Draft of introduction #18
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content/02.introduction.md
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| - A sentence about why do we care about pediatric. We should mention something about the number of samples available from pediatric tumors being low compared to adult tumors and limited by institution, so it's even more important to make data available to all researchers. | ||
| - To fill this unmet need, we developed and currently maintain the Single-cell Pediatric Cancer Atlas (ScPCA) Portal, an open-source data resource for single-cell and single-nuclei RNA sequencing data of pediatric tumors | ||
| With the growing number of single-cell RNA-seq datasets, efforts have emerged to create central, harmonized sources for datasets. | ||
| By harmonizing data across multiple studies and diseases, researchers can better perform joint analysis, taking advantage of more samples to complete their analysis and illuminate previously unknown similarities across different samples and disease types. |
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I don't know what "perform joint analysis" means exactly here. As discussed in Slack, I'm going to try stacking my edits, and I may take this out or reword & try to retain your meaning.
content/02.introduction.md
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| These mechanisms have focused on making large quantities of harmonized data from normal tissue or adult tumor samples available to the public, but there are considerably less efforts to harmonize and publicize data from pediatric tumors. | ||
| Pediatric cancer is much less common than adult cancer, so the number of available samples from pediatric tumors is smaller compared to the number of adult tumors. | ||
| Additionally, not every institution has access to data from pediatric tumors. | ||
| These two reasons make it imperative to provide harmonized data from pediatric tumors to all pediatric cancer researchers. |
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It might be worth citing something that talks about this imperative. I don't have a specific example at my fingertips, but I expect an appropriate citation to exist.
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Before you approve this, do we want to try and find a reference for here?
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Yea, I just realized that.
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Okay, I don't know how we feel about this, but I tried to find a reference that stated the incidence of pediatric cancer is lower than adult cancer. There doesn't seem to be a paper that talks about this, since most of them talk about the incidence of pediatric vs young adult cancer without talking about adult cancer. But I did find mention of the incidence rate on the NCI website, so I added that in as reference.
Then for the comment about not everyone having access to samples from pediatric tumors, I found a paper that measures incidence in the US, including breaking it down by region. They note differences be regions, which to me implies different research institutions in different regions of the country have different access to patient samples.
I added these two in f351f13.
The last reference I added is a summary about the lack of databases focused on pediatric cancer. We don't need to include them all, but I just wanted to bring them up as options. This is added in 845ba66.
…edits Adding my edits to introduction
content/02.introduction.md
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| To ensure that all current and future data on the Portal are uniformly processed, we created scpca-nf, a Nextflow-based open-source pipeline (https://github.com/AlexsLemonade/scpca-nf). | ||
| Using a consistent pipeline for all data increases transparency and allows users to perform analysis across multiple samples and projects without having to do any re-processing. | ||
| The scpca-nf workflow uses alevin-fry for fast and efficient quantification of gene expression for all samples on the Portal, including single-cell RNA-seq data and any associated ADT/CITE-seq or cell hash data, spatial transcriptomics data, and bulk RNA-seq data. |
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I missed this earlier - we should cite alevin-fry here.
Co-authored-by: Jaclyn Taroni <[email protected]>
Closes #16
Here I'm replacing the outline with the actual text for the introduction. I mostly followed what I had in the outline.
A few questions: