– a public effort to discover cat genetic variation and to improve feline & human health!
Precise determination of the genome of a species is important to the understanding disease and for the development of diagnostic and screening tests that will improve disease treatment. The genome has been sequenced in humans, dogs, horses, cattle, cats, and several other species. Unfortunately, the genomic sequence has only been determined in a single cat. Cinnamon was an Abyssinian cat from the University of Missouri whose genome was sequenced in 2007. Because the genome was mapped in a single animal, and since less robust methodologies were used, we lack the information needed to develop tests that may help in the identification of mutations and treatment of disease.
We propose to spearhead a project that will sequence the genome of 99 cats in order to:
– Improve coverage of the cat genome
– Improve future assemblies of the cat genome
– Identify normal and abnormal genetic variation
– Identify causative mutations for specific health concerns
– Allow veterinary hospitals to provide individual genome sequencing for cats for state of the art health care (similar to the developing standard of care for humans)
Coordination by the Lyons Feline Genetics Laboratory will ensure that:
– Different cats from different breeds and locations are sequenced to maximize variation detection
– Similar technologies are used to facilitate efficient data management, transfer and variant identification
– Data quality is high and consistent
– Data is publicly available so that all members of the research community can benefit in a non-competitive and collaborative manner
– Researchers less familiar with genomics research and large scale bioinformatics will have a resource for data interpretation
It is important to remember that this project will also benefit human health because understanding disease in cats may help treatment in human beings. Indeed, the Lyons Feline Genetics Laboratory has been funded by the National Institutes of Health because their work in cats may be ultimately used to help human beings.
The cats and the funding for the project will come from various sources (internal, external, public, private, government, and foundation) including:
– Lyons’ laboratory cats with disease models
– Lyons’ Laboratory cats from different breeds and world populations
– Researchers with cats of interest
– Lay public with cats of interest
– Private companies with a cat of interest
A FaceBook and other website pages are proposed to support the project and to raise funds from the community – including public, private, university and government funding.
Currently, pricing from The McDonnell Genome Institute at Washington University in St. Louis is being considering to support the project including:
- One library preparation (~$100)
- Illumina XTen sequencing (~$1,900 per cat for 30x coverage)
Overall, the Lyons’ Laboratory requires a means to accept funding from various sources to support the project and a means to sub-contract the technology groups to produce and distribute the data. The data is meant to be publicly available, however, phenotypes of interest do not need to be divulged.
Each cat is estimated to cost $3,000 USD, including:
– Lyons laboratory maintenance of project websites
– Payment to veterinary clinics for collection of a 3 – 6 ml EDTA blood sample and overnight shipment to the Lyons laboratory at MU for DNA isolation ($150.00) (when required)
– DNA isolation using organic preps (Phenol:chloroform) by the Lyons Laboratory
– Delivery of DNA to library preparation group (No cost if MU)
-Preparation and quantification of two different insert size libraries per cat
– Delivery of library to sequencing center (No cost if MU)
– 30x sequence of pooled libraries – Illumina XTen 150 bp paired-end reads
– Hard drives for data, transfer of data to Lyons’ laboratory, participating laboratory and shared site at Maverix Biomics
– Data analysis and browser presentation at Maverix Biomics site ($1,000)
Memo of Understanding (MOU)
28 October 2014
Precise determination of the genome of a species is important to understanding disease and for the development of diagnostic and screening tests that will improve disease treatment. The genome has been sequenced in humans, dogs, horses, cattle, cats, and several other species. Unfortunately, the genomic sequence has only been determined in a single cat. Cinnamon was an Abyssinian cat from the University of Missouri whose genome was sequenced in 2007. Because the genome was mapped in a single animal, and since less robust methodologies were used, we lack the information needed to develop tests that may help in the identification of mutations and treatment of disease.
