Genomic Sequencing Assay

1. Introduction and Aims for the Coursework

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 CW1 (“the Review”) you will be asked to write a short review (2000 words) on one such genomic sequencing assay. The final essay will be due in week 12 (45% of total module mark) but you will be asked to submit a draft for Peer Review in week (3% of module mark for providing feedback on submissions of others). There will also be a 2% mark for announcing your chosen topic and interests at the end of Week 5. In total this coursework accounts for 50% of the module mark.

This coursework is designed to allow you to become more knowledgeable about a topic (from the lens of genomics) that you are interested in. Additionally, it will enhance your knowledge of workflows/pipelines and jargon in field of Genomics (some of which will be introduced in this class). Finally, this will be an oppurtunity for you to practise drafting, reviewing and writing literature reviews, which almost all of you will do for your final year project/dissertation.

2. Choosing a Topic/Assay to Review

For CW1 you are asked to choose one genomic sequencing assay to focus your review on. There are several ways to go about finding an assay.

Ideally, you should pick a sequencing assay in your area of interest in biology. One way to find an appropriate genomic sequencing assay is to start with a simple google search for “Genomic applications in X”, where “X” is your specific area of interest in biology. For e.g. X could be “conservation”, “verterbrate development”, “animal breeding” or “schizophrenia”. The more specific “X” is, the easier the next bit will be for you. This search will give you a broad array of results. but going through some of these will start giving you some idea of what kind of assays are being used in this area. You can then pick one of these assays and use that for your CW1 review. Note the assay you choose does not thave to be from the poster. If in doubt, please check with me.

Alternatively, you can also have a look at Illumina’s “For all you seq” poster to find information on a sequencing assay to write your review. A better, more focussed and update way to search this poster is to use Illumina’s Sequencing Method Explorer. Note, you have to choose an assay that was published after 2011 and before 2019. The reference for each assay listed on the All you can seq poster can also be found on the poster. Finally, please note Illumina’s poster/web page may note include applications available to newer generation Long Read Sequencing technology (eg. Oxford Nanopore or PacBio) which may have applications not viable for Illumina short read sequencing.

As before is you are unsure about anything, please contact me.

3. Important Dates for CW1

1. Friday Week 5 23:59, CW1-Part 1-Topic Announcement: This is the absolute deadline for picking a topic/sequencing assay and posting it on the CW1-Part 1 Topic Announcement discussion forum along with 2-3 sentences explaining why you chose this topic/assay. This activity is worth 2% of the total module mark and will be an oppurtunity for me to make sure you are not off-track. Additionally, this is an absolute deadline, you may let me know about your topic earlier. Multiple people can choose the same assay for their review. Feel to post questions about other folk’s topics and interests.
2. Friday Week 10 23:59 and 22nd April 2022, 17:00, CW1-Part 2-Peer Review: Submit a draft for Peer Review feedback via Turnitin by Friday Week 10 23:59 . See details below on expectations of for the Peer Review Exercise. This Peer Review Exercise is meant to provide with additional feedback to potentially improve your writing for final submission. Please note extensions are not possible for this part of the coursework due to time limits for completing the review. Please complete your reviews by 22nd April 2022, 17:00.
3. Friday Week 12 23:59, CW1-Part 3-Final Submission: Submit the final Review via Turnitin. See details below on criteria for marking the final submission.

4. 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.

The example review article on RNAseq gives an example of a review that covers most if not all of the desired content above. This example is of course a published article by a professional researcher and I do not expect such a high level of detail from your work but it is something to aim towards.

5. 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, the review article on RNAseq and the review article on ChIPseq are included for your guidance. It is recommended you read these and study the structure of these articles. Not only will this be helpful for constructing your review, it will also help later when covering these topics in Weeks 6-9. Note: you do not need to have your text in columns as per the example articles. You do need to have the following:

1. Give your review an appropriate title.
2. A short abstract between 50-75 words to attract the attention of the reader.
3. 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.
4. 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. Make sure to have complete captions for your figures in your own words. See this page to understand what constitutes a complete figure caption.
5. 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.
6. 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.

Please make sure to write in scientific/academic English and cite/reference properly. If you are unsure about these make sure to review Sections 3 (Scientific Writing), and 6 (Citing/Referencing) from A Handbook of Writing and Presentation Skills for Science Students.

6. Finding and Using Sources for your Review

This CW is a literature review and as such requires looking up the relevant sources to support your writing. In this particular case, your sources should all be from scientific journal articles. A minimum of 8 sources are required. There is no maximum, but sources numbering over 20 is probably a bit overkill for this assessment. Writing a good review will require that you read all your sources end-to-end multiple times.

One of your sources will be the publication first describing the sequencing/genotypinc assay you picked (the one on the All you can seq poster or elsewhere). This source will include all the information to describing the assay, potential applications and also important background material. There might be additional sources about background (likely other Review papers or descriptions of older methods) cited in the Introduction of this source that you can also use. These sources will help you regarding points 1,2 and 5 from 4. Content of the Review above. There might be sources referring to other methods that you may choose to compare to help in addressing point 3 from 4. Content of the Review above.

The remainder of your sources should cover papers that employ the assay you choose (I will show how to do this in class but basically you want to find papers that use your chosen method). Depending on your assay (how popular and/or how recent it is) you may have 10-100s of these sources. You will have to be selective and pick ones that demonstrate the applicability of the assay or new/unique insights gained from the use of the assay. You could also restrict these to be in particular organisms (example only in verterbates) or addressing specific topics (only investigations in to disease), depending on your interest. You might have to read through a lot of titles/abstracts to select the sources appropriate for your review. These sources will help you regarding points 3,4 and 5 from 4. Content of the Review above.

7. Instructions and Rationale for Peer Review of Draft submission in Week 10 (CW1 – Part 2)

For part 2 of CW1 you are expected to submit a draft for Peer Review at the end of Week 10. Although it is expected that “revised” work (i.e. after review and feedback) will be superior to “draft” work, the term “draft” should not be construed to mean hastily-conceived, incomplete, or poorly-composed. Those students who present the best possible “draft” work will get the most out of the review and revision process. However, please note that extensions to this part of the coursework are not possible, and you should submit whatever work you have produced by the deadline in order to participate in the Peer review activity.

In all aspects, the draft should be as complete as possible. However, please note that the mark associated with the Peer review activity is not for the quality of your draft, but instead for reviewing work by two other anonymous authors. A good essay should be well-researched, well written, interesting and easy to read and understand for any one of your peers. Additionally , participating in peer review can help you in the following:

• Learn how to read carefully, with attention to the details of a piece of writing (whether their own or another writer’s);
• Learn how to strengthen their writing by taking into account the responses of actual and anticipated readers;
• Make the transition from writing primarily for themselves or for an instructor to writing for a broader audience–a key transition for students as they learn to write university-level papers and as they prepare for post-graduate work;
• Learn how to formulate and communicate constructive feedback on a peer’s work;
• Learn how to gather and respond to feedback on their own work.

Your own exeprience of the peer review process and feedback from your peers could help you potentially improve your final submission. Please make sure to read your assigned reviews carefully and provide feedback that is constructive and to the best of your ability. I would expect each review to take a minimum of roughly one hour.

You can only provide reviews if you make a submission by the deadline (Friday Week 10, 23:59). If you have any general questions about the peer review process for CW1, please post it on the Discussion Forum.

8. Final Submission (CW1 – Part 3)

The final submission is worth 45% of the total module mark and will be graded according to the marking criteria attached to the Turnitin submission for part 3. It is hoped that students make use of any insight and/or feedback to improve their final submissions after completion of the Peer review activity (CW1 Part 2).