Defining mtDna Haplogroups

Over the course of typing mtDNA samples from various populations, researchers have observed that individuals often cluster into haplogroups that can be defined by particular polymorphic nucleotides (see Wallace et al. 1999, Ruiz-Pesini et al. 2004). These haplogroups were originally defined in the late 1980s and 1990s by grouping samples possessing the same or similar patterns when subjected to a series of restriction enzymes that were used to separate various mtDNA types from diverse populations around the world (Table 10.8). Mitochondrial DNA haplogroups have now been correlated to HV1/HV2 polymorphisms as well as entire mtGenome variation. Haplogroups A, B, C, D, E, F, G, and M are typically associated with Asians while most Native Americans fall into haplogroups A, B, C, and D. Haplogroups L1, L2, and L3 are African, and haplogroups H, I, J, K, T, U, V, W, and X are typically associated with European populations (Wallace et al. 1999).

Along the same lines as the multiplex SNP detection assay described above for resolving samples containing the most common HV1/HV2 types, Brandst├Ątter et al. (2003) described a multiplex SNP system for categorizing European Caucasian haplogroups. This approach involves the analysis of 16 coding region SNPs to aid assignment of individual samples into one of the nine major European Caucasian mtDNA haplogroups listed above. For example, the presence of a cyto-sine at position 7028 indicates that the sample can be grouped into haplogroup H as opposed to the other groups whose individuals possess a thymine at 7028.

Another SNP typing assay was recently reported to examine 17 coding region SNPs in a single multiplexed detection assay (Quintans et al. 2004). A SNaPshot reaction (see Chapter 8) is used to probe the following mtDNA nucleotide positions: 3010, 3915, 3992, 4216, 4336, 4529, 4580, 4769, 4793, 6776, 7028, 10398, 10400, 10873, 12308, 12705, and 14766. This assay was capable of


Coding Region

Control Region Polymorphisms



(*not including 263G, 315.1C)

A (Asian) B (Asian) C (Asian) D (Asian) H (Caucasian) H1 (Caucasian) H2 (Caucasian) H3 (Caucasian) H4 (Caucasian) H5 (Caucasian) H6 (Caucasian) H7 (Caucasian) I (Caucasian) J (Caucasian) J1 (Caucasian) J2 (Caucasian) K (Caucasian) L1 (African)

U5 (Caucasian) V (Caucasian) W (Caucasian)


9 bp deletion, 16159C 13263G

2092T, 5178A, 8414T 7028C, 14766C 3010A

1438A, 4769A






1719A, 8251A, 10238C 4216C, 12612G, 13708A 3010A

7476T, 15257A 12372A, 14798C 2758A, 3594T, 10810C

3594T 3594C

10400T, 10873C

709A, 1888A, 4917G, 10463C, 13368A, 14905A, 15607G, 15928A, 8697A


4580A, 15904T

709A, 1243C, 8251A, 8697G, 8994A

16233T, 16290T, 16319A, 235G 16217C, 16189C 16233T, 16298C, 16327T 16362C

73A and lack of CRS differences* 73A and lack of CRS differences* 73A and lack of CRS differences* 73A and lack of CRS differences* 73A and lack of CRS differences* 73A and lack of CRS differences* 73A and lack of CRS differences* 73A and lack of CRS differences* 16223T, 199C, 204C, 250C 16069T, 16126C, 295T 462T 195C

16224C, 16311C

16187T, 16189C, 16223T, 16278T, 16311C

16223T, 16278T 16223T

16223T, 16298C 16126C, 16294T

16270T 16298C, 72C

16223T, 189G, 195C, 204C, 207A

X (Caucasian)

1719A, 6221C, 8251G, 14470C 16189C, 16223T, 16278T, 195C

Table 10.8 Major mitochondrial haplogroups and the specific polymorphisms in the coding region or control region that define them (see Finnila et al. 2001, Herrnstadt et al. 2002, Brandstatter et al. 2003, Kong et al. 2003, Allard et al. 2004, Quintans et al. 2004). Note that not all haplogroups, which have been defined in the literature, are listed here.

breaking 266 samples into 20 different mtDNA haplogroup designations and aided in resolving some of the most common type (i.e., 263G, 315.1C) haplogroup H samples from one another.

Forensic population databases have been analyzed in terms of haplogroup information to aid in quality control of samples contained within a population group (Allard et al. 2002, Budowle et al. 2003, Allard et al. 2004).

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