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VALIDATION OF THE Y-STR SYSTEMS BY RELIAGENE, Y-
PLEXTM 5 AND Y-PLEXTM 6, ON THE ABI PRISM ® 3100

presented by
HEATHER D. WOOD

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MS. degree in Forensic Science

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2/05 czfilRC/Dateouejnddp. 15

VALIDATION OF THE Y-STR SYSTEMS BY RELIAGENE, Y-PLEXTM 5 AND Y-
PLEXTM 6, ON THE ABI PRISM® 3100

By

Heather D. Wood

A THESIS

Submitted to
Michigan State University
in partial fulfillment of the requirements
for the degree of
MASTER OF FORENSIC SCIENCE
CRIMINAL JUSTICE

2005

ABSTRACT

VALIDATION OF THE Y-STR SYSTEMS BY RELIAGENE, Y-PLEXTM 5 AND Y-
PLEXTM 6, ON THE ABI PRISM® 3100

By
Heather D. Wood

Y-STR analysis can be useful when autosomal DNA typing fails. Particularly
mmmmfltmmblemscanafisevvithamm analysis, whenthere isa
high female DNA! low male DNA ratio, when no sperm cells are present (e.g.
azoospcrmic semen, blood, saliva, fingernail scrapings), or when there is more than one
male assailant. There are several Y-STR amplification systems that have been generated,
some of which are commercially available.
The Reliagene Y-STR systems Y-PLEX'” 5 and Y-PLEXTM 6 enable simultaneous
amplification of eleven loci on the Y- chromosome. The overall goal of this project was
to validate these Y-STR systems for analysis on an ABI Prism® 3100 genetic analyzer at
the Michigan State Police Forensics Science Division. This was accomplished by
conducting studies to determine the minimum sensitivity of each Y-PLEXTM system, the
precision ofallele sizing using both an ABI Prism® 310 and 3100 genetic analyzer, and
the concordance between the two instruments. Finally, an interethnic study was
conducted by analyzing approximately 100 samples from three ethnic groups, Caucasian,
Afi'ican American and Hispanic. The minimum sensitivity for the Y-PLEXNS and Y-
PLEXTM6 systems were 0.3125ng and 1.25ng respectively. In the interethnic study an
increase in the haplotype diversity and the number of unique haplotypes was observed
when comparing the haplotypes containing the 11 loci of ir-PLEX1M 5 and 6 compared to

the haplotypes containing either the Y-PLEXTM 5 or 6 loci alone

ACKNOWLEDGMENTS

I would like to acknowledge my committee members, Dr. David Foran, Dr. Jay
Siege], Dr. Nibedita Mahanti, and Dr. Chris Smith. I would like to especially thank Dr.
Siegel for giving me this opportunity and Dr. Foran for being so patient with me. In
addition I would like to thank the Michigan State Police personnel at the Forensic
Science Division in Lansing, M1 for allowing me the opportunity to perform my thesis

research intheir lab.

iii

TABLE OF CONTENTS

LIST OF TABLES .......... v
LIST OF FIGURES ............................................................................... vi
INTRODUCTION ................................................................................. 1
MATERIALS AND METHODS ................................................................. 8
RESULTS .......................................................................................... 14
DISCUSSION ....................................................................................... 18
APPENDD( ........................................................................................... 27
BIBLIOGRAPHY .................................................................................. 70

iv

LIST OF FIGURES

Figurel ........................................................................................ 62
Figure2 ........................................................................................ 62
Figure3 ........................................................................................ 63
Figure4 ........................................................................................ 63
FigureS ........................................................................................ 64
Figure6 ........................................................................................ 64
Figure? ........................................................................................ 65
Figure8 ........................................................................................ 65
Figure 10 ....................................................................................... 66
Figure 11 ....................................................................................... 67
Figure 12 ....................................................................................... 68
Figure 13 ....................................................................................... 68
Figure 14 ....................................................................................... 69

Introduction:

Establishing the identification of a perpetrator is crucial to solving a crime.
During the commission of a crime evidence may be transferred from victim to perpetrator
and vice versa. Evidence may also be transferred from the victim and perpetrator to the
crime scene thus placing them at that scene. Physical evidence transferred during the
commission of a crime such as a sexual assault, homicide, or burglary can be very
valuable in solving the case.

The powerful DNA typing technology used by forensic scientists today makes it
possible to potentially identify the perpetrator. The standard method of nuclear DNA
typing utilizes the polymerase chain reaction (PCR) to amplify a series of short tandem
repeats (STRS). A STR region consists of a specific sequence of between 2 and 6 DNA
nucleotides that are tandemly repeated (Ayub et al., 2000). STR regions can consist of
simple tandem repeats such as (AGAT)n or compound tandem repeats such as
(T CT G/T CTA)n and are distributed throughout the human genome. At any given STR
location or locus (plural loci) STRs may vary in size based on the number of repeats, thus
generating different alleles. A high degree of discrimination among individuals (except
identical twins) can be accomplished when multiple STR loci are examined. The forensic
community routinely uses multiplex PCR systems to amplify up to 15 different autosomal
(non-sex chromosomes) loci in a single tube reaction. Most forensic labs have adopted
the use of the 13 core tetrameric STR loci that were selected by the Federal Bureau of
Investigations to constitute the core of the United States national database CODIS

(Combined DNA Index System).

STR Typing

STR amplification systems exist for autosomal and Y chromosome (male specific
sex chromosome) typing. Autosomal chromosomes are inherited as homologous pairs
(one fi'om each parent) therefore, for each STR locus an individual has two alleles. For
example at the STR locus D31358 an individual could have one chromosome that has 12
tandem repeats while the other chromosome has 18, resulting in the genotype 12/18. The
fi'equency of this combination can be calculated for the population or ethnic group under
consideration. The product rule can then be applied when calculating the autosomal
profile frequency because the STR loci used in forensics are inherited independently of
one another. The autosomal genotypic fi'equencies for each allele are multiplied to obtain
a statistic that states the likelihood that another person would share the same profile. For
example, within a given population or ethnic group, if the genotype 12/18 for the
autosomal STR locus D31358 occurs at a frequency of 8.2% and the genotype 19/24 for
the autosomal STR locus FGA occurs at a frequency of 1.7% then the two fiequencies
would be multiplied together to determine the profile fiequency for D31358 and FGA
which would mm in 0.14% of this population or group. As can be seen, the level of
discrimination increases as one increases the number of STR loci examined. When using
the 13 CODIS loci the random match probability can reach one in a trillion or higher,
thus resulting in a high level of discrimination.

Y-STR Typing

Although autosomal typing systems have proven to be very successful in forensic

casework, there are cases when autosomal DNA typing fails. Particularly true in sexual

assaults, problems can arise with autosomal analysis when there is a high female DNA/

low male DNA ratio, when no sperm cells are present for differential extraction (e. g.
azoospermic semen, blood, saliva, fingernail scrapings), or when there is more than one
maleassailant. Whentheseparationofmaleandfemalecellsisnotpossible,theend
result is a profile containing up to fotn' or more alleles per locus, making interpretation
very difficult ifnot impossible. In these cases, Y chromosome STR analysis can aid in
successfully obtaining a male specific profile or profiles. Furthermore, Y chromosome
testingismucheasierthanautosomal S'I'Rprofileanalysiswhenanalyzingmixturesas
there is only one allele per locus per male.

Y-STR analysis does lmve limitations compared to autosomal STR analysis.
Bwausethe Ychromosomeispasseddownfrom fathertosonwithoutrecombinationthe
males inthat particularpaternal lineage will have the same haplotype (Y-STR profile),
making exclusion of males fiom the same paternal lineage impossible. Also, the product
ndecannotbeappliedwhencalctdafingthehaplotypefiequencybeeausetheY
clnornosomeisinheritedintact. lnstead,thecountingmethodisusedtoestimateY-STR
haplotype fi'equency. This involves counting how many times a haplotype occurs in a set
ofsunplestdren from aspecific populationorethnic group. Obviouslythe largerthe
sample size the more reliable is this fi'equency estimate.

The Y chromosome

TheYchromosomeis60megabases(Mb)insize,approximatelyone—thirdthe
size of the X We (Skaletsky et al., 2003). It is the smallest chromosome in the
humangenome,afactthatcanbeatuibutedtogenelossresultingfiomtheY
chromosome’s indility to repair itself via homologous recombination as autosomal and

thefernaleXchromosomescanMarshallGraves,2004). Onlythepseudoautosomal

regions (PARS), located at the terminal tips ofthe Y chromosome, participate in
recombination with the X chromosome during male meiosis. The PARs account for 5%
oftheYchmmosomeandtheremaimng95%istermedthemn-mcombiningY(NRY)or
as male specific Y (MSY) (Skaletsky et al., 2003).
TheYchmmosomewasoncethoughtofasadegenaategeneticwastelandthat
onlyservedthepuposeofmalesexdetermimtion. But,thatwayofthinkinghasbeen
drastically changed based on DNA sequence dataof the MSY. Skaletsky etal., (2003)
buihedanSYuacombirflionofhetaochmmfinmdthreeclassesofemhmmafic
sequences:X-transposed,X-degenerate,andampliconic. 'l‘heheterochronnticregionis
cow oftwo highly repetitive seqtmce families (DYZl and DYZZ), 3.4 Mb ofX-
hamposedsequencesrepflcatedfiomflieXchrunosomeleasdemflfionyeusam
8.4MbofX-degareratesapremesthdmerunmntsofmdentaNosomesfiomwhich
themodandeYclnmnosomevolvedanddrerunairfinglOleofanSYis
Wofdreunpliconicmgimcontaining8mspecificgenesma02003;
Skaletskyetal.,2003). Interestingly,these8genesuepreaemintwocopiesfacingeach
othaanirmrhngesmdmedbyZ—UOKblengthspacerseqmncesmaozom;
Rozenetal.,2003). Ithasbeenshowntlntwhenthere'namutuioninonecopyofa
mapdEcganitiscareaedorrephcedbydreothacopybygeneconversion
(Marshall Graves, 2004; Rozenet al., 2003).
YMMarkers
TheYchromosomehmborsmanymarkersflratcanbeusedforidemitypupoaes
MmeYsinglemlwfidepdymphismsW-SNPS),andY-

STRs. Sex identification is readily achieved by amplifying either the sex-determining

gene of the Y (SRY), or the amelogenin gene. The SRY gene is responsible for testicular
determination (Quintana-Marci and Fellows, 2001). The amelogenin gene encodes
proteins found in tooth enamel, and is located on both the X and Y chromosomes in
slightly different lengths due to a 6 base pair deletion within intron 1 on the X
chromosome, making it an ideal sex discriminatory tool (Nakatani et al., 1991).

Y-STRs and Y-SNPs can be used for several human identity applications such as
male specific DNA amplification in rape cases, paternity testing involving male children,
missing person cases, human migration and evolution studies, and historical and
genealogical research (Butler, 2003). Because of Y-SNPs low generational mutation rate

of 2.0 X 10 '8 (2.0 mutations out of 100,000,000 father/son pairs analyzed) (Jobling,

2001), they are most useful in studies with long historical time lines. Y-SNPs have also
been investigated for forensic use because of their male specificity, the ability to analyze
highly degraded DNA (40 to 50 base pair fragments), and the potential for automation
(Jobling, 2001; Sanchez et al., 2003; Vallone and Butler, 2004). It has also been
suggested that Y-SNPs can be used to determine the ethnic background of a perpetrator
(Jobling, 2001), however, Vallone and Butler (2004), determined that when looking at 50
different Y-SNPs, the ethnicity of US. male DNA samples cannot be inferred most
times. Y-SNP analysis will most likely not overtake the use of Y-STRs in forensics, but
they may be used to support Y-STR data.

Y-S‘I'Rs are more applicable to forensic science because they have a greater
discriminatory power per locus than Y-SNPs due to higher mutation rates and an

increased number of alleles per marker. Kayser and Sajantila (2001) estimated that Y-

STRs used in forensics have an average generational mutation rate of 2.8 X 10 ‘3 (2.8

mutations per 1000 father/son pairs analyzed) when they investigated 4,999 male
germline transmissions fiom confirmed father/son pairs. Although, over 200 Y-STRs
have been identified, only a small subset is used extensively in forensic analysis (Butler,
2003). In 1997 the Ernopean forensic community decided on a core set of Y-STR loci
termed the “minimal haplotype” that includes DYSl9, DYS385 a/b, DYS389I,
DYS389II, DYS390, DYS391, DYS392, and DYS393 (Roewer et al., 2001). The
European “extended haplotype” includes the minimal haplotype loci plus YCAII a/b
(Roewer et al., 2001). In early 2003 the US Scientific Working Group on DNA Analysis
Methods (SWGDAM) selected a core set of loci that includes the minimal haplotype plus
DYS438 and DYS439, which is referred to as the US. haplotype (Butler, 2003). Of the
minimal haplotype loci, only DYS393 and DYSl9 occur on the short arm of the Y
chromosome, the remaining loci are located on the long arm (Butler, 2003). The minimal
haplotype has been used extensively used for population studies (Bosch et al, 2002 and
Schoske et al., 2004) and thousands of minimal haplotype profiles are located in the Y-
STR haplotype reference database fi'om several difl‘erent regions including Europe and
the United States (Roewer et al., 2001).
Y-STR Amplification Systems

There are several Y-STR amplification systems that have been generated, some of
which are commercially available. Commercial kits containing the US. haplotype
include Reliagene systems (Y-PLEX1M 5 and Y—PLEXTM 6, Y-PLEXm 12) and
PowerPlex® Y by Promega. Y-PLEXTM 5 enables simultaneous amplification of five
loci on the Y- chromosome including DYS389I, DYS389II, DYS439, DYS438, and

DYS392. Y-PLEX'“ 6 enables simultaneous amplification of six loci including

DY8393, DYSl9, DYSB89II, DYS390, DYS391, and DYS385. Therefore, Y-PLEXTM 5
and 6 together contain the US. haplotype with DYS389II overlapping between the two
systems. Y-PLEXT” 12 is a compilation of the Y-STRs in Y-PLEX‘“ 5 and 6 plus the
amelogenin marker. PowerPlex® Y enables simultaneous amplification of the US.
haplotype Y-STRs plus DYS437. These commercially available kits enable the forensic
community to easily perform Y-STR typing.

Other non-commercially available Y-STR amplification kits include multiplex
systems containing the US. and European extended haplotype plus other polymorphic Y-
STR loci (Butler et al., 2002; Schoske et al., 2004), multiplex systems containing the US.
haplotype plus other polymorphic loci (Bosch et al., 2002), and multiplex systems that
contain other polymorphic Y-STR loci (Hanson and Ballantyne, 2004). The overall goal
of designing a Y-STR multiplex is to generate a set of markers that can be amplified in
one multiplex reaction and has high discriminating power. The investigation of other
polymorphic Y-STR loci to be included in forensic evaluation is beneficial because by
increasing the number of polymorphic Y-STR loci the power of discrimination increases,
however, in all cases these must be validated.

