Professional Documents
Culture Documents
Lectura 3. Frecuencia Alélica-Allele Frequencies For 26miniSTRs
Lectura 3. Frecuencia Alélica-Allele Frequencies For 26miniSTRs
htm
*
Official Disclaimer: Contribution of the U.S. National Institute of Standards and
Technology. Not subject to copyright. Certain commercial equipment, instruments and
materials are identified in order to specify experimental procedures as completely as
possible. In no case does such identification imply a recommendation or endorsement by
the National Institute of Standards and Technology nor does it imply that any of the
materials, instruments or equipment identified are necessarily the best available for the
purpose. Points of view in this document are those of the authors and do not necessarily
represent the official position or policies of the U.S. Department of Justice.
Sources of Support: National Institute of Justice (NIJ) funded the work described here
through an interagency agreement with the NIST Office of Law Enforcement Standards.
KEYWORDS: forensic science, population genetics, DNA typing, DNA profiling, short tandem repeats,
STR, miniSTR, D1GATA113E02, D1S1627, D1S1677, D2S441, D2S1776, D3S3053, D3S4529,
D4S2364, D4S2408, D5S2500, D6S474, D6S1017, D8S1115, D9S1122, D9S2157, D10S1248, D10S1435,
D11S4463, D12ATA63A05, D14S1434, D17S974, D17S1301, D18S853, D20S482, D20S1082,
D22S1045, U.S. Caucasian, African American, and U.S. Hispanic populations
Page 1 of 6
Allele Frequencies for 26 MiniSTR Loci http://www.cstl.nist.gov/biotech/strbase/NISTpop.htm
including 265 Caucasian, 260 African American, and 140 Hispanic, were extracted for
DNA, quantified, diluted to approximately 1 ng/µL, and separated into seven 96-well
plates as previously described (1). Twenty new miniSTR markers were identified and
chosen based on their size and location on certain chromosomes and are described in an
accompanying publication (2, co-submitted). The candidate loci are all either located on
chromosomes that differ from the 13 CODIS core loci or are at least ~ 50 MB apart from
an existing CODIS locus on the same chromosome, and therefore likely unlinked from
that particular marker. These 20 new loci were selected following the criteria (i.e. high
heterozygosity and low allele spread) described in Coble and Butler (3). They are listed
samples were tested with the original 6 miniSTR loci (NC01 and NC02) described in the
Coble 2005 paper (3). A revised nomenclature is used for several of these loci (2).
Foster City, CA) using 1 ng of population sample DNA, 1X GeneAmp® PCR Gold buffer
Corporation, Cleveland, OH), 0.2 µM primers (2), 1 U AmpliTaq Gold DNA polymerase
(Applied Biosystems), and 0.16 mg/mL BSA (Sigma-Aldrich, St. Louis, MO), in a 10 µL
total reaction volume. The PCR amplification conditions using the 9700 were as follows:
denaturation for 10 min at 95ºC, amplification for 28 cycles of 1 min at 94ºC, 1 min at
59ºC, and 1 min at 72ºC, extension for 45 min at 60ºC, and a final soak at 25ºC.
by adding 1 µL PCR product and 0.35 µL GS500-LIZ internal size standard (Applied
Page 2 of 6
Allele Frequencies for 26 MiniSTR Loci http://www.cstl.nist.gov/biotech/strbase/NISTpop.htm
Prism® 3100 Genetic Analyzer without prior denaturation of samples. POP™-6 (Applied
Biosystems) rather than POP™-4 was utilized for higher resolution separations on a 36
cm array. Samples were injected electrokinetically for 10 s at 3 kV. Bins and panels
were created in GeneMapperID from population information (data not shown) and used
to determine allele calls for the population samples. At least two separate alleles were
sequenced at each STR locus to provide appropriate allele repeat numbers (2).
A total of 665 unique miniSTR profiles were evaluated for each new marker: 663
males and 2 females. The resultant data were evaluated using the PowerMarker statistics
test p-values and Polymorphism Information Content (PIC) in the three U.S. populations
http://www.cstl.nist.gov/biotech/strbase/NISTpop.htm .
References
1. Butler J.M., Schoske R., Vallone P.M., Redman J.W., Kline M.C. (2003) Allele
frequencies for 15 autosomal STR loci on U.S. Caucasian, African American, and
Hispanic Populations. J Forensic Sci 48(4): 908-911.
2. Hill C.R., Coble M.D., Kline M.C., Butler J.M. (2006) Development of additional
new miniSTR loci for improved analysis of degraded DNA samples. Co-
submitted to J Forensic Sci.
3. Coble M.D. and Butler J.M. (2005) Characterization of new miniSTR loci to aid
analysis of degraded DNA. J Forensic Sci 50: 43-53.
4. Liu J. and Muse S.V. (2005) PowerMarker: Integrated analysis environment for
genetic marker data. Bioinformatics 21(9): 2128-2129.
http://statgen.ncsu.edu/powermarker/index.html, v3.24
Page 3 of 6
Allele Frequencies for 26 MiniSTR Loci http://www.cstl.nist.gov/biotech/strbase/NISTpop.htm
TABLE 1 -- U.S. Caucasian, African American, and Hispanic allele frequencies for 26 new miniSTR loci
Page 4 of 6
Allele Frequencies for 26 MiniSTR Loci http://www.cstl.nist.gov/biotech/strbase/NISTpop.htm
Page 5 of 6
Allele Frequencies for 26 MiniSTR Loci http://www.cstl.nist.gov/biotech/strbase/NISTpop.htm
D20S1082 D22S1045
Allele Total Cauc. Afr. Am. Hisp. Allele Total Cauc. Afr. Am. Hisp.
8 0.0008 0.0019 8 0.0038 0.0097
9 9
10 0.0045 0.0116 10 0.0204 0.0428 0.0179
11 0.4639 0.5604 0.3263 0.5357 11 0.1193 0.1396 0.1304 0.0607
12 0.0633 0.0698 0.0695 0.0393 12 0.0317 0.0151 0.0564 0.0179
13 0.0489 0.0057 0.1100 0.0179 13 0.0076 0.0094 0.0039 0.0107
14 0.1642 0.1132 0.2413 0.1179 14 0.0597 0.0585 0.0798 0.0250
15 0.2003 0.1925 0.1815 0.2500 15 0.3293 0.3321 0.2588 0.4536
16 0.0512 0.0509 0.0579 0.0393 16 0.2832 0.3623 0.1868 0.3107
17 0.0030 0.0075 17 0.1337 0.0792 0.2101 0.0964
18 0.0091 0.0038 0.0156 0.0071
N 664 265 259 140 19 0.0023 0.0058
H(ob) 0.6958 0.6528 0.7915 0.6000
P 0.0789 0.2827 0.5150 0.1146 N 663 265 257 140
PIC 0.6725 0.5908 0.7504 0.5851 H(ob) 0.7840 0.7849 0.8171 0.7214
P 0.0453 0.9191 0.2013 0.1133
PIC 0.7418 0.6853 0.8027 0.6348
N: sample size; H(ob): observed heterozygosity; P : Hardy-Weinberg equilibrium, exact test; PIC: polymorphism information content
Page 6 of 6