A SNP panel and online tool for checking genotype concordance through comparing QR codes.
In the current precision medicine era, more and more samples get genotyped and sequenced. Both researchers and commercial companies expend significant time and resources to reduce the error rate. However, it has been reported that there is a sample mix-up rate of between 0.1% and 1%, not to mention...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2017-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC5604942?pdf=render |
| _version_ | 1811197305892634624 |
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| author | Yonghong Du Joshua S Martin John McGee Yuchen Yang Eric Yi Liu Yingrui Sun Matthias Geihs Xuejun Kong Eric Lingfeng Zhou Yun Li Jie Huang |
| author_facet | Yonghong Du Joshua S Martin John McGee Yuchen Yang Eric Yi Liu Yingrui Sun Matthias Geihs Xuejun Kong Eric Lingfeng Zhou Yun Li Jie Huang |
| author_sort | Yonghong Du |
| collection | DOAJ |
| description | In the current precision medicine era, more and more samples get genotyped and sequenced. Both researchers and commercial companies expend significant time and resources to reduce the error rate. However, it has been reported that there is a sample mix-up rate of between 0.1% and 1%, not to mention the possibly higher mix-up rate during the down-stream genetic reporting processes. Even on the low end of this estimate, this translates to a significant number of mislabeled samples, especially over the projected one billion people that will be sequenced within the next decade. Here, we first describe a method to identify a small set of Single nucleotide polymorphisms (SNPs) that can uniquely identify a personal genome, which utilizes allele frequencies of five major continental populations reported in the 1000 genomes project and the ExAC Consortium. To make this panel more informative, we added four SNPs that are commonly used to predict ABO blood type, and another two SNPs that are capable of predicting sex. We then implement a web interface (http://qrcme.tech), nicknamed QRC (for QR code based Concordance check), which is capable of extracting the relevant ID SNPs from a raw genetic data, coding its genotype as a quick response (QR) code, and comparing QR codes to report the concordance of underlying genetic datasets. The resulting 80 fingerprinting SNPs represent a significant decrease in complexity and the number of markers used for genetic data labelling and tracking. Our method and web tool is easily accessible to both researchers and the general public who consider the accuracy of complex genetic data as a prerequisite towards precision medicine. |
| first_indexed | 2024-04-12T01:12:59Z |
| format | Article |
| id | doaj.art-196507326ecc4165b9b929a34b3cd295 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-12T01:12:59Z |
| publishDate | 2017-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-196507326ecc4165b9b929a34b3cd2952022-12-22T03:54:03ZengPublic Library of Science (PLoS)PLoS ONE1932-62032017-01-01129e018243810.1371/journal.pone.0182438A SNP panel and online tool for checking genotype concordance through comparing QR codes.Yonghong DuJoshua S MartinJohn McGeeYuchen YangEric Yi LiuYingrui SunMatthias GeihsXuejun KongEric Lingfeng ZhouYun LiJie HuangIn the current precision medicine era, more and more samples get genotyped and sequenced. Both researchers and commercial companies expend significant time and resources to reduce the error rate. However, it has been reported that there is a sample mix-up rate of between 0.1% and 1%, not to mention the possibly higher mix-up rate during the down-stream genetic reporting processes. Even on the low end of this estimate, this translates to a significant number of mislabeled samples, especially over the projected one billion people that will be sequenced within the next decade. Here, we first describe a method to identify a small set of Single nucleotide polymorphisms (SNPs) that can uniquely identify a personal genome, which utilizes allele frequencies of five major continental populations reported in the 1000 genomes project and the ExAC Consortium. To make this panel more informative, we added four SNPs that are commonly used to predict ABO blood type, and another two SNPs that are capable of predicting sex. We then implement a web interface (http://qrcme.tech), nicknamed QRC (for QR code based Concordance check), which is capable of extracting the relevant ID SNPs from a raw genetic data, coding its genotype as a quick response (QR) code, and comparing QR codes to report the concordance of underlying genetic datasets. The resulting 80 fingerprinting SNPs represent a significant decrease in complexity and the number of markers used for genetic data labelling and tracking. Our method and web tool is easily accessible to both researchers and the general public who consider the accuracy of complex genetic data as a prerequisite towards precision medicine.http://europepmc.org/articles/PMC5604942?pdf=render |
| spellingShingle | Yonghong Du Joshua S Martin John McGee Yuchen Yang Eric Yi Liu Yingrui Sun Matthias Geihs Xuejun Kong Eric Lingfeng Zhou Yun Li Jie Huang A SNP panel and online tool for checking genotype concordance through comparing QR codes. PLoS ONE |
| title | A SNP panel and online tool for checking genotype concordance through comparing QR codes. |
| title_full | A SNP panel and online tool for checking genotype concordance through comparing QR codes. |
| title_fullStr | A SNP panel and online tool for checking genotype concordance through comparing QR codes. |
| title_full_unstemmed | A SNP panel and online tool for checking genotype concordance through comparing QR codes. |
| title_short | A SNP panel and online tool for checking genotype concordance through comparing QR codes. |
| title_sort | snp panel and online tool for checking genotype concordance through comparing qr codes |
| url | http://europepmc.org/articles/PMC5604942?pdf=render |
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