A phasing and imputation method for pedigreed populations that results in a single-stage genomic evaluation

Background

Efficient, robust, and accurate genotype imputation algorithms make large-scale application of genomic selection cost effective. An algorithm that imputes alleles or allele probabilities for all animals in the pedigree and for all genotyped single nucleotide polymorphisms (SNP) provides a framework to combine all pedigree, genomic, and phenotypic information into a single-stage genomic evaluation.

Methods

An algorithm was developed for imputation of genotypes in pedigreed populations that allows imputation for completely ungenotyped animals and for low-density genotyped animals, accommodates a wide variety of pedigree structures for genotyped animals, imputes unmapped SNP, and works for large datasets. The method involves simple phasing rules, long-range phasing and haplotype library imputation and segregation analysis.

Results

Imputation accuracy was high and computational cost was feasible for datasets with pedigrees of up to 25 000 animals. The resulting single-stage genomic evaluation increased the accuracy of estimated genomic breeding values compared to a scenario in which phenotypes on relatives that were not genotyped were ignored.

Conclusions

The developed imputation algorithm and software and the resulting single-stage genomic evaluation method provide powerful new ways to exploit imputation and to obtain more accurate genetic evaluations.     

Anti-alpha-fodrin antibodies do not add much to the diagnosis of Sjögren's syndrome

The presence of anti-alpha-fodrin autoantibodies has been reported to be a highly specific and sensitive test for the diagnosis of Sj?gren's syndrome (SjS). We looked (in Nijmegen) for anti-alpha-fodrin, anti-Ro60, and anti-La autoantibodies in a cohort of 51 patients with rheumatic diseases (primary SjS [21], secondary SjS 6, rheumatoid arthritis [RA] 12, systemic lupus erythematosus [SLE] 6, and scleroderma 6) and in 28 healthy subjects, using ELISA, immunoblotting, and immunoprecipitation. The same samples were analyzed with an alternative anti-alpha-fodrin ELISA in Hanover. The Nijmegen ELISA of the sera from primary SjS showed sensitivities of 43% and 48% for IgA- and IgG-type anti-alpha-fodrin antibodies, respectively. The Hanover ELISA showed sensitivities of 38% and 10% for IgA- and IgG-type anti-alpha-fodrin antibodies, respectively. The ELISAs for alpha-fodrin showed six (Nijmegen) and four (Hanover) anti-alpha-fodrin-positive RA sera. IgA and IgG anti-fodrin antibodies were also present in four patients with secondary SjS. The sensitivities of Ro60 and La-antibodies in the Nijmegen ELISA were 67% and 62%, respectively. Unlike anti-alpha-fodrin antibodies, all anti-Ro60 and anti-La positive sera could be confirmed by immunoblotting or RNA immunoprecipitation. Thus, anti-Ro and anti-La autoantibodies were more sensitive than anti-alpha-fodrin autoantibodies in ELISA and were more frequently confirmed by other techniques. Anti-La antibodies appear to be more disease-specific than anti-alpha-fodrin antibodies, which are also found in RA sera. Therefore, the measurement of anti-alpha-fodrin autoantibodies does not add much to the diagnosis of Sj?gren's syndrome.     

The variability of the hepatitis B virus genome: statistical analysis and biological implications

A statistical analysis of the nucleotide sequence variability in 14 published hepatitis B virus (HBV) genomes was carried out using parametric and nonparametric methods. A parametric statistical model revealed that the different regions of the genome differed significantly in their variability. The conclusion was supported by a nonparametric kernel-density model of the HBV genome. Genes S, C, and P, region X, the precore region, and the pre-S2/pre-S1 regions were ranked in order of increasing variability. In many instances, conserved regions of the genome identified with sequences of known function in HBV biology. However, other characterized regions (such as pre-S) showed much variability despite the involvement of their encoded peptides in specific functions. Point mutations that may result in the formation of stop codons and amino acid changes may affect the clinical picture of HBV infection and may be reflected in atypical serological patterns.      

Clinical and angiographic results with the ACS MULTI-LINK DUET trade mark Coronary Stent System - the DUET Study

BACKGROUND: The DUET Study is a multicenter prospective efficacy and safety evaluation of the ACS MULTI-LINK DUET coronary stainless steel balloon-expandable stent. AIMS: The primary objective was to determine the one-month incidence of MACE (major adverse cardiac events). The secondary objectives were the acute success rate, the restenosis and reocclusion rates (assessed by quantitative coronary angiography (QCA)) at six months and the occurrence of MACE in hospital and at six months. METHODS: Two hundred and ten patients were enrolled between February and June 1998 in 18 European centers. Successful stent placement was achieved in 209 patients. All patients were treated with ticlopidine 500 mg/day for one month and with aspirin >/=100 mg/day. To allow the investigators to gain familiarity with the stent system, the first one to three patients per center formed a separate lead-in population leaving an intention-to-treat population of 157 patients. The majority of the intention-to-treat population were male (79%); 28% had unstable angina, 69% had stable angina, 44% had had a previous myocardial infarction, 15% had had a previous percutaneous transluminal coronary angioplasty, and 3% had a history of stroke. The target vessel was 38.5% left anterior descending artery, 20.5% left circumflex artery and 41.0% right coronary artery. RESULTS: All but one of the intention-to-treat patients were effectively stented (17 required multiple stents). Six-month angiographic follow-up was available in 90% of the intention-to-treat population. Minimal lumen diameter (MLD) postprocedure was 2.61 +/- 0.33 mm, with a residual diameter stenosis of 16%. Six-month follow-up data showed an MLD of 1.87 +/- 0.56 mm with a residual diameter stenosis of 36%. The binary restenosis rate (>/=50% residual stenosis) was 15.6%. Up to one month following the procedure 94.9% of the population was MACE-free, with two subacute occlusions. At six months all patients were alive, of whom 82.8% were MACE-free, and 73% were free of anginal complaints. CONCLUSION: The results observed in the current DUET registry are comparable to data of other balloon-expandable-stent trials, with a low incidence of clinical events at follow-up.     

