Evaluation and Verification of a microRNA Panel Using Quadratic Discriminant Analysis for the Classification of Human Body Fluids in DNA Extracts
There is significant interest in the use of miRNA analysis for forensic body fluid identification. Demonstrated co-extraction and detection in DNA extracts could make the use of miRNAs a more streamlined molecular body fluid identification method than other RNA-based methods. We previously reported...
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MDPI AG
2023-04-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/5/968 |
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| author | Ciara Rhodes Carolyn Lewis Kelsey Price Anaya Valentine Mary-Randall A. Creighton Edward Boone Sarah Seashols-Williams |
| author_facet | Ciara Rhodes Carolyn Lewis Kelsey Price Anaya Valentine Mary-Randall A. Creighton Edward Boone Sarah Seashols-Williams |
| author_sort | Ciara Rhodes |
| collection | DOAJ |
| description | There is significant interest in the use of miRNA analysis for forensic body fluid identification. Demonstrated co-extraction and detection in DNA extracts could make the use of miRNAs a more streamlined molecular body fluid identification method than other RNA-based methods. We previously reported a reverse transcription-quantitative PCR (RT-qPCR) panel of eight miRNAs that classified venous and menstrual blood, feces, urine, saliva, semen, and vaginal secretions using a quadratic discriminant analysis (QDA) model with 93% accuracy in RNA extracts. Herein, miRNA expression in DNA extracts from 50 donors of each body fluid were tested using the model. Initially, a classification rate of 87% was obtained, which increased to 92% when three additional miRNAs were added. Body fluid identification was found to be reliable across population samples of mixed ages, ethnicities, and sex, with 72–98% of the unknown samples classifying correctly. The model was then tested against compromised samples and over biological cycles, where classification accuracy varied, depending on the body fluid. In conclusion, we demonstrated the ability to classify body fluids using miRNA expression from DNA extracts, eliminating the need for RNA extraction, greatly reducing evidentiary sample consumption and processing time in forensic laboratories, but acknowledge that compromised semen and saliva samples can fail to classify properly, and mixed sample classification remains untested and may have limitations. |
| first_indexed | 2024-03-11T03:42:37Z |
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| id | doaj.art-5fb4eb6c2f7f4ab4818d198dd026b4eb |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T03:42:37Z |
| publishDate | 2023-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-5fb4eb6c2f7f4ab4818d198dd026b4eb2023-11-18T01:28:40ZengMDPI AGGenes2073-44252023-04-0114596810.3390/genes14050968Evaluation and Verification of a microRNA Panel Using Quadratic Discriminant Analysis for the Classification of Human Body Fluids in DNA ExtractsCiara Rhodes0Carolyn Lewis1Kelsey Price2Anaya Valentine3Mary-Randall A. Creighton4Edward Boone5Sarah Seashols-Williams6Department of Forensic Science, Virginia Commonwealth University, P.O. Box 843079, 1015 Floyd Ave., Richmond, VA 23284-3079, USADepartment of Forensic Science, Virginia Commonwealth University, P.O. Box 843079, 1015 Floyd Ave., Richmond, VA 23284-3079, USADepartment of Forensic Science, Virginia Commonwealth University, P.O. Box 843079, 1015 Floyd Ave., Richmond, VA 23284-3079, USADepartment of Forensic Science, Virginia Commonwealth University, P.O. Box 843079, 1015 Floyd Ave., Richmond, VA 23284-3079, USACenter for Biological Data Science, Virginia Commonwealth University, P.O. Box 842030, 1015 Floyd Ave., Richmond, VA 23284-2030, USADepartment of Statistical Sciences and Operations Research, Virginia Commonwealth University, P.O. Box 843083, 1015 Floyd Ave., Richmond, VA 23284-3083, USADepartment of Forensic Science, Virginia Commonwealth University, P.O. Box 843079, 1015 Floyd Ave., Richmond, VA 23284-3079, USAThere is significant interest in the use of miRNA analysis for forensic body fluid identification. Demonstrated co-extraction and detection in DNA extracts could make the use of miRNAs a more streamlined molecular body fluid identification method than other RNA-based methods. We previously reported a reverse transcription-quantitative PCR (RT-qPCR) panel of eight miRNAs that classified venous and menstrual blood, feces, urine, saliva, semen, and vaginal secretions using a quadratic discriminant analysis (QDA) model with 93% accuracy in RNA extracts. Herein, miRNA expression in DNA extracts from 50 donors of each body fluid were tested using the model. Initially, a classification rate of 87% was obtained, which increased to 92% when three additional miRNAs were added. Body fluid identification was found to be reliable across population samples of mixed ages, ethnicities, and sex, with 72–98% of the unknown samples classifying correctly. The model was then tested against compromised samples and over biological cycles, where classification accuracy varied, depending on the body fluid. In conclusion, we demonstrated the ability to classify body fluids using miRNA expression from DNA extracts, eliminating the need for RNA extraction, greatly reducing evidentiary sample consumption and processing time in forensic laboratories, but acknowledge that compromised semen and saliva samples can fail to classify properly, and mixed sample classification remains untested and may have limitations.https://www.mdpi.com/2073-4425/14/5/968forensic sciencebody fluid identificationmicroRNAquadratic discriminant analysis (QDA) |
| spellingShingle | Ciara Rhodes Carolyn Lewis Kelsey Price Anaya Valentine Mary-Randall A. Creighton Edward Boone Sarah Seashols-Williams Evaluation and Verification of a microRNA Panel Using Quadratic Discriminant Analysis for the Classification of Human Body Fluids in DNA Extracts Genes forensic science body fluid identification microRNA quadratic discriminant analysis (QDA) |
| title | Evaluation and Verification of a microRNA Panel Using Quadratic Discriminant Analysis for the Classification of Human Body Fluids in DNA Extracts |
| title_full | Evaluation and Verification of a microRNA Panel Using Quadratic Discriminant Analysis for the Classification of Human Body Fluids in DNA Extracts |
| title_fullStr | Evaluation and Verification of a microRNA Panel Using Quadratic Discriminant Analysis for the Classification of Human Body Fluids in DNA Extracts |
| title_full_unstemmed | Evaluation and Verification of a microRNA Panel Using Quadratic Discriminant Analysis for the Classification of Human Body Fluids in DNA Extracts |
| title_short | Evaluation and Verification of a microRNA Panel Using Quadratic Discriminant Analysis for the Classification of Human Body Fluids in DNA Extracts |
| title_sort | evaluation and verification of a microrna panel using quadratic discriminant analysis for the classification of human body fluids in dna extracts |
| topic | forensic science body fluid identification microRNA quadratic discriminant analysis (QDA) |
| url | https://www.mdpi.com/2073-4425/14/5/968 |
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