Criteria to evaluate patterns of segmental and complete aneuploidies in preimplantation genetic testing for aneuploidy results suggestive of an inherited balanced translocation or inversion

Snider, Alyssa; Darvin, Tristan; Spor, Lauren; Akinwole, Adedoyin; Cinnioğlu, Cengiz; Kayalı, Refik

doi:10.1016/j.xfre.2020.12.003

Cited by 3 publications

(3 citation statements)

References 30 publications

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“…With the 0.5 Mbases bin matrix applied in the analysis, a smoothing window of 6 bins and a calling limit of 20 bins, the application has a theoretical resolution of around 10 Mbases. This is comparable with the common resolution for PGT-A using aCGH or NGS (6-10 Mbases) (Snider et al, 2021). Average Q-score of all nanopore-sequenced samples was 8.…”

Section: Quality Control and Genome Coverage For Nanopore Sequencing ...supporting

confidence: 74%

Evaluation of nanopore sequencing on polar bodies for routine pre-implantation genetic testing for aneuploidy

Oberle

Hanzer

Kokocinski³

et al. 2023

Preprint

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STUDY QUESTION: Is nanopore sequencing for PGT-A analysis of pooled polar bodies a reliable, fast, and cost-effective method and applicable for routine diagnostics in human reproductive care? SUMMARY ANSWER: Nanopore sequencing of pooled polar bodies (PB) revealed high concordance rate with traditional array comparative genomic hybridization (aCGH) analysis and the nanopore sequencing workflow was fast (feasible in under 5 hours) and cost-effective (100-150 Euro per sample), allowing fresh embryo transfer. WHAT IS KNOWN ALREADY: PGT-A using PB biopsy derives a clinical benefit by reducing number of embryo transfers and miscarriage rates but is currently not cost-efficient. Results are often unclear and require expert review. Nanopore sequencing technology opens possibilities by providing cost-efficient, fast sequencing results with uncomplicated sample preparation workflows. Interrogating the polar bodies avoids harming the embryo itself and is the only option for PGT-A in some jurisdictions. STUDY DESIGN, SIZE, DURATION: In this prospective clinical trial, 102 pooled PB samples from 20 patients treated for infertility between March and December 2022 were analyzed for aneuploidy using nanopore sequencing technology and compared with aCGH results generated as part of the clinical routine. All patients participating in this trial were treated for infertility at Wunschbaby Institut Feichtinger (WIF) in Vienna and chose aneuploidy screening of their polar bodies. All patients provided written informed consent. PARTICIPANTS/MATERIALS, SETTING, METHODS: PB samples were analyzed by aCGH for routine PGT-A. Aliquots of whole-genome amplified DNA were anonymized and prepared for sequencing by end-prepping, barcoding and adapter ligation. Samples were pooled equimolar for sequencing on a Nanopore MinION machine. Samples were sequenced for up to 9 hours for 6 pooled PB samples. Whole-chromosome copy-numbers were called by a custom bioinformatic analysis software after alignment and pre-processing. Automatically called results were compared to aCGH results. MAIN RESULTS AND THE ROLE OF CHANCE: In total, 99 pooled polar body samples were compared, three samples were excluded because of failed or uninterpretable results. Overall, the Nanopore sequencing workflow showed high concordance rates with aCGH: 96 of 99 samples were consistently detected as euploid or aneuploid (concordance=97%, specificity = 0.957, sensitivity = 1.0, PPV = 0.906, NPV = 1.0) and 91 samples showed a fully concordant karyotype (92%). Chromosomal aneuploidies analyzed in this trial covered all 23 chromosomes with 98 trisomies, 97 monosomies in 70 aCGH samples. Detailed calculation of time and cost for the nanopore sequencing workflow was performed for different scenarios. Time calculation revealed that the whole nanopore workflow is feasible in under 5 hours (for one sample) with maximum time of 16 hours (for 12 samples in parallel). This enables fresh PB euploid embryo transfer. Material cost for the whole workflow range between 100Euro and 150Euro, including sequencing cost of only 40Euro per sample, resulting in cost-efficient aneuploidy screening. LIMITATIONS, REASONS FOR CAUTION: For some samples, the reference result remained unclear, due to increased noise and limited resolution of the aCGH method. In particular, the small chromosomes show higher variability in both platforms and manual review is often required. A larger study with follow-up data or a clinical non- selection trial would be beneficial for increased confidence. WIDER IMPLICATIONS OF THE FINDINGS: This is the first clinical study, systematically comparing nanopore sequencing for aneuploidy of pooled polar bodies with standard detection methods. High concordance rates confirmed feasibility of nanopore technology for this application. Additionally, the fast and cost-efficient sequencing workflow reveals clinical utility of this technology, making polar body PGT-A clinically attractive. STUDY FUNDING/COMPETING INTEREST(S): The study was funded by the Wunschbaby Institut Feichtinger, Dr. Wilfried Feichtinger GmbH. The authors declare no competing conflict of interest. TRIAL REGISTRATION NUMBER: Not available

