HLA At-A Glance

The Human Leukocyte Antigen (HLA) genes are those which are responsible for detecting foreign substances and triggering the immune system. Such HLA screening includes the detection of drug molecules, bacteria and viruses as well as the process of self recognition, such as the screening of tumor cells and autoimmunity. HLA variation is, of course, also the basis for organ transplant rejection. As a result, complex HLA genetic testing is now the standard of care for all of transplantation medicine, performed on @100,000 individuals per year worldwide and, as such, is the recognized gold standard for the field of personalized medicine.

A complex “HLA-like” genetic test is ideally suited to microarray technology, since microarrays can easily detect one thousand to one million local DNA changes in parallel. In spite of that apparently-ideal fit, there are only  a  couple  of microarray tests used in HLA testing today; the reason being that the existing microarray technologies were developed as research tools, not as a platform for clinical or public health screening. Thus, in their current form, microarrays are too complex, too expensive, and require a sample size that is too big to be implemented, practically, as part of large scale genetic testing.� However, GMSbiotech has solved this issue with its high resolution low cost micro array platform.

Beyond organ transplantation and vaccine response, there is now very strong evidence that personal variation in the HLA genes is also directly related to personal variation in the risk of viral infection; the risk of inflammatory joint disease; and very importantly, the dose limiting inflammatory response to drugs, known as “drug rash” or in extreme cases, the life-threatening Stevens-Johnson Syndrome (SJS).

Table I. The Current Role (late 2008) for High Resolution HLA-B Testing: For AIDS Risk, Acacabir Pharmacogenomics, Reactive  Arthritis & other HLA-based diseases.

HLA-B Allele Clinical Indication correlated with Allele Comments Relative to Clinical Utility of HLA-B screening Ref.


Ebola. Protective (with B*14). Non-Fatal response to Ebola

B*07 + B*14 are highly enriched in those who survive



Chlamydia trachomatis. Protective against blindness from Chlamydia trachomatis

Predictive of those who do not develop blindness



Ebola. Protective, (along with B*07). Non-Fatal response to Ebola

B*07 + B*14 are highly enriched in those who survive



Ebola. Sensitizes (with B*67) a Fatal response to Ebola

B*67 + B*15 highly enriched in those who perish



Adverse Drug Response. Carbamazepine induced Stevens-Johnson in Chinese

FDA: All Chinese should be screened before Rx



Adverse Drug Response. Carbamazepineinduced Stevens-Johnson in Chinese

Only solid psychiatric marker for pharmacogenomics



Lukemia in children. ALL high leukocyte counts at presentation

B*17 and A*33 may combine to predict male relapse



Ankylosing Spondylitis. (reactive arthritis). B*27 explains 50% of risk

Severity of reactive arthritis strongly correlated with B*27



Ankylosing Spondylitis (reactive arthritis). B*27 plus IL-1 explain 75% of risk

Severity of reactive arthritis strongly correlated with B*27



Ankylosing Spondylitis. (reactive arthritis). B*27 Correlates with increased arthritic pain in Reactive arthritis after a triggering infection

Severity of reactive arthritis strongly correlated with B*27



Reactive Arthritis. B*27 associated with Enhanced Risk of severe Reactive arthritis

Clinical B*27 Review in Nature



Chrone’s Disease. HLA-B27 appears to convey a very high risk of developing axial inflammation in Crohn's disease.

B*27 not associated with absolute Chrone’s risk, but with subsequent inflammation.



HIV-1. All B*27 alleles Protective, HIV-1 Elite Controller

Also seems to correlate with early work on vaccines



HIV-1. All B*27 alleles Protective, HIV-1 Elite Controller

HIV-1 can mutate out of suppression faster in B*27,Relative to B*57



HIV-1. B*3501 is protective for HIV progression, Other B*35 alleles show rapid HIV progression

As for B*57, a subtle change in B*35 allele has significant effects



Diabetes. Type I diabetes genetic risk explained by B*39 Plus HLA-DQB1 and HLA-DRB1

High profile whole genome scanning study in Nature



Cervical Cancer. Enhanced squamous cell cervical cancer RISK with one or more; A*0201-Cw*0501 DRB1*0401-DQB1*0301

