Annotation of Genome Variants
The major goal for genomics is that to determining the sequence of molecules that make up the genomic content of an organism. The genes are contained in the chromosomes and it can be further described as containing the fundamental units of heredity. These genes are known as transcriptional unit, those regions of chromosomes that under appropriate circumstances are capable of producing RNA then these RNA is translated into molecules of protein.
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Basically human genome variants causes’ difference between individuals include the exchange of genes during meiosis and various mutational events. The usual reasons for genetic variation exists between populations one is all about Natural selection and the other one is Neutrality of most mutations due to the random drift. Studies proved that Human genome variants have both evolutionary significance and medical applications. Evolutionary significance is to understand ancient human population as well as how the different human groups are biologically related to one another, in the case of medicine some disease causing alleles occur more often in people from specific geographical regions.
A specific condition which may cause by the alteration or mutation of a specific gene will lead to particular disorders; these single gene disorders are often heritable so that single gene disorder may be at risk for passing the condition onto their children.
The fact is quite essential to know that how do mutations occur in genome. Gene mutation is a permanent change in DNA sequence that makes up a gene.
The mutations can occur in two ways, one can be through inherited from a parent or acquired during a person’s lifetime.
Mutations passed from parent to child are called hereditary mutations or germ line mutations. This type of mutations is present throughout a person’s life in virtually every cell cycle in the body. Some mutations are called De novo mutations, these kinds of mutations are occur only in egg or sperm cell, or those that occur just after fertilization, so this mutations are also called new mutation. Denovo mutations may specify genetic disorders in which an affect child has a mutation in every cell, but it has no family history of the disorder. But in the case of acquired mutations occur in the DNA of individual cells at some time during a person’s life. Environmental factor such as ultraviolet radiation from the sun or can be the cause of these mutation. Also it can occur if mistake is made as DNA copies itself during cell division (mitosis) so that it cannot be passed in to the next generation, but in the failure in the DNA mechanism then the mutation can be passed to future copies of the altered cell.
Single cell within an early embryo may also occur mutation in single cell .As all the cell divide during growth and development, the individual will have some cells with the mutation and some cells without the genetic change and this situation is called mosaicism.
Some genetic changes are very rare; others are common in the population. Genetic changes that occur in more than 1% of the population are called polymorphisms. These are considered to be as a normal variation in the DNA.
Any way by changing gene’s instruction for making a protein a mutation can cause the protein to malfunction or to be missing entirely. Here we can say that the condition caused by mutation in one or more genes is called a genetic disorder, these genetic disorder causes the disease by making a gene function improperly.
There are number of ways of alteration can be happen in DNA sequence, depends up on their occurring place and alteration in the function of essential proteins gene mutations have varying effects on health. Basically the types of
Missense mutation will make a change in one DNA base pair that results in the substitution of one amino acid for another in the protein made by a gene.
An insertion changes the number of DNA bases in a gene by adding a piece of DNA. As a result, the protein made by the gene may not function
Deletion changes the number of DNA bases by removing a piece of DNA .The deleted DNA may alter the function of the resulting proteins, so the small deletions may remove one or a few base pairs within a gene, while larger deletion can remove an entire gene or several neighbouring genes.
Duplication in DNA sequence will alter the function of the resulting protein a duplication consists of a piece of DNA that is abnormally copied one or more times.
Frame shift mutation is a type of mutation occurs when the addition or loss of DNA bases changes a gene’s reading frame. Basically a reading frame consists of groups of 3 bases that each code for one amino acid. A frame shift mutation shifts the grouping of these bases and challenges the code for amino acids. Then the resulting protein is usually non-functional, so that the frame shift mutation can be Insertions, deletion.
Repeat expansion is a kind of nucleotide repeats which are short DNA sequence that are repeated a number of times in a row. A tri nucleotide repeat is made up of 3-base-pair sequence, and a tetra nucleotide repeat is made up of 4-base-pair sequences. A repeat expansion is a mutation that increases the number of times that the short DNA sequence is repeated. This type of mutation can cause the resulting protein to function improperly.
Mutation and Disease
DNA is constantly subject to mutations, accidental changes in its code. Mutations can lead to missing or malformed proteins, and that can lead to disease.
