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Something else interesting I found on my journey was connectomics, a field of omics which is dedicated to explore the mapping of the brain's neural network to better understand neurological diseases. I thought it would be interesting and this paper is a good introduction to this omics field: https://www.nature.com/articles/nrn3901

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This was a great to take a step back and remember that all the data should interconnect in some way or other. It is a humble reminder of how complex the human body is.
• How many omics technologies did they find in their literature search?
They found 107 articles exploring 13 omics layers.
• What did you think of the way they presented the results of each omics individually?
It was well structured into the different omics sections and the evidence from the primary studies were simplified and allowed for contextual understanding of the advancements made in these different fields. However, it was difficult to try to pinpoint how all these layers interact with each other to produce overall function. The integromics section tackling were overlap occurs was a perfect example of how these different interactions are integral to each other. Hopefully, more studies will follow this integromics study to provide a complete picture of cell activity.
• How might you have improved on the integrated omics studies that have been conducted?
The research can be improved with more replication of the studies, larger populations studied, newer technologies used. To improve the presentation of the data, I believe the best way to go about it would be to trace the phenotypic aspects of the disease back through omics interactions. To elaborate, each section would be a different aspect of the disease, and we would explore the advent of the phenotype through all the omics data available starting with genomics and its regulations such as with epigenomics, then go through the different layers of expression with transcriptomics and proteomics, then the metabolomics, and finally the macro structures such as connectomics.
• What did you think of the conclusions that the authors drew from their research?
They were correct that they integrated a lot of information from different studies. However, they were not precise in the limitations of the study, but proposed appropriate future research avenues and improvements in communicating the information. However, it was not very comprehensive, there was little interpretation and critical analysis of the data, nor much integration of the data to be clinically applicable.

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Here is what I thought for the final journal club, really enjoyed this module!

How many omics technologies did they find in their literature search?

The literature research they performed found 107 articles alongside 13 omics technologies

What did you think of the way they presented the results of each omics individually?

I thought that the results of each omics technology were presented well and with clarity but the entangled web of how these omics technologies interconnect was not clearly investigated and to better and more clearly show this the paper could have linked them better.

How might you have improved on the integrated omics studies that have been conducted?

A way to improve upon the presentation could be to involve a larger set of omics technologies and data as well as the previously mentioned connection of the different technologies.

What did you think of the conclusions that the authors drew from their research?

Whilst the research in the paper collated together significant information it did not answer what was posed at the start of the paper, there was no complete conclusion found and no implications for future research and further compilation of the research should occur.

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•	 How many omics technologies did they find in their literature search?
•	107 articles were found; grouped into 13 omics layers genomics–DNA level, transcriptomics, epigenomics, proteomics, ncRNomics, interactomics, metabolomics, glycomics, lipidomics, phenomics, environmental omics, pharmacogenomics, and integromics.
•	 What did you think of the way they presented the results of each omics individually? 
•	I thought that they presented the data well, and separating it into each omics sections made it clear and easy to understand. However, the interactions between each of these sections could have been explored further.
•	 How might you have improved on the integrated omics studies that have been conducted?
•	As mentioned earlier, the connecting the omics sections could have been looked into. Furthermore, increase the cohort size and keeping up with current omics technology would also improve these integrated studies.
•	What did you think of the conclusions that the authors drew from their research? 
•	The paper did not talk much about limitations which made it difficult to draw conclusions. Furthermore, they appreciate that this is a complex disease and only talked about more studies should explore Parkinson’s disease which is not specific. Further treatments can also be based on the information available. 

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·       How many omics technologies did they find in their literature search?

There are 13 different omics technologies found in the literature search of this paper, with a total of 107 articles.

·       What did you think of the way they presented the results of each omics individually?

The layout of the paper is so easy to follow especially for readers who are not specialist with a focus on the function of genomics at the end. However, this paper was not critical and concise enough, but rather descriptive. Moreover, it has not shown a full clear picture of the relationship between the different omics.

·        How might you have improved on the integrated omics studies that have been conducted?

One way to improve the conducted integrated omics studies is to increase the sample size while including a broader variety of omics technologies.

·       What did you think of the conclusions that the authors drew from their research?

