Journal: Genome Research

Article Title: RNA-seq as a tool for evaluating human embryo competence

doi: 10.1101/gr.252981.119

Figure Lengend Snippet: Experimental overview. ( A ) Preimplantation human development time-course depicting our comparative analytical approach. Samples were processed from blastocyst stage embryos and assessed for morphokinetic criteria and morphology before biopsy. One trophectoderm (TE) biopsy was processed for DNA-based preimplantation genetic testing for aneuploidy (PGT-A), one was harvested for RNA-seq, and the remaining whole embryo (WE) was also processed for RNA-seq. ( B ) Representative image of a blastocyst. ( C ) Data overview table. Embryos (E1-39) for which we have morphokinetic data are shaded in green; those for which DNA-based PGT-A yielded a result are depicted in blue; and those for which we have RNA-seq of either WE or TE biopsy are labeled in black and gray, respectively.

Article Snippet: TE biopsies obtained for the purposes of PGT-A were placed in a proprietary DNA buffer, snap frozen on dry ice, and transferred to storage at – 80°C until analysis was completed by Invitae.

Techniques: RNA Sequencing, Labeling

Journal: Genome Research

Article Title: RNA-seq as a tool for evaluating human embryo competence

doi: 10.1101/gr.252981.119

Figure Lengend Snippet: RNA-based embryo sex chromosome content. ( A ) Chromosome Y–specific gene TPM sums for all WEs (black; left ) and TE biopsy samples (gray; right ), respectively. Embryos are on the x -axis and are ordered by Chromosome Y TPM sum. Dashed line indicates sum of 25 TPM threshold for evidence of a Y Chromosome in the sample. Red letters indicate sex chromosome status as determined by DNA-based PGT-A: M = XY; F = XX; U = Undefined. ( B ) Chromosome X Z -score profiles for all WE and TE biopsy samples, respectively. ( C ) Chromosome Y TPM sums for paired WE–TE samples (from the same embryo). Red letters indicate PGT-A results. Black dot indicates WE sample; gray dot, TE sample.

Article Snippet: TE biopsies obtained for the purposes of PGT-A were placed in a proprietary DNA buffer, snap frozen on dry ice, and transferred to storage at – 80°C until analysis was completed by Invitae.

Techniques:

Journal: Genome Research

Article Title: RNA-seq as a tool for evaluating human embryo competence

doi: 10.1101/gr.252981.119

Figure Lengend Snippet: RNA-based digital karyotype. ( A ) Overview of WE digital karyotypes. Embryos are on the x -axis and chromosomes are on the y -axis. Gray indicates Z -score within the normal range (±2); red, a gain (>2 Z -score); and blue, a chromosomal loss (<−2 Z -score). Red text indicates results of DNA-based PGT-A where applicable. ( B ) Boxplot of Pearson correlation coefficients comparing Z -score profiles from unpaired (black; from different embryos) or paired (red; from the same embryo) WE and TE samples. ( C ) Z -score profiles for paired WE and TE biopsy samples. Black dot indicates Z -score ( y -axis) of WE; gray dot, Z -score of TE biopsy. Red triangles indicate outlying Z -scores. Chromosomes indicated along the x -axis. ( D ) Distribution of Z -score differences between WE and TE biopsy for paired samples (originating from the same embryo). Red lines indicate E8 Chromosome 17 and E35 Chromosome 4 as outliers.

Article Snippet: TE biopsies obtained for the purposes of PGT-A were placed in a proprietary DNA buffer, snap frozen on dry ice, and transferred to storage at – 80°C until analysis was completed by Invitae.

Techniques: