Haplotype assembly of autotetraploid potato using integer linear programing
Siragusa, Enrico ; Haiminen, Niina ; Finkers, Richard ; Visser, Richard ; Parida, Laxmi - \ 2019
Bioinformatics 35 (2019)18. - ISSN 1367-4803 - p. 3279 - 3286.
SUMMARY: Haplotype assembly of polyploids is an open issue in plant genomics. Recent experimental studies on highly heterozygous autotetraploid potato have shown that available methods do not deliver satisfying results in practice. We propose an optimal method to assemble haplotypes of highly heterozygous polyploids from Illumina short-sequencing reads. Our method is based on a generalization of the existing minimum fragment removal model to the polyploid case and on new integer linear programs to reconstruct optimal haplotypes. We validate our methods experimentally by means of a combined evaluation on simulated and experimental data based on 83 previously sequenced autotetraploid potato cultivars. Results on simulated data show that our methods produce highly accurate haplotype assemblies, while results on experimental data confirm a sensible improvement over the state of the art. AVAILABILITY AND IMPLEMENTATION: Executables for Linux at http://github.com/Computational Genomics/HaplotypeAssembler. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Efficient algorithms for polyploid haplotype phasing
He, Dan ; Saha, Subrata ; Finkers, Richard ; Parida, Laxmi - \ 2018
BMC Genomics 19 (2018)Supplement 2. - ISSN 1471-2164
Background: Inference of haplotypes, or the sequence of alleles along the same chromosomes, is a fundamental problem in genetics and is a key component for many analyses including admixture mapping, identifying regions of identity by descent and imputation. Haplotype phasing based on sequencing reads has attracted lots of attentions. Diploid haplotype phasing where the two haplotypes are complimentary have been studied extensively. In this work, we focused on Polyploid haplotype phasing where we aim to phase more than two haplotypes at the same time from sequencing data. The problem is much more complicated as the search space becomes much larger and the haplotypes do not need to be complimentary any more. Results: We proposed two algorithms, (1) Poly-Harsh, a Gibbs Sampling based algorithm which alternatively samples haplotypes and the read assignments to minimize the mismatches between the reads and the phased haplotypes, (2) An efficient algorithm to concatenate haplotype blocks into contiguous haplotypes. Conclusions: Our experiments showed that our method is able to improve the quality of the phased haplotypes over the state-of-the-art methods. To our knowledge, our algorithm for haplotype blocks concatenation is the first algorithm that leverages the shared information across multiple individuals to construct contiguous haplotypes. Our experiments showed that it is both efficient and effective.
Genetic and antigenetic charactersation of serotype a FMD viruses from East Africa to select new vaccine strains.
Bari, F.D. ; Parida, S. ; Tekleghiorghis, T. ; Dekker, A. ; Sangula, A. ; Reeve, R. ; Haydon, D.T. ; Paton, D.J. - \ 2014
Vaccine 32 (2014)44. - ISSN 0264-410X - p. 5794 - 5800.
mouth-disease virus - middle-east - foot - sites - identification - conservation - strategies - protection - evolution - spread
Vaccine strain selection for emerging foot-and-mouth disease virus (FMDV) outbreaks in enzootic countries can be addressed through antigenic and genetic characterisation of recently circulating viruses. A total of 56 serotype A FMDVs isolated between 1998 and 2012, from Central, East and North African countries were characterised antigenically by virus neutralisation test using antisera to three existing and four candidate vaccine strains and, genetically by characterising the full capsid sequence data. A Bayesian analysis of the capsid sequence data revealed the viruses to be of either African or Asian topotypes with subdivision of the African topotype viruses into four genotypes (Genotypes I, II, IV and VII). The existing vaccine strains were found to be least cross-reactive (good matches observed for only 5.4–46.4% of the sampled viruses). Three bovine antisera, raised against A-EA-2007, A-EA-1981 and A-EA-1984 viruses, exhibited broad cross-neutralisation, towards more than 85% of the circulating viruses. Of the three vaccines, A-EA-2007 was the best showing more than 90% in-vitro cross-protection, as well as being the most recent amongst the vaccine strains used in this study. It therefore appears antigenically suitable as a vaccine strain to be used in the region in FMD control programmes.
