Multi-ancestry genome-wide analysis identifies shared genetic effects and common genetic variants for self-reported sleep duration

Both short (≤6 h per night) and long sleep duration (≥9 h per night) are associated with increased risk of chronic diseases. Despite evidence linking habitual sleep duration and risk of disease, the genetic determinants of sleep duration in the general population are poorly understood, especially outside of European (EUR) populations. Here, we report that a polygenic score of 78 European ancestry sleep duration single-nucleotide polymorphisms (SNPs) is associated with sleep duration in an African (n = 7288; P = 0.003), an East Asian (n = 13 618; P = 6 × 10-4) and a South Asian (n = 7485; P = 0.025) genetic ancestry cohort, but not in a Hispanic/Latino cohort (n = 8726; P = 0.71). Furthermore, in a pan-ancestry (N = 483 235) meta-analysis of genome-wide association studies (GWAS) for habitual sleep duration, 73 loci are associated with genome-wide statistical significance. Follow-up of five loci (near HACD2, COG5, PRR12, SH3RF1 and KCNQ5) identified expression-quantitative trait loci for PRR12 and COG5 in brain tissues and pleiotropic associations with cardiovascular and neuropsychiatric traits. Overall, our results suggest that the genetic basis of sleep duration is at least partially shared across diverse ancestry groups.

O-301 Genome-wide association study identified meiotic variant associated with aneuploid pregnancy loss

Study question

Which single nucleotide variant (SNVs) are associated with aneuploid pregnancy loss?

Summary answer

We identified a SNV on MEIG1 gene, which are associated with meiosis/spermiogenesis.

What is known already

Recurrent pregnancy loss (RPL) refers to the loss of two or more pregnancies, with a frequency of 5%. Chromosomal abnormalities in embryos are found in 80% of first trimester miscarriages, 86% of which are aneuploid. Recently, embryonic aneuploidy was found to be the most common cause of RPL, with a frequency of 40-50%. Most trisomy miscarriages are of maternal origin, with errors occurring during meiosis of the oocyte. Chromosome segregation abnormalities in oocytes are thought to be an event associated with increasing maternal age, but in addition, maternal genetic causes are thought to contribute.

Study design, size, duration

A Genome wide association study (GWAS) was performed on a clinically well characterized cohort of 189 women with RPL whose previous aborted conceptus was ascertained to be an aneuploid embryo. Samples were mainly collected from 2007 to 2018 mainly at Nagoya City University Hospital. For control samples, we used 1157 samples from the population-based prospective cohorts that included fertile women.

Participants/materials, setting, methods

All patients underwent a systematic examination. Patients with antiphospholipid syndrome, an abnormal chromosome in either partner, or uterine anomaly were excluded. Patients whose previously miscarried POC exhibited triploidy or 45, X were excluded. DNA was isolated from stored EDTA-blood samples and genotyped by Axiom Japonica-array v2659,503 SNVs). For the GWAS, a chi-squared test was applied to a two-by-two contingency table in allele frequency model.

Main results and the role of chance

The mean (SD) ages and number of previous miscarriages of the patients were 36.8 (4.3) and 3.09 (1.13). GWAS data revealed 5 SNVs with suggestive significance (p < 9.46e-06). The SNVs that showed the most significant associations (P = 1.06E-06, OR = 1.72) was located on meiosis/spermiogenesis associated 1 (MEIG1) gene under an allelic model after Bonferroni correction considering the number of analyzed SNVs. The SNV rs7908491 was reported as a splicing QTL in the MEIG1 gene, which is a meiosis/meiosis-associated factor and is plausibly associated with chromosome aneuploidy. This is the first GWAS in patients with RPL caused by aneuploidy.

Limitations, reasons for caution

Since this study was conducted in a single center and had a small sample size, it needs to be replicated in different centers with more subjects and on an international scale. Whole genome imputation analysis will be performed to detect SNVs with more significant associations.

Wider implications of the findings

Our findings demonstrate that a specific genotype of MEIG1 gene can be a risk factor for aneuploid pregnancy loss. The establishment of clinically applicable maternal germ cell markers could identify groups for whom PGT would be more useful or provide patients with counseling that provides prognostic information about pregnancy.

