Improved eye- and skin-color prediction based on 8 SNPs

abstract: ...Aim To improve the 7-plex system to predict eye and skin color by increasing precision and detailed phenotypic descriptions. Methods Analysis of an eighth single nucleotide polymorphism (SNP), rs12896399 ( SLC24A4 ), showed a statistically significant association with human eye color ( P =0.007) but a rather poor strength of agreement (=0.063). This SNP was added to the 7-plex system (rs12913832 at HERC2 , rs1545397 at OCA2 , rs16891982 at SLC45A2 , rs1426654 at SLC24A5 , rs885479 at MC1R , rs6119471 at ASIP , and rs12203592 at IRF4 ). Further, the instruction guidelines on the interpretation of genotypes were changed to create a new 8-plex system. This was based on the analysis of an 803-sample training set of various populations. The newly developed 8-plex system can predict the eye colors brown, green, and blue, and skin colors light, not dark, and not light. It is superior to the 7-plex system with its additional ability to predict blue eye and light skin color. Results The 8-plex system was tested on an additional 212 samples, the test set. Analysis showed that the number of positive descriptions for eye colors as being brown, green, or blue increased significantly ( P =6.98e-15, z-score: -7.786). The error rate for eye-color prediction was low, at approximately 5%, while the skin color prediction showed no error in the test set (1% in training set). Conclusions We can conclude that the new 8-plex system for the prediction of eye and skin color substantially enhances its former version.

...). This SNP was added to the 7-plex system (rs12913832 at HERC2 , rs1545397 at OCA2 , rs16891982 at SLC45A2 , rs1426654 at SLC24A5 , rs885479 at MC1R , rs6119471 at ASIP , and rs12203592 at IRF4 ). Further, the instruction guidelines on the interpretation of genotypes were changed to create a new 8-plex system. This was based on the analysis of an 803-sample training set of various populations. The newly developed 8-plex system can predict the eye colors brown, green, and blue, and skin colors light

... elsewhere ( 17 ). TaqMan PCR assay Allelic discrimination was performed by polymerase chain recation (PCR)-based TaqMan assays in the presence of two different fluorescently labeled probes, which allow for the detection of both alleles in a single reaction (Applied Biosystems Inc, Foster City, CA, USA): rs12913832 ( HERC2 ), rs1545397 ( OCA2 ), rs1426654 ( SLC24A5 ), rs16891982 ( SLC45A2 ), rs885479 ( MC1R ), rs6119471 ( ASIP ), rs12203592 ( IRF4 ), and rs12896399 ( SLC24A4 ) using optimized PCR

... are shared ( Figure 1 ). The newly-designed 8-plex system was established on 803 samples (training set) ( Table 1 ). Figure 1 Single nucleotide polymorphisms used for eye- and skin-color prediction based on the 8-plex system: rs12203592, rs12896399, rs12913832, rs16891982, and rs6119471 are used to predict eye color; rs12913832, rs16891982, rs6119471, rs1426654, rs885479, and rs1545397 are used to predict skin coloration. Table 1 Eye-color prediction: outcome for training set (n=803) Population

... not blue (ie, brown or green) or not brown (ie, green or blue). Further distinctions for predicting eye color as being brown, green, or blue are dependent on the genotypes of three additional SNPs: rs12203592, rs16891982, and rs6119471 ( Figure 2 ). Brown eye color is predicted by the following genotype combinations: A/A or G/A at rs12913832, plus either G/G at rs6119471, or C/C at rs16891982; green eye color is predicted by G/G at rs12913832 plus C/C at rs16891982, or by G/A at rs12913832 plus T/T at rs12203592; and blue eye color is predicted by G/G at rs12913832 plus T/T at rs12203592. Figure 2 Schematic representation of the eye-color predictor (8-plex system): Step 1: eye color is predicted of being not brown (ie, green or blue) or not blue (ie, brown or green). Eye color can be further refined as being brown, green, or blue, depending on homozygous genotypes of rs16891982, rs6119471, and rs12203592. Step 2: follows only if step 1 results in not brown or not blue. Brown eye color is

... more stringent conditions: G/G at rs12913832, plus G/G at rs16891982, and A/A at rs1426654. Non-light skin color (ie, medium or dark) is predicted by G/G at rs6119471. Table 3 shows the outcome for skin color of the 803 training samples. Since this predictor utilizes only homozygous genotypes, the outcome can be inconclusive (ie, no prediction could be made). Of 803 samples tested, 600 (75%) predictions were made, resulting in only 4 errors (1%). The four erroneous predictions described skin color

... significantly ( P =6.98e-15, z-score: -7.786) while keeping the error rate low. Discussion The newly developed 8-plex system demonstrated improved results compared with the former 7-plex system ( 17 ) by its ability to predict blue eye and light skin color. The number of positive descriptions for eye color increased significantly ( P =6.98e-15, z-score: -7.786), while keeping a low error-rate at approximately 5%. In more detail, the 7-plex system utilizes seven SNPs (rs12913832, rs16891982, rs6119471

infinome is an experiment to study aging. Link your 23andMe account for personalized reports.

SNP: rs6119471

linkouts : SNPedia

Images from Open Access Papers

Search Results from Open Access Papers