Whole genome sequencing increases molecular diagnostic yield compared with current diagnostic testing for inherited retinal disease

Abstract not availableJamie M. Ellingford, Stephanie Barton, Sanjeev Bhaskar, Simon G. Williams, Panagiotis I. Sergouniotis, James O, Sullivan, Janine A. Lamb, Rahat Perveen, Georgina Hall, William G. Newman, Paul N. Bishop, Stephen A. Roberts, Rick Leach, Rick Tearle, Stuart Bayliss, Simon C. Ramsden, Andrea H. Nemeth, Graeme C.M. Blac

Evaluating the contribution of rare variants to type 2 diabetes and related traits using pedigrees

Significance Contributions of rare variants to common and complex traits such as type 2 diabetes (T2D) are difficult to measure. This paper describes our results from deep whole-genome analysis of large Mexican-American pedigrees to understand the role of rare-sequence variations in T2D and related traits through enriched allele counts in pedigrees. Our study design was well-powered to detect association of rare variants if rare variants with large effects collectively accounted for large portions of risk variability, but our results did not identify such variants in this sample. We further quantified the contributions of common and rare variants in gene expression profiles and concluded that rare expression quantitative trait loci explain a substantive, but minor, portion of expression heritability.</jats:p

Whole genome sequences are required to fully resolve the linkage disequilibrium structure of human populations

Background: An understanding of linkage disequilibrium (LD) structures in the human genome underpins much of medical genetics and provides a basis for disease gene mapping and investigating biological mechanisms such as recombination and selection. Whole genome sequencing (WGS) provides the opportunity to determine LD structures at maximal resolution. Results: We compare LD maps constructed from WGS data with LD maps produced from the array-based HapMap dataset, for representative European and African populations. WGS provides up to 5.7-fold greater SNP density than array-based data and achieves much greater resolution of LD structure, allowing for identification of up to 2.8-fold more regions of intense recombination. The absence of ascertainment bias in variant genotyping improves the population representativeness of the WGS maps, and highlights the extent of uncaptured variation using array genotyping methodologies. The complete capture of LD patterns using WGS allows for higher genome-wide association study (GWAS) power compared to array-based GWAS, with WGS also allowing for the analysis of rare variation. The impact of marker ascertainment issues in arrays has been greatest for Sub-Saharan African populations where larger sample sizes and substantially higher marker densities are required to fully resolve the LD structure. Conclusions: WGS provides the best possible resource for LD mapping due to the maximal marker density and lack of ascertainment bias. WGS LD maps provide a rich resource for medical and population genetics studies. The increasing availability of WGS data for large populations will allow for improved research utilising LD, such as GWAS and recombination biology studies.Reuben J. Pengelly, William Tapper, Jane Gibson, Marcin Knut, Rick Tearle, Andrew Collins and Sarah Enni

The distribution of runs of homozygosity in the genome of river and swamp buffaloes reveals a history of adaptation, migration and crossbred events

Background: Water buffalo is one of the most important livestock species in the world. Two types of water buffalo exist: river buffalo (Bubalus bubalis bubalis) and swamp buffalo (Bubalus bubalis carabanensis). The buffalo genome has been recently sequenced, and thus a new 90&nbsp;K single nucleotide polymorphism (SNP) bead chip has been developed. In this study, we investigated the genomic population structure and the level of inbreeding of 185 river and 153 swamp buffaloes using runs of homozygosity (ROH). Analyses were carried out jointly and separately for the two buffalo types. Results: The SNP bead chip detected in swamp about one-third of the SNPs identified in the river type. In total, 18,116 ROH were detected in the combined data set (17,784 SNPs), and 16,251 of these were unique. ROH were present in both buffalo types mostly detected (~ 59%) in swamp buffalo. The number of ROH per animal was larger and genomic inbreeding was higher in swamp than river buffalo. In the separated datasets (46,891 and 17,690 SNPs for river and swamp type, respectively), 19,760 and 10,581 ROH were found in river and swamp, respectively. The genes that map to the ROH islands are associated with the adaptation to the environment, fitness traits and reproduction. Conclusions: Analysis of ROH features in the genome of the two water buffalo types allowed their genomic characterization and highlighted differences between buffalo types and between breeds. A large ROH island on chromosome 2 was shared between river and swamp buffaloes and contained genes that are involved in environmental adaptation and reproduction

A genetically unique Chinese cattle population shows evidence of common ancestry with wild species when analysed with a reduced ascertainment bias SNP panel

