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Construction and validation of a new set of autosomal microhaplotypes of InDels for human identification and analysis of degraded and mixtured samples

Grant number: 22/13924-5
Support Opportunities:Regular Research Grants
Duration: June 01, 2023 - May 31, 2025
Field of knowledge:Biological Sciences - Genetics - Human and Medical Genetics
Principal Investigator:Erick da Cruz Castelli
Grantee:Erick da Cruz Castelli
Host Institution: Faculdade de Medicina (FMB). Universidade Estadual Paulista (UNESP). Campus de Botucatu. Botucatu , SP, Brazil
Associated researchers:Celso Teixeira Mendes Junior ; Marianna Maia Taulois do Rosário ; Michel Satya Naslavsky

Abstract

Identifying a suspect from a degraded sample and/or a sample composed of several unbalanced genetic profiles is a great challenge in forensic genetics. The use of STRs (short tandem repeats) markers by Polymerase Chain Reaction (PCR) and capillary electrophoresis (EC) represent the gold standard for DNA forensic analysis. However, this methodology has important limitations in the face of these forensic challenges. New markers, classified as microhaplotypes, have shown promising results for human identification, ancestry estimation, deconvolution of DNA profiles, and obtaining genetic profiles from degraded samples. Such microhaplotypes are constituted by two or more polymorphisms, such as STRs, SNPs (single nucleotide polymorphisms), and InDels (insertion-delection), also called DIPs (deletion-insertion polymorphisms), and occurring in a short segment of DNA (<200bp ). Compared to STRs, InDels typically have smaller amplification products, considerably lower mutation rates, and do not produce artifacts called stutters (which impair the detection and interpretation of mixtures). Compared to SNPs, InDels are length polymorphisms, which makes EC analysis possible, a technology widely present in forensic laboratories. However, the degree of polymorphism, considered its main limitation, can be increased when multiple InDels nearby form haplotypes, called multi-InDels. In this way, we propose constructing and validating a new set of autosomal multi-InDels markers, consisting of two or more InDels loci in short DNA segments, which have a high power of discrimination and exclusion. We will computationally explore sequencing data from publicly available complete genomes (Project 1000 genomes and HGDP) and Brazilians (Project SABE) to detect valid candidate regions for application in Brazil and other populations. Such microhaplotypes will be organized in a multiplex assay for analysis by capillary electrophoresis, which will facilitate transferring this technology to forensic laboratories. Then, we will test this new set of markers in real cases, enabling the resolution of civil and criminal cases involving critical samples. (AU)

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