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Immunogenetics

, Volume 70, Issue 9, pp 571–583 | Cite as

Nomenclature for the KIR of non-human species

  • James Robinson
  • Lisbeth A. Guethlein
  • Giuseppe Maccari
  • Jeroen Blokhuis
  • Benjamin N. Bimber
  • Natasja G. de Groot
  • Nicholas D. Sanderson
  • Laurent Abi-Rached
  • Lutz Walter
  • Ronald E. Bontrop
  • John A. Hammond
  • Steven G. E. Marsh
  • Peter Parham
Open Access
Original Article

Abstract

The increasing number of Killer Immunoglobulin-like Receptor (KIR) sequences available for non-human primate species and cattle has prompted development of a centralized database, guidelines for a standardized nomenclature, and minimum requirements for database submission. The guidelines and nomenclature are based on those used for human KIR and incorporate modifications made for inclusion of non-human species in the companion IPD-NHKIR database. Included in this first release are the rhesus macaque (Macaca mulatta), chimpanzee (Pan troglodytes), orangutan (Pongo abelii and Pongo pygmaeus), and cattle (Bos taurus).

Keywords

KIR Nomenclature Variant Allele Gene Database Sequence 

Introduction

The KIR locus has been studied in a number of non-human species primates and is characterized by high levels of allelic polymorphism, haplotypic polymorphism in the number of genes, and extensive duplication and recombination (Hammond et al. 2016; Parham 2004). These factors have made it difficult to assign orthologues and have led to a number of different nomenclature systems being used to name genes and alleles. This report describes a common framework and guidelines for KIR nomenclature in non-human species. These have been developed by taking advantage of lessons learned in the development of a nomenclature system for the human KIR (Marsh et al. 2003).

General naming guidelines

To provide consistency with the IPD-MHC Database (Maccari et al. 2017), the non-human KIR nomenclature adopts the same four-character prefix used for species designation in the naming of MHC alleles (de Groot et al. 2012; Ellis et al. 2006; Klein et al. 1990). Also, genes and alleles will be named based on the conventions that have been adopted for the human KIR system (Marsh et al. 2003) that are based on the structures of the molecules they encode. The first digit following the KIR acronym corresponds to the number of Ig-like domains in the polypeptide and the “D” denotes “Domain.” The D is followed by either an “L” indicating a “Long” cytoplasmic tail, an “S” indicating a “Short” cytoplasmic tail or a “P” for pseudogenes. In addition, the inclusion of a “W” indicates “Workshop” following the “L,” “S,” or “P” to indicate any sequence that by phylogenetic analysis is sufficiently divergent to be considered a “new” gene, but lack either genomic sequencing or family studies to demonstrate that it does define a new gene and not a divergent lineage a known gene. Tables 1, 2, and 3 list the current gene designations and their previous names. Symbols for genes are italicized (e.g., Mamu-KIR3DL01), whereas symbols for proteins are not italicized (e.g., Mamu-KIR3DL01). Alleles follow the same conventions as gene names.
Table 1

Gene designations and their previous names

Species

KIR gene designation(s)

Previous KIR gene designation(s)

Rhesus macaque (Mamu)

Mamu-KIR1D

KIR1D, Mamu-KIR1D

Mamu-KIR2DL04

2DL501NK, 2DL503NK, KIR2DL4, KIR2DL4.1, MmKIR2DL4

Mamu-KIR3DL01

2DL426NK, 3DL34, KIR3DL, KIR3DL-like_1, KIR3DL1, KIR3DL1-like1, KIR3DL12, KIR3DL13, KIR3DL14, KIR3DL15, KIR3DL19, KIR3DL1_variant_2, KIR3DL2, KIR3DL2-old, KIR3DL3, KIR3DL4, KIR3DL5