Trial registration number

not applicable

A primary canine and an impacted permanent canine with infection potentially induced an intracranial abscess

Intracranial abscess is a rare but life-threatening disease. There have been no reports on intracranial abscess induced by the residual primary tooth and the impacted successive permanent tooth with infection. We report on an interesting case of a 29-year-old man suffering from an epidural abscess, potentially caused by an infection of the residual primary maxillary right canine and the impacted permanent maxillary right canine. The patient recovered completely after prolonged antibiotic treatment and extraction of both of the suspected teeth. Fusobacterium sp. was isolated from the culture of a peripheral blood sample. This case alerts us to realize that the lack of suitable and timely intervention in oral conditions might produce a harmful effect on general health.

Charge transfer to ground-state ions produces free electrons

Inner-shell ionization of an isolated atom typically leads to Auger decay. In an environment, for example, a liquid or a van der Waals bonded system, this process will be modified, and becomes part of a complex cascade of relaxation steps. Understanding these steps is important, as they determine the production of slow electrons and singly charged radicals, the most abundant products in radiation chemistry. In this communication, we present experimental evidence for a so-far unobserved, but potentially very important step in such relaxation cascades: Multiply charged ionic states after Auger decay may partially be neutralized by electron transfer, simultaneously evoking the creation of a low-energy free electron (electron transfer-mediated decay). This process is effective even after Auger decay into the dicationic ground state. In our experiment, we observe the decay of Ne²⁺ produced after Ne 1s photoionization in Ne-Kr mixed clusters.

Time-Resolved Measurement of Interatomic Coulombic Decay Induced by Two-Photon Double Excitation of Ne_{2}

The hitherto unexplored two-photon doubly excited states [Ne^{*}(2p^{-1}3s)]_{2} were experimentally identified using the seeded, fully coherent, intense extreme ultraviolet free-electron laser FERMI. These states undergo ultrafast interatomic Coulombic decay (ICD), which predominantly produces singly ionized dimers. In order to obtain the rate of ICD, the resulting yield of Ne_{2}^{+} ions was recorded as a function of delay between the extreme ultraviolet pump and UV probe laser pulses. The extracted lifetimes of the long-lived doubly excited states, 390(-130/+450)  fs, and of the short-lived ones, less than 150 fs, are in good agreement with ab initio quantum mechanical calculations.

Slow Interatomic Coulombic Decay of Multiply Excited Neon Clusters

Ne clusters (∼5000  atoms) were resonantly excited (2p→3s) by intense free electron laser (FEL) radiation at FERMI. Such multiply excited clusters can decay nonradiatively via energy exchange between at least two neighboring excited atoms. Benefiting from the precise tunability and narrow bandwidth of seeded FEL radiation, specific sites of the Ne clusters were probed. We found that the relaxation of cluster surface atoms proceeds via a sequence of interatomic or intermolecular Coulombic decay (ICD) processes while ICD of bulk atoms is additionally affected by the surrounding excited medium via inelastic electron scattering. For both cases, cluster excitations relax to atomic states prior to ICD, showing that this kind of ICD is rather slow (picosecond range). Controlling the average number of excitations per cluster via the FEL intensity allows a coarse tuning of the ICD rate.

Towards characterization of photo-excited electron transfer and catalysis in natural and artificial systems using XFELs

The ultra-bright femtosecond X-ray pulses provided by X-ray Free Electron Lasers (XFELs) open capabilities for studying the structure and dynamics of a wide variety of biological and inorganic systems beyond what is possible at synchrotron sources. Although the structure and chemistry at the catalytic sites have been studied intensively in both biological and inorganic systems, a full understanding of the atomic-scale chemistry requires new approaches beyond the steady state X-ray crystallography and X-ray spectroscopy at cryogenic temperatures. Following the dynamic changes in the geometric and electronic structure at ambient conditions, while overcoming X-ray damage to the redox active catalytic center, is key for deriving reaction mechanisms. Such studies become possible by using the intense and ultra-short femtosecond X-ray pulses from an XFEL, where sample is probed before it is damaged. We have developed methodology for simultaneously collecting X-ray diffraction data and X-ray emission spectra, using an energy dispersive spectrometer, at ambient conditions, and used this approach to study the room temperature structure and intermediate states of the photosynthetic water oxidizing metallo-protein, photosystem II. Moreover, we have also used this setup to simultaneously collect the X-ray emission spectra from multiple metals to follow the ultrafast dynamics of light-induced charge transfer between multiple metal sites. A Mn-Ti containing system was studied at an XFEL to demonstrate the efficacy and potential of this method.

