Population and performance analyses of four major populations with Illumina's FGx Forensic Genomics System

Jennifer Churchill Cihlar, Nicole M.M. Novroski, Jonathan L. King, Lay Hong Seah, Bruce Budowle

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)81-92
Number of pages12
JournalForensic Science International: Genetics
Volume30
DOIs
StatePublished - 1 Sep 2017

Fingerprint

Genomics
Single Nucleotide Polymorphism
Population
Alleles
Southwestern United States
Phenotype
High-Throughput Nucleotide Sequencing
Validation Studies
Population Characteristics
Genetic Markers
Population Groups
Hispanic Americans
Gene Frequency
African Americans

Keywords

  • Allele frequencies
  • DNA Signature Prep kit
  • FGx Forensic Genomics System
  • ForenSeq™
  • Major populations
  • Population genetics
  • SNP
  • STR

Cite this

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abstract = "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.",
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Population and performance analyses of four major populations with Illumina's FGx Forensic Genomics System. / Cihlar, Jennifer Churchill; Novroski, Nicole M.M.; King, Jonathan L.; Seah, Lay Hong; Budowle, Bruce.

In: Forensic Science International: Genetics, Vol. 30, 01.09.2017, p. 81-92.

Research output: Contribution to journalArticle

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