Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™

M Eduardoff; T E Gross; C Santos; M de la Puente; D Ballard; C Strobl; C Børsting; N Morling; L Fusco; C Hussing; B Egyed; L Souto; J Uacyisrael; D Syndercombe Court; Á Carracedo; M V Lareu; P M Schneider; W Parson; C Phillips; EUROFORGEN-NoE Consortium; W Parson; C Phillips

doi:10.1016/j.fsigen.2016.04.008

Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™

M Eduardoff, T E Gross, C Santos, M de la Puente, D Ballard, C Strobl, C Børsting, N Morling, L Fusco, C Hussing, B Egyed, L Souto, J Uacyisrael, D Syndercombe Court, Á Carracedo, M V Lareu, P M Schneider, W Parson, C Phillips, EUROFORGEN-NoE ConsortiumW Parson, C Phillips

31 Citations (Scopus)

Abstract

The EUROFORGEN Global ancestry-informative SNP (AIM-SNPs) panel is a forensic multiplex of 128 markers designed to differentiate an individual's ancestry from amongst the five continental population groups of Africa, Europe, East Asia, Native America, and Oceania. A custom multiplex of AmpliSeq™ PCR primers was designed for the Global AIM-SNPs to perform massively parallel sequencing using the Ion PGM™ system. This study assessed individual SNP genotyping precision using the Ion PGM™, the forensic sensitivity of the multiplex using dilution series, degraded DNA plus simple mixtures, and the ancestry differentiation power of the final panel design, which required substitution of three original ancestry-informative SNPs with alternatives. Fourteen populations that had not been previously analyzed were genotyped using the custom multiplex and these studies allowed assessment of genotyping performance by comparison of data across five laboratories. Results indicate a low level of genotyping error can still occur from sequence misalignment caused by homopolymeric tracts close to the target SNP, despite careful scrutiny of candidate SNPs at the design stage. Such sequence misalignment required the exclusion of component SNP rs2080161 from the Global AIM-SNPs panel. However, the overall genotyping precision and sensitivity of this custom multiplex indicates the Ion PGM™ assay for the Global AIM-SNPs is highly suitable for forensic ancestry analysis with massively parallel sequencing.

Original language	English
Journal	Forensic Science International: Genetics
Volume	23
Pages (from-to)	178-189
Number of pages	12
ISSN	1872-4973
DOIs	https://doi.org/10.1016/j.fsigen.2016.04.008
Publication status	Published - 1 Jul 2016

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Eduardoff, M., Gross, T. E., Santos, C., de la Puente, M., Ballard, D., Strobl, C., Børsting, C., Morling, N., Fusco, L., Hussing, C., Egyed, B., Souto, L., Uacyisrael, J., Syndercombe Court, D., Carracedo, Á., Lareu, M. V., Schneider, P. M., Parson, W., Phillips, C., ... Phillips, C. (2016). Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™. Forensic Science International: Genetics, 23, 178-189. https://doi.org/10.1016/j.fsigen.2016.04.008

Eduardoff, M, Gross, TE, Santos, C, de la Puente, M, Ballard, D, Strobl, C, Børsting, C , Morling, N, Fusco, L, Hussing, C, Egyed, B, Souto, L, Uacyisrael, J, Syndercombe Court, D, Carracedo, Á, Lareu, MV, Schneider, PM, Parson, W, Phillips, C, EUROFORGEN-NoE Consortium, Parson, W & Phillips, C 2016, 'Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™', Forensic Science International: Genetics, vol. 23, pp. 178-189. https://doi.org/10.1016/j.fsigen.2016.04.008

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title = "Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM{\texttrademark}",

abstract = "The EUROFORGEN Global ancestry-informative SNP (AIM-SNPs) panel is a forensic multiplex of 128 markers designed to differentiate an individual's ancestry from amongst the five continental population groups of Africa, Europe, East Asia, Native America, and Oceania. A custom multiplex of AmpliSeq{\texttrademark} PCR primers was designed for the Global AIM-SNPs to perform massively parallel sequencing using the Ion PGM{\texttrademark} system. This study assessed individual SNP genotyping precision using the Ion PGM{\texttrademark}, the forensic sensitivity of the multiplex using dilution series, degraded DNA plus simple mixtures, and the ancestry differentiation power of the final panel design, which required substitution of three original ancestry-informative SNPs with alternatives. Fourteen populations that had not been previously analyzed were genotyped using the custom multiplex and these studies allowed assessment of genotyping performance by comparison of data across five laboratories. Results indicate a low level of genotyping error can still occur from sequence misalignment caused by homopolymeric tracts close to the target SNP, despite careful scrutiny of candidate SNPs at the design stage. Such sequence misalignment required the exclusion of component SNP rs2080161 from the Global AIM-SNPs panel. However, the overall genotyping precision and sensitivity of this custom multiplex indicates the Ion PGM{\texttrademark} assay for the Global AIM-SNPs is highly suitable for forensic ancestry analysis with massively parallel sequencing.",

