Evaluation of the Ion AmpliSeq™ PhenoTrivium Panel: MPS-Based Assay for Ancestry and Phenotype Predictions Challenged by Casework Samples
Abstract
:1. Introduction
2. Materials and Methods
2.1. Panel Design
2.2. Reference Samples
2.3. Sensitivity Study
2.4. Casework Samples
2.5. Library Preparation and Sequencing
2.6. Data Analysis
Phenotype and Ancestry Predictions
3. Results
3.1. Coverage and Sensitivity
3.2. Reference Samples
3.2.1. Phenotype Predictions
3.2.2. Ancestry Predictions
European Samples
Non-European Samples
Admixed Samples
3.3. Casework Samples
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Mean p-Values for Each HIrisPlex-S Category among Tested Reference Samples | Example | Prediction | Number of Predictions per Category (Incorrect Ones in Red) | ||||||
---|---|---|---|---|---|---|---|---|---|
EYE COLOR | Blue | Intermediate | Brown | ||||||
0.900 | 0.061 | 0.039 | Blue | ||||||
0.097 | 0.123 | 0.780 | Brown | ||||||
0.336 | 0.240 | 0.424 | Inconclusive | ||||||
HAIR COLOR | Color | Shade | |||||||
Blond | Brown | Red | Black | Light | Dark | ||||
0.212 | 0.103 | 0.678 | 0.007 | 0.969 | 0.031 | Red | |||
0.758 | 0.185 | 0.041 | 0.017 | 0.986 | 0.014 | Light blond to blond | |||
0.582 | 0.315 | 0.066 | 0.037 | 0.935 | 0.065 | Blond to dark blond | |||
0.302 | 0.553 | 0.058 | 0.088 | 0.821 | 0.179 | Light brown to brown | |||
0.206 | 0.619 | 0.012 | 0.163 | 0.525 | 0.475 | Brown to dark brown | |||
0.013 | 0.330 | 0.000 | 0.657 | 0.026 | 0.974 | Dark brown to black | |||
SKIN COLOR | Very Pale | Pale | Inter. | Dark | Dark/ Black | ||||
0.204 | 0.705 | 0.091 | 0.004 | 0.000 | Very pale to pale | ||||
0.046 | 0.492 | 0.454 | 0.008 | 0.000 | Pale to intermediate | ||||
0.005 | 0.068 | 0.878 | 0.050 | 0.004 | Intermediate | ||||
0.003 | 0.021 | 0.497 | 0.458 | 0.024 | Intermediate to dark | ||||
0.001 | 0.006 | 0.262 | 0.721 | 0.010 | Dark | ||||
0.000 | 0.000 | 0.000 | 0.001 | 0.999 | Dark to black |
Admixture (by Converge) | LR (by Snipper) | Population Likelihoods FROG (Highest) | Y-Lineage |
---|---|---|---|
Sample 1 (Japan) billion times more likely EA than SA and AME | Sample 1 (Japan) Japanese 1.3 × 10−51 Mainland Japanese 1.9 × 10−52 | O1b2 P49 | |
Sample 2 (China) billion times more likely EA than AME and SA | Sample 2 (China) Yi (Sichuan) 1.1 × 10−51 | O2 M122 | |
Sample 3 (Vietnam) billion times more likely EA than AME and SA | Sample 3 (Vietnam) Hakka 1.1 × 10−46 Lao Long 8.3 × 10−47 Mainland Japanese 7.8 × 10−47 | N/A | |
Sample 4 (Japan) billion times more likely EA than SA and AME | Sample 4 (Japan) Mainland Japanese 7.2 × 10−53 Okinawa Japanese 4.4 × 10−53 Japanese 2.2 × 10−53 | N/A | |
Sample 5 (Turkey) 18.94 times more likely EU than SA and billion than OCE | Sample 5 (Turkey) Iranians 2.0 × 10−41 Pathan 6.9 × 10−42 Turks 3.1 × 10−42 | R1b1a1b M269 | |
