Reference no: EM133181446

Question: You have received a set of somatic mutations identified in a multiple myeloma cancer tumour sample. Tumours contain many somatic mutations and some of these have an active role in cancer (referred to as driver mutations), while many other mutations occur in the unstable cellular environment they do not have a role in the disease (referred to as passenger mutations). To understand better the patient's cancer you are going to use bioinformatics resources to analyse each of the mutations and assess:

1) if they are likely to have a functional effect
2) if they are more likely to be driver or passenger mutations

Greater emphasis should be placed on analysis of the functional effect (i.e. Point 1 above).
You will write up the findings of your analysis as a scientific report.

Many bioinformatics databases and web servers have been introduced in the lectures and practical sessions, it is up to you to decide which of them you are going to use. It may be that some resources are relevant for a particular mutation but not for another (e.g. some mutations will be present in protein coding regions, while others will not be).

You are expected to use PolyPhen-2, this method has been introduced in the lectures but not in the practical sessions, it is therefore down to you to work out how to use it. This represents a common task in biosciences research, where new tools are introduced and you need to work out how to use them.

For each mutation you should combinethe results obtained from the analyses to suggest for each mutation if it has a functional effect and if it is more likely to be a driver or a passenger mutation and the evidence that supports your decision.

Preparing your reassessment

• Your coursework should be submitted as a scientific report containing each of the sections listed below. You mustuse the word file available on Moodleto write your report. This file includes the layout of the two compulsory tables.

• The word limit for the report is 2000 words (excluding tables, figures, legends and references), this is a MAXIMUM word limit.

• There is also a limit of up to eight tables or figures (i.e. combined total number of tables and figures.) This is a maximum - you do not need to have eight tables/figures. The two compulsory tables are included in this limit (details of their content are provided below). Figures may have multiple parts (e.g. A, B, C) as you often see in papers but each figure must fit on a single page, although the legend may be on a separate page. Note each whole figure should have a single legend, not a legend per part of a figure. If you are unsure what this means then please look at a figure in a paper (e.g. the Multiple myeloma cancer genomics paper from week 8).

• All figures and tables should have a title and a figure/table number and a legend describing them. They must also be referred to in the text. The legends can only be used to explain the figure/table and each legend has a maximum word count of 150words. i.e. do not try to use figure legends to get around the word limit. Any information that is important to your analysis should appear in the main text not only in a figure/table legend.

• The marks associated with each section are displayed below with details of the information that should be included.

• You are expected to include references formatted in a uniform style throughout, you can decide what style to use. I recommend using a reference manager, which will enable you to easily insert and edit the references present in your document.

• The report should be clearly presented. There are no marks specifically assigned for presentation of the coursework but this will factor in all of the individual sections (including referencing, figure and table formats). This means that the scientific data should be presented using a simple, clear, functional style. It is NOT an exercise in desktop publishing.

Attachment:- Bioinformatics.rar