PMID- 32312742
OWN - NLM
STAT- MEDLINE
DCOM- 20210720
LR  - 20211001
IS  - 1549-5469 (Electronic)
IS  - 1088-9051 (Print)
IS  - 1088-9051 (Linking)
VI  - 30
IP  - 4
DP  - 2020 Apr
TI  - Complete characterization of the human immune cell transcriptome using accurate 
      full-length cDNA sequencing.
PG  - 589-601
LID - 10.1101/gr.257188.119 [doi]
AB  - The human immune system relies on highly complex and diverse transcripts and the 
      proteins they encode. These include transcripts encoding human leukocyte antigen 
      (HLA) receptors as well as B cell and T cell receptors (BCR and TCR). Determining 
      which alleles an individual possesses for each HLA gene (high-resolution HLA 
      typing) is essential to establish donor-recipient compatibility in organ and bone 
      marrow transplantations. In turn, the repertoires of millions of unique BCR and 
      TCR transcripts in each individual carry a vast amount of health-relevant 
      information. Both short-read RNA-seq-based HLA typing and BCR/TCR repertoire 
      sequencing (AIRR-seq) currently rely on our incomplete knowledge of the genetic 
      diversity at HLA and BCR/TCR loci. Here, we generated over 10,000,000 full-length 
      cDNA sequences at a median accuracy of 97.9% using our nanopore sequencing-based 
      Rolling Circle Amplification to Concatemeric Consensus (R2C2) protocol. We used 
      this data set to (1) show that deep and accurate full-length cDNA sequencing can 
      be used to provide isoform-level transcriptome analysis for more than 9000 loci, 
      (2) generate accurate sequences of HLA alleles, and (3) extract detailed AIRR 
      data for the analysis of the adaptive immune system. The HLA and AIRR analysis 
      approaches we introduce here are untargeted and therefore do not require prior 
      knowledge of the composition or genetic diversity of HLA and BCR/TCR loci.
CI  - (c) 2020 Cole et al.; Published by Cold Spring Harbor Laboratory Press.
FAU - Cole, Charles
AU  - Cole C
AD  - Department of Biomolecular Engineering, Cellular, Cellular, and Developmental 
      Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA.
FAU - Byrne, Ashley
AU  - Byrne A
AD  - Department of Molecular, Cellular, and Developmental Biology, University of 
      California Santa Cruz, Santa Cruz, California 95064, USA.
FAU - Adams, Matthew
AU  - Adams M
AD  - Department of Molecular, Cellular, and Developmental Biology, University of 
      California Santa Cruz, Santa Cruz, California 95064, USA.
FAU - Volden, Roger
AU  - Volden R
AD  - Department of Biomolecular Engineering, Cellular, Cellular, and Developmental 
      Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA.
FAU - Vollmers, Christopher
AU  - Vollmers C
AD  - Department of Biomolecular Engineering, Cellular, Cellular, and Developmental 
      Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA.
LA  - eng
GR  - R35 GM133569/GM/NIGMS NIH HHS/United States
GR  - T32 HG008345/HG/NHGRI NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
DEP - 20200420
PL  - United States
TA  - Genome Res
JT  - Genome research
JID - 9518021
RN  - 0 (DNA, Complementary)
RN  - 0 (Receptors, Immunologic)
SB  - IM
MH  - Alleles
MH  - Alternative Splicing
MH  - *DNA, Complementary
MH  - Female
MH  - *Gene Expression Profiling/methods
MH  - Gene Expression Regulation
MH  - Genomics/methods
MH  - *High-Throughput Nucleotide Sequencing/methods
MH  - Histocompatibility Testing
MH  - Humans
MH  - Immune System/*cytology/*metabolism
MH  - Male
MH  - Mutation
MH  - Receptors, Immunologic
MH  - *Transcriptome
PMC - PMC7197476
EDAT- 2020/04/22 06:00
MHDA- 2021/07/21 06:00
PMCR- 2020/10/01
CRDT- 2020/04/22 06:00
PHST- 2019/09/14 00:00 [received]
PHST- 2020/04/03 00:00 [accepted]
PHST- 2020/04/22 06:00 [pubmed]
PHST- 2021/07/21 06:00 [medline]
PHST- 2020/04/22 06:00 [entrez]
PHST- 2020/10/01 00:00 [pmc-release]
AID - gr.257188.119 [pii]
AID - 10.1101/gr.257188.119 [doi]
PST - ppublish
SO  - Genome Res. 2020 Apr;30(4):589-601. doi: 10.1101/gr.257188.119. Epub 2020 Apr 20.