HLA class I sequence-based typing using DNA recovered from frozen plasma

Journal of Immunological Methods

Volumn 382, Issue 1-2, 2012, Pages 40-47

  Cotton, Laura A ^a   Rahman, Manal Abdur ^a   Ng, Carmond ^b   Le, Anh Q ^a   Milloy, M J ^b   Mo, Theresa ^b   Brumme, Zabrina L ^a,b  

^a SIMON FRASER UNIVERSITY   (Canada)

^b ST PAUL S HOSPITAL   (Canada)

Author keywords

Human leukocyte antigen (HLA) class I; Plasma; Sequence based typing; Ultrasensitive

Indexed keywords

FRESH FROZEN PLASMA; GENOMIC DNA; HLA A ANTIGEN; HLA ANTIGEN CLASS 1; HLA B ANTIGEN; HLA C ANTIGEN;

ARTICLE; BLOOD; BLOOD SAMPLING; CHROMATOGRAPHY; CLINICAL ARTICLE; DNA EXTRACTION; DNA SEQUENCE; GENE AMPLIFICATION; GENE LOCUS; GRANULOCYTE; HUMAN; PERIPHERAL BLOOD MONONUCLEAR CELL; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RETROSPECTIVE STUDY;

ADOLESCENT; ADULT; ALLELES; BASE SEQUENCE; CHILD; CRYOPRESERVATION; DNA; GENES, MHC CLASS I; HISTOCOMPATIBILITY TESTING; HUMANS; LEUKOCYTES, MONONUCLEAR; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; YOUNG ADULT;

EID: 84863599412     PISSN: 00221759     EISSN: 18727905     Source Type: Journal    
DOI: 10.1016/j.jim.2012.05.003     Document Type: Article

References (33)