Mamu-KIR3DL02

KIR3DL-like_3, KIR3DL2, KIR3DL21, KIR3DL21-like1

Mamu-KIR3DL04

KIR3DL11

Mamu-KIR3DL05

3DL7b-3DL40, KIR3DL, KIR3DL-3, KIR3DL16, KIR3DL7, KIR3DL7-like2, KIR3DL07

Mamu-KIR3DL06

KIR3DL6

Mamu-KIR3DL07

2DL420, KIR3DL, KIR3DL18, KIR3DL7, KIR3DL7-like1, KIR3DL7-like3, KIR3DL03

Mamu-KIR3DL08

KIR3DL, KIR3DL-like_2, KIR3DL17, KIR3DL8, KIRDL8, Mamu-KIR3DL04, Mamu-KIR3DL4

Mamu-KIR3DL10

3DL10-2DL501, 3DL3NK, KIR3DL, KIR3DL10, KIR3DL9, Mamu-KIR3DL05

Mamu-KIR3DL11

KIR3DL, KIR3DL-1, KIR3DL-6, KIR3DL-7, KIR3DL11

Mamu-KIR3DL20

KIR3DL20, KIR3DL20_variant_2, KIR3DL06, KIR2DL5

Mamu-KIR3DLW03

KIR3DL-4, KIR3DL-5, KIR3DL-like1-BNB, KIR3DL21

Mamu-KIR3DLX1

KIR3DL0

Mamu-KIR3DS01

KIR3DH-7, KIR3DH1, KIR3DH5, Mamu-KIR3DS01-JHB-HEFGH,

Mamu-KIR3DS02

3DH2, 3DH42, KIR3DH-like_5, KIR3DH-like_6, KIR3DH10, KIR3DH12, KIR3DH13, KIR3DH14, KIR3DH15, KIR3DH16, KIR3DH2

Mamu-KIR3DS03

KIR3DH3, KIR3DH8, KIR3DH9

Mamu-KIR3DS04

KIR3DH-1, KIR3DH4, KIR3DH6

Mamu-KIR3DS05

KIR3DH1, KIR3DM-1, KIR3DM1, KIR3DM6, KIR_Partial_Sequence_1

Mamu-KIR3DS06

KIR3DH-4, KIR3DH-like8, KIR3DH-like_7, KIR3DH18,

Mamu-KIR3DSW07

KIR3DH-5, KIR3DH7, Mamu-KIR3DS07-JHB-HO

Mamu-KIR3DSW08

KIR3DH-2, KIR3DH-3, KIR3DH-4, KIR3DH-5, KIR3DH-like_1, KIR3DH-like_2, KIR3DH-like_3, KIR3DH-like_4, KIR3DH21, KIR3DSW08

Mamu-KIR3DSW09

KIR3DH-8, KIR3DH20, KIR3DH5, KIR3DH5-like1, mmKIR3DH-1

Table 2

Gene designations and their previous names

Species

KIR gene designation(s)

Previous KIR gene designation(s)

Chimpanzee (Patr)

Patr-KIR2DL4

 

Patr-KIR2DL5

 

Patr-KIR2DL6

Pt-NewII

Patr-KIR2DL7

 

Patr-KIR2DL8

Pt-NewIII

Patr-KIR2DL9

 

Patr-KIR3DL1

Pt-KIR3DL1/2, Pt-KIR3DL3, Pt-KIR3DL1, Pt-KIR3DL2

Patr-KIR3DL3

Patr-KIRC1, Pt-NewI

Patr-KIR3DL4

 

Patr-KIR3DL5

 

Patr-KIR3DS6

Pt-KIR3DL6

Table 3

Gene designations and their previous names

Species

KIR gene designation(s)

Previous KIR gene designation(s)

Orangutan (Poab)

Poab-KIR2DL10

Popy-KIR2DL10, 2DLA

Poab-KIR2DL11

Popy-KIR2DL11, 2DLB

Poab-KIR2DL12

Popy-KIR2DL11, 2DLC

Poab-KIR2DL5

Popy-KIR2DL5. 2DL5

Poab-KIR2DS10

2DSD/2DSA

Poab-KIR2DS13

Popy-KIR2DS13, 2DSC1/2DSB

Poab-KIR2DS14

Popy-KIR2DS14, 2DSB/2DSD2, 2DSA/2DSD1

Poab-KIR3DL1

Popy-KIR3DL1, 3DLH, 3DLC, 3DLD2, 3DLD1, 3DLA, 3DLI, 3DLB

Poab-KIR3DL3

Popy-KIR3DL3, 3DL3

Poab-KIR3DS1

Popy-KIR3DS1, 3DS1

Poab-KIRDP

Popy-KIRDP, DP

Orangutan (Popy)

Popy-KIR2DL11

Popy-KIR2DLB

Popy-KIR2DL12

Popy-KIR2DLC

Popy-KIR2DL5

 

