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Concept of Cytogenetics and Molecular Karyotyping

Discuss about the Cytogenetics for Several Hereditary Diseases.

The abnormalities in the genetic formation of human beings can give rise to several hereditary diseases (Ettorre 2013). The alteration in the DNA sequence due mutation is mainly responsible for the genetic diseases. The mutation can be caused by the alteration can be of single-base mutation, where alteration occurs in just one gene. The alternation can also occur in multiple genes. The diagnosis of these genetic disorders occurs during the time right after birth or even after the many years. The muscular dystrophy is one of the most common forms of genetic disorder, where a child faces weakness while doing movement. Besides, muscular dystrophy, there are many other forms of muscular disorder that can occur due to the genetic disorders. A child can also face mental and physical developmental delay due to genetic disease like Down syndrome.

 In this study report, the analysis of a 5-year-old infant, who is suffering from weakness in the lower muscle and developmental delay, is done. The genetic disorder that the child is suffering is being identified with the result that is obtained from the molecular karyotyping. The ways the function of the gene is altered is also discussed by mentioning the changes that took place at the molecular DNA level.

 The cytogenetics is a special branch of the study of genetics, which deals with the structure and function of human chromosome. The G-banding is a special staining technique that is used to identify the structure of a chromosome within the cell (Hamerton 2013). With the help of the result of the G-banding, it is possible to discover the genetic disease. The change in the structure of a human chromosome can compromise the developmental process of a human. The abnormality in the formation of the chromosome can occur during the time of fetal development. The structural change within a chromosome can disrupt the function of the gene, which in turn can affect the process of synthesis and functioning of proteins. The cytogenetic analysis needs to perform in every new born baby to diagnosis if there is any genetic disease. The data that is obtained from the result of the cytogenetic analysis help in accurate diagnosis of a genetic disorder that a child is suffering.

The molecular karyotyping is a biological technique that is able to detect a disorder in the sequence of the DNA. All the genetic disorders like developmental delay, congenital, autism and many more can be identified with the help of this technology (Stephanie et al. 2013). The base pair position of a DNA sequence is done with the support of the sequencing. If the base pair of chromosome 2 is number 1 and the last base pair is 243,199,373, then it indicates that the base of DNA in chromosome 2. In the band that is obtained from the experiment of molecular karyotyping the number 2 is the chromosome location within the band. 243 is the genomic position on chromosome 3 that is the first breakpoint and 373 is the genomic position of the end breakpoint. The position between the first and the end genomic point is deleted or duplicated due to the molecular mutation that leads to genetic disease (Patassini et al. 2013). 

Description of the DMD Gene

 The DMD is one of the major genes that is found in the human body has the information stored that is required for synthesis of the protein called dystrophin. This protein is located in the muscle cells and helps in the movement of the skeletal and cardiac muscle. It is also present in the nerve cells of the brain in negligible amount (Strmecki et al. 2014). The dystrophin protein is of rod-shaped that helps to connect the muscle fiber and cytoskeleton. The DMD gene covers 2.3 megabases and the locus at the X-chromosome is at Xp21, which consists of 0.08% of the human genome. The RNA that is transcribed from the DNA of the gene consists of 2100 kilobase, and the transcription process takes nearly 16 hours. The processed mRNA that is the end-product of the first transcript is of 14.0-kilo base (Dick et al. 2013).

 The dystrophin is a cohesive type of protein that helps to link the actin filaments of the protein that is present in the plasma of the muscle tissues. Hence the protein is able to get support from inside the surface of sarcolemma. The dystrophin also provides support to the fiber of the muscle and thereby help in the reducing the muscle stiffness.  

