Multiplex–PCR of short amplicons for mtDNA sequencing from ancient DNA

Abstract

We here describe a multiplex–PCR method to generate six overlapping short amplicons (100–130 bp) in two separate PCR reactions of non-overlapping fragments for full sequencing of the whole hypervariable region I (HV1). The performance of this multiplex system has been evaluated not only on ancient bone remains (5000–4000 BP) but also on different forensic samples with highly degraded DNA (bone remains, hair shafts, …) that yielded negative PCR results with the mtDNA amplification strategies usually employed in forensic genetics. The multiplex–PCR methodology described in this study also illustrates a potential high throughput strategy to reconstruct the sequence of both coding and non-coding regions of the mtDNA genome from ancient DNA.