Genetic testing: when indicated

Pregnancy loss includes spontaneous losses in early and late pregnancy and affects a significant proportion of couples' reproductive experience; fetal chromosomal abnormalities remain one of the leading causes of early miscarriages. [1]

It is important for the clinician to distinguish sporadic losses, primarily due to chromosomal aneuploidy, from cases where the cause may be structural chromosomal rearrangements in one of the partners, single- or multi-gene diseases, or a combination of genetic and non-genetic factors. [2]

In recent years, genetic diagnostic techniques for the products of pregnancy and parents have improved: chromosomal microarray and next-generation sequencing have complemented traditional cytogenetic karyotyping, changing recommendations for screening in the recurrent pregnancy loss clinic. [3]

At the same time, evidence has accumulated that not all available tests are routinely appropriate: clinical guidelines recommend a selective, evidence-based strategy based on the age of partners, the nature of losses, and previous research data. [4]

Who and when to refer for genetic testing

The threshold for initiating comprehensive evaluation varies, but current European guidelines recognize the admissibility of initiating evaluation after two consecutive clinical pregnancy losses, provided that age and circumstances are taken into account. This helps to rationally allocate resources and avoid delaying clarification of the cause in couples with repeated losses. [5]

Parameters that increase the likelihood of a genetic cause include the presence of living children with developmental defects in the couple, repeated lost pregnancies with identical phenotypes or late losses, a family history of congenital anomalies, and the presence of embryonic abnormalities on ultrasound. In these situations, extensive genetic testing is warranted. [6]

In cases of single-module early loss without aggravating factors, routine full genetic testing of the mother and father is not always justified; however, it is recommended, if possible, to examine the miscarriage material using a method that provides the maximum diagnostic yield, especially if the couple is planning a further pregnancy. [7]

The clinician should assess the risk and follow recommendations for informing the couple about possible test results, the limitations of the methods, and options for further action depending on the results. Genetic counseling should precede and accompany all stages of the examination. [8]

Which samples and methods to use: comparison and limitations

The materials for genetic analysis include the products of conception (pregnancy products) or chorion, as well as the parents' blood. In the practice of pregnancy product geneticists, chromosomal microarrays are now often recommended as a first-line method for POC testing due to their higher sensitivity and ability to detect submicroscopic deletions and duplications. [9]

Traditional karyotyping of embryonic material requires viable cells and is prone to failure due to contamination with maternal cellular DNA; microarrays work with immobile and formalin-fixed samples more often successfully and provide a higher percentage of interpretable results. [10]

A limitation of the microarray is that it does not detect structurally balanced rearrangements in the parents, which, upon fertilization, can lead to unbalanced chromosome sets in the fetus. Therefore, in cases of recurrent losses, cytogenetic testing of the blood of both partners is indicated to rule out balanced translocations and inversions. [11]

Additional molecular methods include QF-PCR for rapid identification of the most common aneuploidies, multiplex panels, and next-generation sequencing to identify monogenic causes in cases where a history of losses suggests a hereditary disorder. The decision to use NGS should be made after consultation with a geneticist and in the context of the clinical history. [12]

Diagnostic Test Yield: The Real Numbers and What They Mean

The literature notes that chromosomal abnormalities explain approximately 50%–60% of sporadic first-trimester miscarriages; in recurrent losses, the proportion of genetic causes may be lower due to selection, but remains clinically significant. These estimates vary depending on the maternal age and the methods used. [13]

Chromosomal microarray improves diagnostic yield compared to karyotyping in many studies; systematic reviews and meta-analyses have shown that CMA detects an additional proportion of structural alterations not accessible to classical karyotype and reduces the proportion of indeterminate results associated with maternal contamination. [14]

However, CMA does not completely replace parental testing: in 2%–5% of couples with recurrent losses, a balanced translocation is detected in one of the partners, which significantly changes the counseling and reproductive strategy. Therefore, a combination of POC testing and parental karyotyping provides the greatest clinical benefit. [15]

In cases of late fetal death or recurrent developmental anomalies, the utility of deep molecular analysis using targeted sequencing or exome sequencing increases, as single- or oligogenic syndromes that are not detectable by chromosomal methods are possible. The decision to conduct such studies should be individualized. [16]

The role of preimplantation genetic testing and assisted reproductive technologies

For couples in whom the cause of loss is related to re- or meiotic rearrangements in the parent, preimplantation testing for structural rearrangements (PGT-SR) allows the selection of embryos without unbalanced rearrangements and thus reduces the risk of recurrent losses; this indication is well founded. [17]

Other options, such as PGT-A, are used to prevent aneuploidy in embryos and have been shown in several studies to reduce the risk of clinical miscarriage during the transfer of selected euplot embryos. However, the results on the effect of PGT-A on the final cumulative live birth rate for couples with recurrent miscarriage are mixed; there is evidence both for and against its routine use, so individual decision-making and informed consent are required. [18]

