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-733 Implementing preconception expanded carrier screening in a universal healthcare system: insights from a cost-effectiveness analysis

Study question

Would reimbursement of expanded carrier screening (ECS) panels of different gene content be cost-effective in a universal healthcare system?

Summary answer

Both tested ECS panels would be cost-effective if reimbursed by the Italian national healthcare system for a population without personal/familiar or racial/ethnic preconception genetic risks.

What is known already

Collectively, Mendelian diseases are a significant cause of infant mortality and hospitalization. Current preconception screening strategies test a limited number of individuals based on self-reported personal/familiar or racial/ethnic background. Consequently, the majority of at risk couples (ARCs) remain hidden in the general population. If adopted at a population level, multiplex platforms can thus improve screening effectiveness by allowing rapid ECS for a large number of conditions. Available economic evaluations assume the perspective of private/commercial payers. However, the decision to reimburse ECS in a tax-based national healthcare system would benefit from a cost-effectiveness analysis from the perspective of the public payer.

Study design, size, duration

This cost-effectiveness decision model compared lifetime costs and effects of two preconception ECS panels (i.e., “Strategy A1” (testing Cystic Fibrosis, Spinal-Muscular-Atrophy, Beta Thalassemia, Phenylketonuria and Fragile-X-Syndrome) and “Strategy A2” (testing “Strategy A1” + 16 common severe highly-penetrant childhood conditions in the Mediterranean population)) with no screening (“Strategy B”). We embraced the perspective of the Italian National Healthcare System. The time horizon for each condition equals an affected child’s life expectancy.

Participants/materials, setting, methods

We included couples seeking pregnancy without personal/familiar or racial/ethnic genetic risk. The cost-effectiveness analysis was based on a decision tree model where: i) the ECS panels sensitivity was 100%; ii) the probability for at risk couples (ARCs) to be risk-adverse was 77% based on data available from the literature; iii) all the forms of intervention that risk-adverse couples opted for lowered to zero the risk to conceive an affected child for the considered conditions.

Main results and the role of chance

Unitary cost of €240 for Strategy A1 and of €270 for Strategy A2 for each couple were estimated through a market analysis simulating a public ECS provision. For risk-adverse couples, the cost of intervention was estimated as equal to €8,376. This resulted from the weighted mean of the cost of the different options available (i.e., in vitro fertilization (IVF) with preimplantation testing for monogenic disorders (PGT-M) or, in case of natural conception, prenatal diagnosis and, eventually, termination of pregnancy). Strategy A1 was dominant versus no screening: Strategy A1 entailed savings equal to €1,395 and an incremental benefit of 0.0154 life years gained. Strategy A2 was dominant versus no screening: Strategy A2 entailed savings of €2,273 and an incremental benefit of 0.0238 life years gained. Strategy A2, when compared with Strategy A1, entailed an incremental cost of €649 and higher health benefits (0.7688 life years gained) (incremental cost-effectiveness ratio (ICER): €844).

Limitations, reasons for caution

This decision analytic model relies on input parameters on costs and life expectancy associated to each Mendelian disease derived from the literature. However, the feasibility to generate experimental evidence to inform this type of studies is very limited. The cost-effectiveness profiles established are valid under the assumptions listed.

Wider implications of the findings

Cost-effectiveness analyses like the one performed are useful policy tools to inform decisions regarding preconception screening programs for detectable severe recessive highly penetrant early-onset genetic conditions.

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

P–530 The use of wide thresholds for detecting intermediate chromosomal CNV up to 80% doesn’t improve PGT-A ability to discriminate true mosaic from uniformly aneuploid embryos

Study question

What is the effect of varying diagnostic thresholds on the accuracy of Next Generation Sequencing (NGS)-based preimplantation genetic testing for aneuploidies (PGT-A)?

Summary answer

When single trophectoderm biopsies are tested, the employment of 80% upper threshold increases mosaic calls and false negative aneuploidy results compared to more stringent thresholds.