Compared to the study conducted, the conclusion was relatively short and repeating what has been said in the study before, it also lacked direction for future research.

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How many omics technologies did they find in their literature search?

13 different omic technologies were reviewed in the literature search.

What did you think of the way they presented the results of each omics individually?

In terms of the actual layout of the paper, it was easy to follow. However, as we have learned in the past, all omics disciplines are interconnected. To have a better flow in the paper, the authors could have structured it in a way where the proceeding omics technology merged into the succeeding one.

How might you have improved on the integrated omics studies that have been conducted?

Going on from what I mentioned in the previous answer, a way to improve this literature search would be to connect all the omic 'dots'. There needs to be a more comprehensive literature search with larger cohorts. Also, instead of regurgitating what has been claimed by previous research, the authors could have identified areas which needed more attention. However, for what it is worth, this review is a good paper which has a lot of the up-to-date research compiled in one place.

What did you think of the conclusions that the authors drew from their research?

What is interesting is despite the authors indirectly implying limitations in the study, there was no explicit reflection of the same. Also, all this review did was that it compiled research into one paper. Although that is useful, it is, in a way, incomplete. The research question posed at the start was not answered, and it yielded no clinically relevant conclusions.

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Question 1. How many omics technologies did they find in their literature search?

Thirteen layers of omic technology was found in this literature.

Question 2. What did you think of the way they presented the results of each omics individually?

The presentation was in my opinion was clear and I like how it showed the contribution of each omics field.

Question 3. How might you have improved on the integrated omics studies that have been conducted?

Two studies were in silico and therefore suffer potentially suffer from the limitations of the computational methods used. I also believe there could have been greater analysis and reflection within the studies as a whole, as it may have made understanding the connection between the integrated omics easier. As with many integrated studies, standardisation throughout would help to increase its validity.

Question 4. What did you think of the conclusions that the authors drew from their research?

There was a lack of review on the potential limitations and how they may have affected the results or how these limitations could be avoided in future. It also seemed to lack an answer to the proposal.

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Week 5 Journal club - Cardiovascular disease and gut microbial metabolites

How many omics technologies did they find in their literature search?

The authors discuss 13 different omics layers, ranging from genomics and transcriptomics to environmental- and pharmacogenomics. They reviewed a total of 107 articles.

What did you think of the way they presented the results of each omics individually?

This structure made it easier to read at first (especially when the reader isn’t familiar with many of the omic layers discussed) but gave a fairly fragmented view of PD mechanisms.

The integromics and discussion sections provide some more information about AD-associated genes involving multiple layers, however I believe a more integrated structure would have benefited this review.

How might you have improved on the integrated omics studies that have been conducted?

Clearly, more studies are needed that integrate multiple omic techniques to investigate PD mechanisms. As others have mentioned, most integromic studies reviewed here were performed in silico only and may benefit from in vitro or in vivo confirmation. Further

functional studies are necessary to uncover important causal mechanisms of PD.

What did you think of the conclusions that the authors drew from their research?

I don’t think there was sufficient discussion of the limitations of omic techniques reviewed, as well as their actual relevance to disease. Overall, the review provided some useful insight into the different types of omics used in PD research but did not provide many novel interpretations or suggestions for future research.

Best wishes,

Johanna

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How many omics technologies did they find in their literature search?

13 omics layers were found in the literature.

What did you think of the way they presented the results of each omics individually?

Main message was on how gene expression was regulated in PD at different omics layer and how they interact each other with regards to phenotype.

How might you have improved on the integrated omics studies that have been conducted?

Data interpretation and analysis by integrative models should address the signalling pathways leading to PD.

What did you think of the conclusions that the authors drew from their research?

Application of multi-omics approach for particular disease at a personal level can formulate the prevention or treatment which can tailor the individual needs.

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13 omics fields were reviewed. I think the way the authors presented their findings individually made it easy to understand.

They progressed from DNA (genomics) level down metabolomics, phenomics and integrative omics. In the review, they tried to link each layer as they moved down the list.

The lack of overlap in gene expression along the different omics layers makes it difficult to pinpoint biomarkers for Parkinson’s disease.

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•	 How many omics technologies did they find in their literature search?