The Online Mendelian Inheritance in Man (OMIM) is an online database that is a catalog of all the genetic disease that occurs in human. This catalog is being regularly updated as new genetic diseases are being discovered. The phenotypes of the genetic diseases are also represented in the OMIM. The genetic disorders that have been recorded in the OMIM are recorded from over 15,000 genes. The link between the phenotype and genotype is also mentioned in the database (Omim.org, 2016). The database is one of the widely used sources for identifying the cause and symptoms related to a genetic disease. Hence, it can act as a reliable source of literature in the medical study and research.

The gene browser is also an important database source that is used in the identification of genetic disorders. It uses the techniques of bioinformatics in order to graphically display the data that is obtained from the molecular karyotyping of a gene. The visual display mapping of the gene helps the researcher to identify the exact point of mutation within a gene. In the given case the UCSC gene browser is used, which is controlled by the University of California in Santa Cruz. This website helps to provide the gene mapping of the gene of several vertebrates and invertebrates. The website is graphically optimized in order to help the user to obtain faster and accurate result of the molecular karyotyping (Duan et al. 2014).    

Gene Mapping of DMD Gene

The OMIM Allelic Variants that is obtained after molecular karyotyping of the given gene sequence is given below:

OMIM Allelic Variants: 300473.0021 Adrenal Hypoplasia, Congenital

OMIM: 300473: DSS-AHC critical region on the X chromosome, gene 1

Amino Acid Replacement: Tyr197Ter

Position: chrX: 30308773-30308773

Band: Xp 21.2

Genomic Size: 1    (Anon, 2016)

Hence, due to the depletion of the 92 kb gene sequence at the X chromosome at locus Xp21(32,699,367-32,791,566) the amino acid Tryptophan at the 197 position of the dystrophin protein is being replaced by a different amino acid that is coded using different codon. Therefore, due to the defect in the DMD gene at the above mentioned locus the child, in this case, is suffering from the Becker’s muscular dystrophy and developmental delay.

The method that was used in the gene mapping, in this case, included loading of the OMIM allelic variant file into the MySQL table that was obtained from the OMIM. The data that was obtained was identified using the corresponding genetic variants that are present in the database of the table. 

Mutation is the prime cause of a genetic disease that occurs within human beings, which occurs due to the alternation or depletion in the sequence of the DNA. The size of the mutation can vary in size as they can affect a single block of DNA or even a large segment of a chromosome. The mutations within a gene can be of hereditary type, where the mutated gene is inherited from the parents (Gerstung et al. 2015). The DNA that is received by an offspring from the sperm and egg cells is already mutated. The child, thus born has a high chance of suffering from genetic disease. On the other hand, acquired mutation occurs during the lifetime of an individual, where changes in the DNA sequence occurs due to some external environmental agents like expose in UV rays of the sun or also due to errors in the process of DNA replication. Acquired mutations occur in the somatic cells and hence cannot be passed to the next generations. In this case, the five-year-old child is suffering from muscular dystrophy that is caused due to the mutation in the DMD gene is of heredity type as it is passed from the X chromosome (Stenson et al. 2014).     

There are more than 1000 types of mutation at the molecular level that can occur in the DMD gene. The defect in the DMD gene can cause weakness in the cardiac and skeletal muscle of the human body. This clinical condition is described as the muscular dystrophy that also can cause developmental delay in children. The muscles that are suffering from the muscular dystrophy can damage due to repeated contraction and relaxation of the muscle (Ishmukhametova et al. 2013). In order for the normal muscle to function properly, only 0.002% of the total muscle protein consists of dystrophin. Nevertheless, in case total absence of this protein, a person suffers from muscular dystrophy. In the case given, the 5-year-old child, who is having weakness in the lower limb muscle, is suffering from muscular dystrophy. The child may not be able to show the physical movement properly and also might have to depend on wheelchair for proper action.

Disease Due to Defect in the DMD Gene

The mutation in the DMD gene can lead to synthesis of partially functioned protein and thereby lead to Becker’s muscular dystrophy (BMD). This BMD is a type of X-linked recessive disorder. The symptoms of this disease include weakness in the muscle movement, muscle cramp, problem in breathing, cardiac trouble, elevated level of creatine kinase in blood and deformities in the skeleton and chest (Angelini 2014).

