TY - JOUR
T1 - Population and performance analyses of four major populations with Illumina's FGx Forensic Genomics System
AU - Churchill, Jennifer D.
AU - Novroski, Nicole M.M.
AU - King, Jonathan L.
AU - Seah, Lay Hong
AU - Budowle, Bruce
N1 - Funding Information:
The authors would like to thank Illumina, in particular Al Bodota, Cydne Holt, and Joe Varlaro, for study support. This work was supported in part by award no. 2015-DN-BX- K067, awarded by the National Institute of Justice, Office of Justice Programs, U.S. Department of Justice. The opinions, findings, and conclusions or recommendations expressed in this publication are those of the authors and do not necessarily reflect those of the U.S. Department of Justice.
Publisher Copyright:
© 2017 Elsevier B.V.
PY - 2017/9
Y1 - 2017/9
N2 - The MiSeq FGx Forensic Genomics System (Illumina) enables amplification and massively parallel sequencing of 59 STRs, 94 identity informative SNPs, 54 ancestry informative SNPs, and 24 phenotypic informative SNPs. Allele frequency and population statistics data were generated for the 172 SNP loci included in this panel on four major population groups (Chinese, African Americans, US Caucasians, and Southwest Hispanics). Single-locus and combined random match probability values were generated for the identity informative SNPs. The average combined STR and identity informative SNP random match probabilities (assuming independence) across all four populations were 1.75E-67 and 2.30E-71 with length-based and sequence-based STR alleles, respectively. Ancestry and phenotype predictions were obtained using the ForenSeq™ Universal Analysis System (UAS; Illumina) based on the ancestry informative and phenotype informative SNP profiles generated for each sample. Additionally, performance metrics, including profile completeness, read depth, relative locus performance, and allele coverage ratios, were evaluated and detailed for the 725 samples included in this study. While some genetic markers included in this panel performed notably better than others, performance across populations was generally consistent. The performance and population data included in this study support that accurate and reliable profiles were generated and provide valuable background information for laboratories considering internal validation studies and implementation.
AB - The MiSeq FGx Forensic Genomics System (Illumina) enables amplification and massively parallel sequencing of 59 STRs, 94 identity informative SNPs, 54 ancestry informative SNPs, and 24 phenotypic informative SNPs. Allele frequency and population statistics data were generated for the 172 SNP loci included in this panel on four major population groups (Chinese, African Americans, US Caucasians, and Southwest Hispanics). Single-locus and combined random match probability values were generated for the identity informative SNPs. The average combined STR and identity informative SNP random match probabilities (assuming independence) across all four populations were 1.75E-67 and 2.30E-71 with length-based and sequence-based STR alleles, respectively. Ancestry and phenotype predictions were obtained using the ForenSeq™ Universal Analysis System (UAS; Illumina) based on the ancestry informative and phenotype informative SNP profiles generated for each sample. Additionally, performance metrics, including profile completeness, read depth, relative locus performance, and allele coverage ratios, were evaluated and detailed for the 725 samples included in this study. While some genetic markers included in this panel performed notably better than others, performance across populations was generally consistent. The performance and population data included in this study support that accurate and reliable profiles were generated and provide valuable background information for laboratories considering internal validation studies and implementation.
KW - Allele frequencies
KW - DNA Signature Prep kit
KW - FGx Forensic Genomics System
KW - ForenSeq™
KW - Major populations
KW - Population genetics
KW - SNP
KW - STR
UR - http://www.scopus.com/inward/record.url?scp=85021250619&partnerID=8YFLogxK
U2 - 10.1016/j.fsigen.2017.06.004
DO - 10.1016/j.fsigen.2017.06.004
M3 - Article
C2 - 28651097
AN - SCOPUS:85021250619
SN - 1872-4973
VL - 30
SP - 81
EP - 92
JO - Forensic Science International: Genetics
JF - Forensic Science International: Genetics
ER -