Development and validation of a next-generation sequencing–based protocol for 24- chromosome aneuploidy screening of embryos Francesco Fiorentino, Ph.D.,

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Development and validation of a next-generation sequencing–based protocol for 24- chromosome aneuploidy screening of embryos Francesco Fiorentino, Ph.D., Anil Biricik, M.Sc., Sara Bono, B.Sc., Letizia Spizzichino, B.Sc., Ettore Cotroneo, B.Sc., Giuliano Cottone, B.Sc., Felix Kokocinski, Ph.D., Claude-Edouard Michel, Ph.D. Fertility and Sterility Volume 101, Issue 5, Pages 1375-1382.e2 (May 2014) DOI: 10.1016/j.fertnstert.2014.01.051 Copyright © 2014 American Society for Reproductive Medicine Terms and Conditions

Figure 1 Graphic representation of copy number changes observed in various aneuploid whole-genome amplification (WGA) products selected from clinical preimplantation genetic screening cycles with embryo biopsy at cleavage stage. Left: results from array-CGH analysis; right: results from next-generation sequencing (NGS)–based 24-chromosome aneuploidy screening analysis derived from the same WGA product as shown in the left panel. Each NGS graph in the right panel indicates the copy number assignments (0, 1, 2, 3, or 4) on the y-axis and the chromosome number on the x-axis. Gains (copy number state >2) and losses (copy number state <2) are seen as horizontal green bars above and below, respectively, the copy number state of 2. (A) Embryo showing monosomy 9. (B) Embryo showing monosomy 7, 18; trisomy 16. (C) Embryo showing trisomy 2, 7, 9, 10, 19, 21, 22; monosomy 5, 13, X. Fertility and Sterility 2014 101, 1375-1382.e2DOI: (10.1016/j.fertnstert.2014.01.051) Copyright © 2014 American Society for Reproductive Medicine Terms and Conditions

Figure 2 Examples of partial aneusomy detection by next-generation sequencing compared with array comparative genomic hybridization. Arrows indicate partial chromosomal imbalances. (A) Embryo showing a 14-Mb segmental duplication on the short arm of chromosome 17. (B) Embryo showing a 20-Mb segmental gain of chromosome 13q. (C) Embryo showing a 17-Mb segmental duplication on the short arm of chromosome 7. Fertility and Sterility 2014 101, 1375-1382.e2DOI: (10.1016/j.fertnstert.2014.01.051) Copyright © 2014 American Society for Reproductive Medicine Terms and Conditions

Supplemental Figure 1 Sample with discordant result showing a false positive call by next-generation sequencing for trisomy 18 (arrow) in addition to true positive calls of loss of chromosomes 13, 15, and 16. (A) Profile from array-CGH analysis. (B) Profile from NGS-based 24-chromosome aneuploidy screening analysis derived from the same WGA product. Fertility and Sterility 2014 101, 1375-1382.e2DOI: (10.1016/j.fertnstert.2014.01.051) Copyright © 2014 American Society for Reproductive Medicine Terms and Conditions

Supplemental Figure 2 Example of 24-chromosome aneuploidy screening result with complex karyotype obtained from whole-genome amplification products sequenced on (A) a Hiseq and (B) a Miseq instrument, showing concordance between the platforms. Fertility and Sterility 2014 101, 1375-1382.e2DOI: (10.1016/j.fertnstert.2014.01.051) Copyright © 2014 American Society for Reproductive Medicine Terms and Conditions