The overall goal of this project was to validate the Reliagene Y-STR systems, Y-
PLEX'“ 5 and Y-PLEX'"6 for analysis on an ABI Prism® 3100 genetic analyzer at the
Michigan State Police Forensics Science Division. This was accomplished by conducting
studies to determine the minimum sensitivity of each Y-PLEXTM system, the precision of
allele sizing using both an ABI Prism® 310 and 3100 genetic analyzer, and the
concordance between the two instruments. Finally, an interethnic study was conducted by

analyzing approximately 100 samples fiom three ethnic groups, Caucasian, Afiican

American, and Hispanic. The results were evaluated using single locus and haplotype
statistics. The data produced were compared to the validation studies of Y--PLEXTM 5
and 6 published by Reliagene.
Materials and Methods:
DNA Samples

A single source semen sample of 4 mL was donated for the sensitivity study. The
samplewasdilutedwith lOmLofsterilewater,and5 plofthedilutedsemenwas
deposited onto three separate 1 cm2 cotton swatches. The swatches were allowed to dry
at room temperature prior to DNA extraction. Forty previously extracted DNA samples
fiom the Scientific Working Group on DNA Analysis Methods (SWGDAM) were
utilized for the concordance study. One hundred fifty three Hispanic, 109 Caucasian, and
101 Afiican American DNA samples for the interethnic study came from anonymous un-
related male human blood samples that were previously extracted by personnel floor the
Michigan State Police Forensic Science Division.
DNA Extraction

The three semen stains were each cut into 8 small pieces, approximately 0.125
cm2 in size, and all 8 pieces were placed into 1 Spin-Ease (Gibco BRL) extraction tube
either labeled A, B, or C. One hundred and fifty pl TNE (10 mM Tris, 0.1 M NaCl,1
mM EDTA), 50 pl of 20% Sarkosyl, 40 pl of 0.39 M dithiothreitol (DTI'), 150 ul of
sterile H20, and 10 pl proteinase K (20mg/ml) were added to each tube and the samples
were mixed and incubated in a 37° C oven overnight. Each sample was placed into a spin
basket, placed back into the corresponding tube, and centrifuged for 5 minutes at 14,000

X g. The spin baskets were removed and 500 pl of phenol/chloroform/isoamyl alcohol

(25:24:1) was added, which was then vortexed and centrifuged for 5 minutes at 14,000 X
g. The aqueous layer was transferred to a Centricon®100 concentrator (Millipore). The
DNA was washed 3 times with 1 ml ofT'E" (10 mM Tris, 0.1 mM EDTA) and each
sample was centrifirged for 15 minutes at 500 X g for each wash. The filtrate was
discarded and the retentate, containing the DNA, was collected by inverting the column
with the attached retentate vial and centrifuging for 3 minutes at 1000 X g. A total of 50
pl was collected for each sample. DNA samples for the concordance study and
interethnic study were previously extracted.
DNA Quantification

Yield gel and slot blot: The Michigan State Police Forensic Science Division
yield gel protocol was followed to assess the quality and quantity of the DNA extracted
fiom the semen stains. A 1:10 dilution was prepared for each of the 3 extracted semen
DNA samples. Four pl of each DNA sample, neat and diluted 1:10, was combined with 2
hr of loading solution (30% glycerol, 0.1% bromophenol blue, in TE“) and added into a
microtiter plate. Three pl of the DNA size standard Lambda HindIII/EcoRI, 6 pl DNA
quantification standards including: 500, 250, 125, 63, 31, and 15ng of DNA, and the
DNA extracted fiom semen, were loaded onto a 1% agarose gel. Electrophoresis was set
at 175 volts for approximately 10 minutes. The gel was photographed and the DNA
samples were evaluated for quality and quantity by comparing them to the band
intensities of the DNA quantification standards.

Based on the yield gel estimates, 1:2, 1:5, and 1:10 dilutions of samples A, B, and
C were quantified by slot blot hybridization using a Quantiblot" kit (Applied

Biosystems) following manufacturer’s recommendations. Enhanced Chemiluminescent

reagent (ECL"‘) (Amersham Biosciences) was used in conjunction with X-ray film to
detect the labeled human DNA bound to the membrane. The quantity of DNA was
estimatedbyvisuallycomparingthebandintensityofthe DNAtestsampletotheband
intensity of the DNA standards (10, 5, 2.5, 1.25, 0.625, 0.3125, and 0.15625 ng) and the
DNA calibrators provided in the kit.

PicoGreeanssay: The concordance and the interethnic studies’ DNA samples
were quantified using a PicoGreen® double stranded DNA quantification assay
(Molecular Probes) and a MRX RevelationTM microtiter plate fluorometer (Dynex). A
master mix of 200 pl 1134 and 1 pl PicoGreen® dye was prepared for each DNA sample.
Two hundred microliters of the master mix was added to 5 pl of each DNA sample. The
DNA standards of 50, 25, 12.5, 6.25, 3.125, 1.5625, 0.78125, 0.3906, 0.1953 ng and the
samples of unknown concentration were added to a 96—well microtiter plate. MRX
RevelationTM software was utilized to extrapolate the concentration of the unknown DNA
samples by comparing their fluorescence intensity to a graph of the known DNA
concentrations (X-axis) versus fluorescent intensity (Y -axis).

DNA Amplification

The DNA from semen samples was diluted to concentrations of 5, 2.5, 1.25,
0.625, 0.3125, 0.1563, and 0.078 ng/pl. Y-PlexWS and Y-Plexm6 Y-STR amplification
systems were used. Each 25 pl reaction contained 5 pl of 5X primer mix, 0.5 pl
AmpliTaq GoldT"(5u/pl), 14.5 pl sterile water, and 5 pl of DNA. Positive (male DNA)
and negative (female DNA) controls were set up with each set of samples. All
experiments used the same PCR conditions except those of the concordance and

interethnic study where the components of the PCR reaction were reduced by half (total

10

volmne of 12.5 pl). Thermocycler conditions for the Y-PLEXT" 5 system were: initial
denaturation of the DNA template at 95°C for 10 minutes; 32 cycles of 94°C for 30
seconds, 56°C for 1 minute, 70°C for 45 seconds; with a fiml extension of 60°C for 60
minutes and the samples were held at 4°C until they were removed. Thermocycler
conditions for the Y-PLEX‘“ 6 system were: initial denaturation 95°C for 10 minutes; 30
cycles of 94°C for 30 seconds, 59°C for 1 minute, 70°C for 1 minute; with a final
extension of 60°C for 60 minutes and the samples were held at 4°C until they were
removed.
Analysis on ABI Prism® 310 Genetic Analyzer

An ABI Prism® 310 genetic analyzer was utilized for the sensitivity,
concordance, and precision of allele sizing studies. The minimum Relative Fluorescence
Units (RFUs) was set at 75. A matrix file was produced using the recommended matrix
standards fiom Applied Biosystems including 5-FAM, HEX, ROX, and TAMRA. A
master mix was prepared containing 24.5 pl of formarnide and 0.5 pl of the recommended
internal lane standard, GeneScan® - 500 [ROX] (Applied Biosystems). One pl of
amplified product was added to a tube containing 25 p1 of mastermix. An allelic ladder
containing all alleles for each locus was run 8 times with each set of samples. The
samples were denatured on a heat block at 95°C for 3 minutes and then placed into an ice
bath for an additional 3 minutes. The collection parameters for the 310 Genetic Analyzer
were as follows: buffer, 1X Genetic Analyzer Buffer; polymer, Performance Optimized
Polymer 4 (POP-4); virtual filter set, A; injection time, 5 seconds; injection voltage, 15.0

kV; run voltage, 15.0 kV; run time, 30 minutes; run temperature, 60°C. Genotyper®

ll

software was used to run the Y—Typer macros, Y-Typer-S 310 and Y—Typer-6 310, for
analysis of the electropherograms.
Analysis on ABI Prism® 3100 Genetic Analyzer

An ABI Prism® 3100 genetic analyzer was utilized for the concordance,
precision of allele sizing, and interethnic studies. The minimum Relative Fluorescence
Units (RFUs) was set at 75. The Promega matrix standards FL, JOE, CXR, TMR and
internal lane standard ILS600 (Promega) were used on the ABI Prism® 3100 for the Y-
PLEXT" 5 and 6 systems because the recommended Y-PLEXT"I 5 and 6 matrix standards
fi'om Applied Biosystems were not made for the ABI Prism® 3100. Afier evaluating the
absorbance and emission spectra of the Promega matrix standards it was determined that
it should be sufficient for the Y-PLEXT" systems (Table 1). A master mix was prepared
containing 24.5 p] of formarnide and 0.5 pl Promega internal lane standard, ILS 600.
One pl of amplified product was added to a tube containing 25 pl of master mix. An
allelic ladder containing all alleles for each locus was run 8 times with each plate of
samples. The samples were denatured on a heat block at 95°C for 3 minutes and then
placed into an ice bath for an additional 3 minutes. The collection parameters for the
3100 Genetic Analyzer were as follows: buffer, 1X Genetic Analyzer Buffer; polymer,
Performance Optimized Polymer 4 (POP-4); virtual filter set, F; injection time, 5
seconds; injection voltage, 15.0 kV; run voltage, 15.0 kV; run time, 30 minutes; run
temperature, 60°C. Genotyper® software was used to run the Y-Typer macros for
analysis of the electropherograms. An allelic size difference was noted between the ABI
Prism® 310 and 3100, which caused a problem with analysis ofthe data fi'om an ABI

Prism® 3100 with Y-PLEXTM 6 samples using the Y-Typer—6 310, but not Y-PLEXm 5

12

using Y-Typer-S 310. The Y-Typer-S macro had a larger base pair tolerance window for
the first allele of each locus. To rectify the problem, the Y-Typer—6 310 macro was re-
written to have a larger base pair tolerance window and saved as Y6-2.
Statistical analysis

Allele andHaploope Frequencies: The counting method was used to determine
how many times each allele for each locus occurred in each ethnic groups and to
determine the number of times a Y-PLEXm 5, Y-PLEXm 6, or Y-PLEXTM 5 + Y-
PLEX1M 6 haplotype occurred in each ethnic group. Allele and haplotype fi'equencies
were calculated by the equation

(# of times allele or haplotype observed)/ (total # of complete haplotypes).

Haplotype autism Diversity, Random Match Probability andDiscrlndmrtory
Capacity: The haplotype diversity, random match probability (RMP), percentage of
rmique haplotypes, and discriminatory capacity were calculated for Y-PLEXT“ 5, Y-
PLEXT'“ 6, and Y-PLEX‘“ 5 and 6 haplotypes for all three ethnic groups. STR diversity
was calculated for all loci in all three ethnic groups. Haplotype and STR diversity were
calculated to determine the probability that two haplotypes or alleles chosen at random
would be different, using

(n/(n-1)) x( 1- sum of(p2)
where n = sample size and p = haplotype fi'equency or allele fiequency.
RMP, or the probability that two haplotypes chosen at random would be the same, was
calculated as

1 —- haplotype diversity.

l3

The percentage of unique haplotypes was calculated by
[# of lmique haplotypes/ total # of haplotypes] x 100.
Discriminatory capacity, or the ability of each Y-STR system to discriminate between
two unrelated individuals, was determined using
[# of difi‘erent haplotypes observed/ total # population samples] x 100.

Results:
1. Sensitivity Study

Tables 2 and 3 contain the results of the minimum sensitivity study of Y-
PLEXTMS and Y-PLEXTM6 that was determined by amplification of a DNA sample fiom
the semen donor with a total of three trials per DNA concentration. For the Y-PLEXTMS
system the profiles obtained by using 0.08 and 0.17 ng of DNA exhibited allele dropout
at locus DYS439 in two out of three trials. When 0.3125 ng and higher quantities were
used, the alleles at all five loci were amplified in the three trials (Table 2). For the Y-
PLEXm6 system the profiles obtained by using 0.03 and 0.17ng of DNA exhibited allele
dropout at all loci. Allele dropout was observed in loci DYSB93, DYSl9, DYS389II and
DYS385a—b with 0.3125 ng of DNA, and DYS393, DYSl9, and DYS389II with 0.625 ng
of DNA. When 1.25 ng and higher quantities of DNA were used, the alleles at all six loci
were amplified in the three trials (Table 3). Based on the quantities tested, minimum
sensitivity for the Y-PLEXTMS and Y-PLEXTM6 systems were 0.3125ng and 1.25ng

respectively.

14

II. Precision of Allele Sizing Study

Allele sizes determined fiom sequencing studies (Sinha et al., 2003a and b) and
the observed size range, mean size, and standard deviation values for each allele in the
allelic ladders fiom this study, are summarized in Table 4. The observed range and
standard deviation ofthe allele fi'agment sizes were higher on the ABI Prism® 3100 than
for the ABI Prism® 310. The standard deviation values ranged from 0.0208 — 0.1471
base pairs and 0.0217 — 0.08141 base pairs for these instruments respectively. The allele
sizes were estimated 1.60 —4.05 base pairs smaller using the ILS 600 size standard on the
ABI Prism® 3100 than when using Genescan® 500 [ROX] size standard on the ABI
Prism® 310.
III Concordance Study

Y-Typer 5 310 made the same Y-PLEXTM 5 allele calls for the 40 SWGDAM
samples run on either the ABI Prism® 310 or 3100. The Y6-2 macro recognized the Y-
PLEXTM6 allelic ladder and made the same allele calls as the Y-Typer 6 310 macro when
analyzing the 40 Y-PLEXTM 6 amplified SWGDAM samples rim on either an ABI
Prism® 310 or 3100. This indicated Y6-2 could be used to analyze Y-PLEXTM 6 data
fiom an ABI Prism® 3100 in further studies. Further, no ‘pull-up’ was observed,
indicating the Promega matrix standards were suitable for the Y-PLEXTM systems.
IV Interethnic Study

Allele frequency values were consistent with data published by Reliagene (Sinha
et al., 2003a and b; 2004) and are graphically illustrated in Figures 1 through 1 1. All of
the loci exhibited a unimodal distribution of allele fiequencies with the exception of loci

DYSB92, DYS438, DYS390, and DYS385a—b. DY8392 (Figure 2) and DYS385a—b

15

(Figure 6) appear bimodal in the three ethnic groups. DYS438 (Figure 1) appears
unimodal in the African American samples and bimodal in the Caucasian and Hispanic
samples. 'DYss90 appears unimodal in Caucasian and Hispanic samples and bimodal in
Afiican American samples.