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•	 How many omics technologies did they find in their literature search?

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13 different “omics layers” are described with the researchers stating they used classification outlines by Pirih and Kunej (2017) plus additional categories of lipidomics, glycomics, and integromics. There were a huge range of methodologies used in the literature for sequencing from RT-qPCR to miRNA microarrays.

·        What did you think of the way they presented the results of each omics individually?

I think there is a clear structure for the literature review and it is interesting to consider the contribution of each area of omics to but also feel it could potentially under-appreciate the interaction of all of the areas in PD. There is some focus at the end of the function of integromics but I feel the offers may have structured the review in this way as a reflection of the lack of studies which consider overlap between omics areas.

·        How might you have improved on the integrated omics studies that have been conducted?

2 of the 4 studies were conducted in silico and therefore potentially subject to limitations based on computer programs. In each of the studies there was also a focus on between 2 or 3 omics approaches and therefore we do not gain a full understanding of the full landscape of omics interactions although this would be a big ask and there are inherent limitations in providing such complex analyses.

·       What did you think of the conclusions that the authors drew from their research?

The conclusions of the study don’t seem to be adding anything to the already published body of research. The authors also make some bold statements in the discussion without evidence i.e. “It is very important to assign biological function to each statistically significant signal or at least define the cellular pathway that a certain gene is involved in. Omics studies usually have no hypothesis, so the results can be very inconsistent and identified signals can have very different cellular functions.” The omics studies are likely to be explaratory and therefore should not be dismissed. It would also be very difficult to assign biological function to every statistically significant signal, especially with no understanding of their interaction and causality, which could lead to false positives and negatives.

The authors also state “so no definite biomarker for predicting the risk for the occurrence of PD or for predicting the course of the disease was identified.” Which is not true, there is strong evidence for imaging and clinical biomarkers perhaps they should have clarified this statement further. doi: 10.3389/fnins.2018.00612 / https://doi.org/10.1016/S1474-4422(19)30024-9

Claire

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How many omics technologies did they find in their literature search?

They included approximately 107 articles in their findings and grouped them into 13 ‘omics’ groups. Of these, we’ve already seen genomics, transcriptomics, epigenomics, proteomics, and metabolomics in this course. The rest I hadn’t yet heard of!

What did you think of the way they presented the results of each omics individually?

I did find that the paper was clear in its division of the different omics, which is helpful for finding specific/relevant information. However, this module has given me a greater understanding of the relationships between the various ‘omics’ and I would have liked to see more of that reflected in this paper.

How might you have improved on the integrated omics studies that have been conducted?

Similar to my last answer, I think greater analysis and reflection within the studies is necessary to understand the connections between the integrated omics. Regarding study design, larger sample size with a greater degree of standardization is necessary.

What did you think of the conclusions that the authors drew from their research?

No reflection on what the limitations of their review and these studies might have in terms of impact on results. In addition, I believe one of the larger purposes of literature reviews like this is to analyze and extrapolate from available studies, and therefore identify gaps in the research and areas of future focus, which they failed to do. However, I do believe this is a good resource for just reviewing the studies that have been done so far, and a good jumping-off point for researchers that do want to look for gaps or analyse the connections between the fields more.

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Hi everyone,

My thoughts for the last journal club:

·       How many omics technologies did they find in their literature search?

The researchers grouped the study into 13 omics layer (transcriptomics, epigenomics, proteomics, ncRNomics, interactomics, metabolomics, glycomics, lipidomics, phenomics  environmental omics, pharmacogenomics, integromics) and each layer uses different technologies (WGS Illumina, NGS RNAseq, microarry analysis, RT-qPCR etc.)

·       What did you think of the way they presented the results of each omics individually?
They present the discovered studies in a very descriptive way. Rather than highlighting the most relevant finding of each layer or study, they only list them one after another.

·       How might you have improved on the integrated omics studies that have been conducted?

From the 13 omics layers mentioned in the papers, integrated omics studies only used up to three layers. Combining more omics layers into a statistical analysis could help to reveal the underlying processes and risk factors of Parkinson’s disease.

·       What did you think of the conclusions that the authors drew from their research?