Responses of woody vegetation to exclusion of large herbivores in semi‐arid savannas

The Nkuhlu large‐scale long‐term exclusion experiment in Kruger National Park was designed to study the long‐term effects of large herbivores on vegetation. One treatment excludes elephants, another excludes all herbivores larger than hares and another one comprises an open, control area. Vegetation monitoring was implemented in 2002 when a baseline survey was conducted prior to exclusion. Monitoring was repeated 5 years after exclusion. Data from the surveys were analysed to establish how structure and composition of woody vegetation had changed 5 years after herbivore exclusion. The analysis showed that neither plant assemblage nor mean vegetation height had changed significantly since exclusion. However, both species richness and density of woody plants increased 5 years after exclusion of all large herbivores, but not after the exclusion of elephants alone. One already common species, Dichrostachys cinerea, became more common after excluding all large herbivores compared with either no exclusion or elephant exclusion, possibly leading to competitive suppression of other species. Species other than D. cinerea tended to either increase or decrease in density, but the changes were insufficient to induce significant shifts in the overall assemblage of woody plants. The results indicate that after 5 years of exclusion, the combined assemblage of large herbivores, and not elephants alone, could induce changes in species richness and abundances of woody plants, but the effect was so far insufficient to induce measureable shifts in the assemblages of woody plants. It is possible that assemblages will change with time and increasing elephant numbers may amplify future changes.     

The importance of information on relatives for the prediction of genomic breeding values and the implications for the makeup of reference data sets in livestock breeding schemes

Background

The theory of genomic selection is based on the prediction of the effects of genetic markers in linkage disequilibrium with quantitative trait loci. However, genomic selection also relies on relationships between individuals to accurately predict genetic value. This study aimed to examine the importance of information on relatives versus that of unrelated or more distantly related individuals on the estimation of genomic breeding values.

Methods

Simulated and real data were used to examine the effects of various degrees of relationship on the accuracy of genomic selection. Genomic Best Linear Unbiased Prediction (gBLUP) was compared to two pedigree based BLUP methods, one with a shallow one generation pedigree and the other with a deep ten generation pedigree. The accuracy of estimated breeding values for different groups of selection candidates that had varying degrees of relationships to a reference data set of 1750 animals was investigated.

Results

The gBLUP method predicted breeding values more accurately than BLUP. The most accurate breeding values were estimated using gBLUP for closely related animals. Similarly, the pedigree based BLUP methods were also accurate for closely related animals, however when the pedigree based BLUP methods were used to predict unrelated animals, the accuracy was close to zero. In contrast, gBLUP breeding values, for animals that had no pedigree relationship with animals in the reference data set, allowed substantial accuracy.

Conclusions

An animal''s relationship to the reference data set is an important factor for the accuracy of genomic predictions. Animals that share a close relationship to the reference data set had the highest accuracy from genomic predictions. However a baseline accuracy that is driven by the reference data set size and the overall population effective population size enables gBLUP to estimate a breeding value for unrelated animals within a population (breed), using information previously ignored by pedigree based BLUP methods.     

A novel tetravalent bispecific TandAb (CD30/CD16A) efficiently recruits NK cells for the lysis of CD30+ tumor cells

To improve recruitment and activation of natural killer (NK) cells to lyse tumor cells, we isolated a human anti-CD16A antibody with similar affinity for the CD16A 158F/V allotypes, but no binding to the CD16B isoform. Using CD16A-targeting Fv domains, we constructed a tetravalent bispecific CD30/CD16A tandem diabody (TandAb®) consisting solely of Fv domains. This TandAb has two binding sites for CD16A and two for CD30, the antigen identifying Hodgkin lymphoma cells. The binding and cytotoxicity of the TandAb were compared with antibodies with identical anti-CD30 domains: (1) a native IgG, (2) an IgG optimized for binding to Fc receptors, and (3) a bivalent bispecific CD30/CD16A diabody. Due to its CD16A-bivalency and reduced k_off, the TandAb was retained longer on the surface of NK cells than the IgGs or the diabody. This contributed to the higher potency and efficacy of the TandAb relative to those of the other anti-CD30 antibodies. TandAb cytotoxicity was independent of the CD16A allotype, whereas the anti-CD30 IgGs were substantially less cytotoxic when NK cells with low affinity CD16A allotype were employed. TandAb activation of NK cells was strictly dependent on the presence of CD30⁺ target cells. Therefore, the CD30/CD16A TandAb may represent a promising therapeutic for the treatment of Hodgkin’s lymphoma; further, anti-CD16A TandAbs may function as potent immunotherapeutics that specifically recruit NK cells to destroy cancer cells.