Sample 6 (Palestina) billion times more likely EU than SA and EA | Sample 6 (Palestina) Turkish Cypriots 6.1 × 10−49 | N/A | |
Sample 7 (Iran) 458 times more likely SA than EU and billion than OCE | Sample 7 (Iran) Iranians 3.9 × 10−48 Turks 7.2 × 10−49 | H1a1a M82 | |
Sample 8 (Uganda) billion times more likely AFR than SA and OCE | Sample 8 (Uganda) Lisongo 1.2 × 10−38 Hausa 1.1 × 10−39 | N/A | |
Sample 9 (Eritrea) billion times more likely SA than EU and AFR | Sample 9 (Eritrea) Ethiopian Jews 9.1 × 10−51 Somalis 1.6 × 10−52 | E1b1b1 M35 | |
Sample 10 (Egypt) 1.36 times more likely EU than SA and billion more than AME | Sample 10 (Egypt) Palestinian Arabs 1.7 × 10−51 | N/A |
Expected Admixture (Based on Provided Data) | Predicted Admixture (Calculated by Converge) | LR (by SNIPPER) | Population Likelihoods FROG (Highest) | Y Lineage |
---|---|---|---|---|
billion times more likely SA than EU and EA | Sample 1 Chuvash 6.2 × 10–53 Qinghai Tibetans 1.1 × 10–53 Khazaks 7.8 × 10–54 | N/A | ||
billion times more likely EU than SA and AME | Sample 2 Italians 7.0 × 10–48 Turks 5.7 × 10–48 Turkish Cypriots 1.2 × 10–48 | N/A | ||
128,027 times more likely EU than SA and billion more than AME | Sample 3 Kairoun,Tunisia 5.9 × 10–49 Smar,South Tunisia 5.9 × 10–50 | J1a P58 | ||
795 times more likely EU than SA and billion more than OCE | Sample 4 Sousse, Tunisia 1.1 × 10–53 Kairoun,Tunisia 1.8 × 10–54 Smar, South Tunisia 1.7 × 10–54 | N/A | ||
221,461 times more likely EU than SA and billion more than AME | Sample 5 Mixed EU 4.8 × 10–46 Russians 2.7 × 10–46 Finns 1.6 × 10–46 | N/A |
Sample and Material | DNA Input (DI) | Used SNPs Maximum: | p-Values | Admixture Converge (% Mean) | Population Likelihoods FROG (Highest) | Y-Lineage | |||||
---|---|---|---|---|---|---|---|---|---|---|---|
Eye Color | Hair Color | Hair Shade | Skin Color | ||||||||
163 Ancestry | 41 Phenotype | 120 Y-SNPs | Blue Inter Brown | Blond Brown Red Black | Light Dark | V Pale Pale Inter Dark B-Dark | |||||
C1 bone | 125 pg (1.4) | 163 | 30 | 110 | 0.001 0.017 0.982 | 0.097 0.645 0.001 0.257 | 0.052 0.948 | 0.000 0.000 0.001 0.192 0.807 | 51.50 SWA 48.50 AFR | Ethiopian Jews 5.7 × 10−52 | Major: E Subhap: E1b1b1 (M35) |
C2 bone | 31 pg (1.2) | 66 | 12 | 29 | NA | NA | NA | NA | |||
C3 trace | 62 pg (1.6) | 154 | 40 | 107 | The exact p-values cannot be published due to an ongoing investigation | ||||||
C4 trace | 125 pg (1) | 163 | 40 | 113 | |||||||
C5 blood | 1 ng (1.1) | 163 | 41 | 116 | 0.932 0.046 0.021 | 0.433 0.046 0.519 0.002 | 1.000 0.000 | 0.098 0.654 0.249 0.000 0.000 | 100 EU | Danes 4.5 × 10−45 Mixed EU 4.0 × 10−45 Irish 3.8 × 10−45 Hungarians 3.7 × 10−45 | Major: R Subhap: R1a1a1b1a2 (Z280) |
C6 blood | 1 ng (0.9) | 162 | 41 | 116 | 0.000 0.002 0.998 | 0.002 0.301 0.000 0.697 | 0.002 0.998 | 0.000 0.000 0.000 0.003 0.997 | 100 AFR | Yoruba 3.1 × 10−34 Zaramo 4.7 × 10−35 Lisongo 3.5 × 10−35 | Major: E Subhap: E1b1a1 (M2) |
