I've drafted two new postcard ideas which can be found here: Dropbox / IGB / Outreach / Images / Postcards / PersonalGenomics-Postcards.pptx

Asparagus anosmia - I see the SNP in the bottom and top genome. I think the top genome might be heterozygous, would need to expand the track height.

Restless legs syndrome - It looks like the SNP might be heterozygous. Might be interesting to say something about what being heterozygous might mean for restless leg syndrome (more restless?). Could pull info from dbSNP or clinvar?

Might be good to include the rs number so people can look up the SNP online.

I've confirmed that both of the SNP's you suspected are heterozygous are indeed heterozygous, so I've gone ahead and updated the description for both postcards with a bit more detail on what having each type of SNP (i.e. homozygous and heterozygous) means for an individual. I've also added the respective rsID's to each postcard.

Ready for review!

I made a few small changes to the text, but otherwise looks good to me.

I think the next step would be for Dr. Loraine to look at the postcards, and once she approves then go ahead and order them.

Questions / Requests for asparagus anosmia card:

"The vertical zoom stripe highlights the site of a SNP (rs4481887) that determines how likely an individual is to smell asparagus metabolites in their urine (i.e., asparagus anosmia)."

• Hey cool! I am top track person! I can 100% smell that stinky smell. Heterozygous and proud!
• But wait...which allele of rs4481887 causes asparagus anosmia? Is it indeed the G allele?
• Does this SNP seriously cause this condition - the inability to smell that stinky smell? So, for example, if a person has "G" only, they cannot smell the smell?
• In the PowerPoint slide notes section, please add link(s) to definitive sources for the SNP function (need references to ClinVar or other respected sites!). This is for speaker background material and possible QR code options

last but not least:

• Is this SNP located in a gene? There's no gene track in this image. Was that on purpose?

Questions / Requests for restless legs syndrome card:

"BTBD9 gene which determines an individual’s likelihood of developing restless legs syndrome. This individual appears to be heterozygous,.."

• Is this SNP itself associated with the trait, or are we showing it because the gene it's in (BTBD9) got flagged as playing a role in the condition through genetic studies or some other method?
• As in above, please provide a link to a page (or pages) with information about this particular SNP and the gene. This is for speaker background material and possible QR code options.
• More specifically: Please provide a reference that establishes that BTBD9 controls likelihood of developing restless legs syndrome.
• I'm confused about what "controls likelihood" means. My understanding (I am not an expert!) of how genetic studies in humans works is that scientists do big whole genome surveys where they look for associations between conditions and genotypes of thousands and thousands of SNPs. They then end up with associations only, consisting of observations that some percentage of study participants with the condition of interest had allele "this-or-that", while the people without the condition (controls) did not have that same allele, as much. So, in the end, having allele "this-or-that" just means your genotype better matches the people with the condition in that one particular study. The term "likelihood" so far as I know is a kind of statistical measure that you calculate using the data from a study, and then hope you can generalize to all humans, not just the people in the study. So I guess I don't understand what it means to "control likelihood" ? Is this how geneticists use the terminology? I just want to be super careful about making sure the postcard text uses the technical terminology properly, while also communicating care and respect for the data donors!
• Is there a specific reason we are using waffly-scientist language, e.g., "appears to be" instead of straight-up "is"? Is there some reason to doubt their genotype? I'm just asking because we science nerds typically use this type of language when we aren't sure about something and want to communicate that lack of certainty to others. If you have doubts about the person's genotype, like if you noticed something weird or funky about the data, describe it here please! Red flags sometimes turn out to be interesting!

Images look OK, but there are a couple of weirdnesses we should maybe fix before printing these:

Both:

• Please make track labels much, much bigger, as big as possible, except for the "Coordinates" track. It can stay the same size.

Restless legs syndrome card only:

• Can you re-do the image with the tabs tray on the left removed or moved back to where it is usually located on the right side? Keep the bottom tabs in a separate window, though. That is good.

Re-assigne to Nowlan Freese to assess / think about my comments above. I wrote a lot and I don't know if I'm being to fussy about all these details!

After talking through each of these points with Dr. Freese, I've made much of the changes suggested above! Here are those answers/changes:

Asparagus anosmia card:

• The A allele is what causes asparagus anosmia, so having the SNP at this site actually decreases a person's likelihood of experiencing the smell!
• I've added a key at the end of the blurb that breaks down how each genotype affects asparagus anosmia.
• I've also linked to a couple of papers and the SNP's listing on dbSNP in the Notes section for reference.
• No, the SNP is not located in a gene, hence the lack of the gene track in this image!

Restless legs syndrome:

• The SNP is what's associated with this trait, not the gene (see the resources I've added to the Notes section of this slide).
• I've changed the wording I used throughout this postcard blurb to be less vague/wishy-washy. I counted alleles at this site and ensured that that individual is indeed heterozygous and changed my wording to match that conclusion.

Overall image quality:

• I increased the text size of the track labels on both images. I also removed that tray tab on the RLS card so that both postcards look consistent. Finally, I centered the SNP on the RLS card (it was off-center before).

Ready for review!
Dropbox > IGB > Outreach > Images > Postcards > PersonalGenomicsPostcards-V2.pptx

The asparagus blurb doesn't make sense:

The vertical zoom stripe highlights...SNP (rs4481887)...associated with the ability to smell asparagus metabolites in urine (i.e., asparagus anosmia).

"Anosmia" means: inability to smell something, not "ability" to smell something. Is this some weird condition where the meaning is reversed?

Instead of "individual" can we just say "person"? It sounds weird and distancing to do that.
When was the last time you heard someone use the word "individual" to describe someone? Watch the news and make a note of when you hear someone use that word. Who are they talking about? (Hint: How do cops refer to people?)

Possible alternative blurb, assuming "asnomia" means "insensitivity":

This image from Integrated Genome Browser shows genome sequence from two people at SNP rs4481887, associated with asparagus anosmia, the inability to smell asparagus metabolites in urine. The person in the bottom row is homozygous for the "G" insensitivity allele and probably can't smell asparagus metabolites. A semi-transparent zoom stripe highlights the SNP. The zoom stripe label reports the genomic position.

I didn't include the genome version since it didn't seem that important and also the title bar shows that. I also didn't include the fact that Nebula did the sequencing because I didn't want to name-drop a company.

That's a typo – the description should read, "...associated with the inability to smell asparagus metabolites in urine (i.e., asparagus anosmia)."

I've added an alternative blurb to the Asparagus anosmia card on the working slide deck/document (see my last comment for the full file path). I also changed the wording on the Restless legs syndrome card to avoid use of the word "individual".

Ready for review.

I made some edits. I hope everybody will be happy with them! I am moving the ticket to "DONE" as I have no further changes to recommend and I think the cards are exactly what we need.

Much appreciation to Paige Kulzer and Nowlan Freese for getting these done!