Combining whole genome sequencing and non-adaptive group testing for large-scale ethnicity screens
Abstract Background Estimating an individual’s ethnicity from genetic data is crucial for analyzing disease association studies, making informed medical decisions, conducting forensic investigations, and tracing genealogical ancestry. Results This work combines non-adaptive group testing using the m...
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BMC
2025-07-01
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| Series: | BMC Bioinformatics |
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| Online Access: | https://doi.org/10.1186/s12859-025-06192-3 |
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| author | Elior Avraham Noam Shental |
| author_facet | Elior Avraham Noam Shental |
| author_sort | Elior Avraham |
| collection | DOAJ |
| description | Abstract Background Estimating an individual’s ethnicity from genetic data is crucial for analyzing disease association studies, making informed medical decisions, conducting forensic investigations, and tracing genealogical ancestry. Results This work combines non-adaptive group testing using the mathematical field of compressed sensing and standard short-read sequencing to allow an up to 4-fold increase in the number of samples in large-scale ethnicity estimates. The method requires no prior knowledge regarding the tested individuals and provides almost identical results compared to testing each individual independently. Our results are based on simulated data, and on simulations based on experimental data from the 1000 Genomes Project and the Human Genome Diversity Project. Conclusions Our computational approach aims to reduce the costs of large-scale ancestry testing by up to 4-fold in many real-life scenarios while not compromising accuracy. We hope this method will allow more efficient large-scale ethnicity screenings. |
| format | Article |
| id | doaj-art-ca59896fab4447b3a66449b94146c247 |
| institution | Kabale University |
| issn | 1471-2105 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj-art-ca59896fab4447b3a66449b94146c2472025-08-20T04:02:42ZengBMCBMC Bioinformatics1471-21052025-07-0126111410.1186/s12859-025-06192-3Combining whole genome sequencing and non-adaptive group testing for large-scale ethnicity screensElior Avraham0Noam Shental1Department of Computer Science, The Open University of IsraelDepartment of Computer Science, The Open University of IsraelAbstract Background Estimating an individual’s ethnicity from genetic data is crucial for analyzing disease association studies, making informed medical decisions, conducting forensic investigations, and tracing genealogical ancestry. Results This work combines non-adaptive group testing using the mathematical field of compressed sensing and standard short-read sequencing to allow an up to 4-fold increase in the number of samples in large-scale ethnicity estimates. The method requires no prior knowledge regarding the tested individuals and provides almost identical results compared to testing each individual independently. Our results are based on simulated data, and on simulations based on experimental data from the 1000 Genomes Project and the Human Genome Diversity Project. Conclusions Our computational approach aims to reduce the costs of large-scale ancestry testing by up to 4-fold in many real-life scenarios while not compromising accuracy. We hope this method will allow more efficient large-scale ethnicity screenings.https://doi.org/10.1186/s12859-025-06192-3Compressed sensingWhole genome sequencingNon-adaptive group testingEthnicity screensAncestry testing |
| spellingShingle | Elior Avraham Noam Shental Combining whole genome sequencing and non-adaptive group testing for large-scale ethnicity screens BMC Bioinformatics Compressed sensing Whole genome sequencing Non-adaptive group testing Ethnicity screens Ancestry testing |
| title | Combining whole genome sequencing and non-adaptive group testing for large-scale ethnicity screens |
| title_full | Combining whole genome sequencing and non-adaptive group testing for large-scale ethnicity screens |
| title_fullStr | Combining whole genome sequencing and non-adaptive group testing for large-scale ethnicity screens |
| title_full_unstemmed | Combining whole genome sequencing and non-adaptive group testing for large-scale ethnicity screens |
| title_short | Combining whole genome sequencing and non-adaptive group testing for large-scale ethnicity screens |
| title_sort | combining whole genome sequencing and non adaptive group testing for large scale ethnicity screens |
| topic | Compressed sensing Whole genome sequencing Non-adaptive group testing Ethnicity screens Ancestry testing |
| url | https://doi.org/10.1186/s12859-025-06192-3 |
| work_keys_str_mv | AT elioravraham combiningwholegenomesequencingandnonadaptivegrouptestingforlargescaleethnicityscreens AT noamshental combiningwholegenomesequencingandnonadaptivegrouptestingforlargescaleethnicityscreens |