Novel method for combined linkage and genome-wide association analysis finds evidence of distinct genetic architecture for two subtypes of autism

The Autism Genome Project has assembled two large datasets originally designed for linkage analysis and genome-wide association analysis, respectively: 1,069 multiplex families genotyped on the Affymetrix 10 K platform, and 1,129 autism trios genotyped on the Illumina 1 M platform. We set out to exploit this unique pair of resources by analyzing the combined data with a novel statistical method, based on the PPL statistical framework, simultaneously searching for linkage and association to loci involved in autism spectrum disorders (ASD). Our analysis also allowed for potential differences in genetic architecture for ASD in the presence or absence of lower IQ, an important clinical indicator of ASD subtypes. We found strong evidence of multiple linked loci; however, association evidence implicating specific genes was low even under the linkage peaks. Distinct loci were found in the lower IQ families, and these families showed stronger and more numerous linkage peaks, while the normal IQ group yielded the strongest association evidence. It appears that presence/absence of lower IQ (LIQ) demarcates more genetically homogeneous subgroups of ASD patients, with not just different sets of loci acting in the two groups, but possibly distinct genetic architecture between them, such that the LIQ group involves more major gene effects (amenable to linkage mapping), while the normal IQ group potentially involves more common alleles with lower penetrances. The possibility of distinct genetic architecture across subtypes of ASD has implications for further research and perhaps for research approaches to other complex disorders as well

Superconductivity in Dense MgB2MgB_2 Wires

$MgB_2$ becomes superconducting just below 40 K. Whereas porous polycrystalline samples of $MgB_2$ can be synthesized from boron powders, in this letter we demonstrate that dense wires of $MgB_2$ can be prepared by exposing boron filaments to $Mg$ vapor. The resulting wires have a diameter of 160 ${\mu}m$, are better than 80% dense and manifest the full $\chi = -1/4{\pi}$ shielding in the superconducting state. Temperature-dependent resistivity measurements indicate that $MgB_2$ is a highly conducting metal in the normal state with $\rho (40 K)$ = 0.38 $\mu Ohm$-$cm$. Using this value, an electronic mean free path, $l \approx 600~\AA$ can be estimated, indicating that $MgB_2$ wires are well within the clean limit. $T_c$, $H_{c2}(T)$, and $J_c$ data indicate that $MgB_2$ manifests comparable or better superconducting properties in dense wire form than it manifests as a sintered pellet.Comment: Figures' layout fixe

Coexistence of the Critical Slowing Down and Glassy Freezing in Relaxor Ferroelectrics

We have developed a dynamical model for the dielectric response in relaxor ferroelectrics which explicitly takes into account the coexistence of the critical slowing down and glassy freezing. The application of the model to the experiment in PMN allowed for the reconstruction of the nonequilibrium spin glass state order parameter and its comparison with the results of recent NMR experiment (Blinc et al., Phys. Rev. Lett. 83, No. 2 (1999)). It is shown that the degree of the local freezing is rather small even at temperatures where the field-cooled permittivity exceeds the frequency dependent permittivity by an order of magnitude. This observation indicates the significant role of the critical slowing down (accompanying the glass freezing) in the system dynamics. Also the theory predicts an important interrelationship between the frequency dependent permittivity and the zero-field-cooled permittivity, which proved to be consistent with the experiment in PMN (A. Levstik et. al., Phys. Rev. B 57, 11204 (1998))

A Review of the Properties of Nb3Sn and Their Variation with A15 Composition, Morphology and Strain State

This article gives an overview of the available literature on simplified, well defined (quasi-)homogeneous laboratory samples. After more than 50 years of research on superconductivity in Nb3Sn, a significant amount of results are available, but these are scattered over a multitude of publications. Two reviews exist on the basic properties of A15 materials in general, but no specific review for Nb3Sn is available. This article is intended to provide such an overview. It starts with a basic description of the Niobium-Tin intermetallic. After this it maps the influence of Sn content on the the electron-phonon interaction strength and on the field-temperature phase boundary. The literature on the influence of Cu, Ti and Ta additions will then be briefly summarized. This is followed by a review on the effects of grain size and strain. The article is concluded with a summary of the main results.Comment: Invited Topical Review for Superconductor, Science and Technology. Provisionally scheduled for July 200

Behavioral and molecular genetics of reading-related AM and FM detection thresholds

Auditory detection thresholds for certain frequencies of both amplitude modulated (AM) and frequency modulated (FM) dynamic auditory stimuli are associated with reading in typically developing and dyslexic readers. We present the first behavioral and molecular genetic characterization of these two auditory traits. Two extant extended family datasets were given reading tasks and psychoacoustic tasks to determine FM 2 Hz and AM 20 Hz sensitivity thresholds. Univariate heritabilities were significant for both AM (h2 = 0.20) and FM (h2 = 0.29). Bayesian posterior probability of linkage (PPL) analysis found loci for AM (12q, PPL = 81 %) and FM (10p, PPL = 32 %; 20q, PPL = 65 %). Bivariate heritability analyses revealed that FM is genetically correlated with reading, while AM was not. Bivariate PPL analysis indicates that FM loci (10p, 20q) are not also associated with reading

