title: New protocol based on massive parallel sequencing for aneuploidy screening of preimplantation human embryos.
abstract: Novel next-generation sequencing procedures have rapidly emerged into the preimplantation genetic screening framework. This work presents the design and validation of a new low-coverage whole-genome sequencing assay for aneuploidy detection in single blastomeres and trophectodermal samples from preimplantation embryos. The validation ensures analytical sensitivity, specificity, robustness, precision, limit of detection, resolution, and reproducibility. Specific parameters to measure the performance are defined, and the results are compared with a standardized array-based method to stablish the concordance. From the single cell genomics point of view, the main novelties are the length of reads of the libraries (150 nucleotides) together with a paired-end strategy and the design of an original algorithm and copy number viewer. A total of 129 samples were included in six experimental runs using a MiSeq Illumina platform. Samples included: single amniocytes, single blastomeres (cleavage-stage embryos), trophectoderm samples (blastocyst), and diluted DNA. Sensitivity and specificity were calculated per chromosome yielding 96% and 99%, respectively. The percentage of concordant samples was 98.2% and all of the aneuploid samples were confirmed. In conclusion, the validation yields highly reliable and reproducible results, representing an accurate and cost-effective strategy for the routine detection of aneuploidy in human embryos.
authors.affiliation: a Reproductive Genetics Unit , Sistemas Genómicos Ltd. , Paterna , Valencia , Spain.
authors.forename: Xavier
authors.initials: X
authors.lastname: Vendrell
authors.affiliation: b Next-Generation Sequencing Laboratory , Sistemas Genómicos Ltd. , Paterna , Valencia , Spain.
authors.forename: Victoria
authors.initials: V
authors.lastname: Fernández-Pedrosa
authors.affiliation: c Bioinformatics Department , Sistemas Genómicos Ltd. , Paterna , Valencia , Spain.
authors.forename: Juan Carlos
authors.initials: JC
authors.lastname: Triviño
authors.affiliation: a Reproductive Genetics Unit , Sistemas Genómicos Ltd. , Paterna , Valencia , Spain.
authors.forename: Rosa
authors.initials: R
authors.lastname: Bautista-Llácer
authors.affiliation: b Next-Generation Sequencing Laboratory , Sistemas Genómicos Ltd. , Paterna , Valencia , Spain.
authors.forename: Carmen
authors.initials: C
authors.lastname: Collado
authors.affiliation: c Bioinformatics Department , Sistemas Genómicos Ltd. , Paterna , Valencia , Spain.
authors.forename: Oscar
authors.initials: O
authors.lastname: Rodríguez
authors.affiliation: a Reproductive Genetics Unit , Sistemas Genómicos Ltd. , Paterna , Valencia , Spain.
authors.forename: Elena
authors.initials: E
authors.lastname: García-Mengual
authors.affiliation: d CREA Reproductive Medicine Center , Valencia , Spain.
authors.forename: Empar
authors.initials: E
authors.lastname: Ferrer
authors.affiliation: d CREA Reproductive Medicine Center , Valencia , Spain.
authors.forename: Carmen
authors.initials: C
authors.lastname: Calatayud
authors.affiliation: d CREA Reproductive Medicine Center , Valencia , Spain.
authors.forename: Miguel
authors.initials: M
authors.lastname: Ruiz-Jorro
mesh_terms: D000465:Algorithms; D000782:Aneuploidy; D006801:Humans; D019836:Preimplantation Diagnosis / Q000379:methods*; D017422:Sequence Analysis, DNA
keywords: Aneuploidy; blastomeres; embryos; next-generation sequencing; preimplantation genetic diagnosis; validation