HLA explains enhanced genetic risk for Cervical cancer. B*4402 is central theme



Beh�et's disease. Autoimmune disease of the vasculature

B*51 is strongly correlated with severity



Gastric Cancer. Reduced risk of gastric cancer

Mediated via H.Pilori infection



HCV.Protective effect

All B*57’s correlated with spontaneous recovery



Adverse Drug Response. Abacavir sensitivity

Large scale US. Screening trail confirms predictive power for ADR



Adverse Drug Response. Abacavir sensitivity

Described as “Gold standard” in 2009 for personalized medicine



Adverse Drug Response. Abacavir sensitivity

NEJM landmark paper. Large scale Australian Screening trail confirms high predictive power for ADR



HIV-1. Protective effect HIV-1, the Elite Controllers. HLA-B and KIR3DL1/KIR3DS1

Clinical Screening is now routine. The best characterized host protective effect in modern infectious disease research




HIV-1. Protective Effect HIV-1 Elite Controller. Highest genetic correlation. HLA-C may be a secondary player

The role of B*5701 in HIV risk upon infection is the gold standard in host effects in infectious disease



HIV-1. Not Protective HIV-1 Elite Controller

B*5701 & B*5702 must be cleanly resolved at high resolution. For HIV progression & Abacvir ADR



HIV-1. Protective Effect HIV-1 Elite Controller

Protective Mechanism is different than for B*5701



Adverse Drug Response. Allopurinol sensitivity in Chinese

Highly predictive of adverse response to allopurinol




HIV-1.Protective Effect HIV-1 Elite Controller

More escape variants than for B*5701



Ebola. Sensitizes (with B*15) Fatal response to Ebola in Uganda

B*67 + B*15 highly enriched in those who perish



Lukemia children. Male ALL relapse in Chinese




1). Sanchez A, Wagoner KE, Rollin PE (2007). Sequence-based human leukocyte antigen-B typing of patients infected with Ebola virus in Uganda in 2000: identification of alleles associated with fatal and nonfatal disease outcomes. J Infect Dis. 196 Suppl 2:S329-36.

2). Abbas M, Bobo LD, Hsieh YH, Berka N, Dunston G, Bonney G, Apprey V, Quinn TC,
West SK (2008) Human Leukocyte Antigen (HLA)-B, -DRB1 and -DQB1 Allotypes Associated with Disease and Protection in Trachoma Endemic Villages. Invest Ophthalmol Vis Sci. Epub, Sept

3). Ferrell PB Jr, McLeod HL. Carbamazepine (2008) HLA-B*1502 and risk of Stevens-Johnson syndrome and toxic epidermal necrolysis: US FDA recommendations. Pharmacogenomics, 10:1543-6.

4). de Leon J (2008). The Promise of Personalized Medicine for CNS Disorders.
Neuropsychopharmacology. Pharmacogenomics: Sep 17. [Epub ahead of print]

5). Ng MH, Lau KM, Hawkins BR, Chik KW, Chan NP, Wong WS, Tsang KS, Shing MM, Li CK (2006).        HLA-B67 may be a male-specific HLA marker of susceptibility to relapsed childhood ALL in Hong Kong Chinese and HLA-A33 or HLA-B17 signifies a higher presentation leukocytosis: A retrospective analysis on 53 transplant candidates (1989-2003). Ann Hematol. 85(8):535-41.

6). Fussell H, Nesbeth D, Lenart I, Campbell EC, Lynch S, Santos S, Gould K, Powis SJ, Antoniou AN.
(2008) Novel detection of in vivo HLA-B27 conformations correlates with ankylosing spondylitis association. Arthritis Rheum. 58(11):3419-24.

7). Reveille JD (2006) Major histocompatibility genes and ankylosing spondylitis. Best Pract Res Clin Rheumatol. 20(3):601-9.

8). Schiellerup P, Krogfelt KA, Locht H (2008). A comparison of self-reported joint symptoms following infection with different enteric pathogens: effect of HLA-B27. J Rheumatol. 35(3):480-7

9). Inman RD (2006). Mechanisms of disease: infection and spondyloarthritis. Nat Clin Pract Rheumatol. 2(3):163-9.