We all start out our lives with some mutations. These mutation inherited from your parents are called germ-line mutations.
Generally some mutations are bad for the human body but some mutations can be beneficial. To keep population healthy genetic mutations create genetic diversity, many mutations have no effect at all and these mutations are called silent mutations. But the common mutations which were most concerned mutations are which causing disease’s mostly those diseases are happening due to the mutation of a single gene. Most inherited genetic diseases are recessive that means a human must inherit two copies of the mutated gene to inherit a disorder. Diseases caused by a one copy of a defective gene are rare.
But the high impact of natural selection make these dominant genetic diseases tend to get weeded out of populations over time, because afflicted carriers are more likely to die before reproducing.
CFTR are one of the mutated genes this will provide instruction for making a protein called the cystic fibrosis transmembrane conductance, regulator. This protein will produce mucus, sweat, saliva, tears and digestive enzymes. CFTR regulates the channels which transport negatively charged particles and positively charged particles. These channels are necessary for the normal function of organs such as the lungs and pancreas. The most common gene changes involves a single base mismatch a misspelling.. Placing the wrong base in the DNA. At other times, a single base may be dropped or added. And sometimes large pieces of DNA are mistakenly repeated or deleted.
Single Gene Disorder:
The condition caused by the alteration or mutation of a specific gene, these single gene disorders are often heritable, so single gene disorder may be at risk for passing the condition onto their children.
Examples for single gene disorders are: – Cystic fibrosis, Sickle cell anaemia, Tay-sachs disease etc.
In this work the influence of bioinformatics and computational biology is very high, because this work can be go forth only with help of Data bases, tools and programming.
The Data base like OMIM plays a key role because OMIM stands for online mendelian inheritance in man. It is a catalogues of all the known disease with the genetic component and link the disease to the relevant genes in the human genome for further research and tools for genomic analysis of catalogued gene. Basically omim is hosted in the US national centre for biotechnology information (NCBI) .Omim is an abstract of human genes and genetic phenotypes that is freely available and updated daily. Information on all known genetic mandalian disorders and over 12,000genes.
So with the help of Natural Language Processing we can extract key words from this data base and compare with symptoms in any case sheet and identify which disease are belongs to mutations.
Natural language processing is a field of computer science which will concerned with interactions between computers and human natural languages. That is the computers should understand human natural language which enables computers to derive meaning from human or natural language input. Computers use, analyze, understand, generate natural language. It’s originates aprox five decades ago with machine translation systems. Currently NLP includes a wide variety of linguistic theories, cognitive models, and emerging approaches.
The interactive application may be classified along the Speech recognition understanding and synthesis, generation, Natural Language Interfaces, Discourse Management, story Understanding and text generation, Interactive machine translation, Intelligent writing assistants. NLP provides mechanisms for incorporating natural language knowledge and modalities into user interfaces.
By the application of NLP we could easily recognize the language that we required, through this way we can extract the keywords from the Omim database and based on the semantic equivalence compare with the case sheet data and find out the disorders. The semantic equivalence can be find out when we integrate the context distance means finding closeness of word meanings model with morphological analysis.
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Then using the tool Alchemyapi which is based on the natural language processing, here API will employ complex linguistic, statistical and natural network algorithms, alchemyapi is able to read and understand text at massive rates of speed. This tool offers a suite of text analysis functions that can add understanding and semantic data to your text content. These functions are all accessed via a REST API and the data is returned as an easy to pores structure that can be integrated in to our application.
So using this application we do keyword extraction – which extract the important terms. Basically keyword are the important topics in our content and can be used to index data, generate tag clouds or for searching. Alchemyapi is capable for finding keywords in text and ranking them. Alchemyapi automatically detects the language of the content and then performs the appropriate analysis. Api puts statistical algorithms and natural LP technology to analyze our content and identify the relevant keywords, and this tool will ranked based on the relevance here the relevance score is calculated for each keyword based on the statistical analysis, and the result are returned sorted by relevancy.
- Ultimately through this work will make doctors to easily recognize the diseases related to the symptoms.
- Also we could recognize which mutation causes certain disorders.
- If we under stood what makes these diseases may be what kind of mutation leads to certain disorders , hopefully we could look forward for the treatments and medicine .
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