A Rare Mutation in the Primer Binding Region of the Amelogenin Gene Can Interfere with Gender Identification

Abstract

PCR amplification of part of the X-Y homologous amelogenin gene with a single primer pair has been used as a sex identification test because it generates different length products from the X and Y chromosomes. Using a commercially available kit that contains amelogenin primers, we report a single phenotypically normal Caucasian male out of 327 males tested to date that failed to show an X chromosomespecific PCR product. Using alternative amelogenin primers external to but encompassing the initial amplicon, an X chromosome-specific product was seen. Sequence analysis of this X-specific PCR product revealed a C to G mutation at the most 3 base of the initial reverse amelogenin PCR primer. An alternative reverse PCR primer with this most 3 base deleted showed X-and Y-specific products from the case study male. Rare mutations that result in a failure to amplify sex chromosome-specific products can result in incorrect gender identification. Amelogenin is a protein of dental enamel that is present on the human X and Y chromosomes, and deletion of this gene causes X-linked amelogenesis imperfecta, a genetic disorder affecting enamel formation.

Genomic identification in the historical case of the Nicholas II royal family

“…Previous reports revealed failure of the amelogenin sex determination tests in some cases. Deletions or mutations in primer binding sites for X and Y chromosome amelogenin homologs occur in human populations and may lead to gender misidentification (11)(12)(13). To avoid this potential problem, we have developed a gender-identification system adapted for the analysis of degraded DNA.…”

Development of SNP-based human identification system

“…The genes encoding amelogenin and zinc finger proteins are routinely used for sex determination [22][23][24]. For STRbased determination of sex, 6 bp deletion polymorphisms located in intron 3 of the amelogenin gene, on the X chromosome, can generally be detected by size differences [23].…”

“…For STRbased determination of sex, 6 bp deletion polymorphisms located in intron 3 of the amelogenin gene, on the X chromosome, can generally be detected by size differences [23]. Previous studies have performed SNP-based sex determination by examining differences in the sequences of the amelogenin genes located on the X and Y chromosomes [9].…”

Null alleles of the X and Y chromosomal amelogenin gene in a Chinese population

“…Commercially available kits for genotyping short tandem repeats (STRs) usually contain the AMEL primers and have been widely used in DNA databasing, forensic casework, prenatal diagnoses, and transplantation monitoring. Several studies have reported mutations in the X or Y homologue of the AMEL gene, which could cause amplification failure of AMELX or AMELY and result in incorrect sex identification [3][4][5][6][7][8][9][10][11][12]. In the Chinese population, however, some scattered cases with AMEL gene mutations have been reported [5][6][7], although no systematic analysis of the frequency data based on large samples has been done.…”