Improved clinical utility of preimplantation genetic testing through the integration of ploidy and common pathogenic microdeletions analyses

• DOI: 10.1093/humrep/dead033
• Publication Date: 2023-02-24T07:20:11Z
• Authors: S Caroselli; M Figliuzzi; L Picchetta; F Cogo; P Zambon; I Pergher; L Girardi; C Patassini; M Poli; D Bakalova; D Cimadomo; N Findikli; O Coban; M Serdarogullari; F Favero; S Bortolato; A Anastasi; F Capodanno; A Gallinelli; F Brancati; L Rienzi; F M Ubaldi; J Jimenez-Almazán; D Blesa-Jarque; J Miravet-Valenciano; C Rubio; C Simòn; A Capalbo
• Keywords: Preimplantation Genetic Diagnosis; Genomic Imprinting; Uniparental disomy

Can chromosomal abnormalities beyond copy-number aneuploidies (i.e. ploidy level and microdeletions (MDs)) be detected using a preimplantation genetic testing (PGT) platform?The proposed integrated approach accurately assesses the most common pathogenic causative of genomic disorders, expanding clinical utility PGT.Standard methodologies employed in for aneuploidy (PGT-A) identify but cannot determine nor presence recurrent MDs responsible disorders. Transferring embryos carrying these can result miscarriage, molar pregnancy, intellectual disabilities developmental delay offspring. The development strategy that integrates their assessment resolve current limitations add valuable information regarding constitution embryos, which is not evaluated PGT providing new knowledge further understanding causes implantation failure early pregnancy loss. To best our knowledge, have never been studied human up to date.This retrospective cohort analysis including blastocyst biopsies collected between February 2018 November 2021 at multiple collaborating IVF clinics from prospective parents European ancestry below age 45, autologous gametes undergoing ICSI all oocytes. Ploidy determination was validated 164 embryonic samples known status (147 diploids, 9 triploids, 8 haploids). Detection nine 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) developed tested 28 positive controls 97 negative controls. Later, methodology blindly applied of: (i) 100 two pronuclei (2PN)-derived blastocysts were previously defined as uniformly euploid by standard PGT-A; (ii) 99 whose transfer resulted loss.The based on targeted next-generation sequencing selected polymorphisms across genome enriched within critical regions included syndromes. Sequencing data allelic frequencies) analyzed probabilistic model estimated likelihood presence, accounting both noise population genetics patterns linkage disequilibrium, LD, correlations) observed 2504 whole-genome 1000 Genome Project database. Analysis phased parental haplotypes obtained single-nucleotide polymorphism (SNP)-array genotyping performed confirm MD.In analytical validation phase, this showed extremely high accuracy classification (100%, CI: 98.1-100%) identification six out eight (99.2%, 98.5-99.8%). improve detection loss heterozygosity (LOH), haploblocks haplotype frequency LOH occurrence reference population, thus developing mathematical models. As result, chr1p36 chr4p16.3 excluded due poor reliability, whilst workflow incorporated DNA enhance MDs. During application one case triploidy among 2PN-derived (-22q11.21) retrospectively identified biopsy specimens transferred miscarriage (ii). For latter case, family-based revealed same different sibling (n = 2/5) non-carrier parents, suggesting germline mosaicism female partner. When are constitution, with and/or aneuploidies, an incidence 1.5% 3/202, 95% 0.5-4.5%) embryos.Epidemiological studies will required assess alterations particularly miscarriages. Despite assay developed, use support diagnostic calling increase precision assay.This novel significantly expands PGT-A integrating (both de novo inherited ones) usually later stage through invasive prenatal testing. From basic research standpoint, help elucidate fundamental biological questions related otherwise embryos.No external funding used 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., C.R. employees Igenomix C.S. head scientific board Igenomix. A.C. L.P. JUNO GENETICS. GENETICS companies reproductive services.N/A.