Complex-Orbital Order in Fe_3O_4 and Mechanism of the Verwey Transition

Electronic state and the Verwey transition in magnetite (Fe_3O_4) are studied using a spinless three-band Hubbard model for 3d electrons on the B sites with the Hartree-Fock approximation and the exact diagonalisation method. Complex-orbital, e.g., 1/sqrt(2)[|zx> + i |yz>], ordered (COO) states having noncollinear orbital moments ~ 0.4 mu_B on the B sites are obtained with the cubic lattice structure of the high-temperature phase. The COO state is a novel form of magnetic ordering within the orbital degree of freedom. It arises from the formation of Hund's second rule states of spinless pseudo-d molecular orbitals in the Fe_4 tetrahedral units of the B sites and ferromagnetic alignment of their fictitious orbital moments. A COO state with longer periodicity is obtained with pseudo-orthorhombic Pmca and Pmc2_1 structures for the low-temperature phase. The state spontaneously lowers the crystal symmetry to the monoclinic and explains experimentally observed rhombohedral cell deformation and Jahn-Teller like distortion. From these findings, we consider that at the Verwey transition temperature, the COO state remaining to be short-range order impeded by dynamical lattice distortion in high temperature is developed into that with long-range order coupled with the monoclinic lattice distortion.Comment: 16 pages, 13 figures, 6 tables, accepted for publication in J. Phys. Soc. Jp

Rare familial 16q21 microdeletions under a linkage peak implicate cadherin 8 (CDH8) in susceptibility to autism and learning disability

Background: Autism spectrum disorder (ASD) is characterised by impairments in social communication and by a pattern of repetitive behaviours, with learning disability (LD) typically seen in up to 70% of cases. A recent study using the PPL statistical framework identified a novel region of genetic linkage on chromosome 16q21 that is limited to ASD families with LD. Methods: In this study, two families with autism and/or LD are described which harbour rare >1.6 Mb microdeletions located within this linkage region. The deletion breakpoints are mapped at base-pair resolution and segregation analysis is performed using a combination of 1M single nucleotide polymorphism (SNP) technology, array comparative genomic hybridisation (CGH), long-range PCR, and Sanger sequencing. The frequency of similar genomic variants in control subjects is determined through analysis of published SNP array data. Expression of CDH8, the only gene disrupted by these microdeletions, is assessed using reverse transcriptase PCR and in situ hybridisation analysis of 9 week human embryos. Results: The deletion of chr16: 60 025 584-61 667 839 was transmitted to three of three boys with autism and LD and none of four unaffected siblings, from their unaffected mother. In a second family, an overlapping deletion of chr16: 58 724 527-60 547 472 was transmitted to an individual with severe LD from his father with moderate LD. No copy number variations (CNVs) disrupting CDH8 were observed in 5023 controls. Expression analysis indicates that the two CDH8 isoforms are present in the developing human cortex. Conclusion: Rare familial 16q21 microdeletions and expression analysis implicate CDH8 in susceptibility to autism and LD

Combined linkage and linkage disequilibrium analysis of a motor speech phenotype within families ascertained for autism risk loci

Using behavioral and genetic information from the Autism Genetics Resource Exchange (AGRE) data set we developed phenotypes and investigated linkage and association for individuals with and without Autism Spectrum Disorders (ASD) who exhibit expressive language behaviors consistent with a motor speech disorder. Speech and language variables from Autism Diagnostic Interview-Revised (ADI-R) were used to develop a motor speech phenotype associated with non-verbal or unintelligible verbal behaviors (NVMSD:ALL) and a related phenotype restricted to individuals without significant comprehension difficulties (NVMSD:C). Using Affymetrix 5.0 data, the PPL framework was employed to assess the strength of evidence for or against trait-marker linkage and linkage disequilibrium (LD) across the genome. Ingenuity Pathway Analysis (IPA) was then utilized to identify potential genes for further investigation. We identified several linkage peaks based on two related language-speech phenotypes consistent with a potential motor speech disorder: chromosomes 1q24.2, 3q25.31, 4q22.3, 5p12, 5q33.1, 17p12, 17q11.2, and 17q22 for NVMSD:ALL and 4p15.2 and 21q22.2 for NVMSD:C. While no compelling evidence of association was obtained under those peaks, we identified several potential genes of interest using IPA. Conclusion: Several linkage peaks were identified based on two motor speech phenotypes. In the absence of evidence of association under these peaks, we suggest genes for further investigation based on their biological functions. Given that autism spectrum disorders are complex with a wide range of behaviors and a large number of underlying genes, these speech phenotypes may belong to a group of several that should be considered when developing narrow, well-defined, phenotypes in the attempt to reduce genetic heterogeneity

Genetic Analysis Workshop 14: microsatellite and single-nucleotide polymorphism marker loci for genome-wide scans.

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A genome-wide scan for common alleles affecting risk for autism

Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 × 10−8. When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner's curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 × 10−8 threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C