Table 5 summarizes the STR (locus) diversity values for the three ethnic groups;
they ranged fiom 0.3018—0.7006 in Caucasians, 0.4634—0.8416 in Afiican Americans,
and 0.4348—0.7986 in Hispanics. The ranking of the loci based on STR diversity values
was different among the three ethnic groups. DYS439 was the most diverse locus in the
Caucasian samples whereas DYS385a—b was the most diverse locus in the Hispanic and
Afiican American samples. DYS393 was the least diverse locus in the Caucasian and
Hispanic samples whereas DYS389I was the least diverse locus in the Afiican American
samples.

Table 6 summarizes the percentages of samples resulting in full profiles, no
profiles, or containing alleles not present in the allelic ladder (off ladder alleles). The
percentage of interethnic samples resulting in full profiles was greater for Y-PLEXTM 5,
84—94%, than Y-PLEXTM 6, 80—88%. Ofi'ladder alleles were observed for loci DY8390,
DYS391, DYS385a-b for up to 13% the three ethnic groups, and for DYS392 in 5% of
the Hispanic samples only. The ofi‘ ladder alleles were not investigated further because
according to the Michigan State Police Forensic Science Division, the raw data have been
misplaced. Reliagene reported off ladder alleles for loci DYSB93, DYSl9, DYS389II,
DY8390, DYSB91, DYS385a-b, and DYS439 (Sinha et al., 2003a and b).

Tables 7a—c summarize the fiequencies of the most common Y-PLEXTM 5 and 6

combined haplotypes in the three ethnic groups. The haplotype frequencies in the Sinha

l6

et al. (2004) dataset and the web based Reliagene U.S. haplotype database are also
included. The most common haplotypes in the Caucasian and Afiican American samples
intheinterethnic study didnotoccurasfiequentlyinthelargerdatasetsofSinhaetal.
(2004) and Reliagene, occurring at 0.03409 in the interethnic study and 0.0129 in the
Reliagene database for the Caucasian samples and 0.0256 to 0.0093 respectively, for
Afiican American samples. This was not seen for the Hispanic samples; the haplotype
fiequency was 0.01709 in the interethnic study, 0.0282 in Sinha et al. (2004), and 0.0155
in the Reliagene database. However, the increase in sample size between Hispanic
databases, differed by only 117 and 454 samples compared to 88 and 1243 for the
Caucasiangloupand78and 1605 intheAfiicanAmerican group.

Tables 8 a-c, 9 H and 10 a—c contain haplotypes and frequencies forthethree
ethnic groups for Y-PLBXT” 5, Y-PLEXTM 6, and Y-PLEXTM 5 and 6. The Y-PLEXTMS
haplotype fiequencies ranged fiom 0.1121 to 0.0093 in the Caucasian samples, 0.1000 to
0.0200 in the Afiican American samples and 0.0859 to 0.0078 in the Hispanic samples.
This is compared to the Y-PLEXTM6 and Y-PLEx'ms + 6 haplotype fiequency ranges.
The Y-PLEXTM6 ranges were fiom 0.0215 to 0.0108 for the Caucasian samples, 0.0455
to 0.0114 for the Afiican American samples, and 0.0296 to 0.0074 for the Hispanic
samples and the Y-PLEXms + 6 ranges were fiom 0.0341 to 0.0114 for the Caucasian
samples, 0.0256 to 0.0128 for the Afiican American samples, and 0.0171 to 0.0085 for
me Hispanic samples. As expected, the Y-PLEXTMS + 6 haplotypes do not occur as

fiequently as the Y-PLEXNS or Y-PLEXTM6 haplotypes, therefore the number of lmique

haplotpr observed is greater. Figures 12 through 14 graphically illustrate the number

17

of unique haplotypes observed in each ethnic group for Y-PLEXTMS, Y-PLEXTM6, and
Y-PLEXTMS + 6.

Tables 11 and 12 summarize the comparison of haplotype diversity,
discriminatory capacity, and the percentage of unique haplotypes observed in the
interethnic study and Sinha et al. (2004). These values increased as the number of loci
analyzed increased from those in Y-PLEXTMS to Y-PLEXT” 6 to Y-PLEXTMS + 6 in
both studies. The haplotype diversity values increased fiom an average of 0.9829 with
the Y-PLEXTM 5 loci to 0.9956 with the Y-PLEXTM6 loci and to 0.9993 with both Y-
1>Ll~3xTM 5 and 6 loci combined in the interethnic study. The haplotype diversity values
reported by Sinha et al. (2004) also increased with the addition of loci but the values were
slightly lower than what was observed in the interethnic study. Discriminatory capacity
values increased fiom an average of 54.1% with Y-PLEXTMS to 81.8% with Y-PLEXTM6
and 94.3% with the Y-PLEXTMS +6 in the interethnic study. The number ofdifferent
lmplotypes was not reported in Sinha et al. (2004) therefore the discriminatory capacity
wasnotcalculated. Theaverage percentage ofrmiquelurplotypesobservcdincachctlmic
group increased fiom 37.9% with Y-PLEXWS to 71.4 % with Y-PLEXTM6 to 89.77 %
with Y-PLEXNS +6intheinterethnic study. ThiswasalsoseenintheSinhaetal.
(2004) but the average percentages were lower.

Discussion:

The Reliagene Y--PLEXTM 5 and 6 systems were validated for analysis on an ABI
Prism®3100inthisstudy. ThesesystemsweregeneratedtobeusedonanABlPrism®
310andABlPrism®377buthavenotbeentestedonanABlPrism® 3100(Sinhaetal.,

2003a and b). Reliagene was contacted and they verified this. Two issues had to be dealt

18

with prior to proceeding with the validation study. First, the matrix standards consisting
of DNA fragments labeled with the dyes needed for the Y-PLEXTM systems, S-FAM,
HEX, TAMRA, and ROX, were not available for the ABI Prism® 3100. Secondly,
becausethelLS6003izestandardwasusedontheABIPrism®3100theallelefiagment
sizesweleestimatedfiom1.60to4basepairssmallerthanontheABlPrism®310using
theGenwcan®500 [ROX] size standard (Table 4). Thiscreated a problem with analysis
withtheY-Typer6310macro.
ABlPrism®3103and31003difi‘erinthemethodofcreatingamathematical
matrix which is created to account for spectral overlap of different fluorescent dyes.
Therefore,thematlixstandardsarenotsynthesizedthesameway. ForanABIPrism®
310eachmatrixstandardsampleisnmindividually;foranABlPrism®3100thematrix
standard samples are run combined. This necessitates the DNA fiagments with the
attacheddyestobeofdifl‘eringlengthstoallowfortheirseparation. Forexample,with
theABIPlism®3100matrixstandardsby Promega(JOE, FL,TMR,andCXR), JOE is
attachedtoal60bpfiagment,FLisattachedtoa250bpfragment,TMRisattachedtoa
300bpfiagrnentandCXRisattachedtoa350bpfi'agment. TheMichiganStatePolice
Forensic Science Division routinely used these matrix standards, therefore they were
considered as an alternative to the Y-PLEXTM matrix standards. the red dyes, ROX and
CXR,andtheyellowdyes,TAMRAandTMR,arefllesamedyeswithdifl‘erentnames.
Thebluedyes, 5-FAMandFL,andthegleendyes,HEXandJOEhavevery similar
absorbmweandemissionspecuadifi‘eringbtho7nmCI‘ablel). Onceevaluatingthe
Wmdanissionspecuaofeachdyeitwasdetermmedmatthermegamauix

standmdswouldbesufficiemfortheY-PLEXmsystemsontheABIPrism3100. When

19

evaluating the electropherograms no ‘pull up’ was observed due to the Promega matrix
standards.

The size difference observed for the allele fi'agments on the ABI Prism® 310 and
3100isatuihnedmmefactthmdifi'emntmtemallanesmndardswereusedoneach
instrument. ThisissupportedbyShewaleetal.(2004)inwhichtheyvalidatedtheY-
max“ 12 system (a kitcomaimngthcv-PLExmsaodolociinone reaction) on both
anABI Prism®310and3100. TheyusedGenescan®500 [ROX]sizestandardonboth
instruments and no difference in allele fragment sizes was observed. The ILS600 size
standardwasalreadyvalidatedforanABIPrism®3100attheMichiganStatePolice
Forensic Science Division therefore it wm used forthe Y-PLEX 5 and 6 systems. The
provided Y-Typermacros, Y-Typer 5 310 and Y-Typer6 310, were successfully used to
analyzeY-PLEXNSdatafiomtheABIPrism®310and3100,andY-PLEXm6data
fiomtheABl Prism®310. However,theY-Typer6310macrowouldnotrecognizethe
alleles ofthe Y-PLEX‘" 6 allelic ladder on the ABI Prism® 3100. The Y-Typer macros
aredesignedtorecognizethefirstalleleofeachlocusoftheallelicladder+or-a
puticularbasepairrange. Themaclocallsthesubsequentallelesofthatlocusbasedon
thesizeofthefirstallele. TheY-Typer5310macroluldalargeenoughbasepair
whulowforthefirstalleleofeachlocusthatwasabletorecognizethefirstallelesofeach
locus in the Y--PLEXTM 5 allelic ladders fiom the ABI Prism® 310 and 3100 even thoufir
theallelcsweresizedlmto4bpsmallerontheABlPrism®3100 However,thiswasnot
thecasewiththeY-Typer6310maclo. Therefore,theY—Typer6310macrowasre-
writtentohavealargerbasepairwindowsothefirstalleleofeachlocuswouldbe

recognized. AccordingtopersomlelatMichiganStatePoliceFmensicScialceDivision

20

the original macros, which were still in the developmental stage, have been misplaced.
Thus the exact size ofthe base pair window cannot be determined. However, the current
available Y-TyperS310andY-Typer6310macroshaveabasepairwindow+or—7
basepairs.

The results obtained fiom the sensitivity study were compared to Reliagene’s
published data (Sinlm et al., 2003a and b). These results showed a minimum sensitivity
of 0.3125 ng of male DNA for Y-PLEXT” 5 with RFU values ranging from 358—1200
ard a minimum sensitivity of 1.25 ng of male DNA for Y-PLEXTM 6 with RFU values
ranging fiom 337—1927 (Tables2and3), while Reliagenereportedaminimlun
sensitivity of0.1 ngofmale DNA for Y-PLExmswitth-‘Uvaluesrangingfrom400—
600 and aminimum sensitivity of0.2 ngofmale DNA for Y-PLEXm6 withRFU values
ranging fiom 300—800(Sirdraetal., 2003aandb). Thedifferences observed between the
twosensifivitystudieswuldbeexplainedbythedifiaminqmfityofdnmfing
temphe. ReliageneexuactedDNAfimnbloodandbuccalcellswabswhereasdried
semenoncottonswatcheswasusedinthisstudy. However,therewasnocleaevidence
ofDNAdegradmioninflresanenDNAsmnplesuheydidnotprodmesmearsonflle
yieldgelandthefirstallelestodropoutwerenotthelargest. Thesensitivitystudy
MhuevmconductedmerelymdaernfimwhmmonsofDNAwouldbe
opfimalfmmemwbsequemexpaimentsdmefmednreadtswuemumveuigmedny
fin-ther.

Whfleconducfingtheinterethmcsurdy,sampleswereexcludediftheydidnm
hveafirllprofileoriftheyeomainedallelesnotpresentintheallelicladder(offladder

alleles)(Table6). Thesesmrplescmrldnotbeinvestigfledfindrerbecmrseaccold'mgto

21

the DNA personnel at the Michigan State Police Forensic Science Division, the raw data
hadbeenmisplaced. OveralLthepercentageofinterethnic samples thatresultedinfull
profiles was greater for Y-PLEXT“ 5 than Y-PLEX‘" 6, largely due to the number of Y-
am“ 6 samples containing orrladder alleles. ln Y-PLEXTM 5 only the locus DYS439
lmdofl‘ladderaflelegoccurringin5%ofthellispanicsmnples. Incontrast,maverage
of8.7%oftlmsamplesfiomallthreeethnicgroupsresultedinofi'ladderallelesforthe
Y-PLEXTM 6 loci, including loci DYS390, DYS391, and/or DYS385. Reliagene reported
ofi'hddu' alleles for loci DYS393, DYSl9, DYS38911, DYS390, DYS391, DYS38Sa-b,
and DYS439 (Sinha at al., 2003a and b). An average «7.3% and 7% ofthe Y—PLEXT"
5d6smnplesrespectivelydidnotlnveafidlprofilewhichcouldbeMMedm
incorrectestimateofDNAconcerm'ationorlowqualityDNA.
ThereadtsofdieimerethnicsmdywereemnpmedmtheresrdtsofSinhaetal.
(2004)apubflcafimmtheeflablishruaofdnfirstU.S.lmkuypedmahaeM
aelllociorY—PLEXWSand6crablss7,ll,12). Theinterethnicstudy’smost
mmmonhaplotypesinthedueeetlnficgrmrpsocamedlessfiequemlyhrthehpr
MofShlmadW)luldreReliagmU.S.haplotypedatabase(Table7).
Sinhaetal.(2004)estdrlishedflleRe1hgeueU.S.lnplotypedmdlmeusig517
”sunflsmmmlqmrdZflmspanicmples. Since
thendusdmalmgownb1243mml605Afiianms-qh,
d454fl’qmicsmnples. Anavelageof72.l%ofthelnplotypesinSinhaetal.(2004)
menniquthaefmethedeaeaseinflrehaaethicsmdy’smostcmmype
Mikhpthmwismmmmgflndifi‘erenminsample

sizeandincreasedmriqumflable 12) Itwasalsoobscrvedtlllthetlleeeflc

22

groupsdidnotsharethemostcommonhaplotypeintheinterethnicstudy. Infactthe
mostcormnonhaplotypeintheHispanicsmnpleswasnotobxrvedintheAfiican
AmericanorCaucasiansamples. WhensearchingtheReliageneU.S.haplotypedmalmse
thismypeocctlredinCaucmimmplesatalowfiequencyofODOManditdidnot
occurintheAfiicanAmericansamples. Kayseretal.(2003)ccncludedtheY—STR
Wfiflammmmmflispanicsamplesbasedon
ananalysisofmolecularvarimrceqrplomh(AMOVA). Theirfindingissqrportedbythe
datapresentedhere.

lnboththemterethnicstudyandsmhaaal.(2004)aninaeaseinthehapknype
divusityaddlepacemageofmithaplotypawasobservedwhencompmingthe
haplotypesconmmmgaelllocioiY-PLExmsmd6comp-edtothehsplotypes
endogeithertle-PLEXNSor6locialoneGableslland12). Thisisexpected
wmidefingflnpowerofdisahrfimlimofalmkflypehaeuseswifitheadrfifimon-
S'I'Rhci. WandybyH-IsonmdBallmlyne(2004),damnsumesanincreasethe
powerofdiscrimimion. T‘lrymmlyzedSOCareashmlesndSlAfihA-aie.
sqks‘finmdlmofdiehqrhtypesweremique. Thisstmlydenmnstratesthat
whenwmbiningasdofhigflypolymplicY—STRstbdisa-in‘nycmciyc-bc
thmmmnecoddexpeaifalnglnrmkmlnbawasuseimpeat
haplotypeswotddoculbecmrseflreYchomsr-mispasseddrmnfiomm»
genermioncompletelyintact.