10). Orchard TR, Holt H, Bradbury L, Hammersma J, McNally E, Jewell DP, Wordsworth BP (2008)
The prevalence, clinical features and association of HLA-B27 in sacroiliitis associated with established Crohn's disease. Aliment Pharmacol Ther. Oct 9, [Epub ahead of print]

11). Kaslow RA, Rivers C, Tang J, Bender TJ, Goepfert PA, El Habib R, Weinhold K, Mulligan MJ (2001) NIAID AIDS vaccine evaluation group. Polymorphisms in HLA class I genes associated with both favorable prognosis of human immunodeficiency virus (HIV) type 1 infection and positive cytotoxic T-lymphocyte responses to ALVAC-HIV recombinant canarypox vaccines. J Virol. 75(18):8681-9.

12). Schneidewind A, Brockman MA, Yang R, Adam RI, Li B, Le Gall S, Rinaldo CR, Craggs
SL, Allgaier RL, Power KA, Kuntzen T, Tung CS, LaBute MX, Mueller SM, Harrer T,McMichael AJ, Goulder PJ, Aiken C, Brander C, Kelleher AD, Allen TM (2007). Escape from the dominant HLA-B27-restricted cytotoxic T-lymphocyte response in Gag is associated with a dramatic reduction in human immunodeficiency virus type 1 replication. J Virol. 81(22):12382-93. Epub 2007 Sep

13). Gao X, Nelson GW, Karacki P, Martin MP, Phair J, Kaslow R, Goedert JJ, Buchbinder S, Hoots K, Vlahov D, O'Brien SJ, Carrington M (2001) Effect of a single amino acid change in MHC class I molecules on the rate of progression to AIDS. N Engl J Med. 344(22):1668-75. Comment in:
N Engl J Med. 2001 Sep 20;345(12):924-5.

14). Nejentsev S, Howson JM, Walker NM, Szeszko J, Field SF, Stevens HE, Reynolds P, Hardy M, King E, Masters J, Hulme J, Maier LM, Smyth D, Bailey R, Cooper JD, Ribas G, Campbell RD, Clayton DG, Todd JA; Wellcome Trust Case Control Consortium (2007). Localization of type 1 diabetes susceptibility to the MHC class I genes HLA-B and HLA-A. Nature. 450(7171):887-92. Epub 2007 Nov 14. Comment in: Nature. 2007 Dec 6;450(7171):799-800.

15). Madeleine MM, Johnson LG, Smith AG, Hansen JA, Nisperos BB, Li S, Zhao LP, Daling JR, Schwartz SM, Galloway DA (2008). Comprehensive analysis of HLA-A, HLA-B, HLA-C, HLA-DRB1, and HLA-DQB1 loci and squamous cell cervical cancer risk. Cancer Res. 68(9):3532-9.

16). Chessman D, Kostenko L, Lethborg T, Purcell AW, Williamson NA, Chen Z, Kjer-Nielsen L, Mifsud NA, Tait BD, Holdsworth R, Almeida CA, Nolan D, Macdonald WA, Archbold JK, Kellerher AD, Marriott D, Mallal S, Bharadwaj M, Rossjohn J, McCluskey J (2008). Human leukocyte antigen class I-restricted activation of CD8+ T cells provides the immunogenetic basis of a systemic drug hypersensitivity.  Immunity. 28(6):822-32. Erratum in: Immunity. 2008 29(1):165.

17). Hirata I, Murano M, Ishiguro T, Toshina K, Wang FY, Katsu K (2007). HLA genotype and development of gastric cancer in patients with Helicobacter pylori infection. Hepatogastroenterology. 54(76):990-4.

18). Chuang WC, Sarkodie F, Brown CJ, Owusu-Ofori S, Brown J, Li C, Navarrete C, Klenerman P, Allain JP (2007). Protective effect of HLA-B57 on HCV genotype 2 infection in a West African population.  J Med Virol. 79(6):724-33.

19). Young B, Squires K, Patel P, Dejesus E, Bellos N, Berger D, Sutherland-Phillips DH, Liao Q, Shaefer M, Wannamaker P (2008) First large, multicenter, open-label study utilizing HLA-B*5701 screening for abacavir hypersensitivity in North America. AIDS. 22(13):1673-5.

