Comprehensive analysis of karyotypic mosaicism between trophectoderm and inner cell mass

Aneuploidy has been well-documented in blastocyst embryos, but prior studies have been limited in scale and/or lack mechanistic data. We previously reported preclinical validation of microarray 24-chromosome preimplantation genetic screening in a 24-h protocol. The method diagnoses chromosome copy number, structural chromosome aberrations, parental source of aneuploidy and distinguishes certain meiotic from mitotic errors. In this study, our objective was to examine aneuploidy in human blastocysts and determine correspondence of karyotypes between trophectoderm (TE) and inner cell mass (ICM). We disaggregated 51 blastocysts from 17 couples into ICM and one or two TE fractions. The average maternal age was 31. Next, we ran 24-chromosome microarray molecular karyotyping on all of the samples, and then performed a retrospective analysis of the data. The average per-chromosome confidence was 99.95%. Approximately 80% of blastocysts were euploid. The majority of aneuploid embryos were simple aneuploid, i.e. one or two whole-chromosome imbalances. Structural chromosome aberrations, which are common in cleavage stage embryos, occurred in only three blastocysts (5.8%). All TE biopsies derived from the same embryos were concordant. Forty-nine of 51 (96.1%) ICM samples were concordant with TE biopsies derived from the same embryos. Discordance between TE and ICM occurred only in the two embryos with structural chromosome aberration. We conclude that TE karyotype is an excellent predictor of ICM karyotype. Discordance between TE and ICM occurred only in embryos with structural chromosome aberrations

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved

Randomized controlled trial comparing traditional with two "mobile" epidural techniques: anesthetic and analgesic efficacy

BACKGROUND: The authors recently showed that “mobile” epidural analgesia, using low-dose local anesthetic-opioid mixtures, reduces the impact of epidural analgesia on instrumental vaginal delivery, relative to a traditional technique. The main prespecified assessment of pain relief efficacy, women's postpartum estimates of labor pain after epidural insertion, did not differ. The detailed analgesic efficacy and the anesthetic characteristics of the techniques are reported here. METHODS: A total of 1,054 nulliparous women were randomized, in labor, to receive boluses of 10 ml 0.25% bupivacaine (traditional), combined spinal-epidural (CSE) analgesia, or low-dose infusion (LDI), the latter groups utilizing 0.1% bupivacaine with 2 µg/ml fentanyl. Visual analog scale pain assessments were collected throughout labor and delivery and 24 h later. Details of the conduct of epidural analgesia, drug utilization, and requirement for anesthesiologist reattendance were recorded. RESULTS: A total of 353 women were randomized to receive traditional epidural analgesia, 351 received CSE, and 350 received LDI. CSE was associated with a more rapid onset of analgesia, lower median visual analog scale pain scores than traditional in the first hour after epidural insertion, and a significant reduction in bupivacaine dose given during labor. Pain scores reported by women receiving LDI were similar to those in the traditional group throughout labor and delivery. Anesthesiologist reattendance was low but greater with each mobile technique. CONCLUSIONS: Relative to traditional epidural analgesia, LDI is at least as effective and CSE provided better pain relief in the early stages after insertion. The proven efficacy of mobile epidurals and their beneficial impact on delivery mode make them the preferred techniques for epidural pain relief in labor