Genome-wide SNP typing of ancient DNA: Determination of hair and eye color of Bronze Age humans from their skeletal remains.

Nicole Schmidt,Katharina Schücker,Thilo Dörk,Ina Krause,Michael Klintschar,Susanne Hummel

doi:10.1002/ajpa.23996

Abstract

A genome-wide high-throughput single nucleotide polymorphism (SNP) typing method was tested with respect of the applicability to ancient and degraded DNA. The results were compared to mini-sequencing data achieved through single base extension (SBE) typing. The SNPs chosen for the study allow to determine the hair colors and eye colors of humans. The DNA samples were extracted from the skeletal remains of 59 human individuals dating back to the Late Bronze Age. The 3,000 years old bones had been discovered in the Lichtenstein Cave in Lower Saxony, Germany. The simultaneous typing of 24 SNPs for each of the ancient DNA samples was carried out using the 192.24 Dynamic Array™ by Fluidigm®. Thirty-eight of the ancient samples (=64%) revealed full and reproducible SNP genotypes allowing hair and eye color phenotyping. In 10 samples (=17%) at least half of the SNPs were unambiguously determined, in 11 samples (=19%) the SNP typing failed. For 23 of the 59 individuals, a comparison of the SNP typing results with genotypes from an earlier performed SBE typing approach was possible. The comparison confirmed the full concordance of the results for 90% of the SNP typings. In the remaining 10% allelic dropouts were identified. The high genotyping success rate could be achieved by introducing modifications to the preamplification protocol mainly by increasing the DNA input and the amplification cycle number. The occurrence of allelic dropouts indicates that a further increase of DNA input to the preamplification step is desirable.

Highlights

Knowledge of our ancestor's outer appearance helps to understand where we come from and the complex process of human migration, pigmentation, and adaptive processes to different climatic conditions (Parra, 2007)
Single nucleotide polymorphisms (SNPs) are the favored genetic markers used for forensic DNA phenotyping approaches (Fareed & Afzal, 2013)
Besides a variety of different phenotyping kits which can be used for eye and hair color prediction (Draus-Barini et al, 2013; Walsh et al, 2013) there is a multitude of methods for analyzing SNPs

Summary

Introduction

Knowledge of our ancestor's outer appearance helps to understand where we come from and the complex process of human migration, pigmentation, and adaptive processes to different climatic conditions (Parra, 2007). KEYWORDS ancient and degraded DNA, eye color, genome wide, hair color, high-throughput SNP typing, phenotype Besides a variety of different phenotyping kits which can be used for eye and hair color prediction (Draus-Barini et al, 2013; Walsh et al, 2013) there is a multitude of methods for analyzing SNPs. When it comes to analyzing degraded DNA samples, the fragmentation of the DNA is a major obstacle.

Results

Conclusion