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Section: Quality Control and Genome Coverage For Nanopore Sequencing ...supporting

confidence: 74%

Evaluation of nanopore sequencing on polar bodies for routine pre-implantation genetic testing for aneuploidy

Oberle

Hanzer

Kokocinski³

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…Of all the possible gametes, only two (the results of alternate segregation) yielded normal (balanced) chromosomes. The others are genetically unbalanced, with adjacent‐1, adjacent‐2, 3:1, or 4:0 disjunctions (Snider et al., 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Identification and interruption of inheritance of familial cryptic translocations: A case report

Ou,

Sun,

Yang

et al. 2024

Molec Gen & Gen Med

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BackgroundCryptic translocations can be identified via genetic analysis of aborted tissues or malformed infants, but it is difficult to deduce the parental origins of the translocations. In the absence of such information, it is not easy to distinguish translocations from normal embryos during pre‐implantation genetic testing, that seeks to block familial transmission of translocations.MethodsHere, we present a new method that detects cryptic translocations and blocks familial transmission thereof. Whole‐genome, low‐coverage mate‐pair sequencing (WGLMPS) revealed chromosome breakpoint sequences, and preimplantation genetic haplotyping (PGH) was then used to discard embryos with cryptic translocations.ResultsCryptic translocations were found in all four families, and familial transmission was successfully blocked in one family.ConclusionWhole‐genome, low‐coverage mate‐pair sequencing combined with preimplantation genetic haplotyping methods powerfully and practically identify cryptic translocations and block familial transmissions.

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“…Prior studies have demonstrated the potential to reveal previously unknown parental findings via PGT-A in trophectoderm biopsies. For example, it has been demonstrated that recurrent segmental imbalances seen in multiple embryos from the same patient can lead to the identification of balanced translocation carrier parents [ 3 – 5 ].…”

Section: Introductionmentioning

confidence: 99%

High-resolution PGT-A results in incidental identification of patients with small pathogenic copy number variants

Leahy,

Marin,

et al. 2023

J Assist Reprod Genet

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Purpose This study aimed to evaluate whether a high-throughput high-resolution PGT-A method can detect copy number variants (CNVs) that could have clinical implications for patients and their embryos. Methods A prospective analysis of PGT-A cases was conducted using a high-resolution SNP microarray platform with over 820,000 probes. Cases where multiple embryos possessed the same segmental imbalance were identified, and preliminary PGT-A reports were issued recommending either parental microarray or conventional karyotyping to identify CNVs or translocations. Results Analysis of 6080 sequential PGT-A cases led to identification of 41 cases in which incidental findings were observed (0.7%) and parental testing was recommended. All cases, in which parental studies were completed, confirmed the original PGT-A incidental findings. In 2 of the cases, parental studies indicated a pathogenic variant with clinical implications for the associated embryos. In one of these cases, the patient was identified as a carrier of a duplication in chromosome 15q11.2:q11.2 (SNRPN + +), which is associated with autism spectrum disorder. In the second case, the patient was heterozygous positive for an interstitial deletion of 3p26.1:p26.3, which is associated with 3p deletion syndrome and had clinical implications for the patient and associated embryos. In each case, parental studies were concordant with PGT-A findings and revealed the presence of an otherwise unknown CNV. Conclusion High-throughput high-resolution SNP array–based PGT-A has the ability to detect previously unknown and clinically significant parental deletions, duplications, and translocations. The use of cost-effective SNP array–based PGT-A methods may improve the effectiveness of PGT by identifying and preventing previously unknown pathogenic CNVs in children born to patients seeking in vitro fertilization.

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Criteria to evaluate patterns of segmental and complete aneuploidies in preimplantation genetic testing for aneuploidy results suggestive of an inherited balanced translocation or inversion

Cited by 3 publications

References 30 publications

Evaluation of nanopore sequencing on polar bodies for routine pre-implantation genetic testing for aneuploidy

Evaluation of nanopore sequencing on polar bodies for routine pre-implantation genetic testing for aneuploidy

Identification and interruption of inheritance of familial cryptic translocations: A case report

High-resolution PGT-A results in incidental identification of patients with small pathogenic copy number variants

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