Detection of recombination events, haplotype reconstruction and imputation of sires using half-sib SNP genotypes

Ferdosi, Mohammad H,Kinghorn, Brian P,van der Werf, Julius H J,Gondro, Cedric BioMed Central 2014 Genetics, selection, evolution Vol.46 No.1

<P><B>Background</B></P><P>Identifying recombination events and the chromosomal segments that constitute a gamete is useful for a number of applications in genomic analyses. In livestock, genotypic data are commonly available for half-sib families. We propose a straightforward but computationally efficient method to use single nucleotide polymorphism marker genotypes on half-sibs to reconstruct the recombination and segregation events that occurred during meiosis in a sire to form the haplotypes observed in its offspring. These meiosis events determine a block structure in paternal haplotypes of the progeny and this can be used to phase the genotypes of individuals in single half-sib families, to impute haplotypes of the sire if they are not genotyped or to impute the paternal strand of the offspring’s sequence based on sequence data of the sire.</P><P><B>Methods</B></P><P>The hsphase algorithm exploits information from opposing homozygotes among half-sibs to identify recombination events, and the chromosomal regions from the paternal and maternal strands of the sire (blocks) that were inherited by its progeny. This information is then used to impute the sire’s genotype, which, in turn, is used to phase the half-sib family. Accuracy (defined as R<SUP>2</SUP>) and performance of this approach were evaluated by using simulated and real datasets. Phasing results for the half-sibs were benchmarked to other commonly used phasing programs – AlphaPhase, BEAGLE and PedPhase 3.</P><P><B>Results</B></P><P>Using a simulated dataset with 20 markers per cM, and for a half-sib family size of 4 and 40, the accuracy of block detection, was 0.58 and 0.96, respectively. The accuracy of inferring sire genotypes was 0.75 and 1.00 and the accuracy of phasing was around 0.97, respectively. hsphase was more robust to genotyping errors than PedPhase 3, AlphaPhase and BEAGLE. Computationally, hsphase was much faster than AlphaPhase and BEAGLE.</P><P><B>Conclusions</B></P><P>In half-sib families of size 8 and above, hsphase can accurately detect block structure of paternal haplotypes, impute genotypes of ungenotyped sires and reconstruct haplotypes in progeny. The method is much faster and more accurate than other widely used population-based phasing programs. A program implementing the method is freely available as an R package (hsphase).</P>

<i>hsphase</i> : an R package for pedigree reconstruction, detection of recombination events, phasing and imputation of half-sib family groups

Ferdosi, Mohammad H,Kinghorn, Brian P,van der Werf, Julius HJ,Lee, Seung Hwan,Gondro, Cedric BioMed Central 2014 BMC bioinformatics Vol.15 No.-

<P><B>Background</B></P><P>Identification of recombination events and which chromosomal segments contributed to an individual is useful for a number of applications in genomic analyses including haplotyping, imputation, signatures of selection, and improved estimates of relationship and probability of identity by descent. Genotypic data on half-sib family groups are widely available in livestock genomics. This structure makes it possible to identify recombination events accurately even with only a few individuals and it lends itself well to a range of applications such as parentage assignment and pedigree verification.</P><P><B>Results</B></P><P>Here we present <I>hsphase</I>, an R package that exploits the genetic structure found in half-sib livestock data to identify and count recombination events, impute and phase un-genotyped sires and phase its offspring. The package also allows reconstruction of family groups (pedigree inference), identification of pedigree errors and parentage assignment. Additional functions in the package allow identification of genomic mapping errors, imputation of paternal high density genotypes from low density genotypes, evaluation of phasing results either from <I>hsphase</I> or from other phasing programs. Various diagnostic plotting functions permit rapid visual inspection of results and evaluation of datasets.</P><P><B>Conclusion</B></P><P>The <I>hsphase</I> package provides a suite of functions for analysis and visualization of genomic structures in half-sib family groups implemented in the widely used R programming environment. Low level functions were implemented in C++ and parallelized to improve performance. <I>hsphase</I> was primarily designed for use with high density SNP array data but it is fast enough to run directly on sequence data once they become more widely available. The package is available (GPL 3) from the Comprehensive R Archive Network (CRAN) or from http://www-personal.une.edu.au/~cgondro2/hsphase.htm.</P>

Melanoma in Iran: a Retrospective 10-Year Study

Ferdosi, Samira,Saffari, Mojtaba,Eskandarieh, Sharareh,Alishahi, Raziyeh,Moghaddam, Mahsa Ghaffari,Ghanadan, Alireza,Shirkoohi, Reza Asian Pacific Journal of Cancer Prevention 2016 Asian Pacific journal of cancer prevention Vol.17 No.6

Background: Melanoma, the most life-threatening type of skin cancer, is a malignant tumor initiating in melanocytes that rapidly metastasizes and causes death. Materials and Methods: In this retrospective study, samples were selected from patients' information files in our Cancer Institute in Tehran with a designed checklist. A total of 322 files were found from 2003 until 2012. Then the raw data were transferred to Statistical Package for Social Sciences (SPSS) software version 16 and additional analysis was performed by Students t-test. The important variables were considered according to the available information from history of pathology including age, gender, occupation, stage and location of tumor. Results: Our data showed that incidence of melanoma has been different in the studied 10-year period according to age. Also, incidence of melanoma was higher in men than women. It was more common in lower limbs. More commonly housewives among women and farmers among men were affected by melanoma. Conclusions: Taken together the descriptive data clarified general aspects of this disease for further screening and interventions.

