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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 System

Allele

D8S1179

14

D21S11

29

D7S820

Alleged Father Allele

Allele

Allele

PI

14

15

1.5002

31

29

32.2

1.3165

8

10

10

11

0.7721

CSF1PO

11

13

8

11

1.2207

D3S1358

15

16

16

18

0.8141

TH01

7

8

7

D13S317

12

D16S539

9

D2S1338 D19S433

1.1351

12

13

1.0348

10

9

11

1.2588

17

19

19

23

1.7668

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

18.2

24

1.3434

24

CPI: 59.2451 PP: 98.3401%

Two examples of common and non common alleles are: System DRB1 DRB1

C 1340, 0407 0301, 1504

AF* 0407 (Freq=0.06428) 0407 (Freq=0.00025)

PI 7.778 2000

Formula 1/2a 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 at: biosyn@biosyn.com or call us at 800-227-0627


High Resolution HLA Analysis in situationsof Marker(STR s) Depletion