What is known already

Trophectoderm (TE) biopsy coupled with NGS-based PGT-A technologies are able to accurately predict Inner Cell Mass’ (ICM) constitution when uniform whole chromosome aneuploidies are considered. However, minor technical and biological inconsistencies in NGS procedures and biopsy specimens can result in subtle variability in analytical results. In this context, the stringency of thresholds employed for diagnostic calls can lead to incorrect classification of uniformly aneuploid embryos into the mosaic category, ultimately affecting PGT-A accuracy. In this study, we evaluated the diagnostic predictivity of different aneuploidy classification criteria by employing blinded analysis of chromosome copy number values (CNV) in multifocal blastocyst biopsies.

Study design, size, duration

The accuracy of different aneuploidy diagnostic cut-offs was assessed comparing chromosomal CNV in intra-blastocysts multifocal biopsies. Enrolled embryos were donated for research between June and September 2020. The Institutional Review Board at the Near East University approved the study (project: YDU/20l9/70–849). Embryos diagnosed with uniform chromosomal alterations (single or multiple) in their clinical TE biopsy (n = 27) were disaggregated into 5 portions: the ICM and 4 TE biopsies. Overall, 135 specimens were collected and analysed.

Participants/materials, setting, methods

Twenty-seven donated blastocysts were warmed and disaggregated in TE biopsies and ICM (n = 135 biopsies). PGT-A analysis was performed using Ion ReproSeq PGS kit and Ion S5 sequencer (ThermoFisher). Sequencing data were blindly analysed with Ion-Reporter software. Intra-blastocyst comparison of raw NGS data was performed employing different thresholds commonly used for aneuploidy classification. CNV for each chromosome were reported as aneuploid according to 70% or 80% thresholds. Categorical variables were compared using Fisher’s exact test.

Main results and the role of chance

In this study, a total of 50 aneuploid patterns in 27 disaggregated embryos were explored. Single TE biopsy results were considered as true positive when they displayed the same alteration detected in the ICM at levels above the 70% or 80% thresholds. Alternatively, alterations detected in the euploid or mosaic range were considered as false negative aneuploidy results. When the 70% threshold was applied, aneuploidy findings were confirmed in 94.5% of TE biopsies analyzed (n = 189/200; 95%CI=90.37–37.22), while 5.5% showed a mosaic profile (50–70%) but uniformly abnormal ICM. Positive (PPV) and negative predictive value (NPV) per chromosome were 100.0% (n = 189/189; 95%CI=98.07–100.00) and 99.5% (n = 2192/2203; 95%CI=99.11–99.75) respectively. When the upper cut-off was experimentally placed at 80% of abnormal cells, a significant decrease (p-value=0.0097) in the percentage of confirmed aneuploid calls was observed (86.5%; n = 173/200; 95%CI=80.97–90.91), resulting in mosaicism overcalling, especially in the high range (50–80%). Less stringent thresholds led to extremely high PPV (100.0%; n = 173/173; 95%CI=97.89–100.00), while NPV decreased to 98.8% (n = 2192/2219; 95%CI=98.30–99.23). Furthermore, no additional true mosaic patterns were identified with the use of wide range thresholds for aneuploidy classification.

Limitations, reasons for caution

This approach involved the analysis of aneuploidy CNV thresholds at the embryo level and lacked from genotyping-based confirmation analysis. Moreover, aneuploid embryos with known meiotic partial deletion/duplication were not included.

Wider implications of the findings: The use of wide thresholds for detecting intermediate chromosomal CNV up to 80% doesn’t improve PGT-A ability to discriminate true mosaic from uniformly aneuploid embryos, lowering overall diagnostic accuracy. Hence, a proportion of the embryos diagnosed as mosaic using wide calling thresholds may actually be uniformly aneuploid and inadvertently transferred.

Trial registration number

N/A

P-536 Pre-selected for an award: Validation of a Next Generation Sequencing (NGS) workflow integrating simultaneous analysis of ploidy, microdeletions and de novo monogenic diseases for expanded preimplantation genetic testing (PGT)

Study question

Can major de novo genetic and chromosomal abnormalities (i.e., ploidy, microdeletions) be effectively tested on a single embryo biopsy specimen using an integrated NGS approach?

Summary answer

The integrated NGS workflow provided high accuracy for multilevel chromosome and genetic abnormalities analysis based on single biopsies expanding PGT informativity to de novo conditions.