Application of non-structural protein antibody tests in substantiating freedom from foot-and-mouth disease virus infection after emergency vaccination of cattle.
Paton, D.J. ; Clerq, K. De; Greiner, M. ; Dekker, A. ; Brocchi, E. ; Bergmann, I.E. ; Sammin, D.J. ; Gubbins, S. ; Parida, S. - \ 2006
Vaccine 24 (2006)42-43. - ISSN 0264-410X - p. 6503 - 6512.
differentiation - surveillance
There has been much debate about the use of the so-called ¿vaccinate-to-live¿ policy for the control of foot-and-mouth disease (FMD) in Europe, according to which, spread of the FMD virus (FMDV) from future outbreaks could be controlled by a short period of ¿emergency¿ vaccination of surrounding herds, reducing the need for large-scale pre-emptive culling of at-risk animals. Since vaccinated animals may become subclinically infected with FMDV following challenge exposure, it is necessary to either remove all vaccinates (vaccinate-to-kill) or to detect and remove vaccinates in which virus is circulating or has established persistent infections (vaccinate-to-live), in order to rapidly regain the most favoured trading status of FMD-free without vaccination. The latter approach can be supported by testing vaccinated animals for the presence of antibodies to certain non-structural proteins (NSP) of FMDV, which are induced by infection with the virus, but not by vaccination with purified FMD vaccines. Using test sensitivity and specificity data established at a recent workshop on NSP assays [Brocchi E, Bergmann I, Dekker A, Paton DJ, Sammin DJ, Greiner M, et al. Comparative performance of six ELISAs for antibodies to the non-structural proteins of foot-and-mouth disease. Vaccine, in press], this paper examines the ways in which serological testing with NSP ELISAs can be used and interpreted and the effect that this will have on the confidence with which freedom from infection can be demonstrated within guidelines specified by the World Animal Health Organisation and the European Commission.
Comparative evaluation of six ELISA's for the detection of antibodies to the non-structural proteins of foot-and-mouth disease virus.
Brocchi, E. ; Bergmann, I.E. ; Dekker, A. ; Paton, D.J. ; Sammin, D.J. ; Greiner, M. ; Graziola, S. ; Simone, F. De; Yadin, H. ; Haas, B. ; Bulut, N. ; Malirat, V. ; Neitzert, E. ; Goris, N. ; Parida, S. ; Sorensen, K. ; Clerq, K. De - \ 2006
Vaccine 24 (2006)47-48. - ISSN 0264-410X - p. 6966 - 6979.
differentiating infection - vaccinated cattle - polyprotein 3abc - recombinant - antigen - baculovirus - strategy - animals - tests - assay
To validate the use of serology in substantiating freedom from infection after foot-and-mouth disease (FMD) outbreaks have been controlled by measures that include vaccination, 3551 sera were tested with six assays that detect antibodies to the non-structural proteins of FMD virus. The sera came from naïve, vaccinated, infected and vaccinated-and-infected animals; two-thirds from cattle, the remainder from sheep and pigs. The assays were covariant for sensitivity, but not necessarily for specificity. A commercial kit from Cedi-diagnostics and an in-house assay from IZS-Brescia were comparable to the NCPanaftosa-screening index method described in the Diagnostic Manual of the World Animal Health Organisation. Using these three tests the specificity and sensitivity for the detection of carriers in vaccinated cattle approaches or exceeds 99% and 90%, respectively.
|Overall report, review of the special programme biotechnology.
Röling, N.G. ; Biggs, S. ; Parida, A. - \ 1996
Unknown Publisher - 45 p.