The conclusion does not really answer the proposal put forward, yet the paper seems useful for someone who is looking for a list of studies on Parkinson. Perhaps the finding that there are only 4 integromics analyses done so far should serve as an incentive for scientists to integrate more omics layers into their future studies.

BW

Clara

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After conducting a database review of the literature available which included omics data associated with Parkinson’s disease,  the authors retrieved 107 articles and categorised them into 13 omics technology groups. I think the presentation of the results was helpful as it clearly explained the role of each omics approach and methods used by that approach to gain the results. It was helpful for someone like myself who is new to this topic. Intergromics was discussed to indicated links between the omics. It was a paper I found easy to read and understand because for the way they presents and explained their results from each approach individually. I thought the conclusions were quite brief but did cover what they had researched and made appropriate suggestions for future research directions and recognition of the need for multilayers studies.

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Journal Club Week 5: Viktorija Kaminskaite

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Journal Club Week 5: Viktorija Kaminskaite

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How many omics technologies did they find in their literature search?

They grouped the studies into 13 different layers of omics: “genomics–DNA level (22 articles), transcriptomics (16 articles), epigenomics (1 article), proteomics (3 articles), ncRNomics (10 articles), interactomics (5 articles), metabolomics (5 articles), glycomics (1 article), lipidomics (1 article), phenomics (3 articles), environmental omics (6 articles), pharmacogenomics (30 articles), and integromics (4 articles)” so 107 articles in total.

Just thought I would put the definitions for the ones we have not come across on the course (and some articles related to each discipline):

ncRNomics - study of non-coding RNA (more on here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6802278/)

interactomics - The study of the interactions between proteins and other components of a cell (more here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4657177/)

glycomics - systematic study of all glycan structures of a given cell type or organism (more here: https://www.ncbi.nlm.nih.gov/books/NBK453015/)

lipidomics - large-scale study of pathways and networks of cellular lipids (more here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5085849/)

phenomics - systematic study of phenotypes (more here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760679/)

environmental omics - “applications of omics technologies including genomics, transcriptomics, proteomics, and metabolomics to better understand the environmental and genetic factors, toxicity mechanisms, and modes of action in response to both acute and chronic exposure to environmental chemical” - there is a really good figure here: https://www.researchgate.net/publication/273992382_Environmental_OMICS_Current_Status_and_Future_Directions

pharmacogenomics - the study of the role of the genome in drug response (more on here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5682947/)

integromics - data-integration issues associated with genomic research (more on this here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC139396/)

What did you think of the way they presented the results of each omics individually?

I personally found it quite helpful, but it seemed quite disjointed in a way. I agree with the others saying that a more in-depth figure showing how different omics fields interact with each other in PD.

How might you have improved on the integrated omics studies that have been conducted?

I think a larger sample size and standardisation would be helpful for this. They did use in silico modelling, so I wonder how these have been validated?

What did you think of the conclusions that the authors drew from their research?

I thought that the conclusion was short and lacked a little bit in that they did not mention future research in this field and methods used (apart from how more studies should explore PD in general).

Vik

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Journal Club Week 5: 22/11/20 

•	How many omics technologies did they find in their literature search? 

In this study, they found 107 articles which were sorted into 13 omics groups. Including genomics, transcriptomics, epigenomics, proteomics, ncRNomics, interactomics, metabolomics, glycomics, lipidomics, phenomics, environmental omics, pharmacogenomics, and integromics… many we have not seen yet in this module! 

However, more studies could have been used but this was limited due to their keywords used in their literature search. 

•	What did you think of the way they presented the results of each omics individually? 

These included several omics being included to each paragraph. I like how tries to link all the information together in the context of the disease, as the omics can correlate and affect each other. In this way, information can be layered nicely with additional findings. But I think it would have been easier to deliver each of these results of each group individually in a clear and concise way, then link them to wider omics technologies. Perhaps a figure would have aided their explanations?  

•	How might you have improved on the integrated omics studies that have been conducted?  

I think a wider range of omics technologies could potentially be considered, potentially those we have not heard much about yet. They also could’ve used an improved disease which was more standardised to improve their integration e.g. with their in silico studies. However, I do understand that some datasets are much larger than others and hence have more data available- thanks for the link about bacomics!