With the exception of DYS392, DYS438, DYS390, and DYS3850-b all loci
WWWofdkleqdnswmaboobsavedmsmhaetal.(2004).

Suchdisuibuionisexpectedforuiaosmellitealleleswhhregmampems. According»

23

the step mutation model, mutations in these microsatellite regions are generally one
repeat larger (step up) or smaller (step down) (Kimura et al., 1978; Walsh, 2001).
Bimodal distribution for loci DYS392, DYS438, DYS390, and DYS385a-b was observed
in the interethnic study and Sinha et al. (2004). Of these four loci only DYS392 and
DYS438 have been tested for an alternative mutational mechanism. Gusmao et al. (2003)
conductedastudy inordertodetermine ifthesetwolocideviated fiomthe stepwise
mutation model, and concluded that the bimodal allele frequency distributions of these
locicanbeexplainedbyhistoricalanddemoglaphiccausesand notanothermutational
mechanism.

The ranking of the STR diversity values of the Y-ST'R loci difi‘ered among the
three ethnic groups (Table 5), as was observed by Schoske et al. (2003). DYS439 was
the most diverse locus in the Caucasian samples whereas DYS385a-b was the most
diverse locusintheHispanicandAfiicanAmelicansamplss DYS393 wastheleast
diveuelocmintheCaucasimamlHispanicsampleswhereasDYS389I wasthe least
diverse locusintheAfiicanAmericansamples. Boschetal. (2002)andSchoskeetal.
(2N4)£olmdDYS393tobetheleastdiverselocus,DYS439tobethesecondmost
diverse locus, and DYS385a-b to be the most diverse locus in Caucasian, African
AmwwmdnflraimPeninadapopldafiomwhenlookingatthe
“minimal”haplotype loci. T‘heSTRdiversityvalueisbasedonhowpolymorphicthe
ST‘Rlocusis,tlurs,it'ndepemlemonthemunberofpotential alleles foraparticular
locus,thecopynlunberofthelocus(e.g. DYS385a—bisatwoccpy kurs)-Ilthedlelic
dhribuiou. Oftheloci WindleU.S.lnplotype,DYS385a-bisthemost

polymorphicbecauseithastuocopiesaaltherearell possiblealleles(Boschetal.,

24

2002; Schoske et al, 2004). Because the two copies do not necessarily have the same
number of repeats per allele, it has the information of two loci. Surprising, DYS385a-b
was not the most polymorphic locus in the Caucasian samples of the interethnic study.
Thiscouldbeexplainedbythesmallsamplesizeandtheoriginofthesamples. In
previous STR diversity studies the sample sizes were larger and the samples were from
all over the U.S. rather than fiom one state. When comparing the allelic distribution of
each locusinFigures 1 through 11 tothe STRdiversityvaluesinTable 5, onecansee
that the loci containing several possible alleles with an even distribution of frequencies
have higher STR diversity values, for example DYS439 (Figure 3). Conversely, a locus
that has few alleles with a high frequency of occurrence has a lower STR diversity value,
for example DYS393 (Figure 7).

Since the time of this study in 2002, two more inclusive Y-ST'R systems have
become available to the forensic community, Y-PLEXTM 12 by Reliagene and
Powerplex® Y by Promega. Both systems have benefits over the separate Y-PLEXTM 5
and 6 systems. They both include the U.S. haplotype, enabling amplification of all loci
usingjustonePCRreactionasapposedtotwo,andweregeneratedtorlmonanABI
Prism® 3100 enabling high throughput analysis. In addition to the U.S. haplotype, the
Y-PLEXTM 12 system contains a sex-typing marker, amelogenin. This is beneficial as a
control for PCR inhibition and to determine the sex of the sample donor(s). A lack of a
male profile could be due to either PCR inhibition or not enough male DNA present in
the sample. lfthere is no male profile or amelogenin peaks in a female/male mixture
then this would lead to the conclusion that there are PCR inhibitors, however, if there is

no male profile but there are amelogenin peaks this indicates the sample is most all

25

female. Powerplex® Y does not contain the amelogenin marker however it does contain
an additional Y-ST'R locus DYS43 7.

Both Reliagene and Promega have established U.S. haplotype databases for their
respective Y-STR systems that are available to the forensic community in order to
estimate a haplotype fiequency (Sinha et al., 2004 and Krenke et al., 2005). It would be
beneficial to one day have an integrated standardized U.S. haplotype database, because
with a larger database a haplotype fiequency would be more reliable.

The Reliagene Y-PLEXTM 5 and 6 systems have been validated for forensic
casework (Sinha et al., 2003a and b), validated for analysis on an ABI Prism® 3100 in
this study, and utilized for the establishment of the first U.S. haplotype database with the
SWGDAM recommended loci (Sinha et al., 2004). It should be noted that the dataset
fiomthecurrent interethnic studywasmuch smallerthanthedatasetreported inSinhaet
al., 2004 and the current Reliagene database, and it was meant only for the validation of
the Y-PLEXTM systems for analysis on an ABI Prism® 3100. Also, Michigan State
Police Forensic Science Division was involved in the validation of the Y-PLEXTM
systems in collaboration with Reliagene, therefore, this interethnic dataset will be added

to the Reliagene database in the future.

26-

 

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27

Table 2

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Trial 1 Trail 2 Trial 3
Sailple Allele Allele call RFU RFU RFU AverageRFU

5 pgnrale DNA DYS3891 12 4634 4189 4669 4497
DYS3891] 28 3261 3576 4033 3623
DYS439 1 1 6215 5162 6628 6002

DYS438 10 6560 5847 6892 6433
DYS392 1 1 6839 7206 6738 6928
2.5 ng male DNA DYS3891 12 2356 3891 3749 3332
DYS3891] 28 1418 2919 3128 2488
DYS439 l l 1497 3065 2763 2442
DYS438 10 3929 5666 471 1 4769
DYS392 1 l 4064 6758 6216 5679
125 ngmale DNA DYS3891 12 2155 2375 2265 2265
DYS3891] 28 1581 1967 1897 1815

DYS439 I 1 1493 1269 1 141 1301
DYS438 10 2361 2406 3354 2707
DYS392 1 1 3987 3734 3962 3894
0.625 ngrnale DNA DYS3891 12 1322 1862 1692 1625
DYS3891] 28 908 1645 1357 1303

DYS439 11 992 660 880 844
DYS438 10 1309 1576 1788 1558
DYS392 1 1 2592 3122 2580 2765

0.3125 rig male DNA DYS3891 12 849 714 937 833
DYS3891] 28 655 514 788 652

DYS439 1 1 430 321 324 358

DYS438 10 813 959 754 842
DYS392 1 l 937 1271 1495 1234

0.17 ngmale DNA DYS3891 12 313 372 477 387
DYS3891] 28 199 260 391 283

DYS439 11 <75 <75 , 155 155

DYS438 10 365 464 496 442

DYS392 l 1 661 621 1088 790

0.08 ng male DNA DYS3891 12 576 <75 465 521
DYS3891] 28 433 <75 346 390

DYS439 11 158 <75 <75 158

DYS438 10 296 <75 241 269

DYS392 11 286 <75 229 258

 

 

 

 

 

 

 

Y-PLEXWS results ofthe three trials ofthe minirnlln sensitivity study for 0.08 to 5 ng ofDNA on an ABI
Prism®310.

28

Table 3

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Trial 1 Trail 2 Trial 3
Sample Allele Allele call RFU RFU RFU AverageRFU
5 ng male DNA DY8393 13 1114 905 1227 1082
DYSI9 14 2332 549 1023 1301
DYS3891] 28 3173 1279 1749 2067
DY8390 23 3775 2446 3432 3218
DYS391 10 6666 4947 6280 5964
DYS385 13 1,609 2523 2634 2255
DYS385 15 1,285 2432 2184 1967
2.54anale DNA DYS393 13 632 598 636 622
DYSI9 14 1279 525 506 770
DYS3891] 28 1450 823 927 1067
DYS390 23 2059 2003 1813 1958
DYS391 10 3762 4019 4169 3983
DYS385 13 1051 1603 1444 1366
DYS385 15 1062 1240 1425 1242
1.25 nLrnsle DNA DYSB93 13 340 338 333 337
DYSI9 14 649 208 287 381
DYS3891] 28 775 261 376 471
DYS390 23 1239 959 878 1025
DYS391 10 1884 1592 2304 1927
DYS385 13 497 740 654 630
DYS385 15 546 688 675 636
0.62541g male DNA DYSB93 13 180 202 <75 191
DYSI9 14 243 <75 <75 243
DYS3891] 28 261 154 <75 208
DY8390 23 607 439 549 532
DYS391 10 946 951 865 921
DYS385 13 277 471 386 378
DYS385 15 245 436 374 352
0.3125 ng male DNA DYS393 l3 <75 <75 <75
DYSI9 l4 <75 <75 <75
DYS3891] 28 <75 <75 <75
DYS390 23 245 299 253 266
DYS391 10 381 615 552 516
DY8385 l3 <75 192 246 219
DYS385 15 <75 245 155 200
0.17 rig male DNA DYS393 l3 <75 <75 <75 <75
DYSI9 l4 <75 <75 <75 <75
DYS3891] 28 <75 <75 <75 <75
DYS390 23 <75 <75 <75 <75
DYS391 10 290 <75 <75 290

 

 

 

 

 

 

 

29

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Table 3 (continued)

DYS385 l3 <75 <75 <75 <75

DYS385 15 <75 <75 <75 <75

0.08 anale DNA DYS393 13 <75 <75 <75 <75
DYSI9 14 <75 <75 <75 <75

DYS38911 28 <75 <75 <75 <75

DYS390 23 <75 <75 <75 <75

DYS391 10 <75 <75 <75 <75

DYS385 13 <75 <75 <75 <75

DYS385 15 <75 <75 <75 <75

 

 

 

 

 

 

 

Y- PLEXW6 results ofthe three trials ofthe minimum sensitivity study for 0.08 to 5 ng of DNA on an
ABI Prism® 310.

30

 

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Table 4
Size on 310 (bases; n=11) Size on 3100 (bases; 11:12)
Locus Allele Se uence Size (bases) Observed range Mean SD. M Mean __S_D_._
DYS3891 11 244 243.73 - 243.81 243.76 0.0217 240.58 - 240.79 240.67 _0_0108_
12 248 247.76 - 247.85 247.80 0.0223 244.61 - 244.85 244.75 0.0645
13 252 251.73 - 251.86 251.81 0.0510 248.76 — 248.95 248.84 00—61
14 256 255.78 - 255.85 255.81 0.0221 252.75 — 253.04 252.93 111%
15 260 259.83 - 259.94 259.88 0.0298 256.82 - 257.12 256.96 0.0794
DYS389II 27 360 362.40 — 362.65 362.55 0.0624 358.37 — 358.67 358.55 0.0981
28 364 366.46 - 366.60 366.51 0.0484 362.45 - 362.77 362.61 0.0789
29 368 370.31 - 370.56 370.42 0.0699 366.36 - 366.87 366.63 0.1471
30 372 374.25 - 374.48 374.38 0.0813 370.46 — 370.78 370.63 0.0937
31 376 378.20 - 378.41 378.33 0.0573 374.40 - 374.75 374.70 0.1086
32 380 382.14 - 382.31 382.24 0.0490 378.61 - 379.07 378.81 0.1298
33 384 386.02 — 386.15 386.10 0.0475 382.58 - 383.03 382.83 0.1417
DYS439 10 241 238.77 - 238.89 238.81 0.0370 235.73 - 235.93 235.82 0.0704
11 245 242.77 — 242.86 242.81 0.0232 239.68 - 240.02 239.82 0.0976
12 249 246.81 - 246.90 246.85 0.0228 243.75 — 244.02 243.93 0.0696
13 253 250.77 — 250.89 250.80 0.0370 247.86 - 248.11 247.97 0.0741
14 257 254.83 - 254.90 254.86 0.0239 251.92 — 252.18 252.05 0.0890
DYS438 8 131 130.99 - 131.14 131.05 0.0541 128.29 — 128.95 128.85 0.1739
9 136 136.18 - 136.32 136.24 0.0575 134.00 - 134.17 134.08 0.0457
10 141 141.55 — 141.67 141.60 0.0549 139.01 — 139.23 139.14 0.0534
11 146 147.14 - 147.19 147.17 0.0130 144.16 — 144.33 144.24 0.0522
12 151 152.67 — 152.80 152.77 0.0486 149.25 - 149.41 149.33 0.0501
13 156 158.21 158.20 0.0271 154.35 — 154.45 154.42 0.0476
DYS392 10 247 247.05 — 247.14 247.09 0.0234 243.97 - 244.14 244.09 0.0741
11 250 250.05 — 250.20 250.11 0.0552 246.89 - 247.12 247.01 0.0653
12 253 253.07 — 253.19 253.16 ‘ 0.0393 249.92 -250.24 250.13 ‘00983
13 256 256.14 - 256.21 256.17 0.0221 253.06 - 253.38 253.21 0.1114
14 259 259.17 - 259.28 259.22 0.0444 256.12 — 256.44 256.27 0.0852
15 262 262.18 — 262.32 262.70 0.0435 259.43 - 259.5 259.46 0.0295
DYS393 11 112 112.8 - 112.90 112.81 0.0443 110.06 — 110.18 110.13 0.0337
12 116 116.71 — 116.84 116.76 0.0445 114.30 — 114.35 114.32 0.0208
13 120 120.66 - 120.81 120.74 0.0452 118.46 - 118.55 118.49 0.0269
14 124 124.72 — 124.85 124.79 0.0441 122.56 — 122.67 122.62 0.0281
15 128 128.77 - 128.88 128.82 0.0549 126.71 - 126.78 126.73 0.0239
16 132 132.78 - 132.95 132.88 0.0513 130.76 — 130.85 130.80 0.0331
17 136 136.90 — 137.02 136.99 0.0437 134.81 - 134.93 134.87 0.0284