author = "M Eduardoff and Gross, {T E} and C Santos and {de la Puente}, M and D Ballard and C Strobl and C B{\o}rsting and N Morling and L Fusco and C Hussing and B Egyed and L Souto and J Uacyisrael and {Syndercombe Court}, D and {\'A} Carracedo and Lareu, {M V} and Schneider, {P M} and W Parson and C Phillips and {EUROFORGEN-NoE Consortium} and W Parson and C Phillips",

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AU - Eduardoff, M

AU - Gross, T E

AU - Santos, C

AU - de la Puente, M

AU - Ballard, D

AU - Strobl, C

AU - Børsting, C

AU - Morling, N

AU - Fusco, L

AU - Hussing, C

AU - Egyed, B

AU - Souto, L

AU - Uacyisrael, J

AU - Syndercombe Court, D

AU - Carracedo, Á

AU - Lareu, M V

AU - Schneider, P M

AU - Parson, W

AU - Phillips, C

AU - EUROFORGEN-NoE Consortium

AU - Parson, W

AU - Phillips, C

PY - 2016/7/1

Y1 - 2016/7/1

N2 - The EUROFORGEN Global ancestry-informative SNP (AIM-SNPs) panel is a forensic multiplex of 128 markers designed to differentiate an individual's ancestry from amongst the five continental population groups of Africa, Europe, East Asia, Native America, and Oceania. A custom multiplex of AmpliSeq™ PCR primers was designed for the Global AIM-SNPs to perform massively parallel sequencing using the Ion PGM™ system. This study assessed individual SNP genotyping precision using the Ion PGM™, the forensic sensitivity of the multiplex using dilution series, degraded DNA plus simple mixtures, and the ancestry differentiation power of the final panel design, which required substitution of three original ancestry-informative SNPs with alternatives. Fourteen populations that had not been previously analyzed were genotyped using the custom multiplex and these studies allowed assessment of genotyping performance by comparison of data across five laboratories. Results indicate a low level of genotyping error can still occur from sequence misalignment caused by homopolymeric tracts close to the target SNP, despite careful scrutiny of candidate SNPs at the design stage. Such sequence misalignment required the exclusion of component SNP rs2080161 from the Global AIM-SNPs panel. However, the overall genotyping precision and sensitivity of this custom multiplex indicates the Ion PGM™ assay for the Global AIM-SNPs is highly suitable for forensic ancestry analysis with massively parallel sequencing.

AB - The EUROFORGEN Global ancestry-informative SNP (AIM-SNPs) panel is a forensic multiplex of 128 markers designed to differentiate an individual's ancestry from amongst the five continental population groups of Africa, Europe, East Asia, Native America, and Oceania. A custom multiplex of AmpliSeq™ PCR primers was designed for the Global AIM-SNPs to perform massively parallel sequencing using the Ion PGM™ system. This study assessed individual SNP genotyping precision using the Ion PGM™, the forensic sensitivity of the multiplex using dilution series, degraded DNA plus simple mixtures, and the ancestry differentiation power of the final panel design, which required substitution of three original ancestry-informative SNPs with alternatives. Fourteen populations that had not been previously analyzed were genotyped using the custom multiplex and these studies allowed assessment of genotyping performance by comparison of data across five laboratories. Results indicate a low level of genotyping error can still occur from sequence misalignment caused by homopolymeric tracts close to the target SNP, despite careful scrutiny of candidate SNPs at the design stage. Such sequence misalignment required the exclusion of component SNP rs2080161 from the Global AIM-SNPs panel. However, the overall genotyping precision and sensitivity of this custom multiplex indicates the Ion PGM™ assay for the Global AIM-SNPs is highly suitable for forensic ancestry analysis with massively parallel sequencing.

U2 - 10.1016/j.fsigen.2016.04.008

DO - 10.1016/j.fsigen.2016.04.008

M3 - Journal article

C2 - 27208666

SN - 1872-4973

VL - 23

SP - 178

EP - 189

JO - Forensic Science International: Genetics

JF - Forensic Science International: Genetics

ER -

Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™

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