Sequencing Summaries of Unusual STR Alleles

For the past several years, our group at NIST has been sequencing unusual STR alleles found by members of the human identity testing community. Some of these alleles possess point mutations in primer binding sites leading to null alleles while others are "off-ladder" variants. Sequencing these unusual alleles helps to reveal the molecular basis for their variation. This site will include summaries of our findings (along with who provided the sample).

Recent Presentations Regarding Findings Through STR Allele Sequencing:

Margaret Kline talk at 57th Annual Meeting of the American Academy of Forensic Sciences (New Orleans, LA), February 25, 2005, "Some Interesting Point Mutations and Deletions Found Through STR Allele Sequencing" [.pdf]

Margaret Kline talk at Bode East Coast Advanced DNA Technology Workshop (Duck Key, FL), May 24, 2005, "Finding Point Mutations, Deletions and New Alleles Through STR Allele Sequencing" [.pdf]

Variant allele characterization


Locus Variant Allele Sample Source Comments
TPOX 10.3 Maryland State Police Deletion of a "G" that is 157 bp from the repeat region under PowerPlex 1.1 and Identifiler primers does not affect primer binding or allele sizing . However, PowerPlex 2.1 and PowerPlex 16 products are 1 bp smaller because they are further away from the repeat and encompass the deletion.
FGA 46.2 Denver Crime Laboratory Checked with Identifiler allelic ladder
D18S51 null allele 18 FSS and Kuwait government lab Base change was a C-to-T transition 172 bp downstream of the repeat region which impacts the ABI D18S51 reverse primer but not the PowerPlex 16 D18S51 reverse primer that is internal to this mutation
D18S51 40 Nebraska State Crime Lab DNA sequence analysis showed 40 GAAA repeats
D18S51 "5.3" DNA Solutions DNA sequence analysis revealed a 9 bp deletion beyond the end of the 8th repeat unit to produce a "5.3" allele
DYS392 "10.2" AFDIL DNA sequence analysis revealed a C-to-G transversion 180 bp upstream of the STR repeat region; the mutation causes an apparent mobility shift of approximately 0.75 bp such that the allele falls outside of the +/-0.5 bp genotyping bin
DYS635 21.3 NIST U.S. population samples DNA sequence analysis revealed a deletion of a "T" in the repeat region; full repeat was [TCTA]4(TGTA)2[TCTA]2(TGTA)2[TCTA]2(TGTA)2 [TCTA]5 TC-A [TCTA]2
Penta D 18 DNA Solutions DNA sequence analysis confirmed 18 repeats
Penta D "8.2" Peter de Knijff's lab at Leiden University DNA sequence analysis revealed a 13 bp deletion prior to a [AAAGA]11 repeat
Penta D 6 Peter de Knijff's lab at Leiden University DNA sequence analysis confirmed 6 repeats
D19S433 "11.3" Peter de Knijff's lab at Leiden University A sequence difference causes a mobility shift relative to the allelic ladder; DNA sequence analysis found [AAGG]12 repeats whereas the nominal allele 12 is [AAGG]3 [AAGT]2 [AAGG]7


Locus duplication or deletion

Butler, J.M., Decker, A.E., Kline, M.C., Vallone, P.M. (2005) Chromosomal duplications along the Y-chromosome and their potential impact on Y-STR interpretation. J. Forensic Sci. 50(4): 853-859.

DYS390 duplication (MN BCA)

DYS390 deletion (CFS Toronto)

DYS392 deletion (MN BCA)

DYS392 deletion (AFDIL)


More information coming soon...

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Last Updated: 09/21/2015