PMID- 28569259
OWN - NLM
STAT- MEDLINE
DCOM- 20180207
LR  - 20181113
IS  - 1476-5470 (Electronic)
IS  - 1466-4879 (Print)
IS  - 1466-4879 (Linking)
VI  - 18
IP  - 3
DP  - 2017 Sep
TI  - Revealing complete complex KIR haplotypes phased by long-read sequencing 
      technology.
PG  - 127-134
LID - 10.1038/gene.2017.10 [doi]
AB  - The killer cell immunoglobulin-like receptor (KIR) region of human chromosome 19 
      contains up to 16 genes for natural killer (NK) cell receptors that recognize 
      human leukocyte antigen (HLA)/peptide complexes and other ligands. The KIR 
      proteins fulfill functional roles in infections, pregnancy, autoimmune diseases 
      and transplantation. However, their characterization remains a constant 
      challenge. Not only are the genes highly homologous due to their recent evolution 
      by tandem duplications, but the region is structurally dynamic due to frequent 
      transposon-mediated recombination. A sequencing approach that precisely captures 
      the complexity of KIR haplotypes for functional annotation is desirable. We 
      present a unique approach to haplotype the KIR loci using single-molecule, 
      real-time (SMRT) sequencing. Using this method, we have-for the first 
      time-comprehensively sequenced and phased sixteen KIR haplotypes from eight 
      individuals without imputation. The information revealed four novel haplotype 
      structures, a novel gene-fusion allele, novel and confirmed insertion/deletion 
      events, a homozygous individual, and overall diversity for the structural 
      haplotypes and their alleles. These KIR haplotypes augment our existing knowledge 
      by providing high-quality references, evolutionary informers, and source material 
      for imputation. The haplotype sequences and gene annotations provide alternative 
      loci for the KIR region in the human genome reference GrCh38.p8.
FAU - Roe, D
AU  - Roe D
AUID- ORCID: 0000-0001-7750-3026
AD  - Bioinformatics Research, National Marrow Donor Program, Minneapolis, MN USA.
AD  - Department of Computer Science and Engineering, University of Minnesota, 
      Minneapolis, MN USA.
FAU - Vierra-Green, C
AU  - Vierra-Green C
AD  - Immunobiology Research, Center for International Blood and Marrow Transplant 
      Research, Minneapolis, MN USA.
FAU - Pyo, C-W
AU  - Pyo CW
AD  - Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, 
      WA, USA.
FAU - Eng, K
AU  - Eng K
AD  - Pacific Biosciences, Menlo Park, CA, USA.
FAU - Hall, R
AU  - Hall R
AD  - Pacific Biosciences, Menlo Park, CA, USA.
FAU - Kuang, R
AU  - Kuang R
AD  - Department of Computer Science and Engineering, University of Minnesota, 
      Minneapolis, MN USA.
FAU - Spellman, S
AU  - Spellman S
AD  - Immunobiology Research, Center for International Blood and Marrow Transplant 
      Research, Minneapolis, MN USA.
FAU - Ranade, S
AU  - Ranade S
AD  - Pacific Biosciences, Menlo Park, CA, USA.
FAU - Geraghty, D E
AU  - Geraghty DE
AD  - Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, 
      WA, USA.
FAU - Maiers, M
AU  - Maiers M
AUID- ORCID: 0000-0002-0198-2064
AD  - Bioinformatics Research, National Marrow Donor Program, Minneapolis, MN USA.
LA  - eng
PT  - Journal Article
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20170601
PL  - England
TA  - Genes Immun
JT  - Genes and immunity
JID - 100953417
RN  - 0 (Receptors, KIR)
SB  - IM
MH  - Chromosomes, Human, Pair 19/genetics
MH  - *Haplotypes
MH  - Humans
MH  - Receptors, KIR/*genetics
MH  - Whole Genome Sequencing/*methods
PMC - PMC5637231
COIS- KE, RH and SSR are employees of Pacific Biosciences. The remaining authors 
      declare no conflict of interest.
EDAT- 2017/06/02 06:00
MHDA- 2018/02/08 06:00
PMCR- 2017/10/12
CRDT- 2017/06/02 06:00
PHST- 2016/11/21 00:00 [received]
PHST- 2017/02/26 00:00 [revised]
PHST- 2017/03/31 00:00 [accepted]
PHST- 2017/06/02 06:00 [pubmed]
PHST- 2018/02/08 06:00 [medline]
PHST- 2017/06/02 06:00 [entrez]
PHST- 2017/10/12 00:00 [pmc-release]
AID - gene201710 [pii]
AID - 10.1038/gene.2017.10 [doi]
PST - ppublish
SO  - Genes Immun. 2017 Sep;18(3):127-134. doi: 10.1038/gene.2017.10. Epub 2017 Jun 1.