What is known already

Current NGS-based methodologies employed in PGT for aneuploidy (PGT-A) do not detect embryo ploidy level nor frequent pathogenic de novo microdeletions below resolution limits. Moreover, despite their considerable incidence and adverse pregnancy outcomes, de novo mutations causing severe dominant monogenic fetal structural defects (FSD) are not investigated during PGT. The development of a single biopsy specimen-based PGT-A sequencing strategy that integrates ploidy and de novo microdeletions/mutations assessment would significantly widen PGT-A diagnostic scope and technical capabilities. This comprehensive approach would provide additional valuable genetic information of unquestionable clinical utility to further refine embryo selection process among those showing euploid profiles.

Study design, size, duration

Chromosomal conditions were validated using 24 embryo rebiopsies and 5 cell lines with both known ploidy level and known microdeletions (-4p; -8q; -1p; -22q; -5p; -15q; -11q). Genotyping for monogenic conditions was validated using 5 genomic DNA samples (33pg/µl) carrying known pathogenic Single Nucleotide Variants (SNVs) in COL1A1, SOS1, PTPN11, TSC2 and FGFR2 genes. To assess technical performance across identified SNPs, genotyping accuracy was evaluated on 17 samples from 5 embryos and 2 cell lines.

Participants/materials, setting, methods

Thirty-two de novo dominant monogenic conditions with FSD and strong gene-disease relationship were tested using a multiplex PCR panel with sequencing for the genes’ whole coding region. Eight common microdeletions ( < 10Mb) syndromes (Wolf-Hirshorn, Langer-Geidion, 1p36 deletion, De George, Cri-du-Chat, Prader-Willy/Angelman, Jacobsen) were tested using B-allelic frequency (BAF) of 356 highly polymorphic Single Nucleotide Polymorphisms (SNPs). These SNPs were also used for ploidy assessment. Library preparation and sequencing were performed on the IonTorrent S5 (ThermoFisher).

Main results and the role of chance

Blinded NGS data analysis confirmed the ploidy status in all (19) samples with known constitution (8 diploids, 7 polyploids, 4 haploids). Specifically, the proportion of heterozygote calls (BAF 40%-60%) was 60.9% (95%CI:47.6-72.8) for diploid samples and < 1% for haploid samples(P < 0.001). All polyploid samples showed a typical splitting of BAF among 3 experimental ranges (20-40%,40%-60%,60-80%): 34.1%,18.2% and 47.7%, respectively. For microdeletions, all interstitial SNPs genotyped showed a loss of heterozygosity (LOH) as expected. The analysis of positive controls consisting of 20 blastocyst rebiopsies and 3 cell lines (-4p: n = 3; -8q: n = 4; -1p: n = 5; -22q: n = 3; -5p: n = 2; -15q: n = 4; -11q: n = 2), allowed to accurately characterize 6 out of the 7 microdeletions (18/23 samples). In particular, all interstitial SNPs genotyped showed a LOH, while diploid controls showed an overall heterozygosity of 30.9% (average number of hetSNP x deletion = 9/28). Only the very small telomeric 1p36 region failed to properly amplify. For monogenic conditions, sequencing analysis of 5 positive gDNA controls confirmed the presence of 4 known SNVs, whilst only 1 did not achieve the minimum coverage for variant calling. Moreover, 4 additional de novo SNVs detected by sequencing analysis in the gene panel on 8 blastocyst rebiopsies were all confirmed by qPCR/Taqman assays.

Limitations, reasons for caution

Positive controls were not available for all genes and microdeletions included in the panel. Moreover, inefficient amplification has affected some target regions and further optimization will be required. However, analytical performance on technical and biological replicates were highly promising for the tested conditions both cell lines and trophectoderm biopsies.

Wider implications of the findings

This study demonstrates that the integration of genotyping and chromosomal analyses can be efficiently achieved in the same NGS workflow. This approach can be employed to expand PGT diagnostic scope to conditions undetectable in parents due to their de novo onset, or that are below the standard PGT-A resolution.

Trial registration number

N/A

P–536 Validation of a Next Generation Sequencing (NGS) workflow integrating simultaneous analysis of ploidy, microdeletions and de novo monogenic diseases for expanded preimplantation genetic testing (PGT)

Study question

Can major de novo genetic and chromosomal abnormalities (i.e., ploidy, microdeletions) be effectively tested on a single embryo biopsy specimen using an integrated NGS approach?

