Evaluation of the Illumina ® Beta Version ForenSeq™ DNA Signature Prep Kit for use in genetic profiling

Churchill, Jennifer D.; Schmedes, Sarah E.; King, Jonathan L.; Budowle, Bruce

doi:10.1016/j.fsigen.2015.09.009

Cited by 201 publications

(188 citation statements)

References 18 publications

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“…SNP coverage for HID-Ion is affected by the number of wells in the sequencing chip which are occupied by Ion Sphere™ Particles (ISP) with monoclonally amplified SNP target that were successfully read 21 . On the other hand, SNP coverage for the MiSeq ® FGx™ is affected by the PCR amplification efficiency, purification, and bead-based library normalization 11 . Increased number of markers multiplexed in one sequencing reaction could also increase variation in coverage of the SNP markers 11 .…”

Section: Resultsmentioning

confidence: 99%

“…On the other hand, SNP coverage for the MiSeq ® FGx™ is affected by the PCR amplification efficiency, purification, and bead-based library normalization 11 . Increased number of markers multiplexed in one sequencing reaction could also increase variation in coverage of the SNP markers 11 . Comparison of the markers’ SNP coverage between the two MPS systems (Figs 2 and 3) showed that MiSeq ® FGx™ achieved higher SNP coverage reads in majority of the markers; however, it also showed higher variation in SNP coverage distribution across samples than the HID-Ion PGM™, with more read outliers observed in the univariate statistical evaluation.…”

Section: Resultsmentioning

confidence: 99%

“…On its own, human identification via SNP markers wasn’t able to gain as much popularity as STRs and mtDNA markers in the forensic community 8–10 . Since the inception of MPS in forensic science, Illumina ® 11 and Life Technologies™ 12–14 developed marker panels with more than 100 SNP loci. The MPS platforms dedicated for forensic genetics are the MiSeq ® FGx™ Forensic Genomics System (Illumina) and the HID-Ion Personal Genome Machine (PGM)™ (Thermo Fisher Scientific).…”

Section: Introductionmentioning

confidence: 99%

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Comparison of Two Massively Parallel Sequencing Platforms using 83 Single Nucleotide Polymorphisms for Human Identification

Apaga

Dennis

Salvador

et al. 2017

Sci Rep

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The potential of Massively Parallel Sequencing (MPS) technology to vastly expand the capabilities of human identification led to the emergence of different MPS platforms that use forensically relevant genetic markers. Two of the MPS platforms that are currently available are the MiSeq® FGx™ Forensic Genomics System (Illumina) and the HID-Ion Personal Genome Machine (PGM)™ (Thermo Fisher Scientific). These are coupled with the ForenSeq™ DNA Signature Prep kit (Illumina) and the HID-Ion AmpliSeq™ Identity Panel (Thermo Fisher Scientific), respectively. In this study, we compared the genotyping performance of the two MPS systems based on 83 SNP markers that are present in both MPS marker panels. Results show that MiSeq® FGx™ has greater sample-to-sample variation than the HID-Ion PGM™ in terms of read counts for all the 83 SNP markers. Allele coverage ratio (ACR) values show generally balanced heterozygous reads for both platforms. Two and four SNP markers from the MiSeq® FGx™ and HID-Ion PGM™, respectively, have average ACR values lower than the recommended value of 0.67. Comparison of genotype calls showed 99.7% concordance between the two platforms.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Comparison of Two Massively Parallel Sequencing Platforms using 83 Single Nucleotide Polymorphisms for Human Identification

Apaga

Dennis

Salvador

et al. 2017

Sci Rep

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“…To ascertain which of the explanations have more support, i.e., wrong categorization of the samples before entering the laboratory or a failure of the panel to resolve, these eight samples were analyzed using the MiSeq FGx Forensic Genomics System. The panel of primers included in the ForenSeq TM DNA Signature Prep Kit (used for library generation) contains 56 AIMs [17] (Supplemental Figure 4, Table 3). African American sample 20882 was classified as Hispanic American by our AIMs panel and the ForenSeq TM panel.…”

