What Are The Best Markers For

Having learned now how to judge measured parameters such as the probability of exclusion for a marker, it is perhaps worthwhile to step back and consider the STR markers under use in human identity applications. Are some markers better than others and if so is it possible to get results from the best markers when partial profiles or mixtures arise (see Chapter 22)?

In human identity testing, a primary goal is to reliably distinguish unrelated individuals from one another (see Chapter 21) or to match related ones through kinship analysis (see Chapter 23). This is done by using polymorphic markers so that we have less of a chance of a type from another individual randomly matching when it should not. In order to have this high discrimination power we typically use approximately a dozen unlinked STR markers. European laboratories are largely using the SGM Plus kit that amplifies 10 STR loci and North American laboratories use the 13 core CODIS loci with sometimes the addition of two more loci depending on the commercial megaplex (see Chapter 5). There are eight STR loci in common between the European and North American STR testing sets: FGA, TH01, VWA, D3S1358, D8S1179, D16S539, D18S51, and D21S11.

The probability of obtaining a match between two distinct and unrelated individuals (random match probability, RMP) provides a useful measure for evaluating the discriminating power of the DNA profiling system (Foreman and Evett 2001). Table 20.8 examines the average random match probabilities for

Table 20.8

Random match probabilities (RMPs) for the commonly used STR markers determined from Caucasian population databases. Power of discrimination (PD) was calculated for the available kits by multiplying the RMPs for the loci included in the kits (see Table 5.3). The CODIS core STR loci and the most commonly used kits are listed in bold font. The 13 CODIS loci data are from FBI data reported in NlJ's The Future of Forensic DNA Testing (2000). The product of these RMPs is 1.7 x 10-15for the 13 CODIS loci. D2S1138 and D19S433 RMP data are from the Identifiler Kit User's Manual from Applied Biosystems while the SE33 information is from the SEfiler Kit User's Manual. The Penta D and Penta E information comes from PowerPlex 16 population data available from Promega Corporation.

Locus

RMP

STR Kit

1/PD

PD

CSF1PO

0.112

PowerPlex 1.1

8.5 x 10-9

1.2 x 108

FGA

0.036

PowerPlex 2.1

5.8 x 10-12

1.7 x 1011

TH01

0.081

PowerPlex 16

3.0 x 10-18

3.4 x 1017

TPOX

0.195

PowerPlex ES

2.0 x 10-11

5.0 x 1010

VWA

0.062

Profiler Plus

1.1 x 10-11

9.4 x 1010

D3S1358

0.075

COfiler

7.7 x 10-7

1.3 x 106

D5S818

0.158

SGM Plus

2.1 x 10-13

4.8 x 1012

D7S820

0.065

Profiler

2.6 x 10-10

3.9 x 109

D8S1179

0.067

Identifiler

4.0 x 10-18

2.5 x 1017

D13S317

0.085

SEfiler

4.1 x 10-15

2.4 x 1014

D16S539

0.089

CTT

1.8 x 10-3

5.7 x 102

D18S51

0.028

CTTv

1.1 x 10-4

9.1 x103

D21S11

0.039

GammaSTR

7.8 x 10-5

1.3 x 104

D2S1338

0.027

FFFL

3.8 x 10-4

2.7 x 103

D19S433

0.087

Penta D

0.059

Penta E

0.03

SE33

0.02

F13A1

0.098

F13B

0.144

FES/FPS

0.172

LPL

0.155

the commonly used STR loci and the various combinations that are available with the use of different commercial kits.

A higher gene diversity (heterozygosity) level will result from having more alleles at a locus and having alleles that are fairly equal in terms of their observed frequency. Note that the RMP value of TPOX is poorer than D16S539 even though they have a similar number of alleles because D16S539 has a better balance of allele frequencies.

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