Mitochondrial DNA tests

From ISOGG Wiki
Jump to: navigation, search
Map of human migration out of Africa, according to mitochondrial DNA. The numbers represent thousands of years before present time. The blue line represents the area covered in ice or tundra during the last great ice age. The North Pole is at the centre. Africa, the centre of the start of the migration, is at the top left and South America is at the far right.

A mitochondrial DNA test (mtDNA test) traces a person's matrilineal or mother-line ancestry using the DNA in his or her mitochondria. mtDNA is passed down by the mother unchanged, to all children. If a perfect match is found to another person's mtDNA test results, one may find a common ancestor in the other relative's (matrilineal) "information table". However, because mtDNA mutations are very rare, the match will not necessarily be within a genealogical time frame.

Contents

What gets tested

mtDNA by current conventions is divided into three regions. They are the coding region (00577-16023) and two hyper-variable regions (HVR1 [16024-16569], and HVR2 [00001-00576]). All test results are compared to the mtDNA of a European in haplogroup H2a2a. This early sample is known as the Cambridge Reference Sequence (CRS). An updated reference sequence was subsequently published and samples are now compared to the revised Cambridge Reference Sequence (rCRS). A list of single-nucleotide polymorphisms (SNPs) is returned. The relatively few "mutations" or "transitions" that are found are then reported simply as differences from the CRS, such as in the examples just below.

In 2012 Behar et al proposed using an inferred ancestral reference sequence known as the Reconstructed Sapiens Reference Sequence.[1] Bandelt et al (2013) questioned the use of the RSRS and proposed the retention of the rCRS.[2] Genetic genealogy companies have continued to report results in comparison with the rCRS. Family Tree DNA report results in comparison with both the rCRS and the RSRS. The Genographic Project currently reports results in comparison with the RSRS.

The two most common mtDNA tests are a sequence of HVR1 and a sequence of both HVR1 and HVR2. Some mtDNA tests may only analyze a partial range in these regions. With falling prices the preferred option is now to test both HVR1 and HVR2. Family Tree DNA stopped offering the basic HVR1 test in May 2013.

Many people are now choosing to have the full mitochondrial genome sequenced (scientifically called the mtDNA genome or mitogenome). This is at times called the mtDNAFullSequence, the Mega Test, or the full mitochondrial sequence (FMS) test.[Footnote 1] An FMS test will report results for all 16,569 bases in the mtGenome and will provide the most detailed subclade assignment. An exact FMS match usually indicates a shared common ancestor within a genealogical timeframe.

Family Tree DNA and GeneBase are the only two companies that currently offer the FMS test. The Genebase FMS test is only available to existing customers as an upgrade. A full sequence test was previously available from the now defunct company Argus Biosciences.

Understanding test results

The most basic of mtDNA tests will sequence hyper-variable Region 1 (HVR1). HVR1 nucleotides are numbered 16024-16569. Some test reports might omit the 16 prefix from HVR1 results, i.e. 519C and not 16519C.

Region HVR1 HVR2
Differences from rCRS 111T,223T,259T,290T,319A,362C Not Tested

More extensive tests will also sequence Hyper Variable Region 2 (HVR2). HVR2 nucleotides are numbered 00001-00576.

Region HVR1 HVR2
Differences from rCRS 111T,223T,259T,290T,319A,362C 073G,146C,153G

Family Tree DNA customers who have ordered a full mitochondrial sequence test from FTDNA can order a custom mtDNA report from ISOGG member Dr Ann Turner to help them understand their results.

mtDNA tree

The most up-to-date version of the mtDNA tree can be viewed at www.phylotree.org. Phylotree is now on Build 16. Updates are released between two and four times a year. As of January 2013 the different testing companies are using different versions of Phylotree. FTDNA is using Build 14, and the Genographic Project is using Build 13 or 14. FTDNA has indicated that they "have plans to upgrade to V15 as part of a coordinated effort with the National Geographic Genographic project".[3] 23andMe uses Phylotree Build 7.

An up-to-date haplogroup assignment can be obtained from James Lick's mtHap utility. This tool is usually updated within 24 hours of the release of each new Phylotree build.

Haplofind is an alternative and less sophisticated tool more suited for batch processing mtDNA full sequence results. It does provide a list of mutations with reported and associated medical implications.

Understanding mtDNA testing

Videos

A video of a presentation by ISOGG member Maurice Gleeson showing how mitochondrial DNA testing can be used in family history research:

Bill Hurst, the administrator of the mtDNA haplogroup K, project, describes how he successfully used mtDNA testing to unravel the tale of two sisters:

mtDNA databases

FTDNA resources

Blog posts

Articles

Resources

References

  1. Behar DM, Van Oven M, Rosset S et al. A "Copernican" reassessment of the human mitochondrial DNA tree from its root. American Journal of Human Genetics 2012; 90 (5): 936.
  2. The case for the continuing use of the revised Cambridge Reference Sequence (rCRS) and the standardization of notation in human mitochondrial DNA studies Bandelt HJ, Kloss-Brandstatter A, Richards MB et al. Journal of Human Genetics 2014 59(2): 66-77.
  3. Family Tree DNA Learning Center. What version of the mtDNA tree does FTDNA use? 1 November 2013.

Footnotes

  1. FMS is a historic industry joke because it is a female test and FGS rhymes with PMS (Pre-Menstrual Syndrome).
  2. The New England Historic Genealogical Society published NEXUS until the Nov-Dec.1999 issue. They replaced it with New England Ancestors which in turn was succeeded by the winter 2010 issue of American Ancestors.

See also

Licence

This article is licensed under the GNU Free Documentation Licence. It incorporates material from the Wikipedia article "Genealogical DNA test".