When I look back on 2018, I see a year dominated in the journals by massively parallel sequencing (MPS) in many facets. While it would be exhausting to detail every relevant paper from the year, I wanted to share some of the themes and a handful of the papers I found interesting when taking a moment to look back.
In-Depth Evaluations of the MiSeq FGx® Forensic Genomics Solution
It was clear from the volume of publications in the forensic genomics journals about MPS that the technology has reached widespread acceptance, with the MiSeq FGx Forensic Genomics Solution represented in the vast majority of the work. The following collection of articles related to evaluating the performance of the Solution, all arrived at similar conclusions:
- The University of Copenhagen published a thorough comparison of the assay and software to solutions available for CE for a variety of sample types, highlighting applications. Namely, the analysis of mixtures and low-level samples outperformed with MPS vs. the legacy CE technology[i].
- A detailed and substantial inter-laboratory effort was published by the EU-funded DNASeqEx project to evaluate its performance. They concluded “the results of this inter-laboratory study confirm that the ForenSeq® DNA Signature Prep Kit is able to sustain reliable and accurate results and thus corroborate earlier findings”[ii].
- The U.S. Federal Bureau of Investigation (FBI) evaluated the technology with reference samples and came to an identical conclusion: “this MPS chemistry and its associated instrument platform and software were determined to be a robust system that yields accurate and reliable data when used with high quality/quantity samples.”[iii]
- The Genomics Center of the AMMS at the Beijing Institute of Radiation Medicine evaluated the system with specific attention paid to the performance relating to input quantity and degradation index (DI) with multiple, interesting findings[iv]. Importantly, they point out that autosomal STRs were more valuable for low input DNA, with SNPs showing their potential in highly degraded samples.
Real World Implications Investigated
A number of laboratories have moved beyond the evaluation phase and begun looking at the Verogen Solution under different optimization parameters and application to real-world situations.
- The Australian Federal Police optimized their operation for a qPCR normalization procedure over the magnetic bead approach described in the ForenSeq DNA Signature Prep Kit Reference Guide[v],[vi].
- Sam Houston State University, in collaboration with the University of North Texas Health Sciences Center (UNTHSC), performed a side-by-side comparison of the MiSeq FGx Forensic Genomics Solution against the HID-Ion AmpliSeq™ Library Kit and ID panel on the Ion PGM™ System. An inhibitor titration showed the Solution outperformed in hematin and calcium and marginally underperformed against melanin and collagen[vii].
- The Institute of Legal Medicine in Ulm, Germany working in collaboration with the Bavarian State Criminal Police Office, Institute of Forensic Sciences, compared CE and MPS in bone samples when identifying human remains. They found that while CE provided adequate discrimination power, the simultaneous inclusion of sex chromosomes, phenotype, and biogeographical ancestry information can promote an investigation “from the ‘passive comparison’ into the ‘active search’ stage”.[viii]
- The Zhongshan School of Medicine at Sun Yat-sen University evaluated the ForenSeq DNA Signature Prep Kit for paternity testing and found it “powerful for paternity and full sibling testing and most second degree relationships including half siblings, grandparent-grandchild and uncle/aunt-nephew/niece”[ix].
Forensic Population Sequencing
The introduction of MPS to forensic genomics provides numerous benefits with considerable excitement around one in particular: significant gains in discrimination power. Isoalleles, or alleles of the same length that differ by the sequence makeup, provide an additional dimension to the data and require these population studies in order to describe the statistical relevance.
- King’s College London kicked off the year with an analysis of 400 samples of White British and British Chinese populations, showing concordance and significant sequence variation for the repeat region[x].
- The University of Copenhagen followed suit with an investigation of 363 Danish population samples, extending the analysis in to the flanking region with similar results as King’s[xi].
- UNTHSC followed up on their previous work but investigated microhaplotypes identifiable in the flanking regions of their 714-sample collection[xii]. They summarize that the haplotypes identified “significantly improve the discrimination power of the multiplex and can facilitate mixture interpretation”[xiii].
- July was a hot month for population sequencing as three separate studies were accepted in to the literature representing global diversity:
- The National Institute of Standards and Technology (NIST) published a foundational study on the 1036 samples of their standard U.S. population set with analysis of the flanking region[xiv].
- The Supreme Prosecutors’ Office in the Republic of Korea reported on a population of 209 Koreans with a wonderful description of the power of discrimination results per locus for MPS vs. CE[xv].
- Finally, the University of Santiago de Compostela with King’s College London published an extensive analysis on the HGDP-CEPH collection of 944 individuals, spanning seven continentally-defined population groups[xvi].
