• Fertilization: eggs are fertilized in the laboratory, usually using a technique called intracytoplasmic sperm injection, in which a single sperm is injected directly into an egg, to reduce the chance of stray genetic material contaminating the sample.
• Growth to the blastocyst stage: embryos are cultured for five to six days until they reach a stage with a distinct outer layer, called the trophectoderm, and an inner cluster of cells that will go on to form the baby.
• Biopsy: a small number of cells are gently removed from the outer trophectoderm layer only, not from the inner cluster that becomes the fetus, and the embryo is then frozen while those cells are sent for genetic analysis.
• Result and selection: once results are available, an embryo found not to carry the familial variant, and generally forming normally, is prioritized for transfer in a later cycle.Preimplantation Genetic Testing for Monogenic Disorders is a laboratory test performed on embryos created through in vitro fertilization, used to check whether an embryo has inherited a specific, already-known genetic change that runs in a family. Unlike general health screening, this test does not look broadly for “any” genetic problem. It is built around one particular change, called a pathogenic/ likely pathogenic variant, that has already been identified in a parent, a previous child, or another close relative through earlier genetic testing and is confirmed to be the cause of a severe genetic condition. Because the change is known in advance, the laboratory can design a test specifically for that family before the embryos are even created.
Couples usually consider this option when they already know they carry, or are affected by, a serious single-gene condition and want to reduce the chance of passing it on to a child. Common reasons for pursuing it include a personal or family history of conditions such as cystic fibrosis, sickle cell disease, spinal muscular atrophy, thalassemia, etc.
The key difference from prenatal diagnosis is timing. Chorionic villus sampling and amniocentesis test a pregnancy that has already begun, which can mean facing a difficult decision about continuing or ending that pregnancy if a result is unfavourable. Preimplantation Genetic Testing for Monogenic Disorders instead identifies which embryos are unaffected before a pregnancy is established, so that only those embryos are considered for transfer. It does not guarantee a pregnancy or a healthy child in every other respect, but it directly addresses the one specific genetic change the family already knows about.
A soft marker is a small finding on ultrasound that is not, by itself, a birth defect or a structural problem. It is usually a minor, harmless variation in how part of the baby’s body looks on the scan, something like a tiny bright spot in the heart or a small amount of extra fluid in a kidney. On their own, soft markers do not cause any health problem for the baby and often disappear later in the pregnancy or go completely unnoticed after birth.
The reason your sonographer or doctor mentioned it is that certain soft markers were found, in older research, slightly more often in babies who also had an extra or missing chromosome, a change called an aneuploidy. Down syndrome, caused by an extra copy of chromosome 21, is the aneuploidy most people think of, but soft markers have also been studied in connection with trisomy 18 and trisomy 13. Because of this old association, ultrasound reports are trained to flag soft markers so that your care team can factor them into your overall picture, alongside any blood or genetic screening you have already had.
It is important to understand that soft markers are common. Most babies with a soft marker have completely typical chromosomes, and the marker itself is simply a normal variation. The finding is a piece of information to be considered in context, not a diagnosis and not, on its own, a reason for alarm. How much weight it should carry depends heavily on what other testing you have already done, which the next questions in this document walk through.
Doctors group findings under the term “soft marker” when they are seen on a routine or detailed anatomy ultrasound, usually performed in the middle of pregnancy, and are not attached to any other structural problem. The most commonly identified soft markers are:
• Echogenic intracardiac focus A small bright spot within one of the heart’s pumping chambers, caused by a tiny area of calcium buildup on the muscle fibers that anchor the heart valves. It has no effect on how the heart works and is seen in a meaningful minority of all pregnancies.
• Choroid plexus cysts Small, fluid-filled pockets within the choroid plexus, a structure inside the brain that produces the fluid surrounding the brain and spinal cord. These cysts form when folds of tissue trap fluid during normal brain development and are found in roughly one to three percent of all pregnancies.
• Echogenic bowel A portion of the baby’s intestine that appears unusually bright on ultrasound, sometimes as bright as bone. This can be a normal variant, though it has a wider range of possible explanations than most other soft markers, discussed further below.
• Urinary tract dilation (mild renal pelviectasis) A small amount of extra fluid within the collecting system of one or both kidneys, usually mild and often resolving on its own before or shortly after birth.
• Shortened humerus or femur An arm bone or thigh bone measuring somewhat shorter than the average expected for the baby’s gestational age, based on standard growth curves.