20a). Phillips EJ, Mallal SA (2008). Pharmacogenetics and the potential for the individualization of antiretroviral  therapy. Curr Opin Infect Dis. 21(1):16-24.
20b). Hammond E, Almeida CA, Mamotte C, Nolan D, Phillips E, Schollaardt TA, Gill MJ, Angel JB, Neurath D, Li J, Giulivi T, McIntyre C, Koultchitski G, Wong B, Reis M, Rachlis A, Cole DE, Chew CB, Neifer S, Lalonde R, Roger M, Jeanneau A, Mallal S (2007). External quality assessment of HLA-B*5701 reporting: an international multicentre survey. Antivir Ther. 12(7):1027-32.

21). Mallal S, Phillips E, Carosi G, Molina JM, Workman C, Tomazic J, J�gel-Guedes E, Rugina S, Kozyrev O, Cid JF, Hay P, Nolan D, Hughes S, Hughes A, Ryan S, Fitch N,Thorborn D, Benbow A; PREDICT-1 Study Team (2008). HLA-B*5701 screening for hypersensitivity to abacavir. N Engl J Med. 358(6):568-79. Comment in: N Engl J Med. 358(6):637-9.  N Engl J Med. 358(23):2514-5; author reply 2515-6. N Engl J Med. 358(23):2515; author reply 2515-6.

22) Carrington M, Martin MP, van Bergen J (2008) KIR-HLA intercourse in HIV disease. Trends Microbiol. 16(12):620-7. Epub 2008 Oct 29.

23). Fellay J, Shianna KV, Ge D, Colombo S, Ledergerber B, Weale M, Zhang K, Gumbs C, Castagna A, Cossarizza A, Cozzi-Lepri A, De Luca A, Easterbrook P, Francioli P, Mallal S, Martinez-Picado J, Miro JM, Obel N, Smith JP, Wyniger J, Descombes P, Antonarakis SE, Letvin NL, McMichael AJ, Haynes BF, Telenti A, Goldstein DB (2007). A whole-genome association study of major determinants for host control of HIV-1. Science. 317(5840):944-7. Comment in: Science. 318(5849):390-1; author reply 390-1.

24). Cadogan M, Dalgleish AG (2008) Chapter 9 HIV Induced AIDS and Related Cancers Chronic Immune Activation and Future Therapeutic Strategies. Adv Cancer Res. 101:349-95.

25). Yu XG, Lichterfeld M, Chetty S, Williams KL, Mui SK, Miura T, Frahm N, Feeney ME, Tang Y, Pereyra F, Labute MX, Pfafferott K, Leslie A, Crawford H, Allgaier R,Hildebrand W, Kaslow R, Brander C, Allen TM, Rosenberg ES, Kiepiela P, Vajpayee M, Goepfert PA, Altfeld M, Goulder PJ, Walker BD (2007). Mutually exclusive T-cell receptor induction and differential susceptibility to human immunodeficiency virus type 1 mutational escape associated with a two-amino-acid difference between HLA class I subtypes. J Virol. 81(4):1619-31.

26a). Chung WH, Hung SI, Chen YT (2007). Human leukocyte antigens and drug hypersensitivity. Curr Opin Allergy Clin Immunol. 7(4):317-23.

26b). Hung SI, Chung WH, Liou LB, Chu CC, Lin M, Huang HP, Lin YL, Lan JL, Yang LC,Hong HS, Chen MJ, Lai PC, Wu MS, Chu CY, Wang KH, Chen CH, Fann CS, Wu JY, ChenYT (2005).
HLA-B*5801 allele as a genetic marker for severe cutaneous adverse reactions caused by allopurinol. Proc Natl Acad Sci U S A. 102(11):4134-9. Erratum in: Proc Natl Acad Sci U S A. 102(17):6237.

27). Chopera DR, Woodman Z, Mlisana K, Mlotshwa M, Martin DP, Seoighe C, Treurnicht F, de Rosa DA, Hide W, Karim SA, Gray CM, Williamson C; CAPRISA 002 Study Team (2008). Transmission of HIV-1 CTL escape variants provides HLA-mismatched recipients with a survival advantage.  PLoS Pathog. 4(3):e1000033.