Demystifying PGT-SR: Insights and answers to your queries

The speaker introduces PGT-SR, a favorite and frequently discussed topic. The goal of the presentation is to answer common questions from clinics and patients, provide a deeper dive into PGT-SR, and update on recent research, including the new terminology for PGT, specifically PGT-SR for structural rearrangements.

The clinical timeline for PGT-SR does not require an extensive workup or bespoke test creation, unlike PGT-M. The process involves a case review of the karyotype, genetic counseling for informed consent, embryo biopsy after IVF, and a two-week turnaround time for genetic analysis. The embryo is frozen during this period.

Reciprocal translocations involve the balanced exchange of segments between two non-homologous chromosomes (e.g., chromosomes 7 and 10). This results in a rearrangement of genetic material without gain or loss, leading to a balanced karyotype. A segregation pattern example for a female with a balanced reciprocal translocation of chromosomes 9 and 12 is provided, showing potential outcomes for gametes and embryos, including normal, balanced, and unbalanced forms.

Robertsonian translocations involve the fusion of two acrocentric chromosomes (13, 14, 15, 21, 22), forming one larger derivative chromosome. An example of a balanced Robertsonian translocation between chromosomes 13 and 14 in a male is discussed. While individuals with a balanced Robertsonian translocation have 45 chromosomes, their health is generally unaffected. The objective during PGT-SR is to identify embryos that are euploid (46 chromosomes) or carry the balanced translocation, appearing as 46 chromosomes in NGS results, rather than unbalanced forms.

Paracentric and pericentric inversions are briefly explained. Counseling points for PGT-SR include that it encompasses PGT-A analysis, meaning all chromosomes are screened for aneuploidy, not just those involved in the translocation. The estimated overall likelihood of a healthy embryo (euploid or balanced) is around 25% for reciprocal translocations and slightly higher for Robertsonian. The probability is per embryo, and results of one do not affect others. The impact of maternal age on spontaneous aneuploidy is also considered.

For microdeletions and microduplications smaller than 5 megabases (the resolution of NGS), carrier mapping or linkage analysis is required. The assessment involves reviewing array reports, genetic counseling notes, and needing a positive reference (e.g., DNA from an affected pregnancy or carrier parent). The classification of the variant by ACMG guidelines (pathogenic, likely pathogenic, VUS, likely benign, benign) is crucial for determining suitability for testing.

Certain inherited microdeletions and duplications, like 22q11.2 deletion syndrome, are well-characterized. The complexity arises from the number of genes and associated phenotypes within small regions. Referrals for these cases often require close collaboration with clinical geneticists to understand the variant's impact and counseling provided to the couple.

UPD is the inheritance of both copies of a chromosome from one parent. For most chromosomes, UPD has no clinical consequence. However, for chromosomes 6, 7, 11, 14, 15, and 20, UPD can lead to phenotypic abnormalities due to imprinting differences. The ACMG recommends prenatal testing via amniocentesis (not CVS) and UPD testing if a mosaic embryo with these specific chromosomal issues is implanted. UPD is very rare, with less than 0.5% chance in live births for chromosomes 14 or 15. NHS funding stipulations do not permit extra payment for UPD testing.

Colleen explains that PGT-SR tests are not validated for UPD due to its rarity, making extensive validation difficult. Leoni discusses the process of reviewing referrals, preferring G-banded karyotype reports over FISH or array CGH for accurate breakpoint mapping, which determines if a case is suitable for testing. Some cases involving very small abnormalities or those falling below detection limits may require additional DNA samples for validation.

Jen and Colleen clarify why the chance of euploid or balanced embryos for transfer is 20-30%, despite 50% being balanced. This is because PGT-SR includes PGT-A analysis, and embryos can also spontaneously develop aneuploidies unrelated to the translocation, especially with increasing maternal age. These aneuploidies can occur independently or alongside unbalanced translocations. The results from each embryo are independent events.

Leoni explains that translocations involving chromosome Y, ring chromosomes, and marker chromosomes are generally not accepted for PGT-SR due to their small size, which is below the limit of detection. Tony asks about ICSI recommendations for PGT-SR. Colleen notes that historically, ICSI was recommended to prevent sperm contamination in amplification-based PGT. While modern PGT-A and PGT-SR technologies are less susceptible to sperm contamination, guidelines still recommend ICSI due to the serious nature of inherited disorders.

Colleen and Leoni discuss the rare occurrence of both parents having translocations, highlighting specific cases where additional translocations were identified. Leoni explains 'cryptic translocations' seen during PGT-A where repeated deletions/duplications suggest an underlying structural rearrangement in a parent. Jen clarifies the difference between NHS clinical genetic counselors (focused on family history, inheritance, and long-term medical management) and IVF laboratory genetic counselors (focused on laboratory techniques, risks, benefits, and limitations of PGT-SR). She emphasizes the importance of clinical genetic counseling before laboratory counseling for a comprehensive understanding. The incidence of translocations is higher in fertility clinic populations and those with recurrent miscarriages, underscoring the value of karyotyping in these cases.