A research community-based project has developed that will sequence the genome of 99 or more cats in order to:
- Improve coverage of the cat genome
- Improve future assemblies of the cat genome
- Identify normal and abnormal genetic variation
- Identify causative mutations for specific health concerns
- Allow veterinary hospitals to provide individual genome sequencing for cats for state of the art health care (similar to the developing standard of care for humans)
The 99 Lives project is being coordinated by the Lyons Feline Genetics Laboratory at the University of Missouri – Columbia to help ensure that:
- Different cats from different breeds and locations are sequenced to maximize variation
- Similar technologies are used to facilitate efficient data management, transfer and variant calling
- Data quality is high and consistent
- Data is publically available so that all members of the research community can benefit in a non-competitive and collaborative manner
- Researchers less familiar with genomics research and large scale bioinformatics will have a resource for data interpretation
- Follow standards and precedence set by human genetics efforts
All data from the project will become publically available, participants that agree to this MOU will have access to data early and prior to publications.
99Lives Researcher Participation Expectations
Participants in the project are expected to provide high quality sequence and deep coverage of a unique cat genome as part of the collaboration.
- Currently, illumina HiSeq 100 bp paired end sequencing reads are supported. Sequencing is performed from two PCR-free libraries per cat of 350 bp and 550 bp for at least 15X coverage; 20X coverage for standard libraries*. Contributors must provide the sequencing details for each genome. *Ajay SS, Parker SC, Abaan HO, Fajardo KV, Margulies EH. Accurate and comprehensive sequencing of personal genomes. Genome Res. 2011 Sep;21(9):1498-505. doi: 10.1101/gr.123638.111. http://genome.cshlp.org/content/21/9/1498.long
- The data needs to be transferred to Maverix Biomics at a cost of $1,000 per cat.
- Maverix Biomics (http://www.maverixbio.com/) is based in San Mateo, CA. The will align the reads to the cat genome Felis_catus-6.2 sequence (http://www.ncbi.nlm.nih.gov/genome/78?genome_assembly_id=22791) and will use FreeBayes to call SNPs. The cat reads and SNPs are overlaid onto a UCSC type browser for easy viewing of the data. Data tables can be accessed that provide the identified SNPs in specific genes, regions, chromosomes, or the entire genome. Maverix will provide a cumulative analysis of the variant calls for all cats after large groups or specific milestones (20, 40, 60, 80 and 99) of new cat genomes have been added to the database. Variant calling to new cat genome assemblies will be conducted when the annotated assemblies are available.
- Once a genome dataset is transferred to Maverix and funds accepted, the contributor will be given access to the website for the 99 Lives cat genome data.
- The Lyons Laboratory may be able to subsidize some data contributions.
Contributors are expected to provide the basic signalment of the cats when possible, such as gender, breed, place of origin, and coat color.
- One of the most significant concerns of a shared resource is the potential for overlapping projects and performing data analyses on contributed genomes that would interfere or “scoop” the research of another contributor. Therefore, the specific phenotype(s) of interest can be withheld from the cat identification information. However, we fully expect a highly cooperative and collaborative effort for participation in the resource.
- Researchers can privately contact a subset of contributors to ask for phenotypes of interest and for collaborative efforts.
- All cats are welcome, including exotic and wild felids.
All contributors to the 99 Lives data resource are expected to be co-authors on the first publication that is produced by each contributor who uses the data resource.
- All funding sources need to be provided for acknowledgements need to be provided and included in each publication and presentation using the 99 Lives resource data.
- All the cat genome data can be downloaded by other investigators who are interested in other data analyses of the cat genome provided they make a contribution to the resource.
- NIH-funded cat sequences will be deposited into NCBI as well as any other sequences volunteered by the researchers.
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99Lives Cat Genome Sequencing Initiative Contributors
The project has developed as collaboration between the University of Missouri – Columbia, College of Veterinary Medicine, and the University of California – Davis but is extended to all researchers interested in feline health care. The Feline Genetics Laboratory of Leslie Lyons, PhD, at the University of Missouri is coordinating the project. For details – please to e-mail; firstname.lastname@example.org or email@example.com or call 01 573 884 2287.
The Lyons’ Feline Genetics Laboratory will provide periodic updates regarding the project to the contributors and the research community.