Electrochemical Properties of a New Green Corrosion Inhibitor Derived from Prosopis farcta for St37 Steel in 1 M Hydrochloric Acid

Morteza Ferdosi Heragh,Hossein Tavakoli 대한금속·재료학회 2020 METALS AND MATERIALS International Vol.26 No.11

This study investigated the effect of different concentrations of Prosopis farcta extract on the electrochemical properties andcorrosion of St37 steel in 1 M hydrochloric acid medium. The investigation showed that Prosopis farcta extract contains amixture of oily compounds, alkaloids, and flavonoids, which give it notable corrosion inhibition ability. The results of Tafelpolarization, electrochemical impedance, and weight loss tests were consistent in confirming the corrosion inhibition effectof this extract. The maximum percentage inhibition achieved in the Tafel test, EIS test, and weight loss test was 91%, 94%,and 82% respectively. Experiments showed that Prosopis farcta extract classifies as a mixed type corrosion inhibitor. Theinhibition effect of this extract is the product of the adsorption of its molecules in the electrolyte–metal interface, and thisadsorption follows Langmuir isotherm. The adsorption activation energy of Prosopis farcta extract for St37 steel in 1 Mhydrochloric acid was calculated to −10.945kJ∕mol , which shows the spontaneity of this adsorption in this system.

Genome-wide association study of body weight in Australian Merino sheep reveals an orthologous region on OAR6 to human and bovine genomic regions affecting height and weight

Al-Mamun, Hawlader A.,Kwan, Paul,Clark, Samuel A.,Ferdosi, Mohammad H.,Tellam, Ross,Gondro, Cedric BioMed Central 2015 Genetics, selection, evolution Vol.47 No.1

<P><B>Background</B></P><P>Body weight (BW) is an important trait for meat production in sheep. Although over the past few years, numerous quantitative trait loci (QTL) have been detected for production traits in cattle, few QTL studies have been reported for sheep, with even fewer on meat production traits. Our objective was to perform a genome-wide association study (GWAS) with the medium-density Illumina Ovine SNP50 BeadChip to identify genomic regions and corresponding haplotypes associated with BW in Australian Merino sheep.</P><P><B>Methods</B></P><P>A total of 1781 Australian Merino sheep were genotyped using the medium-density Illumina Ovine SNP50 BeadChip. Among the 53 862 single nucleotide polymorphisms (SNPs) on this array, 48 640 were used to perform a GWAS using a linear mixed model approach. Genotypes were phased with <I>hsphase</I>; to estimate SNP haplotype effects, linkage disequilibrium blocks were identified in the detected QTL region.</P><P><B>Results</B></P><P>Thirty-nine SNPs were associated with BW at a Bonferroni-corrected genome-wide significance threshold of 1 %. One region on sheep (<I>Ovis aries</I>) chromosome 6 (OAR6) between 36.15 and 38.56 Mb, included 13 significant SNPs that were associated with BW; the most significant SNP was OAR6_41936490.1 (<I>P</I> = 2.37 × 10<SUP>−16</SUP>) at 37.69 Mb with an allele substitution effect of 2.12 kg, which corresponds to 0.248 phenotypic standard deviations for BW. The region that surrounds this association signal on OAR6 contains three genes: <I>leucine aminopeptidase 3</I> (<I>LAP3</I>), which is involved in the processing of the oxytocin precursor; <I>NCAPG non-SMC condensin I complex, subunit G</I> (<I>NCAPG)</I>, which is associated with foetal growth and carcass size in cattle; and <I>ligand dependent nuclear receptor corepressor-like</I> (<I>LCORL</I>), which is associated with height in humans and cattle.</P><P><B>Conclusions</B></P><P>The GWAS analysis detected 39 SNPs associated with BW in sheep and a major QTL region was identified on OAR6. In several other mammalian species, regions that are syntenic with this region have been found to be associated with body size traits, which may reflect that the underlying biological mechanisms share a common ancestry. These findings should facilitate the discovery of causative variants for BW and contribute to marker-assisted selection.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1186/s12711-015-0142-4) contains supplementary material, which is available to authorized users.</P>