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

A draft human pangenome reference

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample

A luminescent solar concentrator with 7.1% power conversion efficiency

The Luminescent Solar Concentrator (LSC) consists of a transparent polymer plate, containing luminescent particles. Solar cells are connected to one or more edges of the polymer plate. Incident light is absorbed by the luminescent particles and re-emitted. Part of the light emitted by the luminescent particles is guided towards the solar cells by total internal reflection. Since the edge area is smaller than the receiving one, this allows for concentration of sunlight without the need for solar tracking. External Quantum Efficiency (EQE) and current-voltage (I-V) measurements were performed on LSC devices with multicrystalline silicon (mc-Si) or GaAs cells attached to the sides. The best result was obtained for an LSC with four GaAs cell power conversion efficiency of this device, as measured at European Solar Test Installation laboratories, was 7.1% (geometrical concentration of a factor 2.5). With one GaAs cell attached to one edge only, the power efficiency was still as high as 4.6% (geometrical concentration of a factor 10). To our knowledge these efficiencies are among. the highest reported for the LSC