Fragmented Nuclear DNA is the Predominant Genetic Material in Human Hair Shafts.

Michael D Brandhagen,Jodi A Irwin,Odile Loreille

doi:10.3390/genes9120640

Abstract

While shed hairs are one of the most commonly encountered evidence types, they are among the most limited in terms of DNA quantity and quality. As a result, nuclear DNA short tandem repeat (STR) profiling is generally unsuccessful and DNA testing of shed hair is instead performed by targeting the mitochondrial DNA control region. Although the high copy number of mitochondrial DNA relative to nuclear DNA routinely permits the recovery of mitochondrial DNA (mtDNA) data in these cases, mtDNA profiles do not offer the discriminatory power of nuclear DNA profiles. In order to better understand the total content and degradation state of DNA in single shed hairs and assess the feasibility of recovering highly discriminatory nuclear DNA data from this common evidence type, high throughput shotgun sequencing was performed on both recently collected and aged (approximately 50-year-old) hair samples. The data reflect trends that have been demonstrated previously with other technologies, namely that mtDNA quantity and quality decrease along the length of the hair shaft. In addition, the shotgun data reveal that nuclear DNA is present in shed hair and surprisingly abundant relative to mitochondrial DNA, even in the most distal fragments. Nuclear DNA comprised, at minimum, 88% of the total human reads in any given sample, and generally more than 95%. Here, we characterize both the nuclear and mitochondrial DNA content of shed hairs and discuss the implications of these data for forensic investigations.

Highlights

Shed hairs are one of the most commonly encountered evidence types [1], and among the most limited in terms of DNA quantity and quality
The overall patterns of mitochondrial DNA (mtDNA) quantity and quality observed within a single hair were the same regardless of DNA purification method
While we have shown here that complete mtGenomes can be recovered from extremely old hair even without enrichment, hybridization capture assays that enrich for mtDNA

Summary

Introduction

Shed hairs are one of the most commonly encountered evidence types [1], and among the most limited in terms of DNA quantity and quality. Nuclear DNA (nuDNA) is generally too low in quantity and quality to permit successful short tandem repeat (STR) typing. The difficulty of successful STR typing of shed hairs is attributed primarily to the keratinization process, which degrades cellular organelles and nucleic acids [4]. Some nuclear DNA is known to persist in telogen hairs, albeit at low quantities and highly variable qualities [4]. Though a number of studies describe the presence, and successful PCR amplification, of autosomal STR markers from telogen hairs [2,8,9,10,11,12], STR typing is not routinely pursued in forensic laboratories for a number of reasons

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