Pregnancy outcomes from more than 1,800 in vitro fertilization cycles with the use of 24-chromosome single-nucleotide polymorphism-based preimplantation genetic testing for aneuploidy.

OBJECTIVE: To measure in vitro fertilization (IVF) outcomes following 24-chromosome single‒nucleotide-polymorphism (SNP)-based preimplantation genetic testing for aneuploidy (PGT-A) and euploid embryo transfer. DESIGN: Retrospective. SETTING: Fertility clinics and laboratory. PATIENT(S): Women 20-46 years of age undergoing IVF treatment. INTERVENTION(S): Twenty-four-chromosome SNP-based PGT-A of day 5/6 embryo biopsies. MAIN OUTCOME MEASURE(S): Maternal age-stratified implantation, clinical pregnancy, and live birth rates per embryo transfer; miscarriage rates; and number of embryo transfers per patient needed to achieve a live birth. RESULT(S): An implantation rate of 69.9%, clinical pregnancy rate per transfer of 70.6%, and live birth rate per transfer of 64.5% were observed in 1,621 nondonor frozen cycles with the use of SNP-based PGT-A. In addition, SNP-based PGT-A outcomes, when measured per cycle with transfer, remained relatively constant across all maternal ages; when measured per cycle initiated, they decreased as maternal age increased. Miscarriage rates were ∼5% in women ≤40 years old. No statistically significant differences in pregnancy outcomes were found for single-embryo transfers (SET) versus double-embryo transfers with SNP-based PGT-A. On average, 1.38 embryo transfers per patient were needed to achieve a live birth in nondonor cycles. CONCLUSION(S): Our findings that SNP-based PGT-A can mitigate the negative effects of maternal age on IVF outcomes in cycles with transfer, and that pregnancy outcomes from SET cycles are not significantly different from those of double-embryo transfer cycles, support the use of SET when transfers are combined with SNP-based PGT-A.

Effects of maternal age on euploidy rates in a large cohort of embryos analyzed with 24-chromosome single-nucleotide polymorphism-based preimplantation genetic screening.

OBJECTIVE: To determine the effect of maternal age on the average number of euploid embryos retrieved during oocyte harvest as part of an in vitro fertilization (IVF) cycle, including the probability of retrieving at least one euploid embryo in a cohort (PrE). DESIGN: Retrospective study. SETTING: Preimplantation genetic screening (PGS) laboratory. PATIENT(S): Women aged 18 to 48 years undergoing IVF treatment. INTERVENTION(S): Use of 24-chromosome single-nucleotide polymorphism (SNP)-based PGS of day-3 and day-5 embryo biopsies. MAIN OUTCOME MEASURE(S): Relationships between maternal age and the rate of embryos that tested as euploid (hereafter referred to as "euploid embryos"), the average number and proportion of euploid embryos per IVF cycle, and PrE. RESULT(S): We analyzed 22,599 day-3 embryos and 15,112 day-5 embryos. In women aged 27 to 35 years, the median proportion of euploid embryos in each cycle remained constant at ∼35% in day-3 biopsies and ∼55% in day-5 biopsies, but it decreased rapidly after age 35. On average, women in their late 20s had four euploid embryos (day 3 or day 5) per cycle, but this number decreased linearly (R(2) ≥ 0.983) after 35 years of age. The effect of maternal age on PrE was similar, with a rapid exponential decline (R(2) = 0.986). Across all maternal ages, the euploid proportion and number of embryos per cycle were counterbalanced, so the number of euploid embryos per cycle was the same for day-3 and day-5 biopsies. This suggests that the loss of embryos from day 3 to day 5 was primarily due to aneuploidy. CONCLUSION(S): Our results confirm the known inverse relationship between advanced maternal age (>35 years) and embryo euploidy, demonstrating that equal numbers of euploid embryos are available at day 3 and day 5.

Detection of Clonal and Subclonal Copy-Number Variants in Cell-Free DNA from Patients with Breast Cancer Using a Massively Multiplexed PCR Methodology.

We demonstrate proof-of-concept for the use of massively multiplexed PCR and next-generation sequencing (mmPCR-NGS) to identify both clonal and subclonal copy-number variants (CNVs) in circulating tumor DNA. This is the first report of a targeted methodology for detection of CNVs in plasma. Using an in vitro model of cell-free DNA, we show that mmPCR-NGS can accurately detect CNVs with average allelic imbalances as low as 0.5%, an improvement over previously reported whole-genome sequencing approaches. Our method revealed differences in the spectrum of CNVs detected in tumor tissue subsections and matching plasma samples from 11 patients with stage II breast cancer. Moreover, we showed that liquid biopsies are able to detect subclonal mutations that may be missed in tumor tissue biopsies. We anticipate that this mmPCR-NGS methodology will have broad applicability for the characterization, diagnosis, and therapeutic monitoring of CNV-enriched cancers, such as breast, ovarian, and lung cancer.

Inference of functional regions in proteins by quantification of evolutionary constraints.

Likelihood estimates of local rates of evolution within proteins reveal that selective constraints on structure and function are quantitatively stable over billions of years of divergence. The stability of constraints produces an intramolecular clock that gives each protein a characteristic pattern of evolutionary rates along its sequence. This pattern allows the identification of constrained regions and, because the rate of evolution is a quantitative measure of the strength of the constraint, of their functional importance. We show that results from such analyses, which require only sequence alignments, are consistent with experimental and mutational data. The methodology has significant predictive power and may be used to guide structure--function studies for any protein represented by a modest number of homologs in sequence databases.