Statement_of_Work_-_SNPs_Edits_9_8_2022_0001.pdf

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I. BACKGROUND

The U.S. Geological Survey (Pennsylvania Cooperative Research Unit) initiated a landscape genetics approach to understanding spread and transmission of chronic wasting disease (CWD) in white-tailed deer at the landscape level in 2014. This landscape-level approach encompassed parts of central Pennsylvania, central Maryland, and northern Virginia but has since expanded to include the entire states of New York, Ohio, and Pennsylvania. Understanding large-scale gene flow across a region can identify the most likely transmission path of CWD because gene flow identifies historic ancestry of deer across a landscape. Combining landscape genetics with CWD surveillance would provide natural resource agencies a more structured approach to surveillance by providing disease units more reflective of the underlying subpopulation structure of deer in a region. Furthermore, assessment and comparison of prion protein gene (PRNP) genotypes of white-tailed deer from areas experiencing various times since establishment of CWD provides an index of risk and likelihood of recovery of sub-populations to disease.

The standard for genetic studies has been to use microsatellites, short, repetitive DNA sequence elements that are highly polymorphic and exhibit variability to differentiate subpopulations of deer. Previous research in the Mid-Atlantic region identified 11 ideal microsatellites for use in delineation of gene flow and subpopulation structuring of white-tailed deer (Miller et al. 2019).

Unfortunately, microsatellites are not comparable across laboratories preventing sharing of genotypes between labs resulting in costly efforts to run genetics at different laboratories for deer across regions or even nationwide. These issues can be addressed by a shift from using microsatellites to using single nucleotide polymorphisms (SNPs) to identify individuals and to make inferences at a population level (Zimmerman et al., 2020; Smith et al. 2007). Comparison studies between SNPs and microsatellites show the vast amount of information that SNPs provide for population analysis and that SNPs perform as well or even outperform microsatellites in determining population structure, genetic diversity, and genetic differentiation (Zimmerman et al., 2020; Lie et al. 2005; Smith et al. 2007). Fortunately, SNPs for white-tailed deer, have recently been developed (White-tailed Deer Genetic Resources) by assessing genetics from a large collection of tissue samples obtained from deer across the Mid-Atlantic and midwestern

United States from 2019 to 2021. Currently in the Mid-Atlantic region, 1,711 deer have been processed for PRNP and over 4,000 deer have been processed at 11 microsatellites. The cost of running SNPs on over 4,000 deer is too high so we will subsample these deer within the region based on previous results of subpopulation structuring from microsatellite analysis.

II. SCOPE

The U.S. Geological Survey (Pennsylvania Cooperative Research Unit) expects the vendor to provide results for extracted DNA provided by U.S. Geological Survey for 1,500 white-tailed deer using the Thermo Fishers Axiom OVSNP60 Genotyping Array, 2 @ #384HT format

(Catalog number: 551367) that contains 72,723 SNPs and is a component of Thermo Fisher’s

Axiom Agrigenomics Genotyping solution where target genomic DNA is prepared and processed on the GeneTitan Multi-Channel instrument. The expected sample matrix is extracted

DNA in the appropriate concentration. The automated process include hybridization of the gDNA to this high-throughput microarray followed by staining, washing, imaging, and output of genotyping data for further analysis. This subsample of white-tailed deer will then be compared https://storymaps.arcgis.com/stories/9794d395588b45d7a055e86bf42d602b

140G0322Q0238amd0001 Page 3 of 3 to PRNP and microsatellite results by the U.S. Geological Survey to identify susceptibility to

CWD, gene flow, and genetic assignment to population of origin similar to previous work in the region.

Period of Performance: 1 October 2022 – 30 September 2023

III. TECHNICAL REQUIREMENTS

This effort requires the vendor to provide:

• Vendor is responsible for procurement of OVSNP60 from Thermo Fisher Scientific

• Period of Samples may be delivered simultaneously or sequentially over the Period of

Performance. Samples can be shipped to match bid (i.e., 384 in 2 separate shipments)

• Request by email for quantity of DNA needed for each sample sent from U.S. Geological

Survey for SNP processing

• Confirmation of number of samples received that are of acceptable quantity of DNA to run SNPs

• Extracted DNA received from U.S. Geological Survey is to be prepared and processed on the GeneTitan Multi-Channel instrument. The automated process include hybridization of the gDNA to this high-throughput microarray followed by staining, washing, imaging, and output of genotyping data for further analysis.

• Further analysis to include the Axiom™ OVSNP60 Genotyping Array, 384HT format

(Catalog number: 551367) available at Thermo Fisher Scientific

(https://www.thermofisher.com/order/catalog/product/551367?SID=srch-srp-551367)

• Quarterly updates on processing of samples sent for SNPs

• Turnaround time for each batch of samples is flexible, preferrable 30 business days

• Individual results sent in text files and VCF files for each deer sample sent to the vendor

• A brief tutorial of the Axiom Analysis Software and what level of access U.S. Geological

Survey will have to the software and length of access to this software after contract ends

IV. DELIVERABLES

The vendor shall provide the following deliverables:

• Readme File: Contains information about each file sent with the results

• Metadata: Metadata for samples that were genotyped

• Text File: A text file with the SNP genotype data for all deer genotyped on the array, as well as information about the quality of each of the SNPs

• VCF file: A VCF file with only genotypes for the SNPs identified as Best and

Recommended by the Axiom Analysis Software.

https://www.thermofisher.com/order/catalog/product/551367?SID=srch-srp-551367