Interatomic Coulombic decay cascades in multiply excited neon clusters

In high-intensity laser light, matter can be ionized by direct multiphoton absorption even at photon energies below the ionization threshold. However on tuning the laser to the lowest resonant transition, the system becomes multiply excited, and more efficient, indirect ionization pathways become operative. These mechanisms are known as interatomic Coulombic decay (ICD), where one of the species de-excites to its ground state, transferring its energy to ionize another excited species. Here we show that on tuning to a higher resonant transition, a previously unknown type of interatomic Coulombic decay, intra-Rydberg ICD occurs. In it, de-excitation of an atom to a close-lying Rydberg state leads to electron emission from another neighbouring Rydberg atom. Moreover, systems multiply excited to higher Rydberg states will decay by a cascade of such processes, producing even more ions. The intra-Rydberg ICD and cascades are expected to be ubiquitous in weakly-bound systems exposed to high-intensity resonant radiation.

Interatomic Coulombic decay (ICD) is a relaxation of an atom in a weakly bound environment by the transfer of excess energy to ionize the neighbouring atom. Here the authors observe intra-Rydberg ICD in neon clusters, which is a decay that involves the ionization of Rydberg atoms in the cluster.

Liquid marbles as a micro-reactor for efficient radical alternating copolymerization of diene monomer and oxygen

Liquid marbles are a novel micro-reactor to efficiently synthesize polyperoxides by the radical alternating copolymerization of the 1,3-diene with oxygen.

Three-dimensional characterization of BaHfO3 precipitates in GdBa2Cu3O7-y flim using STEM tomography

IntroductionSince the discovery of REBa2Cu3O7-y (RE: Rare Earth element, REBCO) superconductors, they have been expected as the best candidates for the power cable application due to its high critical temperature (Tc) and critical current density (Jc). Among those REBCO superconductors, GdBa2Cu3O7-y (GdBCO) have been receiving great interest because they have higher Tc and Jc than YBa2Cu3O7-y [1].GdBCO with various types of precipitates as artificial pinning centers (APCs) have been proposed to minimize the anisotropy of Jc characteristics under the magnetic field. Among those precipitates, BaHfO3 (BHO) was found most effective precipitates as APCs in GdBCO film prepared by pulsed laser deposition (PLD) method [2]. It is therefore necessary to investigate not only the morphologies but also the dispersion of BHO precipitates within the GdBCO, to understand the role of BHO for the superconducting characteristics. In this study, morphologies and dispersions of BHO precipitates were characterized three-dimensional by scanning transmission electron tomography ExperimentalBHO dispersed GdBCO films were fabricated on Hastelloy C-276TM substrates with buffer layers of CeO2/LaMnO3/MgO/ Gd2ZrO7 by PLD method.To observe microstructure of GdBCO film with BHO precipitates, cross-section TEM specimens were prepared by FIB method using Quanta 3D-200 (FEI, USA) with acceleration voltage from 2 to 30 kV. Three-dimensional information such as morphology and dispersion, of BHO precipitates were characterized by electron tomography using STEM-HAADF. Result and discussionFigure 1 shows three-dimensional reconstructed volume of BHO precipitates in GdBCO, which revealed that fine BHO precipitates have rod- and plate-like morphologies with homogeneous dispersion in GdBCO. In addition, growth directions of these precipitates were found with wide angular distributions from growth direction of GdBCO. Anisotropy of Jc in the magnetic fields was probably enhanced by various growth directions and homogeneous dispersion of nanosized BHO within GdBCO.jmicro;63/suppl_1/i26/DFU080F1F1DFU080F1Fig. 1.Three-dimensional reconstructed volume of BHO.

Genetic epidemiology of tooth agenesis in Japan: a population- and family-based study

Tooth agenesis is one of the most common congenital anomalies in humans. However, the etiology of tooth agenesis remains largely unclear, as well as evidence base useful for genetic counseling. Therefore, we estimated the prevalence and sibling recurrence risk, and investigated agenetic patterns systematically. Tooth agenesis was classified into two subtypes: hypodontia (one to five missing teeth) and oligodontia (six or more missing teeth). The prevalence of these two subtypes were 6.8% [95% confidence interval (CI): 6.1-7.7%] and 0.1% (95% CI: 0.04-0.3%), respectively, and sibling recurrence risk of these were 24.5% (95% CI: 13.8-38.3%) and 43.8% (95% CI: 26.4-62.3%), respectively. This result suggests that the severe phenotype, oligodontia, might be mostly transmitted in a dominant fashion. Using a simple statistical modeling approach, our data were found to be consistent with a bilateral symmetry model, meaning that there was equal probability of missing teeth from the right and left sides.

