CUSTOMER SPOTLIGHT
ANNA SKAYA AND DR DAMIAN KAO

Pioneering feline genetics withnext-generation sequencing
Basepaws leverages the Illumina DRAGEN Bio-IT Platform todevelop direct-to-consumer DNA kits that provide cat owners
with insights about their pets' health
TMThere are cat people and there are dog people. That divide evenspills over into the direct-to-consumer (DTC) DNA testing market.
Many products are available to help dog owners access genetic
data about their pets. But cat owners have been left in the dark.
Anna Skaya, founder and CEO of Basepaws, loves cats and saw
that discrepancy as an opportunity.

ANNA SKAYA, FOUNDER AND CHIEF

Basepaws is a pioneering DTC company that has developed
unique feline genetic test kits. Through these tests, Basepaws
seeks to connect people with their pets and improve cat health.
They are building the world’s largest feline genomics database,currently containing tens of thousands of cat genomes. With theirever-growing genomic database, they are constantly learning new
information about cat breeds, traits, and health.

EXECUTIVE OFFICER, BASEPAWS

Whole-genome sequencing for petsMost DTC DNA testing companies use Illumina microarrays to readDNA. While dog DNA testing companies have taken advantage ofcanine microarrays, no feline microarray product was available. “It
was a really difficult problem to solve and nobody was touchingit,” Skaya recalls. Basepaws decided to use next-generation
sequencing (NGS) to develop genetic testing products for cats.

DAMIAN KAO, PHD, CHIEFOPERATING OFFICER, BASEPAWS“Until a few years ago, NGS was too expensive to use for catsand dogs. Basepaws hit that perfect time point in 2018. When wecame on the scene, Illumina had new systems that allowed us todo sequencing at scale and at a cost that was affordable to thepet parent. Our $129 product includes 1× genome coverage andtargeted amplicon sequencing, which allows us to perform genomic
breed similarity analysis and screen for genetic markers associatedwith a variety of diseases and traits.

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"In our hands, using DRAGEN
analysis, we have realized
cost savings of approximately
50%. In terms of computationaltime it’s almost double thespeed compared to the manualmethod."“The breed part identifies the parts of your pet's DNA that are mostsimilar to known breeds. For example, it could be more Siamese or
more Persian. It's fun to know. But the most insightful part has to
do with health markers. We test for 65 different health markers, aswell as 50 markers associated with physical traits and blood type.
Results from the health marker screening can potentially identify
disease-associated genes. We also use shotgun metagenomic
sequencing and oral microbiome analysis to identify microbes
associated with dental disease. With all its versatile uses, webelieve that NGS is a much better technology for our needs.”

Starting from scratch
Damian Kao, PhD, is COO and Head of Science at Basepaws.
He explains that the biggest challenge was not having enoughpublicly available feline genomic data. “Canine research is probably
10 times larger that feline research. We had to do a lot of our own
sequencing to build up our database before we could actually start
producing results for our customers.
“With Illumina NGS technology, we’re able to scan the entire
genome. As our database grows and we sequence more cats,
we can start making genetic associations with diseases that ourcustomers’ cats might have. We will be able to research newmarkers that will ultimately help pet parents everywhere.”Managing genome-scale data
The next challenge, Dr Kao said, was how to manage wholegenome sequencing (WGS) data analysis. “The data sets that we
get back from Illumina sequencing machines are large, a lot larger
than with your traditional microarrays. That makes the analysis
process much slower and more costly. A big challenge is trying tocut down that cost and make things faster.”
The Illumina DRAGEN Bio-IT Platform directly addresses thatchallenge. The DRAGEN platform uses reconfigurable fieldprogrammable gate array (FPGA) technology to deliver accurate,comprehensive, and efficient secondary analysis of NGS data.
DRAGEN Original Read Archive (ORA) is able to compress WGS
data without loss. “Since the DRAGEN platform is built on this FPGA
architecture, it is optimized for WGS data processing.”
Dr Kao explains that the traditional method to process WGS
data involved a four-step open-source software pipeline. TheDRAGEN platform consolidates all those steps into one process.
“The steps that the DRAGEN platform takes over would be four
separate steps. With each step you have to worry about error
handling, quality check, and random errors that might happen.

