Next-generation sequencing can reveal in vitro-generated PCR crossover products: Some artifactual sequences correspond to HLA alleles in the IMGT/HLA database

Tissue Antigens

Volumn 83, Issue 1, 2014, Pages 32-40

  Holcomb, C L ^a   Rastrou, M ^a   Williams, T C ^b   Goodridge, D ^c   Lazaro, A M ^d   Tilanus, M ^e   Erlich, H A ^a,b  

^a ROCHE MOLECULAR SYSTEMS   (United States)

^b CHILDREN S HOSPITAL OAKLAND RESEARCH INSTITUTE   (United States)

^c Conexio Genomics ^*  (Australia)

^d GEORGETOWN UNIVERSITY MEDICAL CENTER   (United States)

^e MAASTRICHT UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

Human leukocyte antigen; IMGT HLA database; Next generation sequencing; PCR crossover

Indexed keywords

DNA; HLA DRB1 ANTIGEN; HLA DRB3 ANTIGEN; HLA DRB4 ANTIGEN; HLA DRB5 ANTIGEN;

ALLELE; AMPLICON; ARTICLE; ARTIFACT; CELL LINE; CROSSING OVER; DNA SEQUENCE; GENE AMPLIFICATION; GENOTYPE; HLA SYSTEM; IN VITRO STUDY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL;

HUMAN LEUKOCYTE ANTIGEN; IMGT HLA DATABASE; NEXT-GENERATION SEQUENCING; PCR CROSSOVER;

ALLELES; ARTIFACTS; CROSSING OVER, GENETIC; DATABASES, NUCLEIC ACID; DIAGNOSTIC ERRORS; DNA; DNA PRIMERS; EXONS; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HISTOCOMPATIBILITY TESTING; HLA-DR ANTIGENS; HUMANS; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA;

EID: 84890731574     PISSN: 00012815     EISSN: 13990039     Source Type: Journal    
DOI: 10.1111/tan.12269     Document Type: Article

References (19)

1. Bentley G, Higuchi R, Hoglund B et al. High-resolution, high-throughput HLA genotyping by next-generation sequencing. Tissue Antigens 2009: 74: 393-403.
2. Holcomb CL, Hoglund B, Anderson MW et al. A multi-site study using high-resolution HLA genotyping by next generation sequencing. Tissue Antigens 2011: 77: 206-17.
3. ™ system for simplified amplicon library preparation. Tissue Antigens 2013: 81: 141-9.
4. Robinson J, Halliwell JA, McWilliam H, Lopez R, Parham P, Marsh SGE. The IMGT/HLA database. Nucleic Acids Res 2013: 41: D1222-7.
5. Saiki RK, Gelfand DH, Stoffel S et al. Primer-directed enzymatic amplification of DNA with a thermal stable DNA polymerase. Science 1988: 239: 487-91.
6. Shuldiner AR, Nirula A, Roth J. Hybrid DNA artifact from PCR of closely related target sequences. Nucleic Acids Res 1989: 17: 4409.
7. Paabo S, Irwin DM, Wilson AC. DNA damage promotes jumping between templates during enzymatic amplification. J Biol Chem 1990: 265: 4718-21.
8. Meyerhans A, Vartanian J-P, Wain-Hobson S. DNA recombination during PCR. Nucleic Acids Res 1990: 18: 1687-91.
9. Song Q, Cao Y, Li Q et al. Artificial recombination may influence the evolutionary analysis of Newcastle disease virus. J Virol 2011: 85: 10409-14.
10. Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Wightman AJ. At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl Environ Microbiol 2005: 71: 7724-36.
11. Fonseca VG, Nichols B, Lallias D et al. Sample richness and genetic diversity as drivers of chimera formation in nSSU metagenetic analyses. Nucleic Acids Res 2012: 40: e66.
12. Gall A, Ferns B, Morris C et al. Universal amplification, next-generation sequencing, and assembly of HIV-1 genomes. J Clin Microbiol 2012: 50: 3838-44.
13. Shao W, Boltz VF, Spindler JE et al. Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of low-frequency drug resistance mutations in HIV-1 DNA. Retrovirology 2013: 10: 18.
14. Erlich HE. HLA DNA typing: past present and future. Tissue Antigens 2012: 80: 1-11.
15. Danzer M, Niklas N, Stabentheiner et al. Rapid, scalable and highly automated HLA genotyping using next-generation sequencing: a transition from research to diagnostics. BMC Genomics 2013: 14: 221.
16. Gorski J, Rollini P, Mach B. Structural comparison of the genes of two HLA-DR supertypic groups: the loci encoding DRw52 and DRw53 are not truly allelic. Immunogenetics 1987: 25: 397-402.
17. Liu CP, Bach FH, Wu S. Molecular studies of a rare DR2/LD-5a/DQw3 HLA class II haplotype. Multiple genetic mechanisms in the generation of polymorphic HLA class II genes. J Immunol 1988: 140: 3631-9.
18. Gorski J, Mach B. Polymorphism of human Ia antigens: gene conversion between two DR beta loci results in a new HLA-D/DR specificity. Nature 1986: 322: 67-70.
19. Garristsen HSP, Fae I, Legath N et al. Identification of a novel HLA-DRB3*01 variant, HLA-DRB3*0114, containing a DRB1 sequence motif by micro-temperature gradient gel electrophoresis confirmed by sequence-based typing. Tissue Antigens 2009: 75: 185-6.