Y-GATA-H4 Nomenclature Differences
In the scientific literature, several different nomenclatures have been published for the Y-STR locus GATA-H4 (White et al. 1999, Gonzalez-Neira et al. 2001, Gusmao et al. 2002, Butler et al. 2002). These differences are illustrated below in Figure 1 on the same reference DNA sequence (GenBank accession G42676). The NIST 20plex primer pair (Butler et al. 2002) only targets the H4.1 repeat region and therefore does not match the ISFG DNA Commission nomenclature recommendations for GATA-H4 (Gusmao et al. 2006).
NIST SRM 2395, which provides a physical standard for human Y-chromosome DNA analysis, follows ISFG guidelines (Bar et al. 1997, Gill et al. 2001) for the NIST H4 primer pair: namely the first consecutive, polymorphic repeat motif starting from the 5’end is TAGA. Unfortunately, in the case of GATA-H4 use of a TAGA vs. a GATA repeat designation results in a difference of one repeat unit, which caused some problem in the past with different genetic genealogy companies (see Figure 1).
The Applied Biosystems Yfiler kit follows the NIST SRM 2395 nomenclature for GATA-H4. In order to convert a Yfiler H4 typing result to Gusmao et al. 2002 designation add +9 repeat units (see Mulero et al. 2006).
Some issues with Y-STR nomenclature in the Genetic Genealogy field are described at http://www.relativegenetics.com/relativegenetics/articles/y-chromosome_testing.htm.
References:
Bar W, Brinkmann B, Budowle B, Carracedo A, Gill P, Lincoln P, Mayr WR, Olaisen B. DNA recommendations: Further report of the DNA Commission of the ISFH regarding the use of short tandem repeat systems. Int.J.Legal Med. 1997;110:175-6.
Butler JM, Schoske R, Vallone PM, Kline MC, Redd AJ, Hammer MF. A novel multiplex for simultaneous amplification of 20 Y chromosome STR markers. Forensic Sci.Int. 2002;129:10-24.
Gill P, Brenner C, Brinkmann B, Budowle B, Carracedo A, Jobling MA, de Knijff P, Kayser M, Krawczak M, Mayr WR, Morling N, Olaisen B, Pascali V, Prinz M, Roewer L, Schneider PM, Sajantila A, Tyler-Smith C. DNA Commission of the International Society of Forensic Genetics: recommendations on forensic analysis using Y-chromosome STRs. Forensic Sci.Int. 2001;124:5-10.
Gonzalez-Neira A, Elmoznino M, Lareu MV, Sanchez-Diz P, Gusmao L, Prinz M, Carracedo A. Sequence structure of 12 novel Y chromosome microsatellites and PCR amplification strategies. Forensic Sci.Int. 2001;122:19-26.
Gusmao L, Gonzalez-Neira A, Alves C, Lareu M, Costa S, Amorim A, Carracedo A. Chimpanzee homologous of human Y specific STRs. A comparative study and a proposal for nomenclature. Forensic Sci.Int. 2002;126:129-36.
Gusmao L, Sanchez-Diz P, Alves C, Quintans B, Garci, Poveda E, Geada H, Raimondi E, Mari, Silva dlF, Vide MC, Whittle MR, Zarrabeitia MT, Carvalho M, Negreiros V, Prieto SL, Riancho JA, Campos-Sanchez R, Vieira-Silva C, Toscanini U, Amorim A, Carracedo A. Results of the GEP-ISFG collaborative study on the Y chromosome STRs GATA A10, GATA C4, GATA H4, DYS437, DYS438, DYS439, DYS460 and DYS461: population data. Forensic Sci.Int. 2003;135:150-7.
Gusmão, L., Butler, J.M., Carracedo, A., Gill, P., Kayser, M., Mayr, W.R., Morling, N., Prinz, M., Roewer, L., Tyler-Smith, C., Schneider, P.M. (2006) DNA Commission of the International Society of Forensic Genetics (ISFG): An update of the recommendations on the use of Y-STRs in forensic analysis. Forensic Sci. Int. 157:187-197 and Int. J. Legal Med. 120: 191-200.
Mulero, J.J., Budowle, B., Butler, J.M., Gusmão, L. (2006) Letter to the Editor--Nomenclature and allele repeat structure update for the Y-STR locus GATA H4. J. Forensic Sci. 51(3): 694.
White PS, Tatum OL, Deaven LL, Longmire JL. New, male-specific microsatellite markers from the human Y chromosome. Genomics. 1999;57:433-7.
Figure 1. The relative location of various PCR primers and designated STR repeat nomenclatures for the Y-STR locus GATA-H4. The reference sequence used is GenBank accession G42676 (submitted May 1999 by White et al.).