Popy-KIR2DS10

Popy-KIR2DSD/2DSA

Popy-KIR2DS13

Popy-KIR2DSC2/2DSB

Popy-KIR2DS14

Popy-KIR2DSB/2DSD2, 2DSA/2DSD1

Popy-KIR2DS15

 

Popy-KIR3DL1

Popy-KIR3DL1, 3DLF, 3DLE2, 3DLE1

Popy-KIR3DL3

Popy-KIR3DL3, 3DL3

Popy-KIR3DS1

Popy-KIR3DS1, 3DS1

Popy-KIRDP

Popy-KIRDP, DP

Reflecting species-specific differences, there have been further additions/modifications to the general nomenclature for rhesus macaque and cattle. As with the human KIR nomenclature, alleles in each series have been named in order of their deposition into a generalist sequence databank, GenBank/EMBL-ENA/DDBJ (Benson et al. 2017; Chojnacki et al. 2017; Mashima et al. 2017). Where the identity is known of the animal providing the sequenced DNA, that information is included in the database, as well as information regarding the origin of the animal. Tables 4, 5, 6, and 7 provide a complete list of genes and alleles currently in the nomenclature, as well as the original name(s), accession number, and reference to the original report of the sequence.
Table 4

Allele designations and their previous names

Gene

Allele designation

Previous designations

Accession number

Reference

Mamu-KIR1D

Mamu-KIR1D*001

KIR1D

AF334634

(Hershberger et al. 2001)

Mamu-KIR1D

Mamu-KIR1D*002

KIR1D,Mamu-KIR1D*00202-JHB-HA

AY728181, GU112257, GU112266, GU112332

(Sambrook et al. 2005) (Blokhuis et al. 2010)

Mamu-KIR2DL04

Mamu-KIR2DL04*001:01

KIR2DL4, KIR2DL4.1, MmKIR2DL4*0010101-JHB

EU702486, AF361088, AF334644, FJ824091, GU112331, GU112318, GU112263, GU112303, GU112287

(Blokhuis et al. 2009a; Blokhuis et al. 2009b; Blokhuis et al. 2010; Grendell et al. 2001; Hershberger et al. 2001)

Mamu-KIR2DL04

Mamu-KIR2DL04*001:02

2DL501NK

GU299490

(Colantonio et al. 2011)

Mamu-KIR2DL04

Mamu-KIR2DL04*002

MmKIR2DL4*0020101-JHB

FJ824092, GU112279

(Blokhuis et al. 2009b; Blokhuis et al. 2010)

Mamu-KIR2DL04

Mamu-KIR2DL04*003

KIR2DL4, MmKIR2DL4*0040101-JHB

AY505486, FJ824093, GU112322, GU112284

(Andersen et al. 2004; Blokhuis et al. 2009b; Blokhuis et al. 2010)

Mamu-KIR2DL04

Mamu-KIR2DL04*004

KIR2DL4

AY728182

(Sambrook et al. 2005)

Mamu-KIR2DL04

Mamu-KIR2DL04*005

MmKIR2DL4*0050101-JHB

FJ824094

(Blokhuis et al. 2009b)

Mamu-KIR2DL04

Mamu-KIR2DL04*006:01

MmKIR2DL4*0060101-JHB

FJ824095

(Blokhuis et al. 2009b)

Mamu-KIR2DL04

Mamu-KIR2DL04*006:02

2DL503NK

GU014298

(Colantonio et al. 2011)

Mamu-KIR2DL04

Mamu-KIR2DL04*007

MmKIR2DL4*0070101-JHB

FJ824096

(Blokhuis et al. 2009b)

Mamu-KIR2DL04

Mamu-KIR2DL04*008:01

MmKIR2DL4*0080101-JHB

FJ824097

(Blokhuis et al. 2009b)

Mamu-KIR2DL04

Mamu-KIR2DL04*008:02

MmKIR2DL4*0080201-JHB

FJ824098, GU112326

(Blokhuis et al. 2009b; Blokhuis et al. 2010)

Mamu-KIR2DL04

Mamu-KIR2DL04*010

MmKIR2DL4*0100101-JHB

FJ824100

(Blokhuis et al. 2009b)

Mamu-KIR2DL04

Mamu-KIR2DL04*011

MmKIR2DL4*0110101-JHB

FJ824101

(Blokhuis et al. 2009b)