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The DRAGEN platform takes care of all those little edge casesand gives out very detailed statistics and metrics that help uscheck quality.”

The benefits of DRAGEN analysis“The three biggest advantages of the DRAGEN platform for us
are speed, cost, and reliability,” says Dr Kao. “Speed and cost are
pretty self-explanatory. Reliability addresses complexity. Because
DRAGEN analysis is just one single step, it makes our processeasier to run.” During promotions on kits, Basepaws can get
10,000 samples back at once, for example. “It quickly becomes
an exercise in how you juggle multiple processes. The DRAGEN
platform actually takes care of the most complicated part.”"With the DRAGEN platform,
we have the report out to ourcustomers in less than a day,where it used to take two or
three days. That’s significant."

Using the DRAGEN platform, Dr Kao says that Basepaws has
minimized the time it takes to return reports to customers. “In ourhands, using DRAGEN analysis, we have realized cost savingsof approximately 50%. In terms of computational time it’s almost
double the speed compared to the manual method. As soon as we
get the data back from a sequencing facility, we can immediately
process it with the DRAGEN platform and have the report out toour customers in less than a day, where it used to take two or threedays. That’s significant.”
According to Dr Kao, “One huge advantage of sequencing technology is that it is organism agnostic. It doesn’t have to be human.
It doesn’t have to be dog. Every animal on this planet has DNA. If
you can sequence it, you can use DRAGEN analysis. We plugged
the DRAGEN platform directly into our pipeline without much effort.
The only thing we had to do was insert the feline reference genomeand just start using it. It was as simple as that.”"The repetitive region data

One unanticipated benefit is the ability to use repetitive region
data. “The DRAGEN platform deals with repetitive regions of thegenome very well. Repetitive regions are usually difficult to deal
with using open-source software, so we used to throw out a lot ofdata.” Dr Kao explains, “The repetitive region data can provide us
with genotypic resolution, which actually informs us a lot about thebreed of the cats. We were never able to utilize it effectively before,
but with the DRAGEN platform, now we're able to.”before, but with the DRAGEN

actually informs us a lot about
the breed of the cats. We were
never able to utilize it effectively

platform, now we're able to."Scaling for rapid growth
The volume of samples Basepaws has received for the past four
years has doubled or tripled each year. Dr Kao explains, “As youscale a business that depends on sequencing, there are several
bottlenecks, including engineering and data processing. We areconstantly thinking: How long does it take to process all this data?

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How do we organize it? How do we store it? Data will never goaway, but it's something that's easily solvable by using the DRAGENplatform.”"One huge advantage ofBasepaws uses Amazon Web Services to run their genomics
pipelines and access the DRAGEN platform. Dr Kao says, “The main
advantage for a small company like ours is that you can just rent
space on their cloud platform, without having to invest in all that
hardware. You literally just have to requisition more servers on theAmazon cloud and you can scale.”

it is organism agnostic. Everysequencing technology is thatanimal on this planet has DNA.
If you can sequence it, you canuse DRAGEN analysis."

Looking to the future
Basepaws has a vision to improve the lives of cats around the world
by understanding, genetically, what makes each cat unique. Skaya
says, “Basepaws has been growing year over year, phenomenallywell. Sequencing cats was a great starting point, but it's definitely
not the end. We're very interested in using our technology to go
after the dog market as well. We're very proud of the fact that weare a sequencing-based company. It allows us to see a lot moredetail. It allows us create a much better product.
“We really love our pets and we've got to take care of them. Our
test is not just a DNA test, it's not just for fun. Your cat can't talk,but their DNA and their microbiome actually can give you answers
that otherwise you wouldn't know.”

Learn more
DRAGEN Bio-IT Platform, illumina.com/products/by-type/informatics-products/dragen-bio-it-platform.html
Basepaws, basepaws.com

1.800.809.4566 toll-free (US) | +1.858.202.4566 tel | techsupport@illumina.com | www.illumina.com© 2022 Illumina, Inc. All rights reserved. All trademarks are the property of Illumina, Inc. or their respective owners.
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