Improved clinical utility of preimplantation genetic testing through the integration of ploidy and common pathogenic microdeletions analyses

STUDY QUESTION

Can chromosomal abnormalities beyond copy-number aneuploidies (i.e. ploidy level and microdeletions (MDs)) be detected using a preimplantation genetic testing (PGT) platform?

SUMMARY ANSWER

The proposed integrated approach accurately assesses ploidy level and the most common pathogenic microdeletions causative of genomic disorders, expanding the clinical utility of PGT.

WHAT IS KNOWN ALREADY

Standard methodologies employed in preimplantation genetic testing for aneuploidy (PGT-A) identify chromosomal aneuploidies but cannot determine ploidy level nor the presence of recurrent pathogenic MDs responsible for genomic disorders. Transferring embryos carrying these abnormalities can result in miscarriage, molar pregnancy, and intellectual disabilities and developmental delay in offspring. The development of a testing strategy that integrates their assessment can resolve current limitations and add valuable information regarding the genetic constitution of embryos, which is not evaluated in PGT providing new level of clinical utility and valuable knowledge for further understanding of the genomic causes of implantation failure and early pregnancy loss. To the best of our knowledge, MDs have never been studied in preimplantation human embryos up to date.

STUDY DESIGN, SIZE, DURATION

This is a retrospective cohort analysis including blastocyst biopsies collected between February 2018 and November 2021 at multiple collaborating IVF clinics from prospective parents of European ancestry below the age of 45, using autologous gametes and undergoing ICSI for all oocytes. Ploidy level determination was validated using 164 embryonic samples of known ploidy status (147 diploids, 9 triploids, and 8 haploids). Detection of nine common MD syndromes (-4p=Wolf-Hirschhorn, -8q=Langer-Giedion, -1p=1p36 deletion, -22q=DiGeorge, -5p=Cri-du-Chat, -15q=Prader-Willi/Angelman, -11q=Jacobsen, -17p=Smith-Magenis) was developed and tested using 28 positive controls and 97 negative controls. Later, the methodology was blindly applied in the analysis of: (i) 100 two pronuclei (2PN)-derived blastocysts that were previously defined as uniformly euploid by standard PGT-A; (ii) 99 euploid embryos whose transfer resulted in pregnancy loss.

PARTICIPANTS/MATERIALS, SETTING, METHODS

The methodology is based on targeted next-generation sequencing of selected polymorphisms across the genome and enriched within critical regions of included MD syndromes. Sequencing data (i.e. allelic frequencies) were analyzed by a probabilistic model which estimated the likelihood of ploidy level and MD presence, accounting for both sequencing noise and population genetics patterns (i.e. linkage disequilibrium, LD, correlations) observed in 2504 whole-genome sequencing data from the 1000 Genome Project database. Analysis of phased parental haplotypes obtained by single-nucleotide polymorphism (SNP)-array genotyping was performed to confirm the presence of MD.

MAIN RESULTS AND THE ROLE OF CHANCE

In the analytical validation phase, this strategy showed extremely high accuracy both in ploidy classification (100%, CI: 98.1-100%) and in the identification of six out of eight MDs (99.2%, CI: 98.5-99.8%). To improve MD detection based on loss of heterozygosity (LOH), common haploblocks were analyzed based on haplotype frequency and LOH occurrence in a reference population, thus developing two further mathematical models. As a result, chr1p36 and chr4p16.3 regions were excluded from MD identification due to their poor reliability, whilst a clinical workflow which incorporated parental DNA information was developed to enhance the identification of MDs. During the clinical application phase, one case of triploidy was detected among 2PN-derived blastocysts (i) and one pathogenic MD (-22q11.21) was retrospectively identified among the biopsy specimens of transferred embryos that resulted in miscarriage (ii). For the latter case, family-based analysis revealed the same MD in different sibling embryos (n = 2/5) from non-carrier parents, suggesting the presence of germline mosaicism in the female partner. When embryos are selected for transfer based on their genetic constitution, this strategy can identify embryos with ploidy abnormalities and/or MDs beyond aneuploidies, with an estimated incidence of 1.5% (n = 3/202, 95% CI: 0.5-4.5%) among euploid embryos.

LIMITATIONS, REASONS FOR CAUTION

Epidemiological studies will be required to accurately assess the incidence of ploidy alterations and MDs in preimplantation embryos and particularly in euploid miscarriages. Despite the high accuracy of the assay developed, the use of parental DNA to support diagnostic calling can further increase the precision of the assay.

WIDER IMPLICATIONS OF THE FINDINGS

This novel assay significantly expands the clinical utility of PGT-A by integrating the most common pathogenic MDs (both de novo and inherited ones) responsible for genomic disorders, which are usually evaluated at a later stage through invasive prenatal testing. From a basic research standpoint, this approach will help to elucidate fundamental biological and clinical questions related to the genetics of implantation failure and pregnancy loss of otherwise euploid embryos.

STUDY FUNDING/COMPETING INTEREST(S)

No external funding was used for this study. S.C., M.F., F.C., P.Z., I.P., L.G., C.P., M.P., D.B., J.J.-A., D.B.-J., J.M.-V., and C.R. are employees of Igenomix and C.S. is the head of the scientific board of Igenomix. A.C. and L.P. are employees of JUNO GENETICS. Igenomix and JUNO GENETICS are companies providing reproductive genetic services.

TRIAL REGISTRATION NUMBER

N/A.

P-036 Analysis of semen cryopreservation in a cohort of cancer patients

Study question

To investigate the possible correlation between different types of cancer and sperm quality in patients preserving their fertility and evaluate the reproductive outcomes of patients

Summary answer

Testicular cancer was associated with lower sperm volumes (p = 0.041), lower total sperm concentration (p = 0.009) and oligozoospermia (p < 0.001) compared to other cancers.

What is known already

The advancement in cancer treatments over the years frequently allowed a remission in most young patients. In males, spermatogonia are sensitive to chemotherapy and radiotherapy, causing an impairment of sperm production and competence. Moreover, up to two-thirds of patients with cancer have impaired semen parameters before any treatment but findings on whether and how specific types of malignancies can alter them remains heterogeneous. Today the advancement of Assisted Reproductive Technologies (ART) made male fertility preservation widely available, therefore counselling and sperm banking should be offered to all men in reproductive age with a diagnosis of cancer before any treatment.

Study design, size, duration

This was an observational cohort study conducted on cancer patients that underwent fertility preservation at the Center of reproductive Medicine and Surgery “P. Bertocchi” at the Department of Obstetrics and Gynecology in AUSL-IRCCS of Reggio Emilia, Italy between 2007 and 2018. The participation to the study was retrospectively proposed to all patients submitted to fertility preservation counselling from January 1st 2007 to March 28th 2018, and prospectively from March 29th 2018 to December 31st 2018.

Participants/materials, setting, methods

Semen parameters regarding volume, concentration, motility, and morphology were assessed according to the WHO criteria of 2010 in semen samples collected before any cancer treatment. Based on the macroscopic and microscopic evaluation of each sample, all those with at least cryptozoospermia were frozen. We also evaluated the reproductive outcomes of patients seeking a pregnancy with sperm frozen before cancer treatments. Semen parameters and pregnancy outcomes were compared between testicular versus other cancers.

Main results and the role of chance

During the study period, 329 patients were included with a mean age at enrollment of 32.7 ± 8.6 years. A successful cryopreservation was achieved in 94.5% of cases; the cryopreservation failed in 5.5% of cases, due to azoospermia or missed delivery samples. More than half of the cryopreservations were performed in patients affected by testicular cancer (53.3%), followed by those affected by Hodgkin (19.3%) and non-Hodgkin Lymphoma (13.5%), reflecting the increased incidence of these cancer histotypes in the age group of 20-40 years. Testicular cancer was associated with lower sperm volumes (p = 0.041) and lower total sperm concentration (p = 0.009) compared to other cancers. No difference was observed about sperm motility and morphology, while oligozoospermia was significantly more frequent in men with testicular cancer (p < 0.001). In the cohort, the 8.4% of patients thawed their samples; the usage rate and the embryo transfer rate were significantly higher (p = 0.04) among those with a testicular cancer, while pregnancy and livebirth rates did not differ between the two groups.

Limitations, reasons for caution

Relevant limitations of the study included: the absence of a follow-up on fertility status after cancer remission, missing data about spontaneous pregnancies, and information on the seminal status of each patient before cancer diagnosis, precluding any etiopathological consideration between neoplastic pathology and seminal parameters.

Wider implications of the findings

Male fertility preservation is feasible, easy to be performed, non-invasive and does not delay cancer treatments. Men affected by testicular cancer had worse semen parameters at cryopreservation, but pregnancy and livebirth rates were similar to those achieved by men with other cancers and similar to those achieved with fresh sperm.

Trial registration number

not applicable

P-555 Improved clinical validity of Preimplantation Genetic Testing for Aneuploidy (PGT-A) using a next-generation sequencing workflow for simultaneous detection of aneuploidy, ploidy and common pathogenic microdeletions

Study question

Can chromosomal abnormalities beyond aneuploidies (i.e., ploidy and microdeletions, MD) be detected on a single trophectoderm (TE) embryo biopsy using a next-generation sequencing (NGS)-based workflow?

Summary answer

This NGS-based integrated approach allows accurate detection of ploidy status and the most common microdeletions from a single TE-biopsy,expanding PGT-A clinical validity and diagnostic capabilities.

