The Human Genome Project, from one perspective, began in 1981 with the publication 1 of the complete sequence of human mitochondrial DNA (mtDNA). The Cambridge reference sequence (CRS), as it is now designated, continues to be indispensable for studies of human evolution, population genetics and mitochondrial diseases. It has been recognized for some time, however, that the CRS differs at several sites from the mtDNA sequences obtained by other investigators 2, 3. These discrepancies may reflect either true errors in the original sequencing analysis or rare polymorphisms in the CRS mtDNA. A further complication is that the original mtDNA sequence was principally derived from a single individual of European descent, although it also contained some sequences from both HeLa and bovine mtDNA (ref. 1). To resolve these uncertainties, we have completely resequenced the original placental mtDNA sample.

The results of the resequencing confirm that there are both errors and rare polymorphisms in the CRS (Table 1). There are 11 nucleotide positions at which the original sequence contains the incorrect nucleotide (all sequences here refer to that of the CRS mtDNA L-strand), one of which involves the CC doublet at positions 3,106 and 3,107 in the original sequence, which is actually a single cytosine residue. The other errors are mistakes in the identification of single base pairs and typically involve the incorrect assignment of a guanine residue. Errors at nt 14,272 and 14,365 result from the use of the bovine mtDNA sequence at ambiguous sites 1. There are an additional seven nucleotide positions at which the original CRS is correct and which represent rare (or even private) polymorphic alleles. Six of these polymorphisms are single base pair substitutions, although one involves the simple repeat of cytosine residues at nt 311–315. The CRS has five residues in this repeat, whereas most other human mtDNAs have six.