Mamu-KIR2DL04

Mamu-KIR2DL04*012

MmKIR2DL4*0120101-JHB

FJ824102

(Blokhuis et al. 2009b)

Mamu-KIR2DL04

Mamu-KIR2DL04*013

MmKIR2DL4*0130101-JHB

FJ824103

(Blokhuis et al. 2009b)

Mamu-KIR2DL04

Mamu-KIR2DL04*014:01

MmKIR2DL4*0140101-JHB

FJ824104, GU112316

(Blokhuis et al. 2009b; Blokhuis et al. 2010)

Mamu-KIR2DL04

Mamu-KIR2DL04*014:02

MmKIR2DL4*0140201-JHB

FJ824105

(Blokhuis et al. 2009b)

Mamu-KIR2DL04

Mamu-KIR2DL04*015:01

MmKIR2DL4*0150101-JHB

FJ824106, GU112313

(Blokhuis et al. 2009b; Blokhuis et al. 2010)

Mamu-KIR2DL04

Mamu-KIR2DL04*015:02

MmKIR2DL4*0150201-JHB

FJ824107, GU112280

(Blokhuis et al. 2009b; Blokhuis et al. 2010)

Mamu-KIR2DL04

Mamu-KIR2DL04*016

MmKIR2DL4*0160101-JHB

FJ824108

(Blokhuis et al. 2009b)

Mamu-KIR2DL04

Mamu-KIR2DL04*017

MmKIR2DL4*0170101-JHB

FJ824109

(Blokhuis et al. 2009b)

Mamu-KIR2DL04

Mamu-KIR2DL04*018

MmKIR2DL4*0180101-JHB

FJ824110

(Blokhuis et al. 2009b)

Mamu-KIR2DL04

Mamu-KIR2DL04*019

MmKIR2DL4*0190101-JHB

FJ824111

(Blokhuis et al. 2009b)

Mamu-KIR2DL04

Mamu-KIR2DL04*020

MmKIR2DL4*0200101-JHB

FJ824112, GU112274

(Blokhuis et al. 2009b; Blokhuis et al. 2010)

Mamu-KIR3DL01

Mamu-KIR3DL01*001

KIR3DL1, 3DL34

AF334616, GU299488

(Colantonio et al. 2011; Hershberger et al. 2001)

Mamu-KIR3DL01

Mamu-KIR3DL01*002

KIR3DL2-old, 2DL426NK

AF334617, GU299488

(Hershberger et al. 2001), (Colantonio et al. 2011)

Mamu-KIR3DL01

Mamu-KIR3DL01*003

KIR3DL3

AF361083, GU112305

(Blokhuis et al. 2010; Grendell et al. 2001)

Mamu-KIR3DL01

Mamu-KIR3DL01*004

KIR3DL4

AF334619

(Hershberger et al. 2001)

Mamu-KIR3DL01

Mamu-KIR3DL01*005

KIR3DL5

AF334620

(Hershberger et al. 2001)

Mamu-KIR3DL01

Mamu-KIR3DL01*006

KIR3DL12

AF361082

(Grendell et al. 2001)

Mamu-KIR3DL01

Mamu-KIR3DL01*007N

KIR3DL13

AF408151

(Grendell et al. 2001)

Mamu-KIR3DL01

Mamu-KIR3DL01*008N

KIR3DL14

AF408152

(Grendell et al. 2001)

Mamu-KIR3DL01

Mamu-KIR3DL01*009N

KIR3DL15

AF408153

(Grendell et al. 2001)

Mamu-KIR3DL01

Mamu-KIR3DL01*010

KIR3DL19

AF408150

(Grendell et al. 2001)

Mamu-KIR3DL01

Mamu-KIR3DL01*011

KIR3DL1_variant_2

AY728187

(Sambrook et al. 2005)

Mamu-KIR3DL01

Mamu-KIR3DL01*012

KIR3DL1*002-BNB, KIR3DL-like_1

EU419033, AY505476, GU112286

(Andersen et al. 2004; Blokhuis et al. 2010; Moreland et al. 2011)

Mamu-KIR3DL01

Mamu-KIR3DL01*013

KIR3DL1*003-BNB

EU419034

(Moreland et al. 2011)

Mamu-KIR3DL01

Mamu-KIR3DL01*014

KIR3DL1*005-BNB

EU419035

(Moreland et al. 2011)