Summary answer

The integrated NGS workflow provided high accuracy for multilevel chromosome and genetic abnormalities analysis based on single biopsies expanding PGT informativity to de novo conditions.

What is known already

Current NGS-based methodologies employed in PGT for aneuploidy (PGT-A) do not detect embryo ploidy level nor frequent pathogenic de novo microdeletions below resolution limits. Moreover, despite their considerable incidence and adverse pregnancy outcomes, de novo mutations causing severe dominant monogenic fetal structural defects (FSD) are not investigated during PGT. The development of a single biopsy specimen-based PGT-A sequencing strategy that integrates ploidy and de novo microdeletions/mutations assessment would significantly widen PGT-A diagnostic scope and technical capabilities. This comprehensive approach would provide additional valuable genetic information of unquestionable clinical utility to further refine embryo selection process among those showing euploid profiles.

Study design, size, duration

Chromosomal conditions were validated using 24 embryo rebiopsies and 5 cell lines with both known ploidy level and known microdeletions (–4p; –8q; –1p; –22q; –5p; –15q; –11q). Genotyping for monogenic conditions was validated using 5 genomic DNA samples (33pg/µl) carrying known pathogenic Single Nucleotide Variants (SNVs) in COL1A1, SOS1, PTPN11, TSC2 and FGFR2 genes. To assess technical performance across identified SNPs, genotyping accuracy was evaluated on 17 samples from 5 embryos and 2 cell lines.

Participants/materials, setting, methods

Thirty-two de novo dominant monogenic conditions with FSD and strong gene-disease relationship were tested using a multiplex PCR panel with sequencing for the genes’ whole coding region. Eight common microdeletions (<10Mb) syndromes (Wolf-Hirshorn, Langer-Geidion, 1p36 deletion, De George, Cri-du-Chat, Prader-Willy/Angelman, Jacobsen) were tested using B-allelic frequency (BAF) of 356 highly polymorphic Single Nucleotide Polymorphisms (SNPs). These SNPs were also used for ploidy assessment. Library preparation and sequencing were performed on the IonTorrent S5 (ThermoFisher).

Main results and the role of chance

Blinded NGS data analysis confirmed the ploidy status in all (19) samples with known constitution (8 diploids, 7 polyploids, 4 haploids). Specifically, the proportion of heterozygote calls (BAF 40%–60%) was 60.9% (95%CI:47.6–72.8) for diploid samples and <1% for haploid samples(P < 0.001). All polyploid samples showed a typical splitting of BAF among 3 experimental ranges (20–40%,40%–60%,60–80%): 34.1%,18.2% and 47.7%, respectively. For microdeletions, all interstitial SNPs genotyped showed a loss of heterozygosity (LOH) as expected. The analysis of positive controls consisting of 20 blastocyst rebiopsies and 3 cell lines (–4p: n = 3; –8q: n = 4; –1p: n = 5; –22q: n = 3; –5p: n = 2; –15q: n = 4; –11q: n = 2), allowed to accurately characterize 6 out of the 7 microdeletions (18/23 samples). In particular, all interstitial SNPs genotyped showed a LOH, while diploid controls showed an overall heterozygosity of 30.9% (average number of hetSNP x deletion=9/28). Only the very small telomeric 1p36 region failed to properly amplify. For monogenic conditions, sequencing analysis of 5 positive gDNA controls confirmed the presence of 4 known SNVs, whilst only 1 did not achieve the minimum coverage for variant calling. Moreover, 4 additional de novo SNVs detected by sequencing analysis in the gene panel on 8 blastocyst rebiopsies were all confirmed by qPCR/Taqman assays.

Limitations, reasons for caution

Positive controls were not available for all genes and microdeletions included in the panel. Moreover, inefficient amplification has affected some target regions and further optimization will be required. However, analytical performance on technical and biological replicates were highly promising for the tested conditions both cell lines and trophectoderm biopsies.

Wider implications of the findings: This study demonstrates that the integration of genotyping and chromosomal analyses can be efficiently achieved in the same NGS workflow. This approach can be employed to expand PGT diagnostic scope to conditions undetectable in parents due to their de novo onset, or that are below the standard PGT-A resolution.