C7 blood | 1ng 1 | 162 | 41 | 116 | 0.000 0.002 0.998 | 0.003 0.264 0.000 0.733 | 0.007 0.993 | 0.000 0.000 0.000 0.060 0.940 | 60.64 SWA 39.36 AFR | Ethiopian Jews 4.1 × 10−57 | Major: E Subhaplo: E1b1b1 (M35) |
C8 blood | 1 ng 0.9 | 161 | 41 | 116 | 0.000 0.002 0.998 | 0.003 0.425 0.000 0.571 | 0.003 0.997 | 0.000 0.000 0.057 0.923 0.020 | 55.18 AFR 41.82 SWA | Somalis 6.7 × 10−57 Ethiopian Jews 6.6 × 10−57 | Major: T Subhaplo: T1a (M70) |
C9 blood | 1 ng 1.6 | 163 | 41 | 115 | 0.000 0.007 0.993 | 0.007 0.246 0.000 0.747 | 0.014 0.986 | 0.000 0.000 0.998 0.002 0.000 | 92.40 EA 7.60 EU | Hakka 3.9 × 10−54 Taiwanese Han 1.0 × 10−54 SF Chinese 5.3 × 10−55 | Major: R Subhaplo: R1b1a1b (M269) |
C10 blood | 1 ng 2.2 | 161 | 41 | 115 | 0.000 0.003 0.997 | 0.001 0.133 0.000 0.866 | 0.003 0.997 | 0.084 0.000 0.976 0.024 0.000 | 95.06 EA 4.94 SA | Lao Long 4.2 × 10−53 | Major: O Subhaplo: O1b1 (F2320) |
C11 blood | 1 ng 7 | 162 | 41 | 108 | 0.911 0.057 0.032 | 0.576 0.379 0.003 0.042 | 0.917 0.083 | 0.021 0.489 0.475 0.011 0.004 | 92.84 EU 5.26 SWA | Irish 2.7 × 10−47 Danes 1.4 × 10−47 Russians 1.1 × 10−47 | Major: R Subhaplo: R1b1a1b (M269) |
C12 blood | 1 ng 1 | 163 | 40 | 116 | 0.00 0.004 0.996 | 0.004 0.311 0.000 0.685 | 0.004 0.996 | 0.000 0.000 0.019 0.965 0.016 | 67.56 SWA 29.35 EU 3.09 SA | Iranians 2.4 × 10−42 Palestinian Arabs 2.1 × 10−42 | Major: I Subhaplo: I2 (M438) |
C13 blood | 1 ng 1 | 161 | 40 | 116 | 0.000 0.002 0.998 | 0.002 0.301 0.000 0.697 | 0.002 0.998 | 0.000 0.054 0.000 0.005 0.995 | 100 AFR | Yoruba 1.1 × 10−29 Ibo 4.9 × 10−30 Lisongo 2.1 × 10−0 | Major: E Subhaplo: E1b1a1 (M2) |
C14 blood | 1 ng 1.3 | 160 | 40 | 115 | 0.012 0.050 0.938 | 0.072 0.706 0.001 0.221 | 0.137 0.863 | 0.000 0.000 0.210 0.339 0.452 | 56.77 EU 27.40 SA 15.83 OCE | Iranians 9.1 × 10−53 | Major: R Subhaplo: R1a1a1b2 (Z93) |
C15 blood | 1 ng 1 | 163 | 41 | 116 | 0.000 0.003 0.997 | 0.002 0.211 0.000 0.787 | 0.004 0.996 | 0.007 0.020 0.644 0.332 0.008 | 76.32 AME 15.06 SWA 8.62 AFR | Ecuadorian Mestizo 2.8 × 10−69 | Major: Q Subhaplo: Q1b1a1a (M3) |
C16 blood | 1 ng 0.8 | 163 | 40 | 116 | 0.028 0.073 0.899 | 0.087 0.492 0.001 0.420 | 0.169 0.831 | 0.113 0.268 0.550 0.045 0.024 | 51.54 SWA 44.23 EU 4.23 SA | Druze 7.9 × 10−48 | Major: J Subhaplo: J2a (M410) |
C17 blood | 1 ng 0.8 | 163 | 40 | 116 | 0.000 0.003 0.997 | 0.001 0.087 0.000 0.912 | 0.003 0.997 | 0.000 0.000 0.997 0.003 0.000 | 95.85 EA 4.15 OCE | Koreans 5.5 × 10−54 Japanese 3.0 × 10−54 | Major: D Subhaplo: D1b (M55) |
Sample | Phenotype Prediction | Phenotype (Photo) | Ancestry Prediction | Place of Birth |
---|---|---|---|---|
C1 | Brown eyes Dark brown to black hair Black skin | No data (body skeletonized) | ADMIXED (AFR-SWA) Likely: East Africa | Eritrea |
C2 | No prediction | No data (body skeletonized) | No prediction | Eritrea |
