Preclinical validation of a targeted next generation sequencing-based comprehensive chromosome screening methodology in human blastocysts.

STUDY QUESTION: Can a novel targeted next generation sequencing (tNGS) platform accurately detect whole chromosome aneuploidy in a trophectoderm biopsy and provide additional information to improve testing? SUMMARY ANSWER: Karyotypes obtained by tNGS were concordant with other validated platforms and single nucleotide polymorphism genotyping information obtained can be used for improved detection and quality control. WHAT IS KNOWN ALREADY: qPCR-based whole chromosome aneuploidy screening is highly accurate in comparison to other common methods and has been shown to improve IVF success in two randomized clinical trials. With aneuploidy screening becoming standard of care in many IVF centres, there is a need to develop platforms with high throughput, low cost capabilities. STUDY DESIGN SIZE, DURATION: Twelve well-characterized cell lines were obtained from a commercial cell line repository and 31 discarded human blastocysts were obtained from 17 IVF patients who underwent comprehensive chromosome screening (CCS). PARTICIPANTS/MATERIAL, SETTING, METHODS: All samples were processed using a unique amplification strategy which directly incorporated sequencing library adapters and barcodes. Sequencing was performed on an Ion Torrent Proton. A custom bioinformatics pipeline was used to determine the karyotype for each sample. The consistency of tNGS diagnoses with either conventional karyotyping of cell lines or quantitative real-time PCR based CCS of blastocyst biopsies was evaluated. MAIN RESULTS AND THE ROLE OF CHANCE: Overall consistency per sample of tNGS based CCS in 5-cell samples from a variety of cell lines was 99.2%. In the blinded analysis of rebiopsies of aneuploid blastocysts, an overall targeted tNGS CCS consistency of 98.7% was observed per sample. These data demonstrate the ability of tNGS based CCS to provide an accurate and high throughput evaluation of aneuploidy in the human blastocyst. LARGE SCALE DATA: Not applicable. LIMITATIONS REASONS FOR CAUTION: This study is limited to whole chromosome aneuploidy, as mosaicism and segmental aneuploidy have not been investigated. WIDER IMPLICATIONS OF THE FINDINGS: These data show an accurate, high throughput method, and with the greater depth of each amplicon sequenced in comparison to commercial kits, there is greater application available for single nucleotide polymorphism based analysis for quality control. STUDY FUNDING/COMPETING INTERESTS: This study was funded through intramural research funds provided by the Foundation for Embryonic Competence. There are no competing interests.

Free vitamin D does not vary through the follicular phase of the menstrual cycle.

The importance of vitamin D (25OHD) in general health and reproductive success has been a focus in the setting of the 25OHD deficiency epidemic. However, there are challenges to understanding 25OHD's effects. The free and bioavailable levels are affected by 25OHD binding protein (DBP) and it is not known how estradiol fluctuations during the menstrual cycle affect these binding parameters. This may impact the most appropriate time to measure 25OHD when determining deficiency. This study characterizes 25OHD throughout the follicular phase of the menstrual cycle. Patients undergoing natural cycle IVF were included. Serum was drawn throughout the follicular phase of the menstrual cycle; 25OHD, DBP, albumin, and estrogen levels were determined for each time point allowing for mathematical calculation of free and bioavailable 25OHD. Early, mid, and late follicular phases were designated by estrogen tertiles among patients. Mean Levels of 25OHD (total, free, bioavailable) and DBP for each tertile were compared with Kruskil-Wallis test for non-parametric groups. Linear regression with GEE was employed due to repeated measures within participants. A total of 33 patients were included with 202 total serum measurements. There was no difference in mean levels of 25OHD (p = 0.77), free 25OHD (p = 0.91), and bioavailable 25OHD (p = 0.76) when measured throughout the follicular phase of the menstrual cycle. Vitamin D metabolism does not fluctuate as estradiol changes in the follicular phase of the menstrual cycle. This data indicates that assessment of 25OHD, in particular when assessed for associations with reproductive outcomes, can be measured reliably at any point during the follicular phase of the menstrual cycle.

Endometrial microbiome at the time of embryo transfer: next-generation sequencing of the 16S ribosomal subunit.

PURPOSE: Characterization of the human microbiome has become more precise with the application of powerful molecular tools utilizing the unique 16S ribosomal subunit's hypervariable regions to greatly increase sensitivity. The microbiome of the lower genital tract can prognosticate obstetrical outcome while the upper reproductive tract remains poorly characterized. Here, the endometrial microbiome at the time of single embryo transfer (SET) is characterized by reproductive outcome. METHODS: Consecutive patients undergoing euploid, SET was included in the analysis. After embryo transfer, performed as per routine, the most distal 5-mm portion of the transfer catheter was sterilely placed in a DNA free PCR tube. Next-generation sequencing of the bacteria specific 16S ribosome gene was performed, allowing genus and species calls for microorganisms. RESULTS: Taxonomy assignments were made on 35 samples from 33 patients and 2 Escherichia coli controls. Of the 33 patients, 18 had ongoing pregnancies and 15 did not. There were a total of 278 different genus calls present across patient samples. The microbiome at time of transfer for those patients with ongoing pregnancy vs. those without ongoing pregnancy was characterized by top genera by sum fraction. Lactobacillus was the top species call for both outcomes. CONCLUSIONS: The data presented here show the microbiome at the time of embryo transfer can successfully be characterized without altering standard clinical practice. This novel approach, both in specimen collection and analysis, is the first step toward the goal of determining physiologic from pathophysiologic microbiota. Further studies will help delineate if differences in the microbiome at the time of embryo transfer have a reliable impact on pregnancy outcome.