What is known already

Standard methodologies employed in PGT-A do not determine embryo ploidy status due to the normalization process during copy-number-variation analysis. Transferring embryos with abnormal ploidy variations is expected to result in miscarriage or molar pregnancy. Common pathogenic MD are undetected as they fall below the PGT-A resolution limit (<10Mb). MD are involved in genomic disorders associated with neurodevelopmental disabilities and multiple congenital anomalies. The development of this sequencing strategy can resolve current limitations and add valuable information regarding the genetic constitution of embryos, which is not usually evaluated in PGT and normally requires the use of later-stage invasive prenatal diagnosis.

Study design, size, duration

Ploidy determination was validated using 244 embryo samples of known ploidy status (226 diploids, 10 triploids, 8 haploids). We analysed nine common MD syndromes (-4p=Wolf-Hirschhorn, -8q=Langer-Giedion, -1p=1p36 deletion, -22q=DiGeorge, -5p=Cri-du-Chat, -15q=Prader-Willi/Angelman, -11q=Jacobsen, -17p=Smith-Magenis) using 24 positive controls (amniocentesis DNA from MD cases or TE biopsies from autosomal monosomy mimicking MD) and 96 negative controls (healthy newborns). Overall, the dataset included 72 cases of individual chromosomal abnormalities and 576 negative cases across the eight MD regions.

Participants/materials, setting, methods

PGT-A products were reamplified and sequenced (IonTorrentS5-ThermoFisher) using a custom AmpliSeq panel targeting 384 regions with at least one Single Nucleotide Polymorphism (SNP) of high B-allelic frequency. A bioinformatic algorithm based on gaussian-mixture modelling of sequencing data was developed. This algorithm calculates the conditional probability of the observed B-allelic ratio for each SNP, depending on the copy number, then estimates the likelihood of ploidy and the presence of MD based on the sequencing outcomes.

Main results and the role of chance

Ploidy was correctly determined in 233/234 cases (Accuracy=99.4%), with only one diploid sample misclassified as triploid (PPV=94.1%, NPV=100%, Non-informative rate=9/243=3.1%).

Microdeletions could be consistently detected with high reliability in 6 out of the 8 considered regions (-8q,-22q,-5p,-15q,-11q and -17p; PPV=98.5%, NPV=99.5%). Detection of microdeletions of 1p and 4p were less reliable due to the presence of recurrent haplotype blocks in the population at those genomic regions, as confirmed by the analysis of a dataset of 2504 whole genome sequencing from One Thousand Genome Project database (1kGP). The only MD false positive case showed extended loss of heterozygosity in the microdeletion region (-22q), which might be related to uniparental disomy or consanguinity and requires further testing in the family.

This analytical framework was blindly applied to: (i) the analysis of 9 embryos from a family affected by DiGeorge syndrome (female partner was carrier of del22.q11.21(20754422-21440514), resulting in all embryos classified consistently with the conventional PGT-M results (using indirect linkage analysis); (ii) the analysis of samples from 99 transferred human euploid embryos resulting in pregnancy losses. No ploidy alteration was detected in miscarried euploid embryos, but 2 microdeletions (-8q, -22q) were found, with an estimated prevalence of 2/99 in the miscarriage population.

Limitations, reasons for caution

Larger cohort studies will be required to accurately assess the incidence of ploidy alterations and microdeletions in preimplantation embryos and particularly in euploid miscarriages. Despite the high accuracy of the assay developed, the use of parental DNA to support diagnostic calling can further increase the precision of the assay.

Wider implications of the findings

This study provides, for the first time, detection of common pathogenic microdeletions and ploidy status from a single TE biopsy, expanding PGT-A clinical validity. This new assay will also help elucidate fundamental biological and clinical questions related to the genetics of implantation failure and pregnancy loss of apparently euploid embryos.

Trial registration number

not applicable

Protein Microarrays and Midtrimester Amniotic Fluids: A Novel Approach for the Diagnosis of Early Intrauterine Inflammation Related to Preterm Delivery

Novel technologies that allow simultaneous assessment of multiple biomarkers provide new and promising diagnostic/prognostic approaches. By protein microarrays, here we analyzed amniotic fluids (AF) from 50 women with preterm delivery (PTD) and 50 control women, who delivered at term. In detail, cytokines, chemokines, matrix metalloproteinases and antigen-specific antibodies were assessed. The AF analysis showed significant differences between women with preterm and term delivery in the levels of IL-1α, IL-1β, IL-4, IL-6, IL-8, MCP-1, IFN-γ and anti-HSV2 IgG. No significant differences were observed in the levels of TNF-α, MMP-2, MMP-9 and specific IgG for seven vertically transmitted pathogens. In conclusion, we demonstrated the feasibility of protein microarrays in the diagnosis of early intrauterine inflammation. The significant association between the increased levels of certain cytokines and preterm delivery argues on their relevance as early pathogenetic markers for identification of risk patients.