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

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[IE4 (confirmed)! I
W819 I 12 I 181 I 18183-18197 1181871005931 17786-17800 [177.94 0.0452
If f 13 l 185 I 18573-18589 1185821005591 18185-18196 l181.92 00304
F l 14 l 189 I 18959-18981 189.73 006021 18588-18601 18592 0.0376
15 l 193 19355-19373 193.64 0.0508 18986-19001 189.92 0.0365
fi 16 197 197.38— 197.53 197.48 0.0354 19389-19401 193.94 00336
17 201 201.35 -201.47 201.39 0.0506 197.87- 197.97 197.91 0.0354
DYS3891] 27 294 29365-29380 293.72 0.0449 29057-29071 290.64 0.0475
28 298 29776-29793 297.83 0.0712 29461-29475 294.67 0.0469
29 302 30201-30214 302.07 0.0549 29863-29879 298.72 0.0457
30 306 306.09 - 306.27 305.98 0.0646 302.64 - 302.79 302.71 00535
31 310 31016-31041 31031 0.0613 30662-30684 306.72 0.0691
32 314 314.36 - 314.60 314.49 0.0789 310.68 - 310.89 310.77 0.0701
33 318 31844-31867 318.59 00603 314.66- 314.85 314.77 0.0654
DYS390 20 178 17943-17964 179.56 0.0613 17545-17557 175.51 0.0369
21 182 183.4- 183.58 183.50 0.0585 17939-17955 179.48 0.0516
22 186 187.39- 187.52 187.43 00486 183.38— 183.51 183.45 0.0356
23 190 191.24- 191.45 191.34 0.0555 187.35 - 187.49 187.43 0.0389
24 194 195.08 - 195.25 195.17 0.0433 191.35 - 191.49 191.41 0.0382
25 198 19900-19914 199.06 0.0602 19534-19546 195.40 0.0371
DYS391 9 245 245.70-24579 245.76 0.0472 242.78 -242.86 242.82 0.0253
10 249 249.68 - 349.88 249.77 0.0602 246.81 - 246.95 246.88 0.0448
11 253 253.82 - 253.91 253.84 0.0433 250.92 — 251.06 251.00 0.0433
12 257 25782-25791 257.87 00537 2550025515 255.06 0.047:
DYS385 8 345 34536-34548 345.41 0.0376 342.35 -342.53 342.45 0.0679
10 352 352.94 - 353.15 353.05 0.0560 350.17 - 350.34 350.27 0.0508
11 356 356.71 - 356.88 356.77 0.0501 353.98 - 354.15 354.09 0.0623
12 359 360.43 - 360.58 360.52 0.0556 357.88 - 358.05 357.95 0.0555
13 363 364.13 - 364.29 364.21 0.0480 361.64 - 361.86 361.75 0.0659
14 367 367.85 - 368.01 367.95 0.0516 365.51 - 365.75 365.62 0.0727
15 370 371.47 - 371.77 371.69 0.0814 369.33 - 369.52 369.45 0.0530
16 374 37534-37547 375.42 0.0487 373.11 -373.41 373.28 0.0933
17 378 379.07 - 379.22 379.14 00598 377.11 — 377.29 377.18 0.0596
18 382 382.75 - 382.90 382.85 0.0462 380.90 - 381.74 381.06 0.0740
19 385 386.48 - 386.67 386.56 0.0573 384.78 - 385.09 384.95 0.0875

 

 

 

 

 

 

 

 

 

 

The precision of migration of alleles in the allelic ladders of Y—PLEXT‘VS and Y—PLEX“ 6 on an ABI Prism® 310 and an ABI Prism® 3100,
Y—PLEX 5 loci include: DYS3891, DYS38911, DYS439, DYS438, and DYS392. Y-PLEX 6 loci include: DYS393. DYS 19. DYS38911.
DYS390, DYS391, and DYS385. DYS389II is the overlapping locus between Y-PLEX 5 and 6, which are different sizes because they have
different primer sets in each system.

Table 5

 

 

 

 

 

 

 

 

 

 

 

Caucasian Afi'ican American Hispanic
Locus STR diversity Rank STR diversitx Rank STR diversity Rank

DYS439 0.7006 1 0.61 17 5 0.6551 5
DYS389II 0.6878 2 0.7646 2 0.7024 2
DYS390 0.6870 3 0.6831 4 0.6510 6
DYS385a/b 0.6273 4 0.8418 1 0.7986 1
DYS438 0.6265 5 0.5857 6 0.6869 3
DYS392 0.5618 6 0.5164 7 0.6683 4
DYS391 0.5446 7 0.4935 9 0.5520 8
DYSI9 0.4734 8 0.7249 3 0.6405 7
DYS3891 0.4576 9 0.4638 10 0.5193 9

DYS393 0.3018 10 0.4943 8 0.4348 10

 

 

 

 

 

 

 

 

STR diversity and ranking for the Y-PLEXTM 5 and 6 loci tested in the three ethnic

groups: Caucasian, African American, and Hispanic.

 

 

 

 

 

 

 

 

 

Table 6
African
Caucasian American Hispanic
Y-PLEXS N=109 N= 110 N= 153
°/o with fiill profile 98 91 84
% excluded due to off ladder allele 0 0 5
% excluded due to no profile 2 9 ll
Y-PLEX6 N=109 N= 110 N=153
% with full profile 85 80 88
% excluded due to off ladder allele 13 7 6
% excluded due to no profile 2 13 6

 

 

 

 

 

 

PamdisuibutionofdleCaucasian, African Amer-imandHispanic samplesthatwere

mlyzed using Y-PLEXTM 5 and 6 containing: a full profile, off ladder alleles, or no

profile.

N = the number of samples tested.

33

 

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.3336 3.8.9... .3. 869...; 2.. a... sea. 38 .5 .6 2.5m a 536

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3.15 was... $8.15 a £3.15 .88... 3338 855.3.
9.815 ”as... @215 .859. .8 A... “15 .3288 8.. 88 :3 .6 9.5m
5 .15 .82.... $15... $15 a as... 65523...
6.85... 86.85... 53.5... 8.325
.2.......v..e.-n..a.v~.°m.m..m. 1 has 65583... 2.. a. 632...... 6.8%... 8558 .82
on 2...:
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9:15 .98... A515 .38... E 615 .83... 38 4... 8 8.5m
.2 .15 a 515 .88... 8.15 ”RS... .88 655235
656%.: 68.88... 86...... £823

 

 

 

 

2.5.2.26.-. 1.33312 1 .3... 65583... o... a. 252...... 56.3.5. 82...... 8888 .82

 

 

 

 

 

 

.K 2.3
@215 .88... $8.15 .28... 6.215 ans... 8358 852.3.
8815 .38... @315 58.32 .8 €31.15 $88... 38 :3 .6 2.5m
E .15 a $15 .38... .315 .848... .38 65568....
656%.: 68.85... :85... 3330

 

 

 

 

2.24126.-.1.1.8.8412 1 5.5.... 6.2.23... 2.. a. 252...... 8.886 8558 .82

an 033.

34

Table 8a

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

# of
DY83891 DYS3 8911 DYS439 DYS438 DYS392 occurrences Frequency
13 29 11 12 13 12 0.1121
13 29 12 12 13 11 0.1028
13 30 10 1 l 1 l 5 0.0467
12 28 l l 10 1 1 5 0.0467
14 30 12 12 13 4 0.0374
13 30 13 12 13 4 0.0374
13 28 12 12 13 4 0.0374
12 29 12 10 l l 3 0.0280
13 29 13 12 13 3 0.0280
12 28 12 10 l l 3 0.0280
13 30 12 12 13 3 0.0280
13 30 l l 12 13 3 0.0280
13 29 12 13 13 2 0.0187
13 28 13 12 13 2 0.0187
13 30 12 10 1 1 2 0.0187
13 30 1 l l l 1 1 2 0.0187
12 27 l l 10 l 1 2 0.0187
13 29 12 9 l l 2 0.0187
13 30 13 1 l 13 1 0.0093
14 29 1 1 12 13 1 0.0093
13 29 10 10 1 1 1 0.0093
12 29 l l 10 1 l 1 0.0093
13 29 12 12 14 1 0.0093
13 28 l 1 12 13 1 0.0093
13 31 12 10 1 1 1 0.0093
14 31 l l 10 12 1 0.0093
13 30 10 1 l l 1 1 0.0093
12 29 10 10 1 1 1 0.0093
12 30 13 10 1 l 1 0.0093
12 28 13 9 ll 1 0.0093
13 29 1 l 1 l 11 1 0.0093
13 31 10 l 1 l 1 1 0.0093
13 29 12 10 1 1 1 0.0093
12 28 13 12 13 1 0.0093
13 29 12 12 12 1 0.0093
14 30 12 13 13 1 0.0093
13 29 12 10 12 1 0.0093
13 30 12 12 14 1 0.0093
13 28 12 12 14 1 0.0093

 

 

 

 

 

 

 

35

 

 

Table 88 (continued)

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

13 30 l 1 9 l3 1 0.0093
14 31 10 1 1 11 1 0.0093
13 29 ll 12 14 1 0.0093
14 32 10 l l l 1 1 0.0093
14 30 13 12 13 1 0.0093
14 30 l 1 12 13 1 0.0093
13 29 14 12 13 1 0.0093
12 31 l 1 10 1 1 1 0.0093
13 29 12 12 13 1 0.0093
13 29 l 1 10 12 1 0.0093
13 30 12 1 l l 1 1 0.0093
13 30 13 1 1 1 l 1 0.0093
15 31 12 10 1 l 1 0.0093
13 31 13 10 l 1 1 0.0093
Caucasian Y-PLEX 5 haplotype frequencies

36

 

Table 8b

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

#of
DYS3891 DYS3891] DYS439 DYS438 DYS392 occurrences Frequency
13 30 12 11 ll 10 0.1000
13 29 12 12 13 8 0.0800
13 31 12 11 11 7 0.0700
13 31 11 ll 11 6 0.0600
13 29 13 12 13 4 0.0400
13 30 13 11 ll 4 0.0400
13 30 ll 11 11 3 0.0300
14 31 12 11 11 3 0.0300
13 29 12 12 14 3 0.0300
12 28 11 11 ll 2 0.0200
14 30 12 12 13 2 0.0200
13 32 11 ll 11 2 0.0200
12 28 ll 10 11 2 0.0200
13 30 12 12 13 2 0.0200
13 29 13 12 13 2 0.0200
13 29 11 10 ll 2 0.0200
13 29 11 10 ll 2 0.0200
12 29 12 ll 11 2 0.0200
13 29 11 12 13 2 0.0200
12 29 13 ll 11 1 0.0100
14 32 13 ll 11 1 0.0100
11 28 12 11 11 1 0.0100
12 29 ll 9 11 1 0.0100
14 32 12 11 ll 1 0.0100
13 30 12 10 11 1 0.0100
13 29 ll 11 11 1 0.0100
13 21 14 11 10 1 0.0100
13 29 12 11 12 1 0.0100
13 33 12 11 11 1 0.0100
13 29 12 12 13 1 0.0100
13 29 12 11 13 1 0.0100
14 31 11 11 11 1 0.0100
12 30 11 10 12 1 0.0100
12 28 12 10 10 1 0.0100
13 30 ll 8 11 1 0.0100
15 32 12 12 11 1 0.0100
12 29 11 11 12 1 0.0100
14 31 11 12 13 1 0.0100
13 31 13 10 ll 1 0.0100

 

37

 

 

Table 8b (continued)

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

13 29 12 13 13 1 0.0100
12 28 ll 12 13 1 0.0100
14 3O 12 11 14 1 0.0100
14 31 10 10 14 1 0.0100
12 28 13 8 11 1 0.0100
13 28 12 12 13 1 0.0100
13 31 13 11 11 1 0.0100
13 31 12 12 11 1 0.0100
12 31 ll 10 11 1 0.0100
13 30 10 11 11 1 0.0100
13 29 12 9 ll 1 0.0100

 

African American Y-PLEXTM 5 haplotype frequencies

38

 

Table 80

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

# of
DYS3891 DYS3891] DYS439 DYS438 DYS392 occurrences Frequency
13 29 ll 12 13 11 0.0859
13 29 12 12 13 7 0.0547
14 30 12 12 13 5 0.0391
13 30 12 12 13 4 0.0313
14 30 10 10 11 3 0.0234
13 31 12 10 11 3 0.0234
13 30 12 11 ll 3 0.0234
13 30 12 10 11 3 0.0234
13 29 11 11 14 2 0.0156
14 31 l3 12 13 2 0.0156
13 29 10 12 13 2 0.0156
12 27 12 10 11 2 0.0156
12 12 28 11 13 2 0.0156
14 29 12 10 11 2 0.0156
13 30 ll 11 11 2 0.0156
13 29 13 10 11 2 0.0156
13 29 12 9 11 2 0.0156
13 31 11 12 14 2 0.0156
13 30 13 12 13 2 0.0156
12 28 11 10 11 2 0.0156
12 29 11 10 11 2 0.0156
12 28 11 9 11 2 0.0156
13 29 13 12 13 2 0.0156
13 29 12 10 14 2 0.0156
14 31 12 10 11 2 0.0156
13 30 ll 11 15 2 0.0156
13 29 11 11 12 1 0.0078
12 29 12 10 11 1 0.0078
13 29 12 ll 13 1 0.0078
14 31 10 10 11 1 0.0078
13 29 12 12 14 1 0.0078
13 28 12 12 14 1 0.0078
13 30 12 9 11 1 0.0078
12 29 12 11 14 1 0.0078
12 28 11 12 14 1 0.0078
13 30 13 11 15 1 0.0078
14 31 12 12 13 1 0.0078
13 30 11 9 11 1 0.0078
13 31 11 11 11 1 0.0078

 

 

 

 

 

 

 

 

39

 

 

ll‘able 8c (continued)