Trial registration number

N/A

Clinical validity and utility of preconception expanded carrier screening for the management of reproductive genetic risk in IVF and general population

STUDY QUESTION

What is the clinical validity and utility of preconception Expanded Carrier Screening (ECS) application on the management of prospective parents?

SUMMARY ANSWER

The high detection rate of at-risk couples (ARCs) and the high proportion opting for IVF/preimplantation genetic testing (PGT) treatment demonstrate the clinical utility of ECS in the preconception space in IVF and general population.

WHAT IS KNOWN ALREADY

About 2-4% of couples are at risk of conceiving a child with an autosomal recessive or X-linked genetic disorder. In recent years, the increasing cost-effectiveness of genetic diagnostic techniques has allowed the creation of ECS panels for the simultaneous detection of multiple recessive disorders. Comprehensive preconception genetic screening holds the potential to significantly improve couple's genetic risk assessment and reproductive planning to avoid detectable inheritable genetic offspring.

STUDY DESIGN, SIZE, DURATION

A total of 3877 individuals without a family history of genetic conditions were analyzed between January 2017 and January 2020. Of the enrolled individuals, 1212 were gamete donors and 2665 were patients planning on conceiving from both the IVF and the natural conception group. From the non-donor cohort, 1133 were analyzed as individual patients, while the remaining ones were analyzed as couples, for a total of 766 couples.

PARTICIPANTS/MATERIALS, SETTING, METHODS

A focused ECS panel was developed following American College of Obstetrics and Gynecology ACOG-recommended criteria (prevalence, carrier rate, severity), including highly penetrant severe childhood conditions. Couples were defined at-risk when both partners carried an autosomal recessive pathogenic/likely pathogenic variant (PLP) on the same gene or when the woman was a carrier of an X-linked PLP variant. ARC detection rate defined the clinical validity of the ECS approach. Clinical utility was evaluated by monitoring ARCs reproductive decision making.

MAIN RESULTS AND THE ROLE OF CHANCE

A total of 402 individuals (10.4%) showed PLP for at least one of the genes tested. Among the 766 couples tested, 173 showed one carrier partner (22.6%), whereas 20 couples (2.6%) were found to be at increased risk. Interestingly, one ARC was identified as a result of cascade testing in the extended family of an individual carrying a pathogenic variant on the Survival Of Motor Neuron 1SMN1 gene. Of the identified ARCs, 5 (0.7%) were at risk for cystic fibrosis, 5 (0.7%) for fragile X syndrome, 4 (0.5%) for spinal muscular atrophy, 4 (0.5%) for Beta-Thalassemia/Sickle Cell Anemia, 1 (0.1%) for Smith-Lemli-Opitz Syndrome and 1 (0.1%) for Duchenne/Becker Dystrophy. Fifteen ARCs were successfully followed up from both the IVF and the natural conception groups. All of these (15/15) modified their reproductive planning by undergoing ART with Preimplantation Genetic Testing for Monogenic disease and Aneuploidies (PGT-M and PGT-A). To date, 6/15 (40%) couples completed their PGT cycle with euploid/unaffected embryos achieving a pregnancy after embryo transfer and three of them have already had an unaffected baby.

LIMITATIONS, REASONS FOR CAUTION

The use of a limited panel of core gene-disease pairs represents a limitation on the research perspective as it can underestimate the rate of detectable carriers and ARCs in this cohort of prospective parents. Expanding the scope of ECS to a larger panel of conditions is becoming increasingly feasible, thanks to a persistent technological evolution and progressive cataloging of gene-disease associations.

WIDER IMPLICATIONS OF THE FINDINGS

These results highlight the potential clinical validity and utility of ECS in reducing the risk of a pregnancy affected by a detectable inheritable genetic condition. The steady reduction in the costs of genetic analyses enables the expansion of monogenic testing/screening applications at the preimplantation stage, thus, providing valid decisional support and reproductive autonomy to patients, particularly in the context of IVF.

STUDY FUNDING/COMPETING INTEREST(S)

No external funding was used for this study. A.C., M.F., S.C., M.P., L.G., and C.P. are employees of Igenomix Italy. C.S. is the head of the scientific board of Igenomix.

TRIAL REGISTRATION NUMBER

N/A.