Section: Resultsmentioning

confidence: 99%

“…SNP typing of eight questionable samples (by ancestry assignment) were analyzed using the Illumina ForenSeq™ DNA Signature Prep Kit as described by Churchill et al [17]. The ancestry assignments between our AIMs panel and that by the AIMs contained within the ForenSeq™ kit were compared for resolving non-concordant population affinity.…”

Section: Concordance Datamentioning

confidence: 99%

Empirical testing of a 23-AIMs panel of SNPs for ancestry evaluations in four major US populations

et al. 2016

Self Cite

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Ancestry informative markers (AIMs) can be used to determine population affiliation of the donors of forensic samples. In order to examine ancestry evaluations of the four major populations in the USA, 23 highly informative AIMs were identified from the International HapMap project. However, the efficacy of these 23 AIMs could not be fully evaluated in silico. In this study, these 23 SNPs were multiplexed to test their actual performance in ancestry evaluations. Genotype data were obtained from 189 individuals collected from four American populations. One SNP (rs12149261) on chromosome 16 was removed from this panel because it was duplicated on chromosome 1. The resultant 22-AIMs panel was able to empirically resolve the four major populations as in the in silico study. Eight individuals were assigned to a different group than indicated on their samples. The assignments of the 22 AIMs for these samples were consistent with AIMs results from the ForenSeq(TM) panel. No departures from Hardy-Weinberg equilibrium (HWE) and linkage disequilibrium (LD) were detected for all 22 SNPs in four US populations (after removing the eight problematic samples). The principal component analysis (PCA) results indicated that 181 individuals from these populations were assigned to the expected groups. These 22 SNPs can contribute to the candidate AIMs pool for potential forensic identification purposes in major US populations.

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Use of Next‐Generation Sequencing in Forensic Genetics

Børsting

Morling

2017

Encyclopedia of Life Sciences

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The main purpose of forensic science institutions is to provide scientifically based investigations to the judicial system and assist society as a whole with objective analyses of evidence. Ten years ago, the invention of clonal amplification by emulsion PCR or bridge PCR inspired a technical revolution in DNA sequencing commonly known as next‐generation sequencing (NGS). New methods and platforms were invented, all with the same purpose of sequencing massive numbers of DNA molecules simultaneously. These methods are of obvious interest to forensic genetic practitioners, who are frequently faced with the challenge of genotyping limited and degraded DNA material extracted from irreplaceable trace samples. NGS may be superior to the existing techniques and offers new exiting possibilities to the end users of forensic investigations. Key Concepts Next‐generation sequencing (NGS) is based on simultaneous clonal amplification of millions of individual DNA molecules and parallel sequencing of the generated products. Fragment length analyses of PCR‐amplified short tandem repeats (STRs) have been the preferred method for human identification in forensic genetic case work for more than two decades. The multiplexing capability of PCR‐NGS and sequencing capacity of NGS platforms make it possible to type different types of markers (STRs, SNPs and INDELs) in one assay, which increases the available information, saves time and reduces the overall cost of the investigation. Human identification and forensic phenotyping may be accomplished simultaneously by typing human identification and phenotypical markers in one PCR‐NGS assay. Detailed sequence information of STRs increases the statistical weight of the DNA evidence and may aid mixture interpretation. Genome or transcriptome sequencing of samples from deceased makes it possible to combine forensic pathology with medical genetics and forensic toxicology with pharmacogenetics.

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Evaluation of the Illumina ® Beta Version ForenSeq™ DNA Signature Prep Kit for use in genetic profiling

Cited by 201 publications

References 18 publications

Comparison of Two Massively Parallel Sequencing Platforms using 83 Single Nucleotide Polymorphisms for Human Identification

Comparison of Two Massively Parallel Sequencing Platforms using 83 Single Nucleotide Polymorphisms for Human Identification

Empirical testing of a 23-AIMs panel of SNPs for ancestry evaluations in four major US populations

Use of Next‐Generation Sequencing in Forensic Genetics

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