As the disease is of X-linked recessive, the gene of this dystrophin protein is located on the X chromosome. As in case of female, there are two X chromosome present, if one of the X chromosomes is carrying the defective gene, the second X chromosome can provide the copy of the working gene. Hence, one X chromosome can provide the alternative for the detective chromosome. Therefore, muscular dystrophy occurs only in man as they have only one X chromosome. Females, who are the carrier of this defective gene, have 50% chance of passing this gene to the next generation. In case of son, the individual will be affected by the disease; on the other hand, if the individual is a daughter, she will be carrier of this defective gene. In case men, who are suffering from BMD will have daughter, who will be carrier of this disease. However, the sons will not inherit the gene for this disease. The chance of suffering from BMD is 1.5 in every 100,000 males. It is important for the person, who is affected by BMD need to have genetic counseling before they are planning to have babies (Zong et al. 2015).     

Duchenne muscular dystrophy (DMD) is another major type of muscular dystrophy, where muscle of the upper legs and pelvis are poorly developed, and the patient is unable to show proper movement. Children, who are suffering from DMD is often seen to display neurological disorder, and other types of mental developmental delay as the dystrophin protein is an important constituent of the muscle tissues that are present in the brain. The child may also lose the ability to walk properly and take the help of wheelchair for proper movement (Yiu and Kornberg 2015).

The gene that is responsible for the synthesis of the dystrophin gene consist of 79 exons and with the help of DNA testing, it is possible to identify the exact location of mutation in the gene of interest (Gil et al. 2013). Muscle biopsy can also be performed, where tissues muscle is extracted from the patient, and the immunochemistry test is performed with it. The positive result of the test will indicate that absence of the DMD protein. There is also the parental test that can be done for the diagnosis of muscular dystrophy.

There is no permanent cure for the treatment of muscular dystrophy. Corticostriods such as the deflazacort and prednisolone can provide short-term relief by providing muscular strength. The beta2-agonists can also provide support to the movement of the muscle. Physical therapy is also one of the popular techniques to help the patients. The use of orthopedic appliances can also provide support to the movement of the child (Mendell et al. 2013).

Conclusion

 In the given case, the 5-year-old child is showing the symptoms of weakness in the limbic muscle, and there is also the developmental delay is suffering from muscular dystrophy. This is a genetic disease that occurs due to the mutation in the X-chromosome at locus Xp21(32,699,367-32,791,566). The change in the DNA sequence has lead defect in the synthesis of the dystrophin protein that is an essential constituent of the skeleton muscle tissues. As this disease is passed from the X-chromosome, the child has inherited this disease from his mother. Moreover, the male infants have higher chance of suffering from this disease as they have only one X-chromosome present. Hence, in most case, the female are the carrier of this disease and males are the sufferer.

The cytogenetics investigation with the help of molecular karyotyping technique is used to diagnosis of this disease. The online database of OMIM is used to refer the gene mapping that is obtained after molecular karyotyping. The UCSC online gene browser is utilized in this case for the diagnosis of this disease. In spite of the fact that is no permanent care for the muscular dystrophy, there are few techniques that can provide temporary relief by providing support to the muscle.

Reference

Angelini, C., 2014. Becker Muscular Dystrophy. In Genetic Neuromuscular Disorders (pp. 13-17). Springer International Publishing.

Anon, (2016). [online] Available at:

https://genome.ucsc.edu/cgi-bin/hgc?gsid=548173917_7bonpjleQ4j6NloFfHjNVHwX5APL&c=chrX&l=24900000&r=37800000&o=30308772&t=30308773&g=omimAvSnp&i=300473.0021 [Accessed 18 Oct. 2016].

