Biochemical and Mutational Analyses of HEXA Assignment

Assignment Task

1. Introduction

You are a bioinformatician working for a hospital. A patient terminated pregnancy of twins during the second trimester, due to apparent developmental abnormalities. Pathological examination of the foetuses suggested many developmental problems in the brain. Genome sequencing of the foetuses revealed single nucleotide mutations in the gene HEXA that may ultimately be responsible for the pathology. Your task is to help the clinical team understand the nature of the pathology, and how foetal development was affected.

RNA was extracted from brain tissue samples and sent for paired end sequencing. The resulting FASTQ files are on cluster for you to analyse. Control healthy brain samples are also available for your analysis. The exact analyses you run are up to you; this is an opportunity to put into practice the skills you have learned during this module.

2. Contents of the report

Your report has a word limit of 2000 words, excluding figure legends and references. It should follow the general structure of an SPF. We expect a (brief) introduction summarising relevant background literature you find, but the focus should be on the writeup of your own analysis: the methods, results and discussion. Methods should include all relevant programs, their versions and the parameters used so that others can replicate the analysis. The results should explain what your analyses revealed, and support the key outputs (including any sanity checking or quality control) with figures as appropriate. The discussion should (briefly) assess your results in the context of the wider literature.

You may wish to include your script files as supplementary files; these will not contribute to the word count, and (if clearly written and well commented) will help us assess your analysis.

We will be assessing:

• your ability to select appropriate types of analysis
• your ability to communicate your results clearly in text and figures
• your ability to place the results you found in the context of the pathology

Topic

• Genome sequencing and resequencing
• Gene expression
• Epigenetics protein interaction
• Epigenetics :Methylation
• Genome wide association studies
• Functional annotation
• Personal  genomics and Ancestry

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