Evaluating Accuracy of DNA Pool Construction Based on White Blood Cell Counts
Pooling individual samples prior to DNA extraction can mitigate the cost of DNA extraction and genotyping; however, these methods need to accurately generate equal representation of individuals within pools. The objective of this study was to determine accuracy of pool construction of blood samples...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2021-02-01
|
| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2021.635846/full |
| _version_ | 1819119756932808704 |
|---|---|
| author | Amy N. Abrams Amy N. Abrams Tara G. McDaneld John W. Keele Carol G. Chitko-McKown Larry A. Kuehn Michael G. Gonda |
| author_facet | Amy N. Abrams Amy N. Abrams Tara G. McDaneld John W. Keele Carol G. Chitko-McKown Larry A. Kuehn Michael G. Gonda |
| author_sort | Amy N. Abrams |
| collection | DOAJ |
| description | Pooling individual samples prior to DNA extraction can mitigate the cost of DNA extraction and genotyping; however, these methods need to accurately generate equal representation of individuals within pools. The objective of this study was to determine accuracy of pool construction of blood samples based on white blood cell counts compared to two common DNA quantification methods. Fifty individual bovine blood samples were collected, and then pooled with all individuals represented in each pool. Pools were constructed with the target of equal representation of each individual animal based on number of white blood cells, spectrophotometric readings, spectrofluorometric readings, and whole blood volume with 9 pools per method and a total of 36 pools. Pools and individual samples that comprised the pools were genotyped using a commercially available genotyping array. ASReml was used to estimate variance components for individual animal contribution to pools. The correlation between animal contributions between two pools was estimated using bivariate analysis with starting values set to the result of a univariate analysis. Adonis test on distance matrix from the animal correlation showed clustering with method, and higher correlations between methods than within (P < 1 × 10–6). White blood cell count was predictive of sample representation when compared to pooling based on DNA concentration. Therefore, constructing pools using white blood cell counts prior to DNA extraction may reduce cost associated with DNA extraction and genotyping and improve representation of individuals in a pool. |
| first_indexed | 2024-12-22T06:09:50Z |
| format | Article |
| id | doaj.art-373c5dc6247a4a3d87f2125070466cdd |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-22T06:09:50Z |
| publishDate | 2021-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-373c5dc6247a4a3d87f2125070466cdd2022-12-21T18:36:16ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-02-011210.3389/fgene.2021.635846635846Evaluating Accuracy of DNA Pool Construction Based on White Blood Cell CountsAmy N. Abrams0Amy N. Abrams1Tara G. McDaneld2John W. Keele3Carol G. Chitko-McKown4Larry A. Kuehn5Michael G. Gonda6Department of Animal Science, South Dakota State University, Brookings, SD, United StatesDepartment of Animal Science, Berry College, Mount Berry, GA, United StatesGenetics, Breeding, and Animal Health Research Unit, U.S. Meat Animal Research Center, USDA-ARS, Clay Center, NE, United StatesGenetics, Breeding, and Animal Health Research Unit, U.S. Meat Animal Research Center, USDA-ARS, Clay Center, NE, United StatesAnimal Health Genomics Research Unit, U.S. Meat Animal Research Center, USDA-ARS, Clay Center, NE, United StatesGenetics, Breeding, and Animal Health Research Unit, U.S. Meat Animal Research Center, USDA-ARS, Clay Center, NE, United StatesDepartment of Animal Science, South Dakota State University, Brookings, SD, United StatesPooling individual samples prior to DNA extraction can mitigate the cost of DNA extraction and genotyping; however, these methods need to accurately generate equal representation of individuals within pools. The objective of this study was to determine accuracy of pool construction of blood samples based on white blood cell counts compared to two common DNA quantification methods. Fifty individual bovine blood samples were collected, and then pooled with all individuals represented in each pool. Pools were constructed with the target of equal representation of each individual animal based on number of white blood cells, spectrophotometric readings, spectrofluorometric readings, and whole blood volume with 9 pools per method and a total of 36 pools. Pools and individual samples that comprised the pools were genotyped using a commercially available genotyping array. ASReml was used to estimate variance components for individual animal contribution to pools. The correlation between animal contributions between two pools was estimated using bivariate analysis with starting values set to the result of a univariate analysis. Adonis test on distance matrix from the animal correlation showed clustering with method, and higher correlations between methods than within (P < 1 × 10–6). White blood cell count was predictive of sample representation when compared to pooling based on DNA concentration. Therefore, constructing pools using white blood cell counts prior to DNA extraction may reduce cost associated with DNA extraction and genotyping and improve representation of individuals in a pool.https://www.frontiersin.org/articles/10.3389/fgene.2021.635846/fullbovinepoolinggenotypingwhite blood cellsDNA quantification |
| spellingShingle | Amy N. Abrams Amy N. Abrams Tara G. McDaneld John W. Keele Carol G. Chitko-McKown Larry A. Kuehn Michael G. Gonda Evaluating Accuracy of DNA Pool Construction Based on White Blood Cell Counts Frontiers in Genetics bovine pooling genotyping white blood cells DNA quantification |
| title | Evaluating Accuracy of DNA Pool Construction Based on White Blood Cell Counts |
| title_full | Evaluating Accuracy of DNA Pool Construction Based on White Blood Cell Counts |
| title_fullStr | Evaluating Accuracy of DNA Pool Construction Based on White Blood Cell Counts |
| title_full_unstemmed | Evaluating Accuracy of DNA Pool Construction Based on White Blood Cell Counts |
| title_short | Evaluating Accuracy of DNA Pool Construction Based on White Blood Cell Counts |
| title_sort | evaluating accuracy of dna pool construction based on white blood cell counts |
| topic | bovine pooling genotyping white blood cells DNA quantification |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2021.635846/full |
| work_keys_str_mv | AT amynabrams evaluatingaccuracyofdnapoolconstructionbasedonwhitebloodcellcounts AT amynabrams evaluatingaccuracyofdnapoolconstructionbasedonwhitebloodcellcounts AT taragmcdaneld evaluatingaccuracyofdnapoolconstructionbasedonwhitebloodcellcounts AT johnwkeele evaluatingaccuracyofdnapoolconstructionbasedonwhitebloodcellcounts AT carolgchitkomckown evaluatingaccuracyofdnapoolconstructionbasedonwhitebloodcellcounts AT larryakuehn evaluatingaccuracyofdnapoolconstructionbasedonwhitebloodcellcounts AT michaelggonda evaluatingaccuracyofdnapoolconstructionbasedonwhitebloodcellcounts |