In all of these studies, the authors concluded that MPS is concordant to CE results with tangible gains in discrimination power.
Massively parallel sequencing witnessed a watershed year in the journals for 2018 and the topics above only scratch the surface. There were other important works published on everything from mtDNA analysis to early efforts with probabilistic genotyping, genetic genealogy to phenotype estimation. If 2018 is any indication, 2019 will be an even more exciting year in the advancement of this technology.
Do you have a project or idea for a study that could advance the field of forensic genomics? We want to hear about it! Contact us to discuss how we might collaborate effectively and make good things happen in 2019!
[i] Hussing, Christian, et al. “Sequencing of 231 Forensic Genetic Markers Using the MiSeq FGx™ Forensic Genomics System – an Evaluation of the Assay and Software.” Forensic Sciences Research, vol. 3, no. 2, Mar. 2018, pp. 111–123., doi:10.1080/20961790.2018.1446672.
[ii] Köcher, Steffi, et al. “Inter-Laboratory Validation Study of the ForenSeq™ DNA Signature Prep Kit.” Forensic Science International: Genetics, vol. 36, 2018, pp. 77–85., doi:10.1016/j.fsigen.2018.05.007.
[iii] Moreno, Lilliana I., et al. “A Closer Look at Verogen’s Forenseq™ DNA Signature Prep Kit Autosomal and Y-STR Data for Streamlined Analysis of Routine Reference Samples.” Electrophoresis, vol. 39, no. 21, Dec. 2018, pp. 2685–2693., doi:10.1002/elps.201800087.
[iv] Zhang, Qingzhen, et al. “Evaluation of the Performance of Illumina’s ForenSeq™ System on Serially Degraded Samples.” Electrophoresis, vol. 39, no. 21, Oct. 2018, pp. 2674–2684., doi:10.1002/elps.201800101.
[v] Mehta, Bhavik, et al. “Comparison between Magnetic Bead and QPCR Library Normalisation Methods for Forensic MPS Genotyping.” International Journal of Legal Medicine, vol. 132, no. 1, 2017, pp. 125–132., doi:10.1007/s00414-017-1591-9.
[vii] Elwick, Kyleen, et al. “Comparative Tolerance of Two Massively Parallel Sequencing Systems to Common PCR Inhibitors.” International Journal of Legal Medicine, vol. 132, no. 4, 2017, pp. 983–995., doi:10.1007/s00414-017-1693-4.
[viii] Kulstein, Galina, et al. “As Solid as a Rock—Comparison of CE- and MPS-Based Analyses of the Petrosal Bone as a Source of DNA for Forensic Identification of Challenging Cranial Bones.” International Journal of Legal Medicine, vol. 132, no. 1, 2017, pp. 13–24., doi:10.1007/s00414-017-1653-z.
[x] Devesse, Laurence, et al. “Concordance of the ForenSeq™ System and Characterisation of Sequence-Specific Autosomal STR Alleles across Two Major Population Groups.” Forensic Science International: Genetics, vol. 34, 2018, pp. 57–61., doi:10.1016/j.fsigen.2017.10.012.
[xi] Hussing, C., et al. “The Danish STR Sequence Database: Duplicate Typing of 363 Danes with the ForenSeq™ DNA Signature Prep Kit.” International Journal of Legal Medicine, 2018, doi:10.1007/s00414-018-1854-0.
[xii] Churchill, Jennifer D, et. al. “Population and performance analyses of four major populations with Illumina’s FGx Forensic Genomics System.” Forensic Science International: Genetics, vol. 30, 2017, pp. 81–92., doi:10.1016/j.fsigen.2017.06.004.
[xiii] King, Jonathan L., et al. “Increasing the Discrimination Power of Ancestry- and Identity-Informative SNP Loci within the ForenSeq™ DNA Signature Prep Kit.” Forensic Science International: Genetics, vol. 36, 2018, pp. 60–76., doi:10.1016/j.fsigen.2018.06.005.
[xiv] Gettings, Katherine Butler, et al. “Sequence-Based U.S. Population Data for 27 Autosomal STR Loci.” Forensic Science International: Genetics, vol. 37, 2018, pp. 106–115., doi:10.1016/j.fsigen.2018.07.013.
[xvi] Phillips, Christopher, et al. “Global Patterns of STR Sequence Variation: Sequencing the CEPH Human Genome Diversity Panel for 58 Forensic STRs Using the Illumina ForenSeq DNA Signature Prep Kit.” Electrophoresis, vol. 39, no. 21, Mar. 2018, pp. 2708–2724., doi:10.1002/elps.201800117.