Abstract P5-13-07: Genetic polymorphism of estrogen metabolizing enzyme CYP17A1 rs743572 impacts on serum testosterone level in Japanese premenopausal women

The incidence of breast cancer in Japanese women has doubled in all age groups over the past two decades. We recently demonstrated that this marked increase is mostly due to an increase in the estrogen receptor (ER)-positive subtype, and we created risk prediction models for ER-positive breast cancer in both pre- and post- menopausal women using genetic factors (single nucleotide polymorphism (SNP)), environmental risk factors, serum hormones and growth factors by logistic regression analysis. Serum level of testosterone, which is the precursor of estradiol in estradiol synthesis, was found to be a risk predictor in both pre- and post- menopausal women. On the other hand, it has been reported that some SNPs, including those of estrogen-related genes such as ESR1 and CYP17A1, are correlated with breast cancer risk by genome-wide association studies. To acquire some insights into this mechanism, we analyzed genetic factors (14 SNPs), serum hormones and growth factors (estradiol, testosterone, prolactin, insulin-like growth factor 1 (IGF1) and IGF binding protein 3 (IGFBP3)) in 913 women with breast cancer and 278 disease-free controls for correlation between them.

Serum testosterone and prolactin levels were significantly higher in ER-positive breast cancer patients than in disease-free controls in both pre- (p<0.0001, p<0.0001) and post- (p<0.0001, p = 0.007) menopausal women, and serum estradiol level was significantly higher in ER-positive breast cancer patients than in disease-free controls only in premenopausal women (p = 0.0005). There were significant differences in serum hormone levels among the women with each SNP genotype (homozygotes of major allele, heterozygotes and homozygotes of minor allele), including testosterone among rs743572 genotype (p = 0.014), estradiol among rs827421 genotype (p = 0.016), IGF-1 among rs6905370 genotype (p = 0.032), and prolactin among rs1042522 genotype (p = 0.035) in premenopausal women, as well as estradiol among rs3803662 genotype (p = 0.027) and IGFBP3 among rs6905370 genotype (p = 0.036) in postmenopausal women. In particular, serum testosterone level was significantly different among the rs743572, which is one of the enzymes that convert testosterone to estradiol, of genotypes (AA: 0.308 +/- 0.180 ng/ml, AG: 0.319 +/- 0.193 ng/ml and GG: 0.380 +/- 0.187 ng/ml, p = 0.014). On the other hand, the rs743572 heterozygotes of CYP17A1 have been reported to have increased breast cancer risk than homozygotes of both the major allele and minor allele in premenopausal women. Further studies are required to clarify this mechanism.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P5-13-07.

Abstract P4-12-06: A mammographic density prediction model using environmental factors, endogenous hormones and growth factors in Japanese women

The incidence of breast cancer in Japanese women has doubled in all age groups over the past two decades, making it important to evaluate breast cancer risk factors in Japanese women. It is well known that mammographic density is positively associated with breast cancer risk in Western countries, and mammographic density is known to be affected by some environmental factors, serum hormones, and growth factors. We performed stepwise variable selection in a multiple regression model with fifteen independent variables as described below, based on the Akaike information criteria (AIC) to build a mammographic density prediction model using a dataset of 1191 women (913 women with breast cancer and 278 disease-free controls). The variables included were: environmental risk factors (body-mass index (BMI), age at menarche, pregnancy, age at first birth, breastfeeding, family history of breast cancer, age at menopause, use of hormone replacement therapy, alcohol intake and smoking), serum hormones and growth factors (estradiol, testosterone, prolactin, insulin-like growth factor 1 (IGF1) and IGF binding protein 3 (IGFBP3)) and mammographic density. The resulting prediction model is:

Mammographic density = + 0.000476 (IGF1) −0.0605 (testosterone) − 0.0508 (IGFBP3) − 0.00683 (age) − 0.0175 (BMI) + 0.00883 (age at menarche) − 0.0153 (breast feeding), (R2 = 0.336).

In this model, IGF1, testosterone, IGFBP3, age, BMI, age at menarche, and breastfeeding were considered to be important factors. IGF1 and age at menarche were positively associated with mammographic density, while on the other hand testosterone, IGFBP3, age, BMI, and breast feeding were negatively associated with mammographic density. Further studies are required to build a modified model incorporating serial measurements of serum hormones and growth factors to take into account time-dependent changes of serum hormones and growth factors, and to assess its accuracy.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P4-12-06.