Mamu-KIR3DL01

Mamu-KIR3DL01*015

KIR3DL1*006-BNB

EU419036

(Moreland et al. 2011)

Mamu-KIR3DL01

Mamu-KIR3DL01*016

KIR3DL1*007-BNB

EU419037, GU112258

(Blokhuis et al. 2010; Moreland et al. 2011)

Mamu-KIR3DL01

Mamu-KIR3DL01*017

KIR3DL12*001-BNB

EU419044

(Moreland et al. 2011)

Mamu-KIR3DL01

Mamu-KIR3DL01*018

KIR3DL2*001-BNB

EU419046

(Moreland et al. 2011)

Mamu-KIR3DL01

Mamu-KIR3DL01*019:01

KIR3DL1*001-BNB

EU419032, GU112300

(Blokhuis et al. 2010; Moreland et al. 2011)

Mamu-KIR3DL01

Mamu-KIR3DL01*019:02

None

GU112283

(Blokhuis et al. 2010)

Mamu-KIR3DL01

Mamu-KIR3DL01*020

KIR3DL1-like1

EU688987

(Moreland et al. 2011)

Mamu-KIR3DL01

Mamu-KIR3DL01*021

KIR3DL

FJ562108

(Bostik et al. 2009)

Mamu-KIR3DL01

Mamu-KIR3DL01*022

None

GU112267

(Blokhuis et al. 2010)

Mamu-KIR3DL01

Mamu-KIR3DL01*023

None

GU112292

(Blokhuis et al. 2010)

Mamu-KIR3DL01

Mamu-KIR3DL01*024

None

GU112321

(Blokhuis et al. 2010)

Mamu-KIR3DL01

Mamu-KIR3DL01*025

None

GU112324

(Blokhuis et al. 2010)

Mamu-KIR3DL01

Mamu-KIR3DL01*026

KIR3DL allele 2

FJ562109

(Bostik et al. 2009)

Mamu-KIR3DL01

Mamu-KIR3DL01*027

KIR3DL allele 3

FJ562110

(Bostik et al. 2009)

Mamu-KIR3DL02

Mamu-KIR3DL02*001

KIR3DL2

AY728188

(Sambrook et al. 2005)

Mamu-KIR3DL02

Mamu-KIR3DL02*002

KIR3DL-like_3

AY505478

(Andersen et al. 2004)

Mamu-KIR3DL02

Mamu-KIR3DL02*003

KIR3DL21*001-BNB

EU419050

(Moreland et al. 2011)

Mamu-KIR3DL02

Mamu-KIR3DL02*004:01

KIR3DL21*003-BNB

EU419052

(Moreland et al. 2011)

Mamu-KIR3DL02

Mamu-KIR3DL02*004:02

KIR3DL21*005-BNB

EU419053

(Moreland et al. 2011)

Mamu-KIR3DL02

Mamu-KIR3DL02*005

KIR3DL21*006-BNB

EU419054

(Moreland et al. 2011)

Mamu-KIR3DL02

Mamu-KIR3DL02*006

KIR3DL21-like1

EU688989

(Moreland et al. 2011)

Mamu-KIR3DL02

Mamu-KIR3DL02*007

None

GU112277

(Blokhuis et al. 2010)

Mamu-KIR3DL02

Mamu-KIR3DL02*008

None

GU112281

(Blokhuis et al. 2010)

Mamu-KIR3DLW03

Mamu-KIR3DLW03*001

KIR3DL21*002-BNB

EU419051

(Moreland et al. 2011)

Mamu-KIR3DLW03

Mamu-KIR3DLW03*002

KIR3DL21*007-BNB

EU419055

(Moreland et al. 2011)

Mamu-KIR3DLW03

Mamu-KIR3DLW03*003

KIR3DL-like1-BNB

EU419031

(Moreland et al. 2011)

Mamu-KIR3DLW03

Mamu-KIR3DLW03*004

KIR3DL-4

FN424253

(Kruse et al. 2010)

Mamu-KIR3DLW03

Mamu-KIR3DLW03*005

KIR3DL-5

FN424256

(Kruse et al. 2010)

Mamu-KIR3DL04

Mamu-KIR3DL04*001:01

KIR3DL11*002-BNB

EU419040

(Moreland et al. 2011)

Mamu-KIR3DL04

Mamu-KIR3DL04*001:02

None

GU112311

(Blokhuis et al. 2010)