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

12 28 1 1 13 13 1 0.0078
12 28 12 12 13 1 0.0078
13 30 l l 10 l 1 1 0.0078
13 31 l l 10 l 1 1 0.0078
13 3O 12 10 14 1 0.0078
13 30 12 10 12 1 0.0078
13 29 12 1 1 14 1 0.0078
13 30 1 l 10 12 1 0.0078
12 29 l 1 12 13 1 0.0078
13 29 10 12 13 1 0.0078
13 29 1 1 13 14 1 0.0078
13 30 10 10 12 1 0.0078
14 30 13 12 13 1 0.0078
13 29 12 12 13 1 0.0078
12 28 13 1 1 1 1 1 0.0078
13 31 13 ll 14 1 0.0078
13 29 11 13 13 1 0.0078
14 29 12 1 1 1 l 1 0.0078
13 29 12 12 13 1 0.0078
13 29 12 12 10 1 0.0078
14 32 1 l 10 1 1 1 0.0078
13 29 12 12 13 1 0.0078
14 32 13 1 1 l4 1 0.0078
14 31 10 1 1 1 1 1 0.0078
13 29 12 12 13 1 0.0078
13 29 12 12 13 1 0.0078
13 29 1 l l2 14 1 0.0078
13 31 13 12 13 1 0.0078
13 30 l l 12 13 1 0.0078
14 30 13 10 l 1 1 0.0078
13 30 13 l 1 l l 1 0.0078
14 31 12 l 1 14 1 0.0078
14 30 12 9 1 1 1 0.0078
14 32 12 10 12 1 0.0078
12 27 12 12 13 1 0.0078
14 30 l l 12 13 1 0.0078
13 29 l l 9 l 1 1 0.0078
13 30 1 l 1 1 13 1 0.0078
13 3 l 12 12 14 1 0.0078
14 32 13 12 13 1 0.0078

 

Hispanic Y-PLBXW 5 Haplotype Frequencies

40

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

mo...

weed _ N_ : N N 3 3
836 _ 3 N— : VN om 3 m.
856 fl 3 3 o. mN E m— 2
88d g 3 o. S N on S m.
856 ~ 2 m. 2 N eN m. 3
aged ~ 3 m. e N N m. m.
386 g m. .1 o. NN N m— E
886 _ 3 o. NN oN m. 2
«Sad _ 3 Z Z N on I N_
35.0 g 2 Z Z N on 3 2
856 _ 2 2 2 .N N 2 2
MNmod m 3 Z : «N N E m—
mchd m 3 2 3 MN N 3 m.
m_No.o N 3 Z S N on 2 m.
336 N 3 o. mN N I 2
m_No.o N 3 m. o. NN N m— m—
m_No.o N 2 S : VN eN 3 m.
386 N 3 m. o. NN wN 3 m—
MNmod m E Z : «N N 3 m—
m_No.o N E S Z N N 3 2
omvod «4 3 I o. «N cm 3 m.
mNmod m E o. o— N am 5 m—
ocwod w 3 Z S «N N 3 2
28d N E 2 Z mN N 3 2
#05362... 328.558 0 mamm>fl a mumm>0 3mm>Q oomm>n newmm>a 3m>n momm>n

a a 2%...

41

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

was... . m. M. o. MN GM .4. N.
«0...... . v. .. o. MN eN m. .4.
mos... . m. .. o. .N mN v. M.
Mos... . v. .. .. VN GM .4. M.
was... . v. N. o. .N N v. v.
was... . .. o. .. .N N v. .4.
mos... . v. o. o. .N oM m. M.
no.0... . v. M. o. NN MN v. M.
was... . m. N. o. N N v. M.
was... . w. w. o. .N oM M. M.
was... . M. .. c. .N GM .4. M.
8...... . e. v. c. MN oM v. M.
was... . m. .. .. NN cM v. M.
Mos... . w. v. .. MN oN e. v.
Mos... . v. .. .. MN OM v. M.
Mos... . M. .. .. NN cM v. M.
was... . M. N. .. MN N v. M.
«0...... . M. N. o. MN MN .4. v.
8...... . v. N. c. MN eN v. M.
8...... . M. .. o. MN oM v. M.
Mos... . n. M. e MN oN m. M.
Mos... . m. M. o. NN N v. M.
Mos... . v. o. .. .N .M m. M.
Mos... . v. o. NN MN .4. M.
was... . m. .. VN OM o. M.
was... . m. v. c. MN eN v. M.
8.0... . h. v. o .N .M v. M.

 

 

 

 

 

 

 

 

 

 

685.85 a 2......

 

 

42

8.8262... 252%.. w qun.-> 53830

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Mos... . v. o. NN MN v. M.
Mo.o.o . v. .. o. .N 0M v. N.
3...... . M. v. .. .N .M o. v.
Mos... . v. .. .. MN MN v. M.
MOE... . w. .. o. N MN M. M.
Mos... . N. M .N .M c. M.
Mos... . M. N. o. NN MN v. M.
8...... . v. .. o. MN MM 0. M.
8...... . v. .. .. NN MN v. M.
Mo.o.o . M. .. .. MN MN w. M.
Mos... . c. 0. MN MN M. o.
Mo.o.o . w. .. o. .N MN v. M.
8.0... . v. M. o. NN .M M. v.
MOS... . h. v. o. MN MM v. N.
Mo.o.o . v. .. .. VN oM M. M.
Mao... . M. N. .. MN MN M. v.
Mos... . v. .. .. MN OM w. M.

 

 

 

 

 

 

 

 

 

 

@8588. «a ”sub

 

 

43

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

2:3 2 2 2 2 2 2 2 2
2:3 2 2 222 2N 2m 2 2
2:3 2 2 2 2 2 2m 2 2
2:3 2 2 2 22 2 2 2 2
2:3 2 2 2 2 2m 2m 2 2
2:3 2 2 2 2 2 on 2 2
2:3 2 2 2 2N on 2 2
2:3 2 2 2 2 2m 3m 2 2
2:3 2 22 22 a 2 2 2
2:3 2 2 22 22 2 2 2 2
2:3 2 2 2 2 2n 2 2 2
2:3 2 2 2 2m 8 2 2
2:3 2 2 2 2 mm 2 2 2
2:3 2 2 2 2N 22m 2 2
2:3 2 2 2 2m 9. 2 2
2:3 2 2 2 2 2m .2 2 2
2:3 2 2 2 2m 8 2 2
2:3 2 2 2 2 2 mm 2 2
2:3 2 2 2 2 a 22m 2 2
2:3 2 2 22 22 MN 2 2 2
223 N 2 2 2 2 2 22m 2 2
223 N 2 2 2 2m 2 2 2
223 N 2 22 2 mm a 2 2
22.23 m 2 2 222 2N 2m 2 2
2223 m 2 22 22 x 22m 2 2
223 2. 2 22 22 «.6. 3m 2 2
28222222 8222288232 .2 22225 a 2225 2225 9225 223226 225 885

 

 

 

 

 

 

 

 

 

£2 22222

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

v..M.M . M. M. .. NN NM M. M.
v..M.M . h. M. .. .N .M M. M.
.156 . .. .. MN MM v. M.
336 . h. M. M. .N .M M. M.
v..M.M . M. M. .. .N .M M. M.
v..M.M . M. M. M. .N .M M. M.
v. .M.M . .. M. N .M M. M.
336 . M. n. M. NN .M M. v.
¢..M.M . M. N. .. VN MN v. N.
356 . M. .. .. VN MM v. M.
v..M.M . n. M. M. .N MM M. M.
336 . M. h. M. .N MM M. M.
336 . v. .. .. .N .M v. M.
356 . M. v. M. .N MN v. v.
v..M.M . w. .. .. MN MM M. M.
v..M.M . M. .. .N MM M. v.
v..M.M . v. M. NN MM 5. M.
356 . M. M. M. .N NM 6. M.
356 . M. h. M. .N MM 5. M.
386 . M. h. M. .N MM 5. M.
356 . v. M. M. NN MN M. M.
«.56 . h. v. M. NN .M h. M.
35... . M. N. M. .N MN v. M.
356 . M. M. .N MM h. v.
v..M.M . N. .. .. MN MN V. M.
v..M.M . M. M. .N MM h. v.
v..M.M . M. M. .N .M M. v.

 

 

 

 

 

 

 

 

 

 

23822222283 22.2 02.22;

 

 

45

8.822.202... 2.2.8.92... M EXmAMS 282.2252 58.2.32

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

v..M.M . M. v. M. MN MN v. M.
33... . M. .. .. VN MM v. v.
v..M.M . M. v. M. .N .M M. M.
v..M.M . n. .. NN .M M. M.
v..M.M . M. v. .. MN MN M. M.
v..M.M . h. M. M .N .M M. M.
v..M.M . M. M. M. NN MM M. M.
35... . M. h. M. .N MM M. M.
336 . v. .. .. MN MN w... M.
v..M.M . M. v. .. NN MN M. M.
v..M.M . M. M. .N .M h. M.
v..M.M . v. .. .. VN MN M. M.
v..M.M . M. M. .. NN MM M. M.
v..M.M . M. .. .. NN .M v. M.
v..M.M . M. .. MN MN M. M.
356 . v. M. .N .M M. v.
35... . n. M. M. .N .M M. v.
v..M.M . M. .. .. MN MN v. M.
356 . h. M. M. .N MN M. w.
3.9.. . M. h. M. .N MM n. M.
v..M.M . v. .. .. VN MN M. M.
35... . M. M. .N MM M. M.
356 . n. M. M. .N MM M. M.
v..M.M . M. .. .N .M M. M.
v..M.M . M. M. .N MM M. v.

 

 

 

 

 

 

 

 

 

 

8222222228. 2a 9223

 

46

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

22223 2 2 2 2 2 mN 3N 2 2
E2223 2 2 22 2 3N 2 2
223 2 2 2 2 NN 2N 2 2
22223 2 2 2 2 2 Nm 2 2
22223 2 2 22 22 3N 22m 2 2
223 2 2 2 22 2 3N 2 2
223 2 2 2 2 2 2 3N 2 2
283 2 2 2 2 VN :2 2 2
2.23 2 2 2 22 VN 3N 2 2
22223 2 2 2 2 2 2m 2 2
E2223 2 2 2 2 MN 3N 2 2
:83 2 2 2 2 2 2 3N 2 2
2223 N 2 22 2 2 3N 2 2
22223 N 2 2 2 2 3N 2 2
2223 N 2 2 2 2 2m 2 2
22223 N 2 2 2 2 on 2 2
22223 N 2 22 2 4N 3N 2 2
2223 N 2 22 22 2N 2m 2 2
22223 N 2 22 22 2 3N 2 2
NNN23 m 2 22 2 X 2 2 2
22223 N 2 N2 22 «N 3N 2 2
22223 n 2 22 22 NN 3N 2 2
NNN3 N 2 22 2 2 2 ON 2 2
22223 N 2 22 22 MN 2. 2 2
NNN23 N 2 2 a 2 22m 2 2
223 2. 2 22 2 2 2 3N 2 2
23222.22 822228822. .2 22 2326 a 2225 2225 22225 222285 225 82.25

0M 0.2.5.2

47

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

MMMMM . v. .. .. MN MM 3 M.
MMMMM . M. M. M. MN MM M. M.
MMMMM . M. M. MN MM M. v.
MMMMM . v. .. .. MN MM v. M.
VMMMM . v. .. MN . M M. M.
MMMMM . w. .. M. .N .M M. M.
MMMMM . v. .. .. MN MN M. M.
MMMMM . N. .. M «N MN M. M.
MMMMM . v. .. .. MN MM v. M.
MMMMM . v. .. M. MN .M M. N.
«MMMM . . . M. MN . M M. M.
MMMMM . M. v. M. MN NM M. M.
~NMMMM . v. . . M. N MN 2.. N.
MMMMM . M. M. M. «N NM M. M.
MMMMM . . . . . MN MN v. M.
MMMMM . M. M. M. .N MM M. M.
MMMMM . N. . . NN MN M. M.
MMMMM . M. v. M. NN MN M. M.
MMMMM . M. M. .. MN MM v. M.
VMMMM . M. M. M. NN MN v. M.
MMMMM . M. M. M. MN MN M. M.
~NMMMM . v. M. M N .M M. M.
MMMMM . M. N. M. N MM M. M.
MMMMM . M. N. M. MN MN M. M.
MMMMM . M. M. .N MM M. v.
~2VMMM.M . M. M. M. MN .M M. N.
MMMMM . M. .. M. MN MN M. M.
302222.228. oM 0322M

 

 

48

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

«MMMM . v. M. .. VN MN v. M.
VMMMM . w. . . M. .N MN v. M.
wMMMM . v. .. .. MN MN v. N.
VMMMM . v. M. M .N .M M. w.
MMMMM . M. M. .N MN v. M.
VMMMM . M. M. M. .N MM M. M.
MMMMM . M. v. M. MN MN M. v.
MMMMM . M. v. M. MN MN M. v.
MMMMM . M. M. M. .N MN M. M.
MMMMM . M. . . M. N MN M. M.
VMMMM . v. M. MN MN e. M.
MMMMM . v. M. «N MM M. M.
MMMMM . M. v. M. .N MM M. M.
MMMMM . M. M. M. MN MN M. N.
MMMMM . w. . . .. MN MM v. M.
MMMMM . M. v. M. .N MN w. M.
MMMMM . M. M. M. MN .M M. M.
MMMMM . M. . . . . VN MM 1. M.
MMMMM . M. w. M. MN NM M. v.
«MMMM . M. M. M. NN MM v. N.
~NMMMM . M. M. M. MN MM v. N.
VMMMM . M. M. M. .N MM v. M.
MMMMM . M. M. M. MN MM M. M.
MMMMM . M. .. .. MN MN v. M.
VMMMM . N. M. MN MN v. N.
MMMMM . M. M. MN .M M. M.
VMMMM . M. M .N MM M. M.

 

 

 

 

 

 

 

 

 

 

302222.228 oM 0.2.2;

 

 

49

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

VMMMM . M. M. M. .N MM M. v.
VMMMM . M. M. M. .N MM M. v.
VMMMM . M. M. M. MN MM v. N.
MMMMM . M. M. M. MN MM M. M.
VMMMM . M. M MN MM M. M.
VMMMM . M. M. MN MM v. M.
VMMMM . M. M. .. .N MM M. M.
MMMMM . v. M. M. MN .M v. N.
~2VMMM.M . M. M. M. MN MM M. M.
MMMMM . M. N. M. MN MN M. M.
MMMMM . M. v. M. MN MN M. v.
MMMMM . M. v. M. NN MN M. v.
MMMMM . w. .. .. vN MN M. M.
MMMMM . M. M. M .N MN M. M.
MMMMM . M. M. .N MM M. M.
VMMMM . v. .. .. MN MM v. M.
VMMMM . M. M. .. .N .M M. M.
MMMMM . M. M. M. NN MM v. N.
MMMMM . v. .. .. MN MM v. M.
VMMMM . M. N. M. NN MN M. e.
MMMMM . M. M. M. MN .M M. N.
MMMMM . M. .. .. .N .M v. M.
vMMMM . M. v. M. «N MM M. M.
VMMMM . M. M. M. .N MN M. v.
MMMMM . M. .. .. VN MN M. M.
MMMMM . M. M. M. MN MN v. M.
MMMMM . M. M. M. .N MM Q. N.

