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Review of Results / Data from 3 Cat DNA Organizations / Companies
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Selected Comparisons for 2 Basepaws Whole Genome Sequencing Results
I have uploaded a report from the UC-Davis VGL, and I will update basepaws reports when they are available (and you can see more notes about basepaws in the Basepaws_Notes subfolder).
I don't have any raw data for the UC-Davis VGL sample, but I do have an earlier blog post for the report for another cat (and I hope some of my re-analysis of the basepaws raw data will hopefully be able to make use of data from the lab that developed that test).
The UC-Davis VGL sample collection was a cytobrush.
I submitted two different samples for Bastu for basepaws. The first was a hair sample, and the second was a swab.
I was sent the swab when I requested higher coverage sequencing data (or, more precisely, I asked about raw data, and I then learned more about the protocol and the option for raw data for higher coverage sequencing).
While I know that extra experiments are required for health / traits (as mentioned this comment for basepaws, and this blog post for human lcWGS analysis), the $95 basepaws kit is meant to cover 0.5x sequencing. So, I paid an additional $1000 for 15x sequencing (as I understand it, for the 2nd sample).
I believe this is the time-line for sample collection / processing:
UC-Davis VGL (Ancestry Test, $120):
Purchased Test on 11/16/2018
Sample Recieved on 11/27/2018
Recieved Report on 2/25/2018 (~so, a little more than 3 months turn-around time)
basepaws (hair sample, $95, ~0.5x sequencing, possibly other types later?):
Purchased Test on 2/24/2019
Activated Kit / Collected Sample on 3/1/2019
Update (6/22): I think there was confusion, but it was decided just to provide ~20x sequencing for my swab sample, so I should only be recieving one report).
basepaws (mouth swab, $1000, ~15x sequencing, with raw data as FASTQ+BAM+gVCF):
Currently, it looks like this is officially available for $499 or $599. Also, I believe currrent customers only recieve FASTQ and gVCF files, without the BAM file. If you look closely, I think that is on the website under "Your cat’s raw whole genome sequencing data on a secure thumb drive:".
Purchased Test on 3/7/2019
Activated Kit / Collected Sample on 3/14/2019
Learned data was available on 5/24/2019 (assuming this was in fact for the 2nd sample)
Data available from AWS S3 bucket on 6/13/2019
Download report on 10/16/2020
I'm not sure if basepaws will implement automatic deposit into the SRA (with owner's permission). However, I have re-uploaded my raw FASTQ files here:
basepaws 15x WGS Read1: https://storage.googleapis.com/bastu-cat-genome/HCWGS0003.23.HCWGS0003_1.fastq.gz
basepaws 15x WGS Read2: https://storage.googleapis.com/bastu-cat-genome/HCWGS0003.23.HCWGS0003_2.fastq.gz
I still have money left from my $300 Google Cloud credit, but I don't know how much the charge is for people to download from a public link. However, that should be available in the immediate future.
I believe that this was order #3277 (canceled, for hair) that was upgraded to order #3405 (to provide mouth swab) with an extra invoice outside of the typical billing system (although I don't think that is necessary anymore).
basepaws Coach My Cat (on sale for $120, but will increase to $300?):
This should be a 12-week program, where I beleive 3 sessions are included for free.
I'm not sure how much genomic information will be considered (since I didn't get a regular kit).
10/31/2019 - Started filling out information on-line ("Health and Wellness Assessment" and "Weekly Cat Journal")
11/10/2019 - Completed 2 of 12 weeks on-line. I encountered a couple issues with scheduling a live session, but it looks like they got fixed later (see 11/20/2019). Either way, I have no complaints about the timing of responses of the chats (with responses within ~24 hours).
11/13/2019 - While there are currently still some bugs to work out (which might have also affected the live sessions), I really did like Week 3 in terms of having substantiative eductional content.
11/20/2019 - The calendar issue has been fixed (you can schedule an earlier session, and hours are more reasonable). I also went back to revise the 11/10/2019 comment.
12/6/2019 - I had a live session with Coach Becky, which I think went well (although I will schedule one earlier in the day next time, if I schedule more of my 3 free sessions).
1/17/2019 - Completed last session out of 12 weeks. I also had 2 more live sessions that I could have scheduled, but I was OK with my one session.
I think they are going to change some things (and provide an offer to see a "re-launch"). However, at least currently, weeks 10-12 not not have a matching YouTube video, and there weren't any quizes for weeks 11 or 12.
basepaws also has educational content within it's blog. On a slightly different note, I have some Data Science courses that I would like to complete first, but I noticed Coursera also had courses from the University of Edinburgh like "The Truth About Cats and Dogs", "EDIVET: Do you have what it takes to be a veterinarian?", and "Animal Behaviour and Welfare". However, those won't provide behavior advice for your own cat.
basepaws (mouth swab, $129.00, Order #8114):
In order to be able to simplify being able to get another report, I ordered another kit (and I waited to be charged the full new amount, to be fair).