• Thickened nuchal fold A slightly increased thickness of the skin fold at the back of the baby’s neck, measured at the same mid-pregnancy scan.
• Absent or underdeveloped nasal bone The bridge of the nose appearing smaller than expected, or not clearly visible, on ultrasound.
• Single umbilical artery An umbilical cord with two blood vessels instead of the usual three, one artery and one vein rather than two arteries and one vein.Each of these findings has its own separate, and often quite different, level of association with chromosome conditions, which is why your care team’s counseling should always be specific to the exact marker found rather than treating “soft marker” as one uniform category.
This is one of the most misunderstood parts of prenatal ultrasound, so it is worth explaining carefully.
Soft markers were first studied in the 1980s and 1990s, before accurate blood-based screening existed. At that time, doctors were looking for any additional clue, however small, that might help identify pregnancies at higher chance for a chromosome condition. Researchers found that certain markers appeared slightly more often, as a group, among pregnancies later confirmed to involve an extra chromosome. This gave rise to the concept of a “likelihood ratio,” a number describing how much a finding should shift your estimated chance up or down from your starting-point risk.The trouble is that these likelihood ratios vary enormously between different studies and different markers, and, more importantly, the tools available today for estimating aneuploidy chance are far more accurate than ultrasound appearance alone. Cell-free DNA screening, a blood test that analyzes small fragments of placental DNA circulating in the pregnant person’s bloodstream, correctly identifies the great majority of pregnancies affected by trisomy 21, 18, or 13, and correctly clears the great majority that are not affected. Because this blood test is so accurate, current guidelines from ACOG and SMFM state plainly that when a soft marker is found in a pregnancy that has already had a negative cell-free DNA or serum screening result, the marker does not meaningfully change that low chance, and additional invasive testing is not recommended for that reason alone.
No. Having a soft marker does not mean your baby has a chromosome condition, and for most soft markers, most of the time, it does not meaningfully raise your baby’s individual chance either.
Two markers deserve a specific mention because their story is a little different from the rest. Choroid plexus cysts and echogenic intracardiac foci were historically associated mainly with trisomy 18 and trisomy 21 respectively, but when they occur as truly isolated findings, meaning no other structural or genetic concern is present, current evidence shows they add very little useful information once modern screening has already been done. Echogenic bowel is somewhat different again: while it is included among the soft markers for chromosome conditions, it has also been associated with a handful of other, non-chromosomal conditions, including cystic fibrosis and, less commonly, an infection acquired during pregnancy or a problem with fetal growth, which is one reason it is evaluated a little more thoroughly than some other markers, independent of aneuploidy risk.
What happens next depends mainly on two things: whether the soft marker is truly isolated, and what aneuploidy screening you have already had.
• Confirming the marker is isolated The first step after any soft marker is identified is usually a detailed anatomy ultrasound, sometimes called a level II scan, performed by a specialist in maternal-fetal medicine or a similarly experienced sonographer. This scan carefully checks every organ system to make sure there is no additional structural finding and no additional soft marker. A marker found together with a structural problem, or together with more than one other soft marker, is handled differently and more individually than a single, truly isolated finding, since the combined chance is higher than any one marker alone would suggest.
• If you have already had cell-free DNA or serum screening with a low-chance result Current guidelines do not recommend pursuing invasive diagnostic testing, meaning chorionic villus sampling or amniocentesis, based on an isolated soft marker alone. Your low-chance screening result already reflects the most accurate information currently available, and the marker does not meaningfully change it.
• If you have not yet had any aneuploidy screening Your care team should walk you through your options, which typically include cell-free DNA screening or, if that is not accessible or affordable, a standard second-trimester blood screening test called a quad screen. This conversation is meant to estimate your individual chance and let you decide, with accurate numbers in hand, whether you want screening, diagnostic testing, or neither.
• If diagnostic testing has already shown a normal chromosome result A soft marker found afterward, or noticed on a later scan, is not considered meaningful for chromosome risk and does not need to be pursued further for that purpose. It may still occasionally warrant simple follow-up, such as confirming a mild kidney finding has resolved, but this is unrelated to chromosome testing.At every step, the decision to pursue further testing is yours to make. A genetic counselor or maternal-fetal medicine specialist can walk through your personal numbers, including your age-related baseline chance, your prior screening results if any, and the specific marker found, so that you are choosing based on your own complete picture rather than the marker in isolation.
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