Dick, E., Kalra, S., Anderson, D., George, V., Ritso, M., Laval, S.H., Barresi, R., Aartsma-Rus, A., Lochmüller, H. and Denning, C., 2013. Exon skipping and gene transfer restore dystrophin expression in human induced pluripotent stem cells-cardiomyocytes harboring DMD mutations. Stem cells and development, 22(20), pp.2714-2724.

Duan, Q., Flynn, C., Niepel, M., Hafner, M., Muhlich, J.L., Fernandez, N.F., Rouillard, A.D., Tan, C.M., Chen, E.Y., Golub, T.R. and Sorger, P.K., 2014. LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. Nucleic acids research, p.gku476.

Ettorre, E., 2013. Reproductive genetics, gender and the body.Routledge.

Gerstung, M., Pellagatti, A., Malcovati, L., Giagounidis, A., Della Porta, M.G., Jädersten, M., Dolatshad, H., Verma, A., Cross, N.C., Vyas, P. and Killick, S., 2015. Combining gene mutation with gene expression data improves outcome prediction in myelodysplastic syndromes. Nature communications, 6.

Gil, M.M., Quezada, M.S., Bregant, B., Ferraro, M. and Nicolaides, K.H., 2013. Implementation of maternal blood cell?free DNA testing in early screening for aneuploidies. Ultrasound in Obstetrics & Gynecology, 42(1), pp.34-40.

Hamerton, J.L., 2013. Human Cytogenetics: Clinical Cytogenetics (Vol. 2). Academic Press.

Ishmukhametova, A., Chen, J.M., Bernard, R., Massy, B., Baudat, F., Boyer, A., Méchin, D., Thorel, D., Chabrol, B., Vincent, M.C. and Khau Van Kien, P., 2013. Dissecting the structure and mechanism of a complex duplication–triplication rearrangement in the DMD gene. Human mutation,34(8), pp.1080-1084.

Mendell, J.R., Rodino?Klapac, L.R., Sahenk, Z., Roush, K., Bird, L., Lowes, L.P., Alfano, L., Gomez, A.M., Lewis, S., Kota, J. and Malik, V., 2013. Eteplirsen for the treatment of Duchenne muscular dystrophy. Annals of neurology, 74(5), pp.637-647.

Omim.org. (2016). About OMIM. [online] Available at: https://www.omim.org/about [Accessed 18 Oct. 2016].

Patassini, C., Garolla, A., Bottacin, A., Menegazzo, M., Speltra, E., Foresta, C. and Ferlin, A., 2013. Molecular karyotyping of human single sperm by array-comparative genomic hybridization. PloS one, 8(4), p.e60922.

Stenson, P.D., Mort, M., Ball, E.V., Shaw, K., Phillips, A.D. and Cooper, D.N., 2014. The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine. Human genetics, 133(1), pp.1-9.

Stephanie, C.Y., Jiang, P., Choy, K.W., Chan, K.C.A., Won, H.S., Leung, W.C., Lau, E.T., Tang, M.H., Leung, T.Y., Lo, Y.M.D. and Chiu, R.W., 2013. Noninvasive prenatal molecular karyotyping from maternal plasma. PloS one, 8(4), p.e60968.

Strmecki, L., Hudler, P., Benedik-Dolni?ar, M. and Komel, R., 2014.De novo mutation in DMD gene in a patient with combined hemophilia A and Duchenne muscular dystrophy. International journal of hematology, 99(2), pp.184-187.

Yiu, E.M. and Kornberg, A.J., 2015. Duchenne muscular dystrophy. Journal of paediatrics and child health, 51(8), pp.759-764.

Zong, L., Guan, J., Ealy, M., Zhang, Q., Wang, D., Wang, H., Zhao, Y., Shen, Z., Campbell, C.A., Wang, F. and Yang, J., 2015. Mutations in apoptosis-inducing factor cause X-linked recessive auditory neuropathy spectrum disorder. Journal of medical genetics, pp.jmedgenet-2014.

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