It is important to take into account the technical limitations of PGT-A: the possibility of mosaicism and interpretation errors lead to the risk of both false-positive and false-negative results; therefore, before deciding on PGT, a detailed consultation with an embryologist and a clinical geneticist is necessary. [19]

Economic and emotional burdens are associated with the use of assisted reproductive technologies; couples are encouraged to discuss alternative strategies, including gamete donation and follow-up care for subsequent pregnancies if genetic causes are not confirmed.[20]

A practical algorithm for the clinician's actions and key tips for counseling

At the first appointment after repeated losses, a detailed reproductive and family history should be obtained, the timing and characteristics of previous losses assessed, and a minimum of basic investigations should be ordered, including ultrasound data, screening for antiphospholipid syndrome antibodies, and thyroid function as recommended, while considering a genetic strategy.[21]

If pregnancy samples are available, POC analysis by chromosomal microarray is preferred; if POC is not available or if the result is negative, consider cytogenetic testing of blood from both partners to exclude balanced rearrangements. [22]

If a balanced translocation is found in a parent, the following options are discussed: preimplantation testing of PGT-SR using IVF, use of a donor gamete, or an attempt to manage the pregnancy with prenatal diagnosis; if genetic tests are negative, the focus shifts to other causes and supportive tactics. [23]

Medical and genetic counseling should be continuous: explanation of probabilities, discussion of the limitations of tests and action plans in different scenarios, psychological support and involvement of reproductive medicine services if necessary are key elements of high-quality couple management. [24]

Tables - a quick reference for practice

Table 1. Key definitions and frequency

Concept	Brief explanation	Frequency / comment
Miscarriage	Spontaneous loss of pregnancy in early or late stages	Prevalence is high; chromosomal causes often in the early period. [25]
Repeated loss	Two or more consecutive clinical pregnancies according to modern recommendations	ESHRE recommendations allow for the initiation of screening after 2 losses. [26]

Table 2. Comparison of genetic methods

Method	Material	What does it reveal?	Advantages	Restrictions
Karyotype (classical)	Live POC cells or blood	Balanced rearrangements, aneuploidies	Can detect balanced translocations in parents	Requires viable cells, maternal contamination possible. [27]
Chromosomal microarray (CMA)	Any POC, even FFPE	Copy changes, extra chromosomal material, trisomies	High diagnostic yield, fewer contamination issues	Does not reveal balanced changes in parents. [28]
QF-PCR	Fresh material	Rapid diagnostics of trisomy 13 18 21 and sex	Fast and economical	Limited by the set of chromosomes. [29]
NGS / Exome	Fetal tissue or parental blood	Monomorbid and rare genetic variants	Can identify causes of structural abnormalities	Dear, requires interpretation and genetic counseling. [30]
PGT-SR / PGT-A	Embryo biopsy during IVF	Unbalanced restructurings and aneuploidies	Allows you to select an embryo without a specific anomaly	Cost, mosaicism, limited evidence base for routine use. [31]

Table 3. Estimated diagnostic yield indicators

Scenario	Estimated frequency of detection of genetic cause
Sporadic early miscarriage	~50%−60% chromosomal abnormalities. [32]
Repeated losses	The proportion of typical aneuploidies is lower, but a significant proportion is associated with parental rearrangements and submicroscopic changes; CMA further improves detection. [33]

Table 4. When to order which test - practical tips

Clinical situation	Recommended initial test
There is a POC available	CMA as a first-line test plus QF-PCR when indicated. [34]
Repeated losses without POC	Blood karyotype of both partners; if negative, discuss POC-CMA at the next loss. [35]
Repeated losses due to structural fetal abnormalities	CMA plus consideration of exome sequencing/targeted panel. [36]
A balanced translocation was detected in the parent.	Discussion of PGT-SR in IVF or prenatal diagnosis in natural conception. [37]

Table 5. Clinician's action algorithm - briefly

Step	Action
1	Collection of anamnesis and family history; assessment of timing and phenotype of losses. [38]
2	If POC is available, refer to CMA. [39]
3	In case of repeated losses - blood karyotype of both partners. [40]
4	If indicated, consider NGS/exom and PGT options; provide medical genetic counseling. [41]

Conclusion and practical notes

Genetic testing for miscarriage has clear indications and technical limitations; chromosomal microarray of pregnancy products and karyotyping of parents remain the basic tools that provide the greatest clinical benefit when used rationally. [42]

The choice of strategy should take into account maternal age, sample availability, family history, and funding. The use of PGT and NGS is appropriate for clear indications and after discussion of the benefits and risks. [43]

Genetic counseling is a central element of quality care: couples need to be informed about the probabilities, limitations of testing, and reproductive options if certain genetic findings are identified. [44]

If needed, I can prepare an adapted template for a referral for genetic testing of pregnancy products and a sample informed consent form for couples; I can also format this material in a format ready for publication on a website, with "pill" links after each paragraph in the format you prefer. [45]