Macaque monkeys are critical in transplantation studies, yet macaque genomics lags significantly behind human genomics. While reliable genotyping methods have been developed for some macaque immune loci, including the major histocompatibility complex region, broader transplant immunogenetics studies in macaques are currently limited by existing methods. Much of the current work in macaque genomics employs whole-exome or whole-genome sequencing; however, these approaches rely on flawed reference genomes and annotations for variant calling, and perform especially poorly in complex immune genes. Long-read RNA sequencing allows for identification of full-length transcript isoforms and phased SNPs from multiple immune gene families simultaneously, without a reference genome. Here we describe whole-transcriptome sequencing of peripheral blood mononuclear cells from one rhesus and one cynomolgus macaque using Pacific Bioscience's long-read RNA sequencing (Iso-Seq) technology performed on a PacBio Sequel machine. We obtained over 800,000 consensus reads per animal, with an average read length of approximately 3000 bases. Using data produced from the PacBio Iso-Seq analysis pipeline (version 4.0.0), we identified reads aligning to expected MHC class I and II alleles. We anticipate that this technology will be useful in characterizing cell type-specific expression of immune gene isoforms in healthy macaques and those undergoing transplant rejection, and may enable identification of biomarkers of rejection.

CITATION INFORMATION: Haj A., Karl J., Wiseman R., O'Connor D. Whole-Transcriptome Sequencing to Identify Macaque Immune Gene Variants Am J Transplant. 2017;17 (suppl 3).

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