Expanded clinical validation of Haploseek for comprehensive preimplantation genetic testing

Zeevi, David A.; Backenroth, Daniel; Hakam-Spector, Elinor; Renbaum, Paul; Mann, Tzvia; Zahdeh, Fouad; Segel, Reeval; Zeligson, Sharon; Eldar‐Geva, Talia; Ben‐Ami, Ido; Ben-Yehuda, Adi; Carmi, Shai; Altarescu, Gheona

doi:10.1038/s41436-021-01145-6

Cited by 10 publications

(18 citation statements)

References 25 publications

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“…The conversion to sequencing-based haplotyping allows single-cell haplotyping in all species. Haploseek combines both sequencing and SNP arrays to profile single cells by utilizing single-cell low-coverage whole-genome sequencing for copy-number profiling and haplotyping, but processes phasing references via SNP arrays to determine maternal and paternal haplotypes ( 9 , 12 ). scHaplotyper demonstrated discrimination and visualization of the inheritance of the haplotypes for PGT-M purposes based on single-cell DNA sequencing by using a Hidden Markov Model on phased SNPs; however, no detailed information was provided on the sequencing process itself ( 31 ).…”

Section: Discussionmentioning

confidence: 99%

“…Human embryos are now frequently genotyped via SNP arrays and subsequently, haplotyped for the generic and genome-wide identification of disease allele inheritance in the diagnostic setting of preimplantation genetic testing for monogenic disorders (PGT-M) ( 23 , 24 , 26–28 ). In recent years, multiple approaches for single-cell haplotyping have been developed, yet only a limited number have been clinically implemented ( 5 , 6 , 9 , 12 , 28–31 ). These first approaches are based on the use of SNP arrays to genotype single-cell and bulk DNA.…”

Section: Introductionmentioning

confidence: 99%

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Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing

Masset

Ding

Dimitriadou

et al. 2022

Nucleic Acids Research

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Single-cell whole-genome haplotyping allows simultaneous detection of haplotypes associated with monogenic diseases, chromosome copy-numbering and subsequently, has revealed mosaicism in embryos and embryonic stem cells. Methods, such as karyomapping and haplarithmisis, were deployed as a generic and genome-wide approach for preimplantation genetic testing (PGT) and are replacing traditional PGT methods. While current methods primarily rely on single-nucleotide polymorphism (SNP) array, we envision sequencing-based methods to become more accessible and cost-efficient. Here, we developed a novel sequencing-based methodology to haplotype and copy-number profile single cells. Following DNA amplification, genomic size and complexity is reduced through restriction enzyme digestion and DNA is genotyped through sequencing. This single-cell genotyping-by-sequencing (scGBS) is the input for haplarithmisis, an algorithm we previously developed for SNP array-based single-cell haplotyping. We established technical parameters and developed an analysis pipeline enabling accurate concurrent haplotyping and copy-number profiling of single cells. We demonstrate its value in human blastomere and trophectoderm samples as application for PGT for monogenic disorders. Furthermore, we demonstrate the method to work in other species through analyzing blastomeres of bovine embryos. Our scGBS method opens up the path for single-cell haplotyping of any species with diploid genomes and could make its way into the clinic as a PGT application.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing

Masset

Ding

Dimitriadou

et al. 2022

Nucleic Acids Research

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“…developed Haploseek, which is based on SNP microarray, whole-genome sequencing, and hidden Markov model (HMM) [83] . This comprehensive method showed 100% concordance on PGT-M and PGT-A/SR results in 73 and 72 embryos, respectively, compared with PCR and VeriSeq-PGS [87] . Furthermore, Xie et al .…”

Section: Novel Pgt Technologiesmentioning

confidence: 99%

A review of pre-implantation genetic testing technologies and applications

Zhao

Kang

et al. 2022

Reproductive and Developmental Medicine

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The first practice of pre-implantation genetic testing (PGT) was reported more than 30 years ago. PGT, originally named pre-implantation genetic screening (PGS) and pre-implantation genetic diagnosis (PGD), is now categorized as PGT for aneuploidies (PGT-A), PGT for monogenic/single-gene defects (PGT-M), and PGT for chromosomal structural rearrangements (PGT-SR). Patients with fertility issues caused by advanced maternal age, carrier status of chromosomal abnormalities, or harboring pathogenic variant(s) are recommended to undergo PGT to increase the possibility of successful live birth and avoid potentially affected newborns. High-throughput techniques, such as DNA microarrays and next-generation sequencing (NGS), have enabled comprehensive screening of all 24 chromosomes, instead of few loci at a time. Furthermore, as a comprehensive PGT, PGT-Plus was enabled by the rapid development of a genome-wide single-cell haplotyping technique to detect embryo aneuploidy, single-gene disorders, and chromosomal aberrations simultaneously using a single universal protocol. In addition, non-invasive approaches enable a more intact embryo during the biopsy procedure, which may avoid potential mosaicism issues at a certain scale by testing spent culture media (SCM). As a novel PGT application, PGT-P detects genome-wide variations in polygenic diseases, which account for a large proportion of premature human deaths and affect a markedly larger population than monogenic diseases, using polygenic risk score calculation to decrease the potential of affecting complex conditions. Owing to the emergence of new technologies recruited to PGTs, more couples with infertility issues have a promising chance of conceiving a healthy baby, ultimately facilitating the human species to live more prosper.

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“…2 Recent advances in shifting towards genome wide single nucleotide polymorphism (SNP) microarrays and next generation senescing (NGS) allowed combining different PGT approaches for screening of chromosomal and genetic disorders. [3][4][5][6][7] However, PGT is invasive and requires obtaining cellular biopsies from the embryos. In addition, false negative assessments may arise due to insufficient genetic amplification and chromosomal mosaicism.…”

Section: Introductionmentioning

confidence: 99%

Delineating the heterogeneity of preimplantation development via unsupervised clustering of embryo candidates for transfer using automated, accurate and standardized morphokinetic annotation

Zabari

Kan‐Tor

et al. 2022

Preprint

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The majority of human embryos, whether naturally or in vitro fertilized (IVF), do not poses the capacity to implant within the uterus and reach live birth. Hence, selecting the embryos with the highest developmental potential to implant is imperative for improving pregnancy rates without prolonging time to pregnancy. The developmental potential of embryos can be assessed based on temporal profiling of the discrete morphokinetic events of preimplantation development. However, manual morphokinetic annotation introduces intra- and inter-observer variation and is time-consuming. Using a large clinically-labeled multicenter dataset of video recordings of preimplantation embryo development by time-lapse incubators, we trained a convolutional neural network and developed a classifier that performs fully automated, robust, and standardized annotation of the morphokinetic events with R-square 0.994 accuracy. To delineate the morphokinetic heterogeneity of preimplantation development, we performed unsupervised clustering of high-quality embryo candidates for transfer, which was independent of maternal age and blastulation rate. Retrospective comparative analysis of transfer versus implantation rates reveals differences between embryo clusters that are distinctively marked by poor synchronization of the third meiotic cell-cleavage cycle. We expect this work to advance the integration of morphokinetic-based decision support tools in IVF treatments and deepen our understanding of preimplantation heterogeneity.

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Expanded clinical validation of Haploseek for comprehensive preimplantation genetic testing

Cited by 10 publications

References 25 publications

Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing

Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing

A review of pre-implantation genetic testing technologies and applications

Delineating the heterogeneity of preimplantation development via unsupervised clustering of embryo candidates for transfer using automated, accurate and standardized morphokinetic annotation

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