PrimeTime_Fall_2018

DNA Matters Tim Kozelsky | DNA & Data Service Analyst | tkozelsky@akaushi.com AKAUSHI BREED GENET ICS

A question I am fre- quently asked is “Which method of DNA collection is best?” The American Akaushi Association (AAA) staff’s response has always been to explain the cost of each method as well as to point out each method’s advan- tages and drawbacks. We

up to another week depending on GeneSeek’s processing load. Once SNP samples are com- plete, I can access the data immediately. The failure rate of SNP processing is a bit higher, but that is expected due to the amount of qual- ity DNA needed in order to get a good profile. So, here is the data: Work Ave. Act. Failure Days to SNPs Orders Samples Failures Lot Size Rate Process Blood 105 3,749 70 36 1.87% 24.04 Hair 45 765 7 17 0.92% 24.86 Tissue 39 1,667 11 43 0.66% 21.8 TSU 35 1,832 24 52 1.31% 25.29 Total 224 8,013 112 36 1.40% 24.00 As you can see, there isn’t much difference in the failure rate regardless of the collection method used, which is the main point to take away from this data. Overall, blood samples are the most popular method, which is likely due to its overall cost and ability to fit into a wide range of ranch operations. Hair samples are a favorite for smaller ranch operations and for ranchers submitting new samples for SNP pro- files on older breeding stock. Datamars Typifix and Allflex ® TSU tissue samples are preferred by larger ranch operations for their ease of use. The bottom line is that the choice of DNA collection method will not have a big impact on the amount of failures you may have or the processing time. The biggest impact on failure rates lies in the way the sample is collected and stored. Blood samples need to contain enough blood so that the circle collection area is completely saturated and soaked through the paper. It also needs to be completely dried before being mailed to the association office. Hair samples need to be free of foreign matter with as many strands placed on the cards as possible. It is recommended that at least 50 strands are pulled. Also, be sure that the root balls are what is placed on the card and not the hair strands themselves. Tissue samples should be taken from the center of the ear where there isn’t as much cartilage mate- rial. Finally, do not use any cleaning or disin- fectant chemicals on the collection area prior to collecting the sample. Apply wormer and fly treatments after the DNA sample is taken. All of these chemicals can inhibit the DNA process-

have also stressed the importance of using the method that best matches the way a rancher works their herd. The tissue and tissue sam- pling units (TSU) methods are very popular for larger ranches that either rope and work cattle out in the fields or want to get as many head through the chute as quickly as possible. The blood method works well for those who dehorn or notch ears. The hair method is most popular with polled breeders who have a good chute to run calves through and that allows safe access to the tail switch. However, given that each op- eration is unique, the ultimate decision can only be made by the rancher. The current price list for samples is as follows: Collection DNA Cost SNPs Kit Processing per Sample Blood $0.50 $18.00 $18.50 Hair $2.00 $20.00 $22.00 Tissue $3.00 $21.00 $24.00 TSU $2.40 $21.00 $23.40 I have been collecting DNA processing data this year to see if there are any differences in failure rates or processing times at the Gene- Seek lab. Before we get into the numbers, I want to explain my calculations. “Actual failure rate” is the total number of failures divided by the total number of samples. “Days to process” is the total time from when I process the DNA and prepare the submission documents to the time DNA profiling is complete. The data only includes single nucleotide polymorphisms (SNP) processing, since we are moving away from the older, short tandem repeat (STR) technology. A quick comparison of the two processing platforms reveals that, on average, it takes 30 days to process STR data, compared to 24 days for SNP. In addition, we have to wait for the lab to send us the STR results data, which can take

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Akaushi Prime Time • Fall 2018

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