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Xia Y, Katz M, Chandramohan D, Bechor E, Podgursky B, Hoxie M, Zhang Q, Chertman W, Kang J, Blue E, Chen J, Schleede J, Slotnick NR, Du X, Boostanfar R, Urcia E, Behr B, Cohen J, Siddiqui N. The first clinical validation of whole-genome screening on standard trophectoderm biopsies of preimplantation embryos. F S Rep 2024; 5:63-71. [PMID: 38524212 PMCID: PMC10958695 DOI: 10.1016/j.xfre.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 03/26/2024] Open
Abstract
Objective To validate the performance of our laboratory-developed whole-genome screening assay within clinical preimplantation genetic testing environments. Design Perform a laboratory-developed whole-genome assay on both cell lines and trophectoderm biopsies, subsequently employing the next-generation sequencing procedure to reach a sequencing depth of 30X. Adhere to the Genome Analysis Toolkit best practices for accuracy, sensitivity, specificity, and precision calculations by comparing samples with references. Our assay was then applied to cell lines and biopsies harboring known pathogenic variants, aiming to ascertain these changes solely from the next-generation sequencing data, independent of parental genome information. Settings Clinical laboratory. Patients Coriell cell lines and research embryos with known chromosomal or genetic variants. Research trophectoderm biopsies from a couple that are heterozygous carriers for distinct variants in the same autosomal recessive gene (HOGA1). Intervention Not applicable. Main Outcome Measures Accuracy, sensitivity, specificity, and precision were assessed by comparing the samples to their references. For samples with known variants, we calculated our sensitivity to detecting established variants. For the research embryos, noncarrier, carrier, and compound heterozygous states of inherited HOGA1 variants were distinguished independently of parental samples. Results Amplification of DNA from cell lines and embryos yielded success rates exceeding 99.9% and 98.2%, respectively, although maintaining an accuracy of >99.9% for aneuploidy assessment. The accuracy (99.99%), specificity (99.99%), sensitivity (98.0%), and precision (98.1%) of amplified genome in the bottle (reference NA12878) and embryo biopsies were comparable to results on genomic DNA, including mitochondrial heteroplasmy. Using our assay, we achieved >99.99% sensitivity when examining samples with known chromosomal and genetic variants. This encompassed pathogenic CFTR, BRCA1, and other variants, along with uniparental isodisomies and microdeletions such as DiGeorge syndrome. Our research study identified noncarrier, carrier, and compound heterozygous states within trophectoderm biopsies while simultaneously screening for 1,300 other severe monogenic diseases. Conclusion To our knowledge, this is the first clinical validation of whole-genome embryo screening. In this study, we demonstrated high accuracy for aneuploidy calls (>99.9%) and genetic variants (99.99%), even in the absence of parental genomes. This assay demonstrates advancements in genomic screening and an extended scope for testing capabilities in the realm of preimplantation genetic testing.
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Affiliation(s)
- Yuntao Xia
- Laboratory Department, Orchid Health, Palo Alto, California
| | - Maria Katz
- Laboratory Department, Orchid Health, Palo Alto, California
| | | | - Elan Bechor
- Laboratory Department, Orchid Health, Palo Alto, California
| | | | - Michael Hoxie
- Laboratory Department, Orchid Health, Palo Alto, California
| | - Qinnan Zhang
- Laboratory Department, Orchid Health, Palo Alto, California
| | - Willy Chertman
- Laboratory Department, Orchid Health, Palo Alto, California
| | | | | | | | | | | | - Xiaoli Du
- Laboratory Department, Orchid Health, Palo Alto, California
| | | | - Eric Urcia
- HRC Fertility-Encino, Encino, California
| | - Barry Behr
- Department of Obstetrics and Gynecology - Reproductive Endocrinology and Infertility, Stanford University, Sunnyvale, California
| | | | - Noor Siddiqui
- Laboratory Department, Orchid Health, Palo Alto, California
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Abu Maizar AM, Urcia E, VerMilyea MD, Marrs R, Ringler GE, Baek K. Fully hatched euploid blastocysts exhibit lower pregnancy outcomes when compared to other blastocyst stages in frozen set cycles. Fertil Steril 2019. [DOI: 10.1016/j.fertnstert.2019.07.515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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