 

 

 

 

 

 

 

 

 

 

232222228 a 02.2.2

 

 

50

3288322 222.2%: M BEES o222222222

 

 

 

 

 

VMMMM . M. M. N. .N MN v. v.
VMMMM . M. v. M .N MN M. M.
VMMMM . . . . . MN MN v. N.
VMMMM . M. v. M. MN MN V. N.
VMMMM . M. N. M. MN MN v. N.

 

 

 

 

 

 

 

 

 

 

€222.88. oM 0323M

 

 

51

 

Table 103

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

52

 

 

DYS385 DYS385 # (,f
DYS3891 DYS389H DYS439 DYS438 DYS3 2 DYS393 DYSI9 DYS38911 DYS390 DYS391 a L occurrences Frequency
13 29 11 12 13 13 14 29 24 11 11 14 3 0.0341
12 28 11 10 11 13 14 28 22 10 13 14 3 0.0341
13 29 12 12 13 13 14 29 24 11 11 14 2 0.0227
13 3O 13 12 13 13 14 30 24 10 11 14 2 0.0227
13 29 12 12 13 13 14 29 25 ll 11 14 2 0.0227
13 30 11 11 11 13 17 30 25 10 10 14 2 0.0227
13 28 12 12 13 13 14 28 24 11 11 14 2 0.0227
12 27 11 10 11 13 14 27 23 10 15 2 0.0227
13 29 11 12 13 13 15 29 24 10 11 15 ] 0.0114
14 30 12 12 13 13 14 30 24 11 11 16 1 0.0114
13 3O 13 11 13 12 14 3O 24 11 11 14 1 0.0114
12 29 12 10 11 13 15 29 22 10 14 14 1 0.0114
14 29 11 12 13 13 14 29 24 11 11 14 A 1 0.0114
12 29 12 10 11 14 15 29 22 10 14 15 1 0.0114
A 30 10 11 11 13 17 3O 25 10 10 _14 1 0.0114
13 29 10 10 11 13 13 29 24 9 13 14 1 0.0114
L 29 11 10 11 14 15 29 24 11 13 16 1 0.0114
L 29 12 12 14 13 14 29 25 11 11 14 1 0.0114
i 28 11 12 13 13 14 28 23 10 11 14 1 0.0114
_13\ 29 12 13 13 13 14 29 23 11 11 14 1 0.0114
1; 31 12 10 11 13 13 31 25 10 16 18 1 0.0114
14 31 11 10 12 13 14 31 24 9 14 17 1 0.0114
12 29 10 10 11 13 14 29 23 10 14 15 1 0.0114
i 30 13 10 11 13 16 3O 24 11 15 15 1 0.0114
L 28 11 10 11 13 14 28 22 10 14 14 1 0.0114
L 29 11 12 13 13 14 29 24 11 11 15 1 0.0114
13 31 10 11 11 13 15 31 24 11 10 14 1 0.0114
L 29 12 10 11 13 14 29 22 10 13 15 1 0.0114
13 29 13 9 11 13 15 29 23 9 13 17 1 0.0114
13 29 11 12 13 13 14 29 23 10 12 14 1 0.0114
1&2 28 13 12 13 14 14 28 23 10 12 13 1 0.0114
1\3 29 13 12 13 13 14 29 23 11 11 14 1 0.0114
L 28 12 10 11 13 15 28 22 10 13 14 1 0.0114
13 ‘ 29 11 12 13 13 14 29 23 11 12 13 1 0.0114
FL 30 13 12 13 13 14 3O 22 11 11 13 1 0.0114
13 28 13 12 13 13 14 28 23 11 11 14 1 0,0114
13 28 12 12 13 13 14 28 23 11 11 14 1 0.0114

 

 

 

Table 10:1 (continued)

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

13 1 29 T 12 1 12 12 13 14 29 24 11 11 11. 1 0.0114
14 1 30 1 12 13 13 13 14 31) 23 11 11 14_. 1 0.111 14
13 30 1 10 11 11 13 16 30 25 10 11 11_ 1 0,0114
13 1 29 1 12 10 12 14 16 29 23 11 14 1_)_ 1 0.0114
13 30 1 12 12 14 13 14 31) 22 11 11 1:: 1 0.0114
13 28 1 12 12 1 14 13 14 28 23 10 11 14_ 1 0.0114
13 30 1 11 1 9 1 13 13 14 30 23 10 14 16_ 1 0.0114
14 30 1 12 1 12 1 13 13 14 30 24 10 11 1::_ 1 0.0114
13 30 1 12 1 10 1 11 13 13 30 24 10 16 11?. 1 0.0114
13 29 1 12 1 13 1 13 13 14 29 24 10 12 1:. 1 0.0114
12 28 1 11 1 10 11 13 14 28 22 1o 13 14_ 1 0.0114
13 30 1 10 1 11 11 13 15 30 24 10 1o 14_ 1 0.0114
13 29 1 11 1 12 14 14 14 29 24 11 10 11“ 1 0.0114
13 29 1 12 1 12 13 14 14 29 24 10 12 14 1 0.0114
30 1 13 12 13 13 14 30 24 11 11 14_ 1 0.0114
29 1 12 12 13 13 14 29 24 10 11 15 1 0.0114
29 1 12 12 13 14 15 29 23 10 11 14_ 1 0.0114
30 1 12 1o 11 12 14 30 23 10 13 15- 1 0.0114
30 1 11 12 13 13 14 30 25 11 11 14- 1 0.0114
29 1 13 12 13 14 15 29 25 11 12 1.11 0.0114
30 1 11 12 1 13 13 15 30 24 11 11 14 1 0.0114
29 1 14 12 1 13 13 14 29 24 11 11 15__ 1 0.0114
30 1 11 12 1 13 13 14 30 24 10 11 14_ 1 0.0114
31 11 10 11 14 15 31 22 10 13 14_. 1 0.0114
13 29 12 12 13 13 14 29 24 11 11 14 1 0.0114
29 11 12 13 13 14 29 24 10 11 14_ 1 0.0114
29 11 10 12 16 15 29 23 10 16 16 1 0.0114
13 29 1 11 12 13 13 14 29 23 11 11 15 1 0.0114
30 1 12 11 1 11 13 16 30 25 10 11 14_ 1 0.0114
13 28 1 12 12 13 13 14 29 24 11 11 14. 1 0.0114
29 1 12 1 12 13 13 14 29 23 10 11 14. 1 0.0114
n 29 1 12 1 12 13 13 14 29 22 11 11 14_ 1 0.0114
n 30 1 13 1 11 11 13 16 30 25 10 11 14. 1 0.0114
n 28 1 12 1 1o 11 13 14 28 22 10 12 16_ 1 0.0114
15 31 1 12 1 10 11 13 16 31 24 9 12 12‘ 1 0.0114
13 29 1 11 1 12 13 13 13 29 24 1o 11 14 1 0.0114
13 29 1 13 1 12 13 13 14 29 23 11 11 14. 1 0.0114
13 31 1 13 1 10 11 14 16 31 24 11 14 1_5__ 1 0.0114
13 30 1 12 1 12 13 12 14 30 24 10 11 14. 1 0.0114

 

 

 

 

 

 

 

 

53

 

 

 

 

 

Table 1011 (continucd)
12 1 29 1 12 1 10 1 11 1 13 1 14 1 29 1 22 1 10 1 14 1 14 1 1 1 11.0114
13 1 30 1 12 1 12 1 13 1 13 1 14 1 30 1 24 1 10 1 11 1—14 1 1 1 (1.0114

Caucasian Y—PLEXTM 5 and 6 haplotype frequencies

54

 

 

1—]
SD
2
(D
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5"

 

 

 
    

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

1
DYS3891 1:YS389H 1 DYS439 1DYS438 DYS392 DYS393 DYS389H 1 DYS390 DYS391 DYS38511 DYS385 b # of occurrences Frequency
L 13 1 29 1 12 1 12 1 13 1 13 1 14 29 24 11 11 14 2 0.0256
L13 1 31 1 11 1 11 1 11 1 13 1 15 31 21 10 16 17 2 0.0256
E3 1 29 1 12 1 12 1 13 1 13 1 14 29 23 11 11 15 1 0.0128
12 1 28 1 11 1 10 1 11 1 13 1 14 28 22 10 14 14 1 0.0128
E4 1 32 1 13 1 11 1 11 1 13 1 15 32 21 10 14 14 1 0.0128
13 1 30 1 12 1 11 1 11 1 14 1 161 30 21 10 18 18 1 0.0128
1 29 1 11 1 10 1 11 1 12 1 141 29 21 10 14 15 1 0,0128
1 32 1 11 1 11 1 11 1 15 1 151 32 21 10 17 17 1 0.0128
1 28 1 12 1 11 1 11 1 13 1 16 28 21 10 15 15 1 0.0128
1 29 1 11 1 9 1 11 1 14 1 15 29 1 22 10 14 15 1 0.0128
1 29 1 12 1 11 1 11 1 14 1 16 29 1 10 16 16 1 0.0128
1 31 1 12 1 11 1 11 1 15 1 15 31 1 10 14 18 1 0.0128
1 29 1 11 1 12 1 13 1 13 1 141 29 1 24 11 11 12 1 0.0128
1 29 1 12 1 12 1 13 1 13 1 14 29 1 24 11 11’ 11 1 0.0128
1 30 1 12 1 11 1 11 1 14 1 16 30 1 21 10 17 18 1 0.0128
1 30 1 13 1 11 1 11 1 14 1 17 30 1 21 10 17 17 1 0.0128
1 32 1 12 1 11 1 11 1 13 1 15 32 21 10 16 18 1 0.0128
1 29 1 12 1 12 1 13 1 13 1 14 29 23 10 11 14 1 0.0128
30 1 12 1 10 1 11 1 13 1 13 30 24 10 13 17 1 0.0128
31 1 12 1 11 1 11 1 13 1 15 31 21 10 1 14 17 1 0.0128
29 1 11 1 11 1 11 1 13 1 14 29 25 11 14 18 1 0.0128
29 1 12 1 12 1 13 1 13 1 14 29 24 10 11 14 1 0.0128
31 1 14 1 11 1 10 1 13 1 15 1 31 21 10 16 18 1 0.0128
31 1 12 1 11 1 11 1 15 1 16 1 31 1 21 10 17 17 1 0.0128
31 1 11 1 11 1 11 1 14 1 15 1 31 1 21 10 16 16 1 0.0128
30 1 12 1 11 1 11 1 14 1 17 1 30 1 21 1o 18 18 1 0.0128
29 1 12 1 11 1 12 1 13 1 14 1 29 1 23 1 11 11 12 1 0.0128
33 1 12 1 11 1 11 1 14 1 17 1 33 1 21 1 1o 18 18 1 0.0128
30 1 12 1 12 1 13 1 13 1 14 1 30 1 24 1 11 11 14 1 0.0128
29 1 12 1 11 1 13 1 13 1 14 1 29 24 1 10 1 12 15 1 0.0128
31 1 11 1 11 1 11 1 13 1 17 1 31 22 10 14 17 1 0.0128
28 1 12 1 10 1 10 1 13 1 15 1 28 22 1o 13 14 1 0.0128
30 1 12 1 11 1 11 1 13 1 17 1 30 21 10 17 18 1 0.0128
30 1 13 1 11 1 11 1 15 1 17 30 1 21 20 17 19 1 0.0128
32 1 11 1 11 1 11 1 15 1 17 32 1 21 10 1 16 19 1 0.0128
30 1 12 1 11 1 11 1 14 1 15 30 1 21 11 1 16 16 1 0.0128
29 1 11 1 11 1 12 1 14 1 14 29 1 21 101 14 16 1 0.0128

 

 

 

 

 

 

 

 

 

 

 

55

 

 

 

 

 

 

 

 

 

Table 10b (continued)
14 1 31
13 3O

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

1 11 1 12 1 13 1 13 1 14 31 24 11 11 14 1 0.0128

1 1 11 1 11 1 11 1 13 16 30 21 10 17 19 1 0.0128

13 1 30 1 11 1 11 1 11 1 13 15 30 21 10 16 17 1 0.0128
13 1 30 1 12 1 12 1 13 1 13 14 30 24 11 11 15 1 0.0128
13 1 29 1 13 1 12 1 13 1 12 14 29 24 11 12 15 1 0.0128
13 1 29 1 13 1 11 1 13 1 13 1 14 29 23 10 11 14 1 0.0128
13 fa 1 12 1 11 1 11 1 14 1 15 31 22 10 17 19 1 0.0128
13 1 31 1 13 1 10 1 11 1 13 1 16 31 24 1o 11 11 1 0.0128
13 1 31 1 11 1 11 w 1 13 1 16 1 31 21 10 15 18 1 0.0128
13 1 29 1 12 1 13 1 13 1 13 1 14 1 29 24 11 11 14 1 0.0128
13 1 31 1 12 1 11 1 11 1 13 1 15 1 31 21 11 16 17 1 0.0128
13 1 31 1 11 1 11 1 11 1 13 1 15 1 31 21 11 13 17 1 0.0128
14 1 32 1 11 1 11 1 11 1 13 1 15 1 32 22 11 15 16 1 0.0128
13 30 1 13 1 11 1 11 1 14 1 16 1 30 21 10 15 15 1 0.0128
13 1 31 1 12 1 11 1 11 1 15 1 15 1 31 21 11 16 , 16 1 0.0128
13 1 29 1 11 1 12 1 13 1 13 14 29 24 11 11 14 1 0.0128
13 1 3o 1 12 1 11 1 11 1 15 16 30 21 10 16 17 1 0.0128
13 1 30 1 12 1 11 1 11 1 13 16 30 21 10 18 18 1 0.0128
12 1 28 1 11 1 12 1 13 1 13 15 28 24 11 11 14 1 0.0128
13 30 1 12 1 11 1 11 1 15 17 30 21 10 17 19 1 0.0128
12 1 29 1 12 1 11 1 11 1 14 15 29 21 10 16 17 1 0.0128
13 1 29 1 12 1 12 1 14 1 13 14 29 25 11 11 13 1 0.0128
14 1 31 1 12 1 11 1 11 1 14 1 15 31 21 10 15 17 1 0.0128
13 1 31 1 12 1 11 1 11 1 14 l 16 1 31 21 10 14 14 1 0.0128
14 1 31 1 10 1 10 1 14 1 13 1 14 1 31 22 11 11 13 1 0.0128
13 1 30 1 12 1 11 1 11 1 13 1 15 1 30 22 11 15 19 1 0.0128
14 1 31 1 12 1 11 1 11 1 13 1 17 1 31 21 10 18 18 1 0.0128
12 1 28 1 13 1 8 1 11 1 13 1 16 1 28 22 11 14 16 1 0.0128
13 1 28 1 12 1 12 1 13 1 13 1 14 1 28 23 11 11 14 1 0.0128
13 3o 1 12 1 11 1 11 1 13 1 16 1 30 21 10 17 18 1 0.0128
13 1 30 1 11 1 11 1 11 1 13 1 15 1 30 22 10 13 15 1 0.0128
13 31 1 13 1 11 1 11 1 13 1 15 1 31 21 9 16 17 1 0.0128
13 1 31 1 12 1 12 1 11 1 13 1 15 1 31 21 1o 16 17 1 0.0128
14 1 30 1 12 1 12 1 13 1 14 1 14 1 30 24 11 11 13 1 0.0128
13 1 32 1 11 1 11 1 11 1 13 1 15 32 21 10 16 18 1 0.0128
13 " 31 1 11 1 11 1 11 1 13 1 15 31 22 11 17 17 1 0.0128
12 1 31 1 11 1 10 1 11 1 13 1 15 31 21 10 14 18 1 0.0128
12 1 28 11 1 10 1 11 1 13 1 16 28 25 11 14 16 1 0.0128

