The hypothesis of the study
This research was conducted in Saudi Arabia to determine the genetic and genomic alterations that underlie classic anirida. Though the topic seems scientific, the researchers did not include the genes the research deals with in the topic. The topic does not give a clear picture of what in deed is in the paper since the contents cannot be read from it by the intended audience. The problem of classic anirida is an appropriate problem that needs researchers to deal with. This is because the information from the previous studies does not tell on the exact cause of the disease thereby requiring the scientists to do genetic and genomic analysis of the disease. According to the author of the study, previous information only showed that the disorder was caused by dominant mutations on the PAX6 gene but when this information is compared to the results of PAX6 analysis, it raises questions as to whether the disorder is as a result of dominant mutation of the PAX6 gene. This is because there are present cases of anirida that show no identifiable PAX6 mutation.
The question the research is revolving was very interesting since they provide the reader with the reason for them to have interest in the research, which is very interesting as far as the cause of PAX6 negative classic aniridia cases is concerned. In their introduction, the researchers used other previous work by other researchers to give relevant literature as to why they were indeed interested in the research. This literature in the introduction is standard in length, and at the end the researchers have explain what they asked in the research. The hypothesis proposed by the researchers of this study is that the individuals with PAX6-negative classic anirida could have gotten it through alterations of regulatory elements of PAX6 genomically or the probability that there is either point or deletion mutations in genes that cause congenital iris problems or disorders.
The authors are not the very first to address the question on the real cause of classic anirida. There has been some other work done by different researchers to come up with the information that the disorder is caused by dominant mutation of PAX6. The researchers of this study therefore checked someone else’s work and came up with the research question based on the results of the previous studies. The researchers base their knowledge about the genotypes associated with the disorder from the work of other researchers.
Methodology
The objective of the method used by the researchers is to find out whether genetic alterations of the PAX6 regulatory elements and mutations in other genes that cause congenital iris problems cause the classic anirida in PAX6 negative classic anirida cases. The method described by the researchers explains how they were able to answer the question for the research. The information the researchers gave is enough to let another researcher repeat the experiment and get reproducible results. The protocol the researchers followed is not complicated, and this is why they did not include any form of a diagram or a table in their explanation of the method. Ethical considerations that were relevant to the research were mentioned where the researchers got the approval of the institutional review board for their study.
The method the researchers employed in their study is indeed appropriate to answer their questions regarding the cause of classic anirida in PAX6 negative classic anirida cases. In general, the sample was taken from patients with classic anirida and their blood samples taken after confirming that they indeed had the disorder, which is characterized by invisible iris, keratopathy and lens opacity. Direct sequencing was done and if PAX6 mutation was not showed, deletion in PAX6 was assessed through multiplex ligation- dependent probe amplification (MLPA). In case there were no PAX6 deletions, sequencing of the candidate genes was done followed by karyotying of the genome through array CGH. The relatives of these patients also underwent the genetic analysis for confirmatory purposes. In the method, the researchers considered their alternative hypothesis. Even if the hypothesis were not cleared identified in the article, they are identified as the researchers’ speculated causes of classic anirida in PAX6 negative classic anirida cases. In their effort to refute their hypothesis, the methodology was centered in trying to test on whether to reject it or accept their hypothesis. DNA was extracted from blood of the patent, quantified through spectrophotometer and amplified via PCR. Coding regions were sequenced along variants in the boundary sites. Following the removal of nucleotides, analysis of the sequence was done and compared to the sequences for reference. Though the methodology used answered the research questions, the researchers did not think of other methods that could be used to give result.
However, the sample size used in this study was not large enough to provide reliable scientific findings that should be documented. This is the reason as to why the interpretation by the author should not be over emphasized until more analysis on the cases is done to confirm the findings of this research.
Results
The researchers have not used graphs and tables to summarize their findings but did it in text. In the results section the researchers have stuck to showing what they found after doing the experiment without going into discussing why the results were the way they were. Of the 12 patients whose analysis was done, 10 of them had PAX6 mutation, while two of them even if showed classic anirida, did not show PAX6 mutation. After further analysis of the two patients without PAX6 mutation, they lacked pharmacological mydriasis and the iris. The conclusion made by the researchers is well supported by the results since in the familia cases all of them showed PAX6 mutation while two of the sporadic cases did not show mutation of the PAX6. The two cases that did not show PAX6 mutation, one was homozygous for the pathogenic missense FOXC1 variant and deletion on 11q24.2 chromosomes. On analyzing the parents, they showed homozygosity for the FOXC1 variant and were heterozygous for the deletion. The other case was idiopathic.
Conclusion
The conclusion was highly supported by the results. Other scientists’ work is used in the conclusion of the study to support the results of the study. As the parents’ results of one of the cases showed, it was supported that there is a recessive cause for any phenotype if there is the presence of a recessive cause. The heterozygous PAX6 mutation underlies the reason for most classic anirida cases even in a setting of enhanced homozygosity in parental ancestry. Deletion in homozygous 11q24.2 or in combination with missense variant in homozygous FOXC1 was speculated to be the cause of classic anirida via array CGH. From other scientists’ work, p.P297S FOXC1 is responsible for altering interactions with factors in the degradation and transactivation of FOXC1.
The study has very many openings for future research since it would be appropriate to determine if the genes contained in the deletion of 11q24.2 have a role in the development of the eye. There is also a possibility that the non coding regulatory regions for PAX6 may appear in 11q24.2. The researchers use other peoples work to clarify on interfamilial phenotypic variability caused by the difference in individual’s background in terms of the genotype and the environment.
The study suggests additional experiment that needs to be carried out to clearly determine the real cause of classic anirida in PAX6 – negative cases. From this study, it was found that there is variation in the genomic copy number and further research is needed to determine this association with classic anirida in the cases where patients lack PAX6 mutation.
The results were clearly discussed by the researchers thereby convincing the reader that indeed their hypothesis was well manipulated to come to the conclusion of the findings. All along their written text, the argument presented are logical and their facts accurate since they well support them with other previous related research. All the important terms used in this study were clearly defined for the reader to understand the concept and intent. All the arguments presented had sufficient evidence through the use of other work by previous researchers. The main p is well supported throughout the text making the text very appropriate (Khan, Aldahmesh & Alkuraya 2011,P8-714).
Reference
Khan, A., Aldahmesh, A. & Alkuraya, S. (2011)Genetic and genomic analysis of classic aniridia in Saudi Arabia. Molecule Version, Biology and genetics in vision research, 17, 708-714