C3 | Brown eyes Light brown to brown hair Pale to intermediate skin | No data (police investigation) | High: Europe | No data |
C4 | Brown eyes Light brown to brown hair Pale to intermediate skin | No data (police investigation) | High: Europe | No data |
C5 | Blue eyes Red hair Pale skin | No data (body decayed) | High: Europe | Russia |
C6 | Brown eyes Black hair Black skin | No data Black hair Black skin | High: Africa Likely: Central/West | Burkina Faso |
C7 | Brown eyes Black hair Black skin | Brown eyes Black hair Black skin | ADMIXED (SWA-AFR) Likely: East Africa | Eritrea |
C8 | Brown eyes Black hair Dark skin | Brown eyes Black hair Dark skin | ADMIXED (SWA-AFR) Likely: East Africa | Ethiopia |
C9 | Brown eyes Black hair Intermediate skin | Brown eyes Black hair Intermediate skin | High: Asia High: East Asia | China |
C10 | Brown eyes Black hair Intermediate skin | Brown eyes Black hair Intermediate skin | High: Asia High: East Asia | Vietnam |
C11 | Blue eyes Blond to light blond hair Pale to intermediate skin | No data (body decayed) | High: Europe | Brazil |
C12 | Brown eyes Black hair Dark skin | No data (body decayed) | ADMIXED (SWA-EU-SA) Likely: Southwest Asia | Iraq |
C13 | Brown eyes Black hair Black skin | No data Black hair Black skin | High; Africa Likely: Central/West | Nigeria |
C14 | Brown eyes Brown to dark brown hair Dark skin to black skin | No data Dark greying hair No data | ADMIXED (EU-SA-OCE) | Afghanistan |
C15 | Brown eyes Black hair Intermediate to dark skin | No data Black hair Intermediate skin | ADMIXED (AME-SWA-AFR) Likely: South America | Mexico |
C16 | Brown eyes Dark brown to black hair Pale to intermediate skin | No data Dark greying hair Intermediate skin | ADMIXED (SWA-EU-SA) Likely: Southwest Asia | Iran |
C17 | Brown eyes Black hair Intermediate skin | No data Dark greying hair Intermediate skin | High: Asia High: East Asia | Japan |
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Diepenbroek, M.; Bayer, B.; Schwender, K.; Schiller, R.; Lim, J.; Lagacé, R.; Anslinger, K. Evaluation of the Ion AmpliSeq™ PhenoTrivium Panel: MPS-Based Assay for Ancestry and Phenotype Predictions Challenged by Casework Samples. Genes 2020, 11, 1398. https://doi.org/10.3390/genes11121398
Diepenbroek M, Bayer B, Schwender K, Schiller R, Lim J, Lagacé R, Anslinger K. Evaluation of the Ion AmpliSeq™ PhenoTrivium Panel: MPS-Based Assay for Ancestry and Phenotype Predictions Challenged by Casework Samples. Genes. 2020; 11(12):1398. https://doi.org/10.3390/genes11121398
Chicago/Turabian StyleDiepenbroek, Marta, Birgit Bayer, Kristina Schwender, Roberta Schiller, Jessica Lim, Robert Lagacé, and Katja Anslinger. 2020. "Evaluation of the Ion AmpliSeq™ PhenoTrivium Panel: MPS-Based Assay for Ancestry and Phenotype Predictions Challenged by Casework Samples" Genes 11, no. 12: 1398. https://doi.org/10.3390/genes11121398