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-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

Effect of mifepristone on the transcriptomic signature of endometrial receptivity

STUDY QUESTION

How does a single dose of mifepristone on Day 2 after the LH peak (LH + 2) affect the endometrial receptivity transcriptome as assessed by the receptive signature established by the endometrial receptivity analysis (ERA)?

SUMMARY ANSWER

A single dose of mifepristone on day LH + 2 renders the endometrium non-receptive by altering the transcriptome associated with endometrial receptivity.

WHAT IS KNOWN ALREADY

Mifepristone is a progesterone receptor modulator that has been shown to alter endometrial receptivity. The ERA is a computational predictor that utilizes gene expression data of 248 genes from next generation sequencing to identify endometrial receptivity status.

STUDY DESIGN, SIZE, DURATION

Endometrial biopsies were collected on day LH + 7 from controls (n = 11) and from women treated with mifepristone (n = 7). For further comparative analysis, samples were also obtained from women in the proliferative phase (n = 7).

PARTICIPANTS/MATERIALS, SETTING, METHODS

Mifepristone treatment consisted of 200 mg administered on day LH + 2. Endometrial biopsies were treated for RNA isolation and cDNA conversion and sequencing. Endometrial receptivity status was assessed by the ERA computational predictor. Differential gene expression between groups was also assessed. Ingenuity Pathway Analysis was used for network analysis. Validation of gene expression results was done by qPCR.

MAIN RESULTS AND THE ROLE OF CHANCE

Control samples were all staged around 'receptive' as would be clinically expected for LH + 7. Treatment samples were all staged as non-receptive (all but one was classified as 'proliferative' and the last as 'pre-receptive'). Differential gene expression analysis yielded 60 differentially expressed genes between the control and treatment groups. Bioinformatic pathway analysis for differential expression showed inactivation of the progesterone and glucocorticoid receptors, consistent with mifepristone action.

LIMITATIONS, REASONS FOR CAUTION

The primary limitations are the relative small number of subjects and the use of a limited gene panel.

WIDER IMPLICATIONS OF THE FINDINGS

This study sheds further light on the endometrial receptivity altering effects of mifepristone and on progesterone action. It further shows the capacity of the ERA to identify pharmacologically induced non-receptive endometrium, which expands its possible use clinically and in research.

STUDY FUNDING/COMPETING INTEREST(S)

C.v.G. and N.R.B. have no conflicts of interest. P.G.L. reports honorarium from University of HK/Shenzhen, other from NIF, India, outside the submitted work. K.G.D. reports consultancy for Bayer AG, Exelgyn, HRA-Pharma, Gedeon Richter, MSD, Mithra, Exeltis and Natural cycles, payment for lectures from Bayer AG, NSD, Ferring, HRA-Pharma, Exelgyn and Exeltis and clinical trials for Bayer AG, MSD, Exeltis, Mithra, HRA-Pharma and Sun Pharma. C.S. has a patent gene expression profile (ERA) issued to Igenomix and is scientific director of Igenomix S.L. M.R., R.N. and J.M.V. are employees of Igenomix S.L.

TRIAL REGISTRATION NUMBER

N/A.