No assembly required: Full-length MHC class I allele discovery by PacBio circular consensus sequencing

Catherine J. Westbrook, Julie A. Karl, Roger W. Wiseman, Suzanne Mate, Galina Koroleva, Karla Garcia, Mariano Sanchez-Lockhart, David H. O'Connor, Gustavo Palacios

Research output: Contribution to journalArticle

28 Citations (Scopus)

Abstract

Single-molecule real-time (SMRT) sequencing technology with the Pacific Biosciences (PacBio) RS II platform offers the potential to obtain full-length coding regions (~1100-bp) from MHC class I cDNAs. Despite the relatively high error rate associated with SMRT technology, high quality sequences can be obtained by circular consensus sequencing (CCS) due to the random nature of the error profile. In the present study we first validated the ability of SMRT-CCS to accurately identify class I transcripts in Mauritian-origin cynomolgus macaques (Macaca fascicularis) that have been characterized previously by cloning and Sanger-based sequencing as well as pyrosequencing approaches. We then applied this SMRT-CCS method to characterize 60 novel full-length class I transcript sequences expressed by a cohort of cynomolgus macaques from China. The SMRT-CCS method described here provides a straightforward protocol for characterization of unfragmented single-molecule cDNA transcripts that will potentially revolutionize MHC class I allele discovery in nonhuman primates and other species.

Original languageEnglish (US)
Pages (from-to)891-896
Number of pages6
JournalHuman Immunology
Volume76
Issue number12
DOIs
StatePublished - Dec 1 2015
Externally publishedYes

Fingerprint

Alleles
Macaca
Complementary DNA
Technology
Macaca fascicularis
Primates
Organism Cloning
China

Keywords

  • Cynomolgus macaques
  • MHC class I
  • PacBio
  • Single-molecule real-time circular consensus sequencing (SMRT-CCS)

ASJC Scopus subject areas

  • Immunology and Allergy
  • Immunology

Cite this

Westbrook, C. J., Karl, J. A., Wiseman, R. W., Mate, S., Koroleva, G., Garcia, K., ... Palacios, G. (2015). No assembly required: Full-length MHC class I allele discovery by PacBio circular consensus sequencing. Human Immunology, 76(12), 891-896. https://doi.org/10.1016/j.humimm.2015.03.022

No assembly required : Full-length MHC class I allele discovery by PacBio circular consensus sequencing. / Westbrook, Catherine J.; Karl, Julie A.; Wiseman, Roger W.; Mate, Suzanne; Koroleva, Galina; Garcia, Karla; Sanchez-Lockhart, Mariano; O'Connor, David H.; Palacios, Gustavo.

In: Human Immunology, Vol. 76, No. 12, 01.12.2015, p. 891-896.

Research output: Contribution to journalArticle

Westbrook, CJ, Karl, JA, Wiseman, RW, Mate, S, Koroleva, G, Garcia, K, Sanchez-Lockhart, M, O'Connor, DH & Palacios, G 2015, 'No assembly required: Full-length MHC class I allele discovery by PacBio circular consensus sequencing', Human Immunology, vol. 76, no. 12, pp. 891-896. https://doi.org/10.1016/j.humimm.2015.03.022
Westbrook, Catherine J. ; Karl, Julie A. ; Wiseman, Roger W. ; Mate, Suzanne ; Koroleva, Galina ; Garcia, Karla ; Sanchez-Lockhart, Mariano ; O'Connor, David H. ; Palacios, Gustavo. / No assembly required : Full-length MHC class I allele discovery by PacBio circular consensus sequencing. In: Human Immunology. 2015 ; Vol. 76, No. 12. pp. 891-896.
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