Literature Review on a Genomic Sequencing Assay

The availability of and drastic reduction in costs of high-throughput sequencing (2nd generation sequencing and beyond) has greatly driven innovation in biology, yielding a plethora of functional genomic assays making use of next generation sequencing. These sequencing assays address specific biological questions in a genome-wide manner for e.g. RNAseq methods seek to quantify genome-wide gene expression which can be used to address a variety of questions (e.g. changes in gene expression due onset of diseases) in disparate biological disciplines (from conservation to cell biology). For the review, you will be asked to write a short review (2000 words) on one such genomic sequencing assay.

Chosen genomic sequencing assay: Digenome-seq

Content of the Review

The review should be written in a language accessible to a reader with the knowledge level of a 2nd year Biology University student (i.e. you and your peers). As far as possible, your review should cover, in the following order with some flexibility, the following content:

1. The background should include the general area of biology, kind of biological questions the assay is designed to investigate and the methods that existed (or not) prior to the assay.
2. A brief description of the assay including any specific and unique details on the laboratory and computational requirements of conducting the assay.
3. Advantages and disadvantages of the method in general or specifically in comparison to other pre-existing methods.
4. A critical synthesis of new and/or unique findings addressing the questions you mentioned in the background (or potentially something new) using the assay in question. These could be a discussion of research highlighting specific applications of the assay or the application of the assay in different contexts.
5. Current limitations, future directions and conclusions.
6. References section in alphabetical order. Ensure that in text citations have also been included. (Harvard Referencing Format).

Layout and Structural Elements of the Review

The layout of the Review is expected to follow the layout of an article from journal Nature Reviews Genetics. Two examples of these can be accessed through the references below and can be used for guidance:

1. Park, P.J., 2009. ChIP–seq: advantages and challenges of a maturing technology. Nature reviews genetics, 10(10), pp.669-680.
2. Wang, Z., Gerstein, M. and Snyder, M., 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nature reviews genetics, 10(1), pp.57-63.

It is recommended you read these and study the structure of these articles. Note: you do not need to have your text in columns as per the example articles.

You do need to have the following:

• Give your review an appropriate title.
• A short abstract between 50-75 words to attract the attention of the reader.
• Use clearly headed sections to structure your review. You can either use the points from Content of the Review above to define your sections or use your own.
• Your review must have a minimum of two figures or a figure and a table. Each figure can have multiple panels. One of the figures must be related to point 2 from the section on Content of the Review above. You can use pre-existing figures (from your readings for example) as long you cite the source. Original figures will be preferred, within reasonable bounds, and will give you more practice in designing your own figures to convey complex biological/technical information.
• Use a Glossary box to explain any terminology/jargon in your own words. This should come at the end of your review, before your references.
• The word count for the final submission (including the abstract but excluding the title and references and the glossary box) should be between 2000  10%  words. Please include a word count at the end of the document.