Purchased Test on 11/1/2019
Activated Kit / Collected Sample on 11/6/2019
E-mail that Sequencing has been started on 11/25/2019
E-mail that Sequencing has been Completed on 12/9/2019 (but report is not ready - that is estimated in another 2-3 weeks).
E-mail that Report is Ready 12/18/2019 (for lcWGS : Amplicon-Seq variants not ready yet).
I am not sure exactly when the mutation results became available but I noticed them in the report on 1/8/2020. I think this was faster than others reported in the Facebook group, so that is pretty good (although e-mail notification may have been nice). However, even if it was 2 months turn-around, that was faster than the previous 3-month turnaround (which was only for raw data - no analysis from basepaws).
If raw data is eventually provided, I am also extremely interested to see samples from the same cat in different batches (since, I would expect low-coverage WGS to be more prone to batch effects, even though I would guess the Amplicon-Seq health markers are mostly OK).
I had a file on my computer noting a "fixed typo" in a report on 3/25/2020. While the file size is different and the font size is different, I haven't been able to find the typo when I checked more recently (and both reports are supposed to be created from version 2.4). So, I changed the name of that files, but I will add a note if I can find a typo (even if compared to my 1st report downloaded on 12/18/2019).
I also ordered a technical replicate (Order #12725) on 3/31/2020 and I received the report on 5/8/2020 (when I also re-downloaded a report for the 1st sample that I submitted).
MyCatDNA / Optimal Selection ($99):
Purchased Test on 10/31/2019
Activated Kit / Collected Sample on 11/4/2019
Recieved Report on 11/25/2019
Recieved e-mail reply about questions on 12/18/2019 (including how to share Bastu's data, which you can view here, with an account)
I guess I will find out if the report is the same, but I started trying to order a MyCatDNA test and I was informed that I had to purchase a test through Optimal Selection (since I was a US customer).
The e-mail receipt came from a "wisdomhealth.com" e-mail. If I try to go to that address, I get re-directed to https://www.wisdompanel.com/. You can't actually order a cat DNA test on that website, but I think this might explain what was meant by "Wisdom Panel for Cats" on this article (even though they didn't mention the UC-Davis VGL)
PetQCheck by Purina (gut microbiome test, list price of $99.00, purchase price for me was $79.00, includes free shipping, Order PQCBP1541):
I don't believe FASTQ files are normally returned. However, before ordering the kit, I double-checked and I was told "We can definitely send the FASTQ files to you....We don’t typically provide this raw data, therefore, could you do the following to make sure that we include them: One of the last questions of the survey asks whether there is anything else we should know about your pet. Can you add a note in this field asking for the FASTQ files?"
Purchased Test on 3/3/2021
- I ordered from from here, a link towards the bottom of this page).
- It also looks like there are other things that can be ordered here.
Kit arrived on 3/8/2021 (but I need to wait until my cat uses the litter box and I am not too busy, in order to collect a fresh sample)
Sample collected and mailed on 3/15/2021.
I recieved a report and raw data on 4/12/2021.
You can see a copy of that report here.
I think the FASTQ files are slightly larger than I should upload to GitHub, so I uploaded those to Google Cloud:
PetQCheck metagenomics Read1: https://storage.googleapis.com/bastu-cat-genome/zr4262_9V3V4_R1.fastq.gz
PetQCheck metagenomics Read2: https://storage.googleapis.com/bastu-cat-genome/zr4262_9V3V4_R2.fastq.gz
I haven't compared AnimalBiome/KittyBiome, but perhaps I can submit samples to multiple companies at the same time as a future experiment. As of 3/2/2021, raw FASTQ files were not provided for KittyBiome (unlike PetQCheck).
basepaws (Dental Health Test, 2 orders, 5 samples purchased, intend to use 4 of the samples):
I moved notes to a README file in a subfolder.
Wisdom Panel (Wisdom Panel Complete for Cats, $129.99, Order #98735):
Purchased Test on 6/19/2021
Kit Arrived and Sample Collected on 6/23/2021
Results returned on 7/6/2021
On 7/9/2021, the company indicated that they use a custom Illuminm Infinium XT genotyping chip to generate the data. They said they do not currently return raw data and there is no timeline about when that may be offered, but they hope to do so in the future.
PetQCheck by Purina (gut microbiome test, list price of $99.00, purchase price for me was $79.00, includes free shipping, Order PQCBP1863):
I purchased a 2nd test (to check changes over time) on 7/10/2021.
Kit arrived on 7/15/2021.
Sample collected and mailed on 7/16/2021.
I recieved a report and raw data on 8/23/2021.
You can see a copy of that report here.
I think the FASTQ files are slightly larger than I should upload to GitHub, so I uploaded those to Google Cloud:
PetQCheck metagenomics Read1: https://storage.googleapis.com/bastu-cat-genome/zr4669_1V3V4_R1.fastq.gz
PetQCheck metagenomics Read2: https://storage.googleapis.com/bastu-cat-genome/zr4669_1V3V4_R2.fastq.gz
PetQCheck by Purina (gut microbiome test, list price of $99.00, purchase price for me was $79.00 + $5.73 in taxes for a total of $84.73, includes free shipping, Order PQCBP2244):
I purchased a 3rd test on 10/25/2021.