African American Y-PLEXTM 5 and 6 haplotype frequencies

 

56

 

 

 

Table lOc

 

 

 
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
   
  
  
  
  
  
  
 
  
  
  
 
  
  

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

DYS3891 1 DYS389H 1 DYS439 1 DYS438 DYS392 DYS393 DY819 DYS38911 DYS390 DYS391 DYS385 a DYS385 b #Ol‘occurrences Frequenc
14 1 30 1 10 1 10 11 13 13 30 24 9 13 14 2 0.0171
13 1 29 1 11 1 12 13 13 14 29 23 11 11 14 2 0.0171
14 1 31 1 13 1 12 13 13 14 31 24 11 11 14 2 0.0171
13 1 29 1 11 1 11 1 12 1 15 17 29 21 1o 15 17 1 0.0085
13 29 1 12 1 12 1 13 1 13 14 29 24 11 11 15 1 0.0085
12 29 1 12 1 10 11 1 14 15 29 23 1-1 14 15 1 0.0085
13 1 29 1 12 1 11 13 1 14 13 29 23 11) 14 18 1 0.0085
13 29 1 11 1 11 14 1 13 14 29 24 11) 15 15 1 0.0085
14 31 1 10 1 10 1 11 1 14 13 31 24 9 13 14 1 0.0085
13 29 1 12 1 12 14 1 12 14 29 23 11 11 14 1 0.0085
13 28 1 12 1 12 14 1 13 14 28 24 1;) 11 14 1 0.0085
13 29 1 1o 1 12 13 13 14 29 24 11 13 14 1 0.0085
13 30 1 12 1 9 11 12 14 3o 24 19 1‘3 15 1 0.0085
12 29 1 12 11 14 13 14 29 23 111 13 18 1 0.0085

29 1 11 12 13 13 15 29 24 11 11 16 1 0.0085
12 28 1 11 12 14 14 13 28 24 11) 15 16 1 0.0085
13 30 1 13 11 15 13 13 30 24 11 14 16 1 0.0085
14 31 1 12 12 13 13 14 31 24 11 11 15 1 0.0085
13 31 1 12 1o 11 12 15 31 23 19 13 18 1 0.0085
12 27 1 12 1 10 11 14 15 27 22 11 12 15 1 0.0085
14 30 1 12 1 12 13 13 14 30 24 11 11 14 1 0.0085
13 29 1 12 1 12 1 13 14 14 29 24 1) 12 15 1 0.0085
13 30 1 11 1 9 1 11 12 14 30 22 13 13 15 1 0.0085
13 31 1 11 1 11 1 11 13 15 31 21 11 16 17 1 0.0085
13 30 1 12 1 12 1 13 1 13 14 30 24 11 11 14 1 0.0085
13 30' 1 12 1 11 1 11 15 16 30 21 1o 17 17 1 0.0085
12 28 1 11 1 13 1 13 13 13 28 24 9 15 18 1 0.0085
13 29 1 12 1 12 1 13 13 15 29 24 11 11 14 1 0.0085
13 29 1 11 1 12 1 13 13 14 29 24 111 11 14 1 0.0085
12 28 1 12 1 11 1 13 14 13 28 23 10 14 19 1 0.0085
14 29 1 12 1 10 1 11 13 16 29 23 10 12 13 1 0.0085
13 29 1 12 1 12 1 13 13 15 29 25 11 12 14 1 0.0085
13 30 1 11 1 10 1 11 13 13 30 23 10 15 16 1 0.0085

31 1 11 1 10 1 11 12 14 31 23 10 13 14 1 0.0085
13 30 1 11 1 11 1 11 13 15 30 21 11 16 18 1 0.0085
13 29 1 11 1 12 1 13 13 14 29 25 11 11 14 1 0.0085

 

 

 

 

 

 

 

 

 

57

 

 

 

 

1'74—

able lOc (continued)

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

1 13 1 30 1 12 1 10 1 14 1 13 14 1 311 1 23 1o. 1 17 17 1 0.0085
L 13 1 30 1 12 1 10 1 12 1 13 13 1 3o 1 25 9 J 18 18 1 0.0085
13 1 30 1 11 1 10 1 12 1 15 16 1 3n 1 23 10 1 15 18 1 0.0085
13 1 3o 1 12 1 1o 1 11 1 12 14 1 311 1 23 10 1 13 15 1 0.0085
13 1 30 1 12 1 11 1 11 1 14 15 1 311 21 10 1 13 16 1 0.0085
12 1729 1 11 1 12 1 13 1 13 1 14 1 29 23 11 11 14 1 0.0085
13 1 3o 1 12 1 11 1 11 1 14 1 15 1 30 21 10 15 16 1 0.0085
13 1 29 1 13 1 10 1 11 1 12 1 14 1 29 23 10 12 19 1 0.0085
13 1 29 1 12 1 9 1 11 1 12 1 14 1 29 25 10 14 19 1 0.0085
14 3o 1 12 1 12 1 13 1 13 1 14 1 30 24 10 11 14 1 0.0085
13 1 30 1 13 1 12 1 13 1 13 1 14 1 30 23 11 11 14 1 0.0085
13 1 29 1 11 1 12 1 13 1 12 1 14 1 29 25 11 11 11 1 0.0085
13 29 1 11 1 12 1 13 1 13 1 14 1 29 23 11 11 14 1 0.0085
13 29 1 1o 1 12 1 13 1 13 1 14 1 29 24 11 13 15 1 0.0085
13 1 29 1 12 1 9 1 11 1 12 1 14 1 29 23 10 14 15 1 010085
13 1 31 1 12 1 1o 1 11 1 13 1 13 I 31 24 1o 15 17 1 0.0085
13 29 1 11 1 13 1 14 1 13 1 14 29 24 11 10 13 1 0.0085
13 1 31 1 11 1 12 1 14 1 13 1 13 31 24 10 14 17 1 0.0085
13 31 1 11 1 12 1 14 1 13 1 13 31 24 10 13 18 1 0.0085
13 29 1 11 1 12 1 13 1 13 14 29 24 11 12 14 1 0.0085
14 1 30 1 12 1 12 1 13 I 13 14 30 24 11 11 14 1 0.0085
12 28 1 11 1 10 1 11 1 13 15 28 23 10 13 14 1 0.0085
13 30 1 10 1 1o 1 12 1 13 13 30 24 9 13 14 1 0.0085
14 1 3o 1 13 1 12 1 13 1 13 1 14 1 30 23 11 11 14 1 0.0085
13 29 1 12 1 10 1 14 1 13 1 14 1 29 24 11 17 17 1 0.0085
13 29 1 12 1 12 1 13 1 12 1 14 1 29 25 10 11 13 1 0.0085
12 28 1 13 1 11 1 11 1 13 1 15 1 28 25 10 11 15 1 0.0085
13 31 1 13 1 11 1 14 1 12 1 13 1 31 23 10 16 19 1 0.0085
13 30 1 11 1 11 1 11 1 14 1 15 1 30 21 10 16 16 1 0.0085
13 29 1 11 1 13 1 13 1 13 1 14 1 29 24 11 11 14 1 0.0085
12 28 1 11 1 10 1 11 1 13 14 1 28 22 10 13 15 1 0.0085
12 29 1 11 1 10 1 11 1 13 15 1 29 22 10 14 16 1 0.0085
14 29 1 12 1 11 1 11 1 13 16 1 29 22 11 12 12 1 0.0085
13 30 1 12 1 10 1 11 1 13 13 1 30 24 1o 16 16 1 0.0085
13 29 1 12 1 12 1 13 1 13 15 29 25 11 12 14 1 0.0085
13 29 1 12 1 12 1 10 1 13 14 29 23 11 11 11 1 0.0085
14 32 1 11 1 10 I 11 1 13 13 32 24 1o 15 16 1 0.0085
13 29 1 11 1 12 1 13 1 12 14 29 24 1o 11 14 1 0.0085
13 30 1 13 1 12 1 13 1 13 14 30 24 1o 11 14 1 0.0085

 

 

 

 

 

 

 

 

 

 

 

 

 

58

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Table lOc (continued)
13 1 29 1 12 12 13 13 14 29 25 11 11 14 1 0.0085
14 1 32 1 13 11 14 13 13 32 23 10 14 17 1 0.0085
13 1 29 1 13 12 13 13 14 29 24 11 11 15 1 0,0085
14 1 31 1 10 11 11 12 15 31 25 10 11 14 1 0.0085
13 1 29 1 12 12 13 1 14 14 29 24 10 12 15 1 0.0085
14 1 30 1 12 1 12 1 13 1 13 14 30 24 11 11 14 1 0.0085
14 1 29 1 12 1 10 1 11 1 13 17 29 24 9 11 12 1 0.0085
13 1 29 1 12 1 12 1 13 1 13 1 14 29 24 10 . 11 14 1 0.0085
13 1 29 1 11 1 12 1 14 1 13 1 13 29 24 1 1 11 14 1 0.0085
13 1 31 1 13 1 12 1 13 1 13 1 15 31 24 10 11 14 1 0.0085
14 1 31 1 12 1 10 1 11 1 13 1 13 31 25 11 14 14 1 0.0085
13 1 30 1 11 1 12 1 13 1 13 1 14 30 24 11 11 14 1 0.0085
14 1 30 1 13 1 10 1 11 1 14 13 30 23 10. 17 17 1 0,0085
13 1 30 1 13 1 11 1 11 1 13 15 3o 20 10 17 19 1 0.0085
13 30 1 12 1 12 1 13 1 13 14 30 24 11 11 14 1 0.0085
13 29 1 12 1 12 1 13 1 13 14 29 24 10 11 15 1 0.0085
14 1 30 1 10 1 1o 11 13 13 30 24 9 13 13 1 0.0085
14 1 31 1 12 1 11 14 13 13 31 25 10 16 16 1 0.0085
13 1 29 1 13 1 10 11 12 14 29 23 10 12 12 1 0.0085
13 1 29 1 11 1 12 13 13 14 29 25 11 11 13 1 0.0085
13 3o 1 11 1 11 15 13 14 30 24 10 15 18 1 0.0085
14 30 1 12 1 9 1 11 12 14 30 23 10 13 17 1 0.0085
13 1 30 1 12 1 10 1 11 1 12 14 30 22 10 13 19 1 0.0085
13 29 1 12 1 12 1 13 1 13 14 29 23 11 11 14 1 0.0085
14 32 1 12 1 10 1 12 1 14 1 15 32 23 10 14 15 1 0.0085
13 30 1 12 1 12 1 13 1 13 1 14 30 24 11 11 15 1 0.0085
13 29 1 11 1 12 1 13 1 13 1 14 29 24 10 11 15 1 0.0085
14 1 31 1 12 1 10 1 11 1 13 1 13 31 23 10 15 18 1 0.0085
13 1 29 1 13 1 12 1 13 1 13 1 14 29 24 11 11 14 1 0.0085
14 30 1 11 1 12 1 13 1 13 14 30 24 11 11 14 1 0.0085
13 1 29 1 11 1 9 1 11 1 12 15 29 23 10 15 19 1 0.0085
13 30 1 11 1 11 1 15 1 13 13 30 24 10 14 17 1 0.0085
13 30 1 11 1 11 1 13 1 13 13 30 24 10 14 14 1 0.0085
13 31 1 12 1 12 1 14 1 13 13 31 24 10 13 18 1 0.0085
12 29 1 11 1 10 1 11 1 13 1 14 29 23 10 14 14 1 0.0085
13 1 29 1 10 1 12 1 13 1 13 1 15 29 24 10 11 13 1 0.0085
14 1 32 1 13 1 12 1 13 1 13 1 14 32 24 10 11 14 1 0.0085
12 28 12 11 1 13 1 13 1 13 28 24 9 14 17 1 0.0085
G

Hispanic Y—PLEXTM 5 and 6 haplotype frequenci s

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

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61

 

 

lemma
lAManNn-dlan
Ell-Chunk:

 

 

 

 

 

 

 

Y— mws allele fieqoency moflocus DYS43?

['19ch

 

DYSSO2

WNW

 

 

 

 

Ymmsmmymorha-Dvsm

62

 

 

 

 

 

Y-mmsmmwahanm”

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Y-mwsmmmormovsam

 

 

 

 

 

 

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65

 

 

 

 

Y-ruzxmoaneum’qhduunvssnn

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v-HEXNGMiuqu-cymiormovssso

 

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DYS391

 

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Y-mmsmmgnhorha-Dvml

67

 

 

 

 

—A
o

Y-PLEXS
m so
0
g so
9
8‘ 40 ~
35 ECaucasian
; so IAfrican American
g 20 Cll-fispanic
C
79
O
[.—

 

0

123456789101112
#ofoocurrences

 

 

 

Histogram of total number of Y-PLEX1M 5 haplotypes and the number of times they
occurred in each population.

Figure 13

 

Y-PLEX 6

 

l Caucasian
l African Am eriean
:1 Hispanic

 

 

Total number 0! haplotypes

 

it of occurrences

 

 

 

Histogram of total number of Y-PLEXTM 6 haplotypes and the number of times they
occurred in each population.

68

Figure 14

 

Y-PLEX 5 and 6

 

 

 

ca

0

D.

2'

2

:1: ICaucasian
S I African American
6) . .

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3

C

E

o

.—

 

1 2 3
# of occurrences

 

 

 

Histogram of total number of Y~PLEXTM 5 and 6 combined haplotypes and the number
of times they occurred in each population.

69

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72

   

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