The challenge of predicting human pigmentation traits in degraded bone samples with the MPS-based HIrisPlex-S system

Magdalena Kukla-Bartoszek; Maria Szargut; Ewelina Pośpiech; Marta Diepenbroek; Grażyna Zielińska; Agata Jarosz; Danuta Piniewska-Róg; Joanna Arciszewska; Sandra Cytacka; Magdalena Spólnicka; Wojciech Branicki; Andrzej Ossowski

doi:10.1016/j.fsigen.2020.102301

The challenge of predicting human pigmentation traits in degraded bone samples with the MPS-based HIrisPlex-S system

Forensic Sci Int Genet. 2020 Jul:47:102301. doi: 10.1016/j.fsigen.2020.102301. Epub 2020 Apr 21.

Affiliations

¹ Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa St. 7, 30-387, Kraków, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa St. 7A, 30-387, Kraków, Poland.
² Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland; The Polish Genetic Database of Totalitarianism Victims, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland.
³ Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa St. 7A, 30-387, Kraków, Poland.
⁴ Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland; The Polish Genetic Database of Totalitarianism Victims, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland; Institut für Rechtsmedizin der Universität München, Nußbaumstr. 26, 80336, München, Germany.
⁵ Department of Forensic Medicine, Jagiellonian University Medical College, Grzegórzecka St. 16, 31-531, Kraków, Poland.
⁶ Biology Department, Central Forensic Laboratory of the Police, Aleje Ujazdowskie 7, 00-583, Warszawa, Poland.
⁷ Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa St. 7A, 30-387, Kraków, Poland; Department of Forensic Medicine, Jagiellonian University Medical College, Grzegórzecka St. 16, 31-531, Kraków, Poland.

PMID: 32387914
DOI: 10.1016/j.fsigen.2020.102301

Abstract

Identification of human remains is an important part of human DNA analysis studies. STR and mitochondrial DNA markers are well suited for the analysis of degraded biological samples including bone material. However, these DNA markers may be useless when reference material is not available. In these cases, predictive DNA analysis can support the process of human identification by providing investigative leads. Forensic DNA phenotyping has progressed significantly by offering new methods based on massively parallel sequencing technology, but the frequent degradation processes observed in skeletal remains can make analysis of such samples challenging. In this study, we demonstrate the usefulness of a recently established Ion AmpliSeq^TM HIrisPlex-S panel using Ion Torrent technology for analyzing bone samples that show different levels of DNA degradation. In total, 63 bone samples at post-mortem intervals up to almost 80 years were genotyped and eye, hair and skin colour predictions were performed using the HIrisPlex-S models. Following the recommended coverage thresholds, it was possible to establish full DNA profiles comprising of 41 DNA variants for 35 samples (55.6%). For 5 samples (7.9%) no DNA profiles were generated. The remaining 23 samples (36.5%) produced partial profiles and showed a clear underperformance of 3 HIrisPlex-S SNPs - rs1545397 (OCA2), rs1470608 (OCA2) and rs10756819 (BNC2), all used for skin colour prediction only. None of the 23 samples gave complete genotypes needed for skin colour prediction was obtained, and in 7 of them (25.9%) the 3 underperformed SNPs were the cause. At the same time, the prediction of eye and hair colour using complete IrisPlex and HIrisPlex profiles could be made for these 23 samples in 20 (87.0%) and 12 cases (52.2%), respectively. Complete HIrisPlex-S profiles were generated from as little as 49 pg of template DNA. Five samples for which the HIrisPlex-S analysis failed, consistently failed in standard STR analysis. Importantly, the 3 underperforming SNPs produced significantly lower number of reads in good quality samples. Nonetheless, the AUC loss resulting from missing data for these 3 SNPs is not considered large (≤0.004) and the prediction of pigmentation from partial profiles is also available in the current HPS tool. The study shows that DNA degradation and the resulting loss of data are the most serious challenge to DNA phenotyping of skeletal remains. Although the newly developed HIrisPlex-S panel has been successfully validated in the current research, primer redesign for the 3 underperforming SNPs in the MPS design should be considered in the future.

Keywords: Forensic DNA Phenotyping; Polish Genetic Database of Totalitarianisms Victims; massively parallel sequencing; prediction reliability; skeletal remains.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Body Remains
Bone and Bones / chemistry*
DNA / genetics
DNA Degradation, Necrotic
DNA Fingerprinting
Eye Color / genetics*
Forensic Genetics / methods
Genotype
Hair Color / genetics*
High-Throughput Nucleotide Sequencing*
Humans
Phenotype
Polymorphism, Single Nucleotide*
Skin Pigmentation / genetics*

Substances

DNA