Kit arrived on 10/29/2021.
Sample collected and mailed on 10/31/2021.
I was informed of a sample mix-up problem on 12/21/2021. I did not recieve a report for the original sample that I submitted.
I recieved a replacement kit on 12/29/2021.
Sample was collected on 1/8/2022.
This replacement sample was mailed on 1/9/2022.
I recieved a report and raw data on 1/30/2022.
You can see a copy of that report here.
You can view the FASTQ files using the links below:
PetQCheck metagenomics Read1: https://storage.googleapis.com/bastu-cat-genome/zr5877_3V3V4_R1.fastq.gz
PetQCheck metagenomics Read2: https://storage.googleapis.com/bastu-cat-genome/zr5877_3V3V4_R2.fastq.gz
basepaws (mouth swab, $429.00, with raw data as FASTQ+gVCF, Order #48757):
I ordered a 2nd Whole Genome Sequencing kit in order to get a 2nd sample with raw data for metagenomics analysis as well as additional reads that could potentially be combined for higher coverage germline analysis.
I purchased this kit on 4/18/2022.
Sample was collected on 4/21/2022 (for ID #31211051000777).
I received an e-mail that "Bastu - ALT (Swab)'s DNA results are here!" on 6/10/2022. However, the link to download a report did not work, and I did not see how to access the raw data. So, I e-mailed the company for troubleshooting.
I also noticed that updated report for my earlier Whole Genome Sequencing kit was also still not ready (even though it had an estimated update date of "Apr 17th - May 1st", and I checked on June 11th).
On 6/13/2022, I received a PDF report via e-mail (which I could also then see in the web interface). I have not yet received the raw data, but my understanding is that is not yet ready to be returned to me (and/or I have not yet received something physically).
On 8/10/2022, I recieve an e-mail to confirm my address in preparation to mail a USB with data to me.
On 8/13/2022, I received a USB drive with data. I then uploaded the data to Google Cloud:
Interleaved FASTQ #1 (Run 186, Lane 1): AB.CN.45.31211051000777.LP.858.D9.L1.R186.WGS.fastq.gz
Interleaved FASTQ #2 (Run 186, Lane 2): AB.CN.45.31211051000777.SP.319.D1.L2.R186.WGS.fastq.gz
Interleaved FASTQ #3 (Run 195, Lane 2): AB.CN.45.31211051000777.SP.329.E1.L2.R195.WGS.fastq.gz
As described here, I also created combined files in the more typical Paired-End format for combined reads:
Combined Basepaws WGS #2 (R1): Basepaws_WGS2_R1.fastq.gz
Combined Basepaws WGS #2 (R2): Basepaws_WGS2_R2.fastq.gz
However, even if I extend the read names to keep track of the source, it will no be possible to run analysis on a per-tile basis or analyze the observed versus expected barcode sequences (as I did for the 1st WGS sample).
PetQCheck "TARGETED HEALTH Advanced Microbiome Screener" by Purina (gut microbiome test, list price of $149.00 + $10.80, includes free shipping, Order PQCBP2700):
I purchased a 4th test on 9/9/2022.
Sample collected after giving Bastu FortiFlora slightly before and a few days after dental cleaning (9/19/2022), with last FortiFlora in wet foot on 9/23/2022.
Sample collected and mailed on 9/28/2022.
I recieved Bastu's results on 10/30/2022, with a report that can be viewed here.
You can view the FASTQ files using the links below:
PetQCheck metagenomics Read1: https://storage.googleapis.com/bastu-cat-genome/zr8725_3V3V4_R1.fastq.gz
PetQCheck metagenomics Read2: https://storage.googleapis.com/bastu-cat-genome/zr8725_3V3V4_R2.fastq.gz
Kidney-Chek ($49.99 for 3 tests, $9.15 for shipping, Order #1393):
I placed an order for 3 tests on 3/11/2023. This a day after Bastu's checkup where the vet said that Bastu showed good kidney function (especially for her age).
The kits arrived on 3/20/2023.
I started to work on collecting samples on 3/25/2023. Each kit contained 2 strips. I encountered a problem with Bastu trying to bite the strip, which caused damage to the pad used for an accessment. This involved throwing out both strips for the first kit.
I also opened the second kit on 3/25/2023. I think Bastu was over-stimulated, and it became harder to swab along the gums. So, instead, I tested a strip on myself. Unlike when the strip was used in Bastu's mouth, the wet strip stayed a slightly darker shade of yellow when used on my mouth. Although I could not get a complete covering without damaging the pad, the part that was moistened in Bastu's mouth was more of a shade of blue.
Darwin's Cats (beta version, $149 for kit that is normally $249, free shipping, Order #128):
On 5/21/2024, I received an e-mail that Darwin's Ark was started for cats. I added information for myself and for Bastu in the on-line system.
On 6/7/2024, I ordered a kit for Bastu.