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Genomics

What is PRSice?

Dr. Muniba Faiza

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Etiology is the study of origination or causation of an event or phenomenon. Genetic etiology is the study of genes responsible for particular traits along with some other genes in an organism. The identification of genetic etiology has become a protocol while studying genotypes and/or phenotypes of individuals. For this, PRS which means, Polygenic Risk Score is calculated. A PRS is the summation of trait-associated alleles across various genetic loci, weighted by effect sizes on a trait of interest. The effect sizes are calculated by the  Genome-Wide Association Studies (GWAS). It has revealed that the genetic basis of most of the complex traits caused by the small effects of hundreds or thousands of variants. The polygenic effects can be considered as the genetic liability to disease risk associated with these genes. PR score was found to be accurate in most of the applications. PRS only considers the variants with P-value threshold, i.e., PT.

PRS is calculated using estimated published GWAS results. This technique was first applied by the International Schizophrenia Consortium (2009), demonstrating that genetic risk for schizophrenia (SCZ) is a predictor of bipolar disorder. It has also been proved as the reliable indicator of genetic liability.

Jack Euesden et al. (2014), introduced a software package to easily calculate the PRS, known as PRSice (means ‘precise’).

They found out the genetic relationship between the Schizophrenia (SCZ) and Major Depressive Disorder (MDD) and significantly proved that PRS of SCZ predicts the status of MDD.

Fig.1

PRSice returns the best fit PRS according to the polygenic risk associated with the alleles responsible for a trait. The main feature of PRSice is that it can easily and automatedly calculate the PRS at any value of P-value threshold, i.e., PT and then identifies the most precise threshold. It only requires the GWAS results of individuals on a base phenotype and genotype data on target phenotype, to calculate the PRS for each individual, and plots a PRS model depicting the fit range of PT value. PRSice can also consider the SNPs in linkage disequilibrium (i.e., an occurrence of a combination of genes in non-random proportions in a population), but it depends on the user whether to use this option or not. PRSice is a command line program that calculates PRS for individuals, under variously specified parameters and reduces the computation time.

For further reading, click here.

For any query, write to [email protected]

Reference:

PRSice: Polygenic Risk Score software —-Jack Euesden*, Cathryn M. Lewis, and Paul F. O’Reilly*

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

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Genomics

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Genozip- a new compression tool for VCF files

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Methods to detect the effects of alternative splicing and transcription on proteins

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Conventionally unconventional: Anecdote of small RNAs discoveries

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Dr. Muniba Faiza

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Mycobacteriophages and their potential as source against Mycobacterial active biomolecules

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So, today is the great festival of Christmas……! Birthday of The Son of God.. And on this Auspicious day, We want to present before you all the power of Nature… How nature itself provides solution against the problem raised within it….. We all are aware of the epidemics of threat created by Mycobaterium tuberculosis and other related species. But, down here in this article we show how nature provides the solution against it.

As we know Bacteriophage (Bacterio= Bacteria’s, Phage= eater) infects several bacterium species. In contrast to it, a Mycobacteriophage is a member of a group of bacteriophages that infect mycobacterial species as their hosts e.g.,  Mycobacterium smegmatis and Mycobacterium tuberculosis, the causative agent of tuberculosis.

The rising incidence of tuberculosis, emergence of multi drug resistance in Mycobacterium tuberculosis and a slow progress in finding new drugs makes mycobacteriophage a potential candidate for its use as a diagnostic and therapeutic tool against TB.

All the characterized Mycobacteriophages are double-stranded DNA (dsDNA) tailed phages belonging to the order Caudovirales. Most are of the family Siphoviridae , characterized by  long flexible non contractile tails, whereas phages of the family Myoviridae, have contractile tails. There is a notable absence of mycobacteriophages from the family Podoviridae (containing short stubby tails), arising the question whether long tails are needed to traverse the relatively thick mycobacterial cell envelope. dsDNA tailed phages are either temperate, forming stable lysogens with a turbid plaque or lytic, forming clear plaques in which the host cells are killed. Mycobacteriophages can also be studied by the morphology of the plaques which vary in size and shape. Plaque morphology also depends on the burst size, which is the number of phage particles released on the lysis of the infected bacteria.

Genometrics of 70 sequenced Mycobacteriophages

Since the mycobacterial cell wall consists of a mycolic acid rich Mycobacterial outer membrane, attached to an arabinogalactan layer that is in turn linked to the peptidoglycan, it poses significant challenge to the phages. This challenge is met by a set of proteins, namely Lysin B proteins that cleave the linkage of mycolic acids to the arabinogalactan layer, holins that regulate lysis timing, and the endolysins (LysinAs) that hydrolyze peptidoglycan.

Phages affect hosts with a holin-endolysin system essential for programmed lysis. Endolysin is  found to be associated with a protein component of the phage tail involved in facilitating the penetration of the murein during injection of the genome into the host. Holins are small membrane proteins that form holes in the membrane through which the endolysin can pass. Holins control the length of the infective cycle for lytic phages so as to achieve lysis at an optimal time.

Endolysins can be a source of potential antibacterial because of its specificity (targeting only a few strains of bacteria) and thus replacing antibiotics (which have a more wide ranging effect), their low probababilty of developing resistance in Mycobacterium and novel mode of action.

Bioinformatics can assist this particular field of research by finding several other proteins existing on this planet or to prepare other such options having similar pharmacophore (physical and chemical attributes) properties. We can demolish the various disease threats by using natural options provided to us and can remain healthy on this planet. The only point to be remembered for this is,

NATURE CAN SATISFY OUR NEEDS, BUT IT CANNOT SUSTAIN OUR GREED….. AS A HEALTHY BODY CONSISTS OF A HEALTHY MIND, THE SAME WAY.. A CONSERVED PLANET CONSERVES ITS SPECIES TOO…..

(A major part of this article consist of some texts copied from

Hatfull, Graham F. “Mycobacteriophages: genes and genomes.” Annual review of microbiology 64 (2010): 331-356.

for any other information related references and queries, please let us know at [email protected]

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Roary: Analysis of Prokaryote Pan Genome on a large-scale

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