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

Estimation of the radial size and density fluctuation amplitude of edge localized modes using microwave interferometer array

A novel technique to estimate the range of radial size and density fluctuation amplitude of edge localized modes (ELMs) in the KSTAR tokamak plasma is presented. A microwave imaging reflectometry (MIR) system is reconfigured as a multi-channel microwave interferometer array (MIA) to measure the density fluctuations associated with ELMs, while electron cyclotron emission imaging (ECEI) system is used as a reference diagnostics to confirm the MIA observation. Two dimensional full-wave (FWR2D) simulations integrated with optics simulation are performed to investigate the Gaussian beam propagation and reflection through the plasma as well as the MIA optical components and obtain the interferometric phase undulations of individual channels at the detector plane due to ELM perturbation. The simulation results show that the amplitude of the phase undulation depends linearly on both radial size and density perturbation amplitude of ELM. For a typical discharge with ELMs, it is estimated that the ELM structure observed by the MIA system has density perturbation amplitude in the range similar to 7 % to 14 % while radial size in the range similar to 1 to 3 cmclos