Reanalysis and review of the Cambridge reference series for human mitochondrial DNA

The Human Genome Project, from a certain point of view, began in 1981 with the publication1 of the entire human mitochondrial DNA (mtDNA) series. The Cambridge Reference Sequence (CRS), as now controlled, remains indispensable for studies. human evolution, population genetics, and mitochondrial disease; however, it has been identified for some time that CRS differs in several versions of mtDNA series received through other researchers2,3. These discrepancies possibly reflect true errors in original sequencing research or polymorphisms in CRS mtDNA. A further complication is that the original mtDNA series was mainly derived from a single individual of European origin, although it also comprises some series of HeLa mtDNA and farm animals (ref. 1). For those doubts, we absolutely resequent the original sample of placenta mtDNA.

The resequencing effects verify that there are infrequent errors and polymorphisms in the CRS (Table 1). There are 11 nucleotide positions in which the original series comprises the correct type nucleotide (all series here refer to that of the L strand of the RSC mtDNA), one of which reaches the CC doublet at positions 3. 106 and 3. 107 in the original series, which is truly an unmarried cytosine residue. Other errors are errors in the identity of unique base pairs and regularly involve the correct assignment of a guanine residue Errors in 14. 272 and 14. 365 nt are the result of the use of the bovine mtDNA series at ambiguous sites. There are seven additional nucleotide positions in which the original CRS is of the correct type and which constitute infrequent (or even private) polymorphic alleles. are substitutions of undeniable base pairs, the undeniable repetition of cytosine residues in nt 311-315 is reached. CRS has five residues in this repetition, while max. imum other human mtDNA have six.

To find out which errors in CRS resulted from the use of HeLa’s mtDNA series, we did series of the entire Mitochondrial Genome of HeLa (data not shown). He is of African descent and differs from the CRS published on various sites. it is possible that simply using the HeLa series was that of nt 14,766 (T vs. C, respectively).

The mtDNA of the revised CRS belongs to the European haplogroup H on the basis of cytosine in nt 14. 766 (instead of thymine in the original CRS) and cytosine in nt 7. 028 (instead of thymine 4, 5, 6). haplogroup H is shown through the absence of any planned restriction adjustment that characterizes other European haplogroups from mtDNA4,6.

If we arrive with the technical errors (8) and errors (3) caused by the speculation of the bovine mtDNA and HeLa series, the overall error frequency for the original CRS research was 0. 07%, highlighting the remarkable feat of Sanger and his colleagues. However, due to its widespread use, we propose that the CRS for human mtDNA be revised as follows: (i) the ten undeniable substitution errors deserve to be corrected; (ii) infrequent polymorphic alleles should be retained (i. e. the revised SCR (RCRS) will have to be a true reference set and not a consensus set); and (iii) the original numbering of the nucleotides must be retained. The last suggestion represents a compromise between accuracy (correction of numbering to account for only residue C at 3,106 and 3,107 nt) and consistency with previous literature. all in the past, adjustments of known series greater than 3,106 nt would create an unacceptable point of confusion.

Issue Date: October 1999

DOI: doi. org/10. 1038/13779

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