•	What did you think of the conclusions that the authors drew from their research? 

The conclusion was brief and did not include future investigations or how these investigations will specifically improve research into Parkinson’s disease. They also did not mention methodological limitations, or how they integrated these omics together and the importance of this.  But perspectives such as the personalised medicines were mentioned, and overall this could be a comprehensive source on PD omics studies thus far. Perhaps this may useful for further targeted research into therapeutics and possible biomarkers. 

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How many omics technologies did they find in their literature search?

They found 107 articles that contained different omics procedures. They sorted them into 13 omics subgroups.

But they are aware that not all published studies are included in their review due to selection of keywords for literature screening.

What did you think of the way they presented the results of each omics individually?

The listing of each omics separately may have been easier to deliver the results of each group properly, which was clear and concise.

How might you have improved on the integrated omics studies that have been conducted?

Like what everyone is saying, increasing the sample size & perhaps combining certain multi-omics technique together and adding other approaches as in the field of functional genomics, RNA-editomics, nutrigenomics, and metagenomics.

What did you think of the conclusions that the authors drew from their research?

Conclusion was short and talked about how more studies exploring the disease are necessary.

Thank you
Aljowhara Alageel

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How many omics technologies did they find in their literature search?
The studies were grouped into 13 omics layers: genomics–DNA level, transcriptomics, epigenomics, proteomics, ncRNomics, interactomics, metabolomics, glycomics, lipidomics, phenomics, environmental omics, pharmacogenomics, and integromics.
What did you think of the way they presented the results of each omics individually?
In my opinion, it's nice how they represented several omics in each paragraphs showing such technologies and their effect on PD diagnosis and prognosis. Yet, they do not show how multi-OMICS correlate with each other. They tend to correlate and affect each other in a different way. Therefore, if Multi-omics were classified together it can enable better understanding and analysis of PD which will lead to a more precise and effective diagnosis for PD patients.
How might you have improved on the integrated omics studies that have been conducted?

The study might be able to increase its sample size and standardization with also integrating multi-omics technique together as mentioned in Q2

What did you think of the conclusions that the authors drew from their research?

The conclusion didn't use future possibilities to tackle, Yet, they demonstrated that with OMICS we can protect our patients in advance of the disease which will enable us to innovate personalized medicines for these patients that could solve there genetic cause. However, they only seem to focus on what they had demonstrated in the study rather than detailing the effects of future research in order to detect the main symptoms in an individual patient much better in advance. Overall, their conclusion was briefly written and the author should've provided a more detailed one for a better understanding of effective diagnosis and prognosis of PD.

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How many omics technologies did they find in their literature search?
Looking at 107 studies, 13 different omics fields were explored. I really found___ interesting

What did you think of the way they presented the results of each omics individually?
I agree with those before that they are kept quite distinct and unlinked, but I do think it is an easy way to present it if you can slowly build on each type by adding in the findings of another omics field. I liked the figure showing the omics but I think if more links could've been established + shown then it would make a useful little diagram to understand how things relate to each other.

How might you have improved on the integrated omics studies that have been conducted?
I think it would be interesting if the study could have used more omics fields we haven't heard of thus far, but as it has already been said, some have much larger datasets available than others. A very niche one I read about recently is bacomics: https://link.springer.com/article/10.1007/s11571-020-09577-7

What did you think of the conclusions that the authors drew from their research?
As everyone has said, the conclusions are a little lacking as they didn't mention future possibilities or methodological limitations to tackle. However it is a start and their resource on PD is interesting and provides an opening for further research into candidate findings, especially if they are highlighted in multiple omics fields. I'm particularly excited for finding an easy cost-effective screening tool to use clinically. I think it would be good to give people the option of knowing sooner and planning for potential challenges and support in advance. I had a patient who came into a Parkinson's clinic with no diagnosis despite onset of symptoms being a decade ago. This is a paper on PD and omics if anyone wants a bit more reading in the area: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7277996/

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Questions:

How many omics technologies did they find in their literature search?

In total 107 articles were explored for omics data, the studies discovered 13 omics groups including new omics not learned in the module.

What do you think of the way they presented the results of each omics individually?