In Hong Kong, there is a cattle population of 3c1,200 individuals of uncertain origin and genetic diversity. This population shows heterogeneous morphology, both in body type and pigmentation. Once used as draught animals by the local farmers, they were abandoned around the 1970s due to changes in the economy, and since then have lived as feral populations. To explore the origins of these cattle, we analysed 3c50k genotype data of 21 Hong Kong feral cattle, along with data from 703 individuals of 36 cattle populations of European, African taurine, and Asian origin, the wild x domestic hybrid gayal, plus two wild bovine species, gaur and banteng. To reduce the effect of ascertainment bias 3c4k loci that are polymorphic in the two wild species were selected for further analysis. The stringent SNP selection we applied resulted in increased heterozygosity across all populations studies, compared with the full panel of SNP, thus reducing the impact of ascertainment bias and facilitating the comparison of divergent breeds of cattle. Our results showed that Hong Kong feral cattle have relatively high levels of genetic distinctiveness, possibly due to the low level of artificial selection, and a likely common ancestry with wild species. We found signs of a putative taurine introgression, probably dating to the import of north European breeds during the British colonialism of Hong Kong. We showed that Hong Kong feral cattle, are distinct from Bos taurus and Bos indicus breeds. Our results highlight the distinctiveness of Hong Kong feral cattle and stress the conservation value of this indigenous breed that is likely to harbour adaptive genetic variation, which is a fundamental livestock resource in the face of climate change and diversifying market demands

Distribution of, and immune response to, chicken anti-αGal immunoglobulin Y antibodies in wild-type and αGal knockout mice

Chicken antibodies (immunoglobulin Y; IgY) to the αGal epitope (galactose α-1,3-galactose) bind to αGal antigens of mouse and porcine tissues and endothelial cells in vitro and block human anti-αGal antibody binding, complement activation and antibody-dependent cell-mediated lysis mechanisms. The activities and toxicity of anti-αGal IgY have not been tested in vivo. In this study, we tested the effects of multiple injections of affinity-purified anti-αGal IgY (AP-IgY) in both wild-type (WT) and α-1,3-galactosyltransferase knockout (Gal KO) mice. WT and Gal KO mice were injected once, twice, three, or four times intravenously (i.v.) with AP-IgY and killed at 1 hr or 24 hr. Mice displayed no toxicity to four injections of AP-IgY. Heart, lung, liver, kidney, spleen and pancreatic tissue were evaluated using immunohistochemical techniques for the presence of the αGal epitope using the GSI-B4 lectin, and for bound IgY, as well as mouse IgM and IgG. The binding of AP-IgY antibodies to the endothelium of WT mouse tissues was essentially identical to the pattern of binding of the GSI-B4 lectin after injection of WT mice and death at 1 hr. WT mice killed 24 hr after i.v. injection of AP-IgY showed little remaining bound IgY in their endothelia, indicating that IgY is cleared over that time period. We also evaluated the blood drawn at the time of death for the presence of anti-αGal IgY, anti-IgY IgM and anti-IgY IgG by enzyme-linked immunosorbent assay. Anti-αGal IgY was almost undetectable in WT mouse sera at all injection and killing times. In contrast, Gal KO mouse sera showed increasing anti-αGal IgY levels until 24 hr after the fourth injection, when anti-αGal IgY levels were almost undetectable. Anti-IgY IgM and IgG levels in WT and Gal KO mouse sera showed a typical increase in anti-IgY IgM 24 hr after the second injection (3 days after the first injection) and an increase in anti-IgY IgG 24 hr after the third injection (5 days after the first injection). These results show that IgY binds to αGal epitopes in the WT mice and is cleared sometime over a 24-hr time period and that IgY is an expected immunogen in mice eliciting a rather typical anti-IgY IgM and IgG response

Production of α-1,3-galactosyltransferase null pigs by means of nuclear transfer with fibroblasts bearing loss of heterozygosity mutations

Hyperacute rejection of porcine organs by old world primate recipients is mediated through preformed antibodies against galactosyl-α-1,3-galactose (Galα-1,3-Gal) epitopes expressed on the pig cell surface. Previously, we generated inbred miniature swine with a null allele of the α-1,3-galactosyltransferase locus (GGTA1) by nuclear transfer (NT) with gene-targeted fibroblasts. To expedite the generation of GGTA1 null pigs, we selected spontaneous null mutant cells from fibroblast cultures of heterozygous animals for use in another round of NT. An unexpectedly high rate of spontaneous loss of GGTA1 function was observed, with the vast majority of null cells resulting from loss of the WT allele. Healthy piglets, hemizygous and homozygous for the gene-targeted allele, were produced by NT by using fibroblasts that had undergone deletional and crossover/gene conversion events, respectively. Aside from loss of Galα-1,3-Gal epitopes, there were no obvious phenotypic differences between these null piglets and WT piglets from the same inbred lines. In fact, congenital abnormalities observed in the heterozygous NT animals did not reappear in the serially produced null animals