Keywords

RNA-seq; genomics; coding-region SNPs; SNPs; forensic genomics; single nucleotide polymorphisms

Abstract

This study explores the use of coding-region, forensically-relevant single nucleotide polymorphisms (SNPs) from RNA sequencing data. SNPs present distinct advantages over short tandem repeat (STR) typing, particularly in niche scenarios, such as in samples with low-quantity DNA templates or in degraded samples with substantially fragmented DNA. While RNA is susceptible to rapid ex-vivo degradation, mRNA has demonstrated unexpected stability in dried body fluid stains, contingent upon the storage conditions. This paper presents a pipeline designed to identify forensically relevant coding region single nucleotide polymorphisms (cSNPs) from RNA-seq data.

The forensically relevant cSNPs utilized in this study were sourced from a previously published paper that identified a panel of 35 body fluid-specific cSNPs. Our pipeline demonstrated effectiveness in identifying forensically relevant cSNPs across various tissue categories. However, the final analysis raises concerns about the overall specificity of this panel of cSNPs and issues with cross-reactivity for different body fluids.

Overall, this study contributes to the advancement of forensic genetics by providing a robust and standardized pipeline for identifying cSNPs from RNA-seq data. While further evaluation and optimization are necessary, the demonstrated efficacy of this pipeline holds promise for enhancing genetic profiling in forensic contexts.

Thesis Completion Year

2024

Thesis Completion Semester

Spring

Thesis Chair

Yooseph, Shibu

College

College of Engineering and Computer Science

Department

Computer Science

Thesis Discipline

Computer Science

Language

English

Access Status

Campus Access

Length of Campus Access

1 year

Campus Location

Orlando (Main) Campus

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