Assessing the performance of multi-InDel panels for human identification among admixed Brazilians

Livia Carla Ramos; Luciellen D G Kobachuk; Douglas Mendes Nadur; Luiza Rauen Sabbag; Marianna Maia Taulois do Rosário; Michel S Naslavsky; Celso Teixeira Mendes-Junior; Erick C Castelli

doi:10.1016/j.fsigen.2024.103161

Assessing the performance of multi-InDel panels for human identification among admixed Brazilians

Forensic Sci Int Genet. 2024 Oct 9:74:103161. doi: 10.1016/j.fsigen.2024.103161. Online ahead of print.

Authors

Livia Carla Ramos¹, Luciellen D G Kobachuk², Douglas Mendes Nadur³, Luiza Rauen Sabbag⁴, Marianna Maia Taulois do Rosário⁵, Michel S Naslavsky⁶, Celso Teixeira Mendes-Junior⁷, Erick C Castelli⁸

Affiliations

¹ São Paulo State University (UNESP), Institute of Biosciences, Botucatu, São Paulo, Brazil; Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit - Unipex, School of Medicine, São Paulo State University - UNESP, Botucatu, São Paulo, Brazil; Superintendência da Polícia Técnico-Científica, Núcleo de Perícias Criminalísticas de Bauru, São Paulo, Brazil. Electronic address: livia.ramos@unesp.br.
² Polícia Científica do Paraná, Seção de Genética Molecular Forense, Curitiba, Paraná, Brazil; Department of Genetics, School of Medicine, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil.
³ São Paulo State University (UNESP), Institute of Biosciences, Botucatu, São Paulo, Brazil.
⁴ Department of Genetics, School of Medicine, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil.
⁵ Polícia Científica do Paraná, Seção de Genética Molecular Forense, Curitiba, Paraná, Brazil.
⁶ Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo (USP), São Paulo, São Paulo, Brazil; Hospital Israelita Albert Einstein, São Paulo, São Paulo, Brazil.
⁷ Department of Chemistry, Forensic and Genomics Research Laboratory, Faculty of Philosophy, Science and Letters at Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP 14040-901, Brazil. Electronic address: ctmendes@ffclrp.usp.br.
⁸ Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit - Unipex, School of Medicine, São Paulo State University - UNESP, Botucatu, São Paulo, Brazil; São Paulo State University (UNESP), Department of Pathology, School of Medicine, Botucatu, São Paulo, Brazil. Electronic address: erick.castelli@unesp.br.

PMID: 39418769
DOI: 10.1016/j.fsigen.2024.103161

Abstract

Insertion/deletion polymorphisms, or InDels, are widely present in the human genome. They have been considered as potential markers for forensic analysis because they can be genotyped using the CE platform and compatible typing techniques used in forensic laboratories. Additionally, InDels have lower mutation rates and often short amplicon sizes, making them ideal for detecting degraded samples. However, most InDels are bi-allelic; therefore, their discrimination power is relatively low. A new set of genetic marker called multi-InDels was reported to improve InDel's informativeness. Multi-InDel markers are generally designated as microhaplotypes encompassing two or more InDels within a short distance, usually less than 200 bp. In this study, we evaluated the applicability of three previously proposed panels of multi-InDel markers, designed for Asian populations, for human identification in Brazil. We assessed all the multi-InDel markers using high-coverage whole-genome sequencing data from a census-based cohort of 1171 Brazilians residing in São Paulo, the largest Brazilian capital. The results showed that most markers are informative for Brazilian individuals since they present more than three frequent haplotypes with different sizes. However, most markers are prone to amplification/sequencing errors due to repetitive or low-complexity regions. Among the tested panels, the one from Huang et al. (2014) is the most promising for forensic use in Brazil, with a combined match probability and cumulative power of exclusion of 4.92 ×10^-14 and 0.9991, respectively. Nevertheless, these values are low compared to the ones obtained with CODIS STRs (short tandem repeats) and larger SNP (single nucleotide polymorphisms) panels. Therefore, new attempts to scan the human genome for highly polymorphic multi-InDel markers are still necessary to obtain a suitable panel of multi-InDels for worldwide populations.

Keywords: Brazilian population; DIP-DIP markers; Deletion/insertion polymorphism (DIP); Forensic genetics; Microhaplotypes; Multi-InDel markers.