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From: Patrick Guinness <>
Subject: [DNA] DYS464 / new primer
Date: Tue, 11 Nov 2003 15:12:36 +0000


Greetings List,

Was I the only person to notice that DYS464 at the NIST site is blank?

http://www.cstl.nist.gov/div831/strbase/str_y464.htm

(Home page
http://www.cstl.nist.gov/div831/strbase/index.htm )


However, an Austrian team has now published a paper with a
different primer (as 13% of their 135 donors showed intermediate
alleles). How many of us have 'ambiguities' at DYS464?

PG

Forensic Science International
Volume 137, Issues 2-3 , 26 November 2003, Pages 221-230

doi:10.1016/j.forsciint.2003.07.002 Cite or link
using doi Copyright ©
2003 Elsevier Ireland Ltd. All rights reserved.

Announcement of population data

Molecular characterization and Austrian Caucasian
population data of the
multi-copy Y-chromosomal STR DYS464

Burkhard Berger, Harald Niederstätter, Anita
Brandstätter and Walther
Parson,

Institute of Legal Medicine, University of Innsbruck,
Müllerstrasse 44,
A-6020, Innsbruck, Austria

Received 5 May 2003; revised 24 July 2003; accepted
30 July 2003. ;
Available online 24 September 2003.


Abstract

DYS464 is a multi-copy STR system with four positions
on the Y-chromosome
(DYS464a, b, c, and d) which was recently identified and
characterized [Forensic
Sci. Int. 130 (2002) 97]. The aims of our study were to
perform a population
study, to estimate the mutation rate and an extensive
sequence analysis in order
to confirm the nomenclature. Fourteen different alleles were
found in an
Austrian population sample with an allele length varying from
9 to 19 repeats.
All alleles were cloned and sequenced. Alleles 9?x2013;19
showed the general
repeat structure (CCTT)n ... (CCTT)2 ... (CCTT)3 ... (CCTT)4
... (CCTT)2 ...
(CCTT)2. The nomenclature is based on the number of repeated
units of the
variable (CCTT)n-stretch only. In 13% of the samples
intermediate alleles,
namely 14.3A, 14.3B and 15.3 were detected. In these alleles
the variable repeat
block is interrupted by a CTT motif (14.3A:
(CCTT)3CTT(CCTT)11; 14.3B and 15.3:
(CCTT)7CTT(CCTT)7/8). A comparison with GenBank entries
revealed the existence
of a length variant due to a deletion of one cytosine in the
5' flanking region
of the first repeat block. We designed an alternative forward primer to
circumvent possible ambiguities in the allele designation. A
total of 54
different genotypes were identified in 135 men corresponding
to a discrimination
capacity (DC) of 40% and a gene diversity (GD) of 0.97. These
values are much
higher than those of other Y-chromosomal short tandem repeats
(Y-STRs). DYS464
has the same haplotype diversity (HD) as the combination of
the five Y-STR loci
with the lowest gene diversities of the Y-STR core set. On
the other hand, a
combination of the three most diverse loci (DYS464, DYS385
and DYS390) has the
same capacity to distinguish between paternal lineages than
the complete minimal
haplotype (minHT) consisting of eight Y-STR loci. In our
population sample the
addition of DYS464 to the minHT increases the number of
different haplotypes
from 110 to 122. The mutation-rate estimate based on the 70
meioses analyzed
amounts to 2.86?10-2 (95% confidence interval 3.5?10-3 to
9.95?10-2). This value
is approximately 10 times higher than the average
mutation-rate estimate for
Y-STRs.

Author Keywords: Y-chromosome; DYS464; Short tandem
repeat; Y-STR; Minimal
haplotype; Population study; Mutation rate; Forensics


Corresponding author. Tel.: +43-512-507-3303; fax:
+43-512-507-2764.


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