Inter- and intra-reproducibility of genotypes from sheep technical replicates on Illumina and Affymetrix platforms

peer-reviewedBackground Accurate genomic analyses are predicated upon access to accurate genotype input data. The objective of this study was to quantify the reproducibility of genotype data that are generated from the same genotype platform and from different genotyping platforms. Methods Genotypes based on 51,121 single nucleotide polymorphisms (SNPs) for 84 animals that were each genotyped on Illumina and Affymetrix platforms and for another 25 animals that were each genotyped twice on the same Illumina platform were compared. Genotypes based on 11,323 SNPs for an additional 21 animals that were genotyped on two different Illumina platforms by two different service providers were also compared. Reproducibility of the results was measured as the correlation between allele counts and as genotype and allele concordance rates. Results A mean within-animal correlation of 0.9996 was found between allele counts in the 25 duplicate samples that were genotyped on the same Illumina platform and varied from 0.9963 to 1.0000 per animal. The mean (minimum, maximum) genotype and allele concordance rates per animal between the 25 duplicate samples were equal to 0.9996 (0.9968, 1.0000) and 0.9993 (0.9937, 1.0000), respectively. The concordance rate between the two different Illumina platforms was also near 1. A mean within-animal correlation of 0.9738 was found between genotypes that were generated on the Illumina and Affymetrix platforms and varied from 0.9505 to 0.9812 per animal. The mean (minimum, maximum) within-animal genotype and allele concordance rates between the Illumina and Affymetrix platforms were equal to 0.9711 (0.9418, 0.9798) and 0.9845 (0.9695, 0.9889), respectively. The genotype concordance rate across all genotypes increased from 0.9711 to 0.9949 when the SNPs used were restricted to those with three high-resolution genotype clusters which represented 75.2% of the called genotypes. Conclusions and implications Our results suggest that, regardless of the genotype platform or service provider, high genotype concordance rates are achieved especially if they are restricted to high-quality extracted DNA and SNPs that result in high-quality genotypes.Financial support from the Irish Department of Agriculture, Stimulus Research Fund project OVIGEN is gratefully acknowledged. The contribution from the International Sheep Genomics Consortium in the development of the low-density custom genotyping platform is also acknowledged

Assessing Aerosol Mixed Layer Heights from the NASA LaRC Airborne HSRL During the DISCOVER-AQ Field Campaigns

No abstract availabl

Risk factors for intimate partner homicide in England and Wales

From Wiley via Jisc Publications RouterHistory: received 2021-10-01, rev-recd 2021-12-18, accepted 2022-01-28, pub-electronic 2022-02-17Article version: VoRPublication status: PublishedAbstract: Intimate partner homicides are often situated within the context of domestic abuse, and although less prevalent than domestic abuse, there have been several multi‐agency approaches to understanding the risk for these fatal crimes. Domestic Homicide Reviews (DHRs) were introduced in 2011 to provide information to help with assessing such risk. This paper aims to analyse DHRs in England and Wales to investigate/determine risk factors for domestic homicide following intimate partner abuse. All publicly available DHRs published between July 2011 and November 2020 where the victim and perpetrator were or had been intimate partners (N = 263) were retrieved from Community Safety Partnership websites in England and Wales. A quantitative design was used to extract data from DHRs, and descriptive and inferential statistics were generated by SPSS 26. Findings identified risk factors relating to domestic abuse, including stalking, separation, and the victim being in a new relationship. Sociodemographic risk factors included higher levels of deprivation, lower income and higher barriers to housing and services. This highlights the role of both individual and sociodemographic factors in domestic homicides, and particularly the need for greater socioeconomic security for victims of domestic abuse. In conclusion, though much of the data is in line with previous research, our analysis highlights the pivotal role of regional poverty, with comfortable socioeconomic conditions offering protection against intimate partner homicides. This research suggests important directions for future research and makes a valuable contribution to a more in‐depth understanding of the relationship between domestic abuse and intimate partner homicide