1. Abbott W.G., Tukuitonga C.F., Ofanoa M., Munn S.R., Gane E.J. Low-cost, simultaneous, single-sequence genotyping of the HLA-A, HLA-B and HLA-C loci. Tissue Antigens 2006, 68:28.
2. Andolfatto S., Namour F., Garnier A.L., Chabot F., Gueant J.L., Aimone-Gastin I. Genomic DNA extraction from small amounts of serum to be used for alpha1-antitrypsin genotype analysis. Eur. Respir. J. 2003, 21:215.
3. Bax M., van Heemst J., Huizinga T.W., Toes R.E. Genetics of rheumatoid arthritis: what have we learned?. Immunogenetics 2011, 63:459.
4. Blomeke B., Bennett W.P., Harris C.C., Shields P.G. Serum, plasma and paraffin-embedded tissues as sources of DNA for studying cancer susceptibility genes. Carcinogenesis 1997, 18:1271.
5. Bodmer J.G., Marsh S.G., Albert E.D., Bodmer W.F., Bontrop R.E., Charron D., Dupont B., Erlich H.A., Fauchet R., Mach B., Mayr W.R., Parham P., Sasazuki T., Schreuder G.M., Strominger J.L., Svejgaard A., Terasaki P.I. Nomenclature for factors of the HLA system, 1996. Tissue Antigens 1997, 49:297.
6. Brumme Z.L., Brumme C.J., Chui C., Mo T., Wynhoven B., Woods C.K., Henrick B.M., Hogg R.S., Montaner J.S., Harrigan P.R. Effects of human leukocyte antigen class I genetic parameters on clinical outcomes and survival after initiation of highly active antiretroviral therapy. J. Infect. Dis. 2007, 195:1694.
7. Brumme Z.L., Brumme C.J., Heckerman D., Korber B.T., Daniels M., Carlson J., Kadie C., Bhattacharya T., Chui C., Szinger J., Mo T., Hogg R.S., Montaner J.S., Frahm N., Brander C., Walker B.D., Harrigan P.R. Evidence of differential HLA class i-mediated viral evolution in functional and accessory/regulatory genes of HIV-1. PLoS Pathog. 2007, 3:e94.
8. Brumme Z.L., Brumme C.J., Carlson J., Streeck H., John M., Eichbaum Q., Block B.L., Baker B., Kadie C., Markowitz M., Jessen H., Kelleher A.D., Rosenberg E., Kaldor J., Yuki Y., Carrington M., Allen T.M., Mallal S., Altfeld M., Heckerman D., Walker B.D. Marked epitope- and allele-specific differences in rates of mutation in human immunodeficiency type 1 (HIV-1) Gag, Pol, and Nef cytotoxic T-lymphocyte epitopes in acute/early HIV-1 infection. J. Virol. 2008, 82:9216.
9. Brumme Z.L., John M., Carlson J.M., Brumme C.J., Chan D., Brockman M.A., Swenson L.C., Tao I., Szeto S., Rosato P., Sela J., Kadie C.M., Frahm N., Brander C., Haas D.W., Riddler S.A., Haubrich R., Walker B.D., Harrigan P.R., Heckerman D., Mallal S. HLA-associated immune escape pathways in HIV-1 subtype B Gag, Pol and Nef proteins. PLoS One 2009, 4:e6687.
10. Brumme C.J., Chan B., Markle T., Carlson J., Martin E., Le A.Q., Penney K., Rahman M., Kuang T., Nassab P., Chopera D.R., Markowitz M., John M., Mallal S., Walker B.D., Koblin B., Mayer K., Brockman M.A., Poon A., Brumme Z.L. Molecular and functional consequences of immune-mediated evolution in HIV-1 Nef during the North American epidemic. AIDS Res. Hum. Retroviruses 2011, 27:A60.
11. Carrington M., O'Brien S.J. The influence of HLA genotype on AIDS. Annu. Rev. Med. 2003, 54:535.
12. Cereb N., Yang S.Y. Dimorphic primers derived from intron 1 for use in the molecular typing of HLA-B alleles. Tissue Antigens 1997, 50:74.
13. Cereb N., Maye P., Lee S., Kong Y., Yang S.Y. Locus-specific amplification of HLA class I genes from genomic DNA: locus-specific sequences in the first and third introns of HLA-A, -B, and -C alleles. Tissue Antigens 1995, 45:1.
14. Cinek O., Wilkinson E., Paltiel L., Saugstad O.D., Magnus P., Ronningen K.S. Screening for the IDDM high-risk genotype. A rapid microtitre plate method using serum as source of DNA. Tissue Antigens 2000, 56:344.
15. Dixon S.C., Horti J., Guo Y., Reed E., Figg W.D. Methods for extracting and amplifying genomic DNA isolated from frozen serum. Nat. Biotechnol. 1998, 16:91.
16. Doxiadis I., Grosse-Wilde H. Typing for HLA class I gene products using plasma as source. Vox Sang. 1989, 56:196.
17. Dunn P.P., Day S., Williams S., Bendukidze N. DNA sequencing as a tissue-typing tool. Methods Mol. Med. 2004, 91:233.
18. Fellay J., Shianna K.V., 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 J.M., Obel N., Smith J.P., Wyniger J., Descombes P., Antonarakis S.E., Letvin N.L., McMichael A.J., Haynes B.F., Telenti A., Goldstein D.B. A whole-genome association study of major determinants for host control of HIV-1. Science 2007, 317:944.
19. Fowke K.R., Plummer F.A., Simonsen J.N. Genetic analysis of human DNA recovered from minute amounts of serum or plasma. J. Immunol. Methods 1995, 180:45.
20. Howell W.M., Carter V., Clark B. The HLA system: immunobiology, HLA typing, antibody screening and crossmatching techniques. J. Clin. Pathol. 2010, 63:387.
21. Jones E.Y., Fugger L., Strominger J.L., Siebold C. MHC class II proteins and disease: a structural perspective. Nat. Rev. Immunol. 2006, 6:271.
22. Kuniholm M.H., Kovacs A., Gao X., Xue X., Marti D., Thio C.L., Peters M.G., Terrault N.A., Greenblatt R.M., Goedert J.J., Cohen M.H., Minkoff H., Gange S.J., Anastos K., Fazzari M., Harris T.G., Young M.A., Strickler H.D., Carrington M. Specific human leukocyte antigen class I and II alleles associated with hepatitis C virus viremia. Hepatology 2010, 51:1514.
23. Lin Z., Floros J. Genomic DNA extraction from small amounts of sera to be used for genotype analysis. Biotechniques 1998, 24:937.
24. Listgarten J., Brumme Z., Kadie C., Xiaojiang G., Walker B., Carrington M., Goulder P., Heckerman D. Statistical resolution of ambiguous HLA typing data. PLoS Comput. Biol. 2008, 4:e1000016.
25. Mallal S., Phillips E., Carosi G., Molina J.M., Workman C., Tomazic J., Jagel-Guedes E., Rugina S., Kozyrev O., Cid J.F., Hay P., Nolan D., Hughes S., Hughes A., Ryan S., Fitch N., Thorborn D., Benbow A. HLA-B*5701 screening for hypersensitivity to abacavir. N. Engl. J. Med. 2008, 358:568.
26. Martin M., Carrington M., Mann D. A method for using serum or plasma as a source of DNA for HLA typing. Hum. Immunol. 1992, 33:108.
27. Miura T., Brumme Z.L., Brockman M.A., Rosato P., Sela J., Brumme C.J., Pereyra F., Kaufmann D.E., Trocha A., Block B.L., Daar E.S., Connick E., Jessen H., Kelleher A.D., Rosenberg E., Markowitz M., Schafer K., Vaida F., Iwamoto A., Little S., Walker B.D. Impaired replication capacity of acute/early viruses in persons who become HIV controllers. J. Virol. 2010, 84:7581.
28. Moore C.B., John M., James I.R., Christiansen F.T., Witt C.S., Mallal S.A. Evidence of HIV-1 adaptation to HLA-restricted immune responses at a population level. Science 2002, 296:1439.
29. Reveille J.D. The genetic basis of spondyloarthritis. Ann. Rheum. Dis. 2011, 70(Suppl. 1):i44.
30. Robinson J., Mistry K., McWilliam H., Lopez R., Parham P., Marsh S.G. The IMGT/HLA database. Nucleic Acids Res. 2011, 39:D1171.
31. Sandford A.J., Pare P.D. Direct PCR of small genomic DNA fragments from serum. Biotechniques 1997, 23:890.
32. Timm J., Li B., Daniels M.G., Bhattacharya T., Reyor L.L., Allgaier R., Kuntzen T., Fischer W., Nolan B.E., Duncan J., Schulze zur Wiesch J., Kim A.Y., Frahm N., Brander C., Chung R.T., Lauer G.M., Korber B.T., Allen T.M. Human leukocyte antigen-associated sequence polymorphisms in hepatitis C virus reveal reproducible immune responses and constraints on viral evolution. Hepatology 2007, 46:339.
33. Wood E., Li K., Miller C.L., Hogg R.S., Montaner J.S., Schechter M.T., Kerr T. Baseline self-perceived risk of HIV infection independently predicts the rate of HIV seroconversion in a prospective cohort of injection drug users. Int. J. Epidemiol. 2005, 34:152.