It does not consider omics as a whole, by separating them it classifies them individually and doesn’t take into consideration the various links between the different omics and that they can have effects on each other. By integrating the different omics, it could help in understanding Parkinson’s disease better.

How might you have improved on the integrated omics studies that have been conducted?

The study could have increased its size and followed a standardised design to improve on integrating omics.

What did you think of the conclusions that the authors drew from their research?

I think the conclusion is somewhat brief, it’s quite basic and doesn’t reflect what they have found or all the different types if omics especially on how to integrate them together, I feel like they’ve only described what they’ve done and mainly focused on various future interests of study without discussion of limitations or future studies in detail however their suggests were interesting, also it doesn’t say how its impacted the omics research community and what it means for development and treatment of diseases.

Francesca Carvalho

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How many omics technologies did they find in their literature search?

The 107 articles found in their search were classified into 13 omics groups. It is interesting to hear about other omics beyond the ones we have already learned about in this module.

It was also discussed that some omics types were not included due to the rapid development and extensiveness of studies into Parkinson’s disease, such as functional genomics, RNA-editomics, nutrigenomics, and metagenomics.

What did you think of the way they presented the results of each omics individually?

The presentation of the omics as separate paragraphs, although I imagine the easiest way for them to structure the paper, does not fully reflect how integrated the omics are. Many of the omics affect and correlate with each other, for example ncRNomics must significantly affect transcriptomics and proteomics. To fully understand a disease such as Parkinson’s disease, the omics need to be considered as a whole.

The integromics section seems to attempt to link omics together, but only by looking at other studies which have done the overlapping rather than finding links between the separate omics studies mentioned in this paper. The integromics studies included also only link genomics-DNA, transcriptomics, proteomics and interactomics, so links between other omics have not been considered at all.

How might you have improved on the integrated omics studies that have been conducted?

A wider range of omics could be considered, though I appreciate the ones chosen are probably the ones with the largest databases (for in silico studies) and are the most relevant and interconnected. The studies could have increased scale and standardisation.

What did you think of the conclusions that the authors drew from their research?

The conclusions do not clearly enough reflect the need to integrate the omics. However, this paper is a step towards that in bringing all the current information on the different omics information together in one place, so further links can potentially be made between the different omics studies. I agree that further multilayer studies should be conducted.

It is interesting that some genes are implicated in Parkinson’s disease through omics such as environmental omics and pharmacogenetics but not currently through omics such as genomics-DNA level and transcriptomics, it would be interesting to see whether further study in the areas of genomics-DNA level and/or transcriptomics also suggests the connection of such genes.

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Apologies again for not being able to participate in the discussion.

How many omics technologies did they find in their literature search?

13 technologies were identified although the categorisation of these is interesting and there is some overlap between the groups such as ncRNomics and transcriptomics.

What did you think of the way they presented the results of each omics individually?

I agreed with everyone that this paper is more of a list and doesn’t integrate the information very well, but some sections are contextualised better than others.

How might you have improved on the integrated omics studies that have been conducted?

Lots of these studies were in silico modelling looking for overlap in analysis. These studies may benefit from standardised study design and data to improve integration.

Would it also be possible in the future to use the information gathered by this paper to design more targeted multi omics investigations looking specifically at those genes and pathways involved in pathogenesis?

What did you think of the conclusions that the authors drew from their research?

The discussion is disjointed and although the paper pulls together a lot of information on PD they fail to discuss the impact or future possibilities of this information. The discussion is also quite limited in its caveats to analysis – barely touching upon methodologies of most of the omics technologies discussed.

They have however successfully created a comprehensive resource on PD omics studies so far and I did think it was interesting that they identified the top 40 implicated pathways in PD and listed many genes that were identified across multiple omics platforms. I think this will be a useful resource for more targeted research into PD biomarkers and therapeutics.

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This week we have been looking into other omic technologies and for this weeks  journal club we have chosen a paper that surveys the literature on the use of many different omics technologies in the context of a complex disease.

Redenšek S, Dolžan V, Kunej T. From Genomics to Omics Landscapes of Parkinson's Disease: Revealing the Molecular Mechanisms. OMICS. 2018;22(1):1–16.