Selection Of Sequence Variants Research Articles

Using imputed whole-genome sequence data to improve the accuracy of genomic prediction for parasite resistance in Australian sheep

BackgroundThis study aimed at (1) comparing the accuracies of genomic prediction for parasite resistance in sheep based on whole-genome sequence (WGS) data to those based on 50k and high-density (HD) single nucleotide polymorphism (SNP) panels; (2) investigating whether the use of variants within quantitative trait loci (QTL) regions that were selected from regional heritability mapping (RHM) in an independent dataset improved the accuracy more than variants selected from genome-wide association studies (GWAS); and (3) comparing the prediction accuracies between variants selected from WGS data to variants selected from the HD SNP panel.ResultsThe accuracy of genomic prediction improved marginally from 0.16 ± 0.02 and 0.18 ± 0.01 when using all the variants from 50k and HD genotypes, respectively, to 0.19 ± 0.01 when using all the variants from WGS data. Fitting a GRM from the selected variants alongside a GRM from the 50k SNP genotypes improved the prediction accuracy substantially compared to fitting the 50k SNP genotypes alone. The gain in prediction accuracy was slightly more pronounced when variants were selected from WGS data compared to when variants were selected from the HD panel. When sequence variants that passed the GWAS - log_{10} (p,value) threshold of 3 across the entire genome were selected, the prediction accuracy improved by 5% (up to 0.21 ± 0.01), whereas when selection was limited to sequence variants that passed the same GWAS - log_{10} (p,value) threshold of 3 in regions identified by RHM, the accuracy improved by 9% (up to 0.25 ± 0.01).ConclusionsOur results show that through careful selection of sequence variants from the QTL regions, the accuracy of genomic prediction for parasite resistance in sheep can be improved. These findings have important implications for genomic prediction in sheep.

0298 Selection of sequence variants to improve dairy cattle genomic predictions

0298 Selection of sequence variants to improve dairy cattle genomic predictions

Sequence variations in HIV-1 p24 Gag-derived epitopes can alter binding of KIR2DL2 to HLA-C*03:04 and modulate primary natural killer cell function.

The aim of this study was to assess the consequence of sequence variations in HLA-C03:04-presented HIV-1 p24 Gag epitopes on binding of the inhibitory natural killer (NK) cell receptor KIR2DL2 to HLA-C03:04. HIV-1 may possibly evade recognition by KIR+ NK cells through selection of sequence variants that interfere with the interactions of inhibitory killer cell immunoglobulin-like receptors (KIRs) and their target ligands on HIV-1 infected cells. KIR2DL2 is an inhibitory NK cell receptor that binds to a family of HLA-C ligands. Here, we investigated whether HIV-1 encodes for HLA-C03:04-restricted epitopes that alter KIR2DL2 binding. Tapasin-deficient 721.220 cells expressing HLA-C03:04 were pulsed with overlapping peptides (10mers overlapped by nine amino acids, spanning the entire HIV-1 p24 Gag sequence) to identify peptides that stabilized HLA-C expression. The impact that sequence variation in HLA-C03:04-binding HIV-1 epitopes has on KIR2DL2 binding and KIR2DL2+ NK cell function was determined using KIR2DL2-Fc constructs and NK cell degranulation assays. Several novel HLA-C03:04 binding epitopes were identified within the HIV-1 p24 Gag consensus sequence. Three of these consensus sequence peptides (Gag144-152, Gag163-171 and Gag295-304) enabled binding of KIR2DL2 to HLA-C03:04 and resulted in inhibition of KIR2DL2+ primary NK cells. Furthermore, naturally occurring minor variants of epitope Gag295-304 enhanced KIR2DL2 binding to HLA-C03:04. Our data show that naturally occurring sequence variations within HLA-C03:04-restricted HIV-1 p24 Gag epitopes can have a significant impact on the binding of inhibitory KIR receptors and primary NK cell function.

Replication kinetics and persistence of a conditionally live attenuated SIV (SIVrtTA) in vivo confers protection against SIVmac239 wild-type challenge in a rhesus macaque model

Vaccination with live attenuated SIV confers potent protection against wild-type SIV challenge in the SIV/macaque model of HIV. Although safety concerns preclude the direct application of this vaccine approach in humans, a clearer understanding of its mechanism of protection may lead to the development of novel AIDS vaccines. A novel live attenuated SIVmac239 Δnef vaccine (SIVrtTA), dependent on doxycycline administration for replication, has been evaluated in vivo and its ability to protect against pathogenic SIV challenge determined. Two groups of six Indian rhesus macaques (Groups A and B) were vaccinated with SIVrtTA with an oral doxycycline dosing regime for 6 months. In Group A, doxycycline was stopped for 8 weeks before wtSIVmac239 challenge. A third group was vaccinated with a conventional SIVmac239Δnef vaccine. In the presence of doxycycline, all 12 macaques receiving SIVrtTA were infected exhibiting peak SIV RNA levels (log10 3-5 SIV RNA copies/ml) which declined in all macaques but persisted at higher levels in three SIVrtTA vaccinates. Levels of virus replication measured by independent qRT-PCR and qDNA PCR assays were lower in SIVrtTA vaccinates compared with the SIVmac239Δnef vaccine which peaked in the log10 4-6 SIV RNA copies/ml range. No escape from doxycycline dependence was identified. Upon challenge with wild-type SIVmac239 and compared with naive challenge controls (Group D), a significant vaccine effect was observed in all three vaccine groups, assessed by the comparative reduction of circulating viral RNA in plasma. Naive wtSIVmac239 challenge controls exhibited ~7 log10 SIV RNA copies/ml at peak which persisted beyond the acute infection phase. This compared with all three vaccine groups where post wtSIVmac239 viral RNA levels were markedly reduced among SIVrtTA vaccinates with a more pronounced vaccine effect among Group A vaccinates. Viral RNA was un-detectable in one SIVrtTA vaccinate (Group A) and in the 2 log10 range in another (Group B). The highest levels of protection in SIVrtTA vaccinates correlated with an enhanced persistence of SIVrtTA as circulating viral RNA in the immediate post-acute infection vaccine period. Retrospective sequence analysis recovered from SIVrtTA vaccinates indicated a selection of sequence variants in the LTR promoter region and the Tat and rtTA genes that do not affect doxycycline control but which may have influenced replication in vivo. Vaccination with SIVrtTA induced a marked vaccine effect which will enable the role of viral persistence to be evaluated in this vaccination strategy. SIVrtTA represents a new tool to develop and design novel AIDS vaccines.

Molecular characterization of CEVd strains that induce different phenotypes in Gynura aurantiaca: structure-pathogenicity relationships

Two Citrus exocortis viroid isolates (CEVd-s and CEVd-129) that induce severe and mild symptoms in Gynura aurantiaca, respectively, have been characterized. They present nucleotide sequences in the pathogenicity motifs P(L), C and P(R) similar to those of "Class A" and "Class B". Infectivity and symptom expression in G. aurantica and tomato were evaluated with a selection of sequence variants recovered from both isolates. As expected, the two variants selected from CEVd-s induced severe symptoms. The variants selected from CEVd-129 induced mild symptoms, except one of them, named MJ, that presented an unusual genotype and induced severe symptoms in G. aurantiaca. The biological properties of MJ show that the two nucleotide changes of the C domain normally associated with the P(L) and P(R) motifs of "Class B" strains are not implicated in symptom expression. The relationship between "Class A" and "Class B" strains with the symptoms induced in clementine trees grafted on trifoliate orange is discussed.