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bioSYNTHESIS
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High Resolution HLA Analysis in situations

of Marker(STR s) Depletion

Introduction
The Human Leukocyte Antigen (HLA) is one of the most
polymorphic gene systems known in humans, comprising of
over 1000 alleles over the Class I (A, B and C) and Class II (DR,
DQ and DP). In fact HLA was used early( since the 70’s) to
determine paternity in the USA and the worldwide.

Marker Exhaustion
In many situations, including closely interbreeding populations ,
the CPI’s (cumulative paternity index) , using the 15 marker
Identifiler (Applied Biosystems, CA, USA), probabilities of
paternity may not reach even 99%; hence most labs make use
of additional STR’s to bring the number over the 99% mark.
However even additional markers(See table 1) may not be
enough( maybe these markers are too common).
Table 1: 21 markers combination listed on the table below

1 D8S1179
2 D21S11
3 D7S820
4 CSF1PO
5 D3S1358
6 THO1
7 D13S17
8 D16S539
9 D2S1338
10 D19S433
11 VWA
12 TPOX
13 D18S51
14 D5S818
15 FGA
16 F13A01
17 F13B
18 FESFPS
19 LPL
20 Penta D
21 Penta E

Usefulness/ Applications
1. Common Alleles
Hence performing high resolution analysis of HLA alleles loci,
can be valuable, as the high polymorphicity of the system most
likely/surely will increase the probability of paternity (PP) over
99%.
 2. Mutations
In cases where there are mutations, HLA analysis will help to confirm paternity or
in inconclusive cases.

3. Disease Association
There are a number of immune related diseases that correlate with specific HLA
alleles.

4. Extended Analysis(instead of VNTR’s)

In cases where a higher CPI is needed, and instead of using hard to find places
that perform VNTR analysis, HLA analysis is able to increase significantly the CPI
values of any given case.

Examples of the usefulness of including HLA data in DNA

analysis (Table 2)

Table 2: Example of 15 markers result:

Child Alleged Father

System Allele Allele Allele Allele PI

D8S1179 14 14 15 1.5002

D21S11 29 31 29 32.2 1.3165

D7S820 8 10 10 11 0.7721

CSF1PO 11 13 8 11 1.2207

D3S1358 15 16 16 18 0.8141

TH01 7 8 7 1.1351

D13S317 12 12 13 1.0348

D16S539 9 10 9 11 1.2588

D2S1338 17 19 19 23 1.7668

D19S433 13 14 13 13.2 0.8381

 vWA 16 19 15 19 3.4626

TPOX 8 11 8 11 1.7902

D18S51 16 17 17 20 1.5253

D5S818 12 11 12 1.4061

FGA 22 24 18.2 24 1.3434

CPI: 59.2451
PP: 98.3401%

Two examples of common and non common alleles are:

System C AF* PI Formula
DRB1 1340, 0407 0407 (Freq=0.06428) 7.778 1/2a
DRB1 0301, 1504 0407 (Freq=0.00025) 2000 1/2a
*Allele Frequency (AF) data is based on Hispanic populations conducted by National Marrow Donor Program
(2007-11-20).

If the HLA-DRB1 locus is added to the table 2 above, the CPI and
PP will be much higher than 15 markers results.
Example of CPI and PP from 2 different DRB1 data that added
to the table 2:
1. CPI with HLA-DRB1 (common allele,0407): 460.796 PP with
HLA-DRB1: 99.78%
2. CPI with HLA-DRB1 (rare allele, 1504): 118490.2
PP with HLAB1: 99.9992%

We can see that even with a common allele one is able to

increase the PP to 99.78% and with a more rare HLA allele
the PP goes up to 99.9992%
Bio-Synthesis Inc. is a Dallas,TX based biotechnology
company , founded in 1984.
We provide a range of services including synthetic
peptides, nucleic acids(DNA, RNA, siRNA) antipeptide
antibodies, PCR kits, cloning services and more.
For further questions or to place orders please write to us
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