Common Nomenclature For Str Alleles

To aid in inter-laboratory reproducibility and comparisons of data, a common nomenclature has been developed in the forensic DNA community. DNA results cannot be effectively shared unless all parties are speaking the same language and referring to the same conditions. (It would do little good to describe the recipe for baking a cake in a language that is not understood by both the recipe giver and the chef. For example, if the recipe says to turn the oven on to 450 degrees Fahrenheit and the chef uses 450 Kelvin (~250°F), the results would be vastly different.) Likewise if one laboratory calls a sample 15 repeats at a particular STR locus and the same sample is designated 16 repeats by another laboratory, a match would not be considered, and the samples would be assumed to come from separate sources. As will be discussed in Chapter 18, the advent of national DNA databases with many laboratories worldwide contributing information has made it crucial to have internationally accepted nomenclature for designating STR alleles.

A repeat sequence is named by the structure (base composition) of the core repeat unit and the number of repeat units. However, because DNA has two strands, which may be used to designate the repeat unit for a particular STR marker, more than one choice is available and confusion can arise without a standard format. Also, where an individual starts counting the number of

->

1 2

3

4 5 6

5'

-TTTCCC TCAT TCAT

TCAT

TCAT TCAT TCAT TCACCATGGA - 3'

3'

- AAAGGG AGTA AGTA

AGTA

AGTA AGTA AGTA AGTGGTACCT - 5'

6

5

4 3 2 1

<-

repeats can also make a difference. With double-stranded DNA sequences being read in the 5' to 3' direction (see Chapter 2), the choice of the strand impacts the sequence designation. For example, the 'top' strand for an STR marker may be 5'-...(GATA)„...-3' while the 'bottom' strand for the same sequence would be 5'-...(TATC)B .-3'. Depending on the sequence surrounding the repeat region, the core repeat could be shifted relative to the other strand (Figure 5.2).

Recognizing the need for standardization in STR repeat nomenclature, a committee of forensic DNA scientists, known as the DNA Commission of the International Society of Forensic Haemogenetics (ISFH), issued guidelines for designating STR alleles in 1994 (Bar et al. 1994) and again in 1997 (Bar et al. 1997). The ISFH is now known as the International Society of Forensic Genetics (ISFG; see http://www.isfg.org/). The ISFG 1994 recommendations focused on allelic ladders and designation of alleles that contain partial repeat sequences. The ISFG 1997 guidelines discuss the sequence and repeat designation of STRs.

When reviewing the STR literature prior to 1997, an individual should keep in mind that repeat nomenclatures often differ from the ISFG 1997 guidelines. This fact can lead to some confusion if one is not careful. For example, early descriptions of the STR locus TH01 by the Forensic Science Service label the repeat TCAT (Kimpton et al. 1993) while Caskey and co-workers described the TH01 repeat as AATG (Edwards et al. 1991).

The latest ISFG recommendations are reviewed below (Bar et al. 1997):

Choice of the Strand

■ For STRs within protein coding regions (as well as in the intron of the genes), the coding strand should be used. This would apply to STRs such as VWA (GenBank: M25716), TPOX (GenBank: M68651), and CSF1PO (GenBank: X14720).

■ For repetitive sequences without any connection to protein coding genes like many of the D#S### loci, the sequence originally described in the literature of the first public database entry shall become the standard reference (and strand) for nomenclature. Examples here include D18S51 (GenBank: L18333) and D21S11 (GenBank: M84567).

Figure 5.2 Example of the DNA sequence in a STR repeat region. Note that using the top strand versus the bottom strand results in different repeat motifs and starting positions. In this example, the top strand has six TCAT repeat units, while the bottom strand has six TGAA repeat units. Under ISFH recommendations (Bar et al. 1997), the top strand from GenBank should be used. Thus, this example would be described as having [TCAT] as the repeat motif. Repeat numbering, indicated above and below the sequence, proceeds in the 5' to 3' direction as illustrated by the arrows.

■ If the nomenclature is already established in the forensic field but not in accordance with the aforementioned guideline, the nomenclature shall be maintained to avoid unnecessary confusion. This recommendation applies to the continued use by some laboratories of the 'AATG repeat' strand for the STR marker TH01. The GenBank sequence for TH01 uses the coding strand and therefore contains the complementary 'TCAT repeat' instead.

Choice of the Motif and Allele Designation

■ The repeat sequence motif should be defined so that the first 5'-nucleotides that can define a repeat motif are used. For example, 5'-GG TCA TCA TCA TGG-3' could be seen as having 3 x TCA repeats or 3 x CAT repeats. However, under the recommendations of the ISFH committee only the first one (3 x TCA) is correct because it defines the first possible repeat motif.

■ Designation of incomplete repeat motifs should include the number of complete repeats and, separated by a decimal point, the number of base pairs in the incomplete repeat. Examples of 'microvariants' with incomplete repeat units include allele 9.3 at the TH01 locus. TH01 allele 9.3 contains nine tetranucleotide AATG repeats and one incomplete ATG repeat of three nucleotides (Puers et al. 1993). Another microvariant example is allele 22.2 at the FGA locus, which contains 22 tetranucleotide repeats and one incomplete repeat with two nucleotides (Barber et al. 1996).

■ Allelic ladders containing sequenced alleles that are named according to the recommendations listed above should be used as a reference for allele designation in unknown samples. Allelic ladders may be commercially obtained or prepared in house and should contain all common alleles.

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