Mamu-KIR3DL04

Mamu-KIR3DL04*001:03

None

GU112319

(Blokhuis et al. 2010)

Mamu-KIR3DL04

Mamu-KIR3DL04*002

KIR3DL11*003-BNB

EU419042

(Moreland et al. 2011)

Mamu-KIR3DL05

Mamu-KIR3DL05*001

KIR3DL16*001-BNB

EU419045

(Moreland et al. 2011)

Mamu-KIR3DL05

Mamu-KIR3DL05*002

KIR3DL7*004-BNB

EU419061

(Moreland et al. 2011)

Mamu-KIR3DL05

Mamu-KIR3DL05*003

KIR3DL7*005-BNB

EU419062

(Moreland et al. 2011)

Mamu-KIR3DL05

Mamu-KIR3DL05*004

KIR3DL7*009-BNB

EU419066

(Moreland et al. 2011)

Mamu-KIR3DL05

Mamu-KIR3DL05*005

KIR3DL7*013-BNB

EU419069

(Moreland et al. 2011)

Mamu-KIR3DL05

Mamu-KIR3DL05*006:01

KIR3DL7-like2

EU688991

(Moreland et al. 2011)

Mamu-KIR3DL05

Mamu-KIR3DL05*006:02

None

GU112293

(Blokhuis et al. 2010)

Mamu-KIR3DL05

Mamu-KIR3DL05*007

KIR3DL-3

FN424252

(Kruse et al. 2010)

Mamu-KIR3DL05

Mamu-KIR3DL05*008

3DL7b-3DL40

GU112291, GU014295

(Blokhuis et al. 2010) (Colantonio et al. 2011)

Mamu-KIR3DL05

Mamu-KIR3DL05*009

None

GU112310

(Blokhuis et al. 2010)

Mamu-KIR3DL05

Mamu-KIR3DL05*010

KIR3DL allele 13

FJ562120

(Bostik et al. 2009)

Mamu-KIR3DL05

Mamu-KIR3DL05*011

KIR3DL allele 14

FJ562121

(Bostik et al. 2009)

Mamu-KIR3DL06

Mamu-KIR3DL06*001

KIR3DL6

AF334621

(Hershberger et al. 2001)

Mamu-KIR3DL06

Mamu-KIR3DL06*002

KIR3DL6*001-BNB

EU419056

(Moreland et al. 2011)

Mamu-KIR3DL07

Mamu-KIR3DL07*001

KIR3DL7

AF334622

(Hershberger et al. 2001)

Mamu-KIR3DL07

Mamu-KIR3DL07*002

KIR3DL18

AF361086

(Grendell et al. 2001)

Mamu-KIR3DL07

Mamu-KIR3DL07*003

KIR3DL7*001-BNB

EU419057

(Moreland et al. 2011)

Mamu-KIR3DL07

Mamu-KIR3DL07*004

KIR3DL7*003-BNB

EU419060

(Moreland et al. 2011)

Mamu-KIR3DL07

Mamu-KIR3DL07*005

KIR3DL7*006-BNB

EU419063

(Moreland et al. 2011)

Mamu-KIR3DL07

Mamu-KIR3DL07*006

KIR3DL7*007-BNB

EU419064

(Moreland et al. 2011)

Mamu-KIR3DL07

Mamu-KIR3DL07*007

KIR3DL7*008-BNB

EU419065

(Moreland et al. 2011)

Mamu-KIR3DL07

Mamu-KIR3DL07*008

KIR3DL7*012-BNB

EU419068

(Moreland et al. 2011)

Mamu-KIR3DL07

Mamu-KIR3DL07*009:01

KIR3DL7-like1, 2DL420

EU688990, GU299489

(Colantonio et al. 2011; Moreland et al. 2011)

Mamu-KIR3DL07

Mamu-KIR3DL07*009:02

None

GU112282

(Blokhuis et al. 2010)

Mamu-KIR3DL07

Mamu-KIR3DL07*010

KIR3DL7-like3

EU688992

(Moreland et al. 2011)

Mamu-KIR3DL07

Mamu-KIR3DL07*011

KIR3DL allele 10

FJ562117

(Bostik et al. 2009)

Mamu-KIR3DL07

Mamu-KIR3DL07*012

KIR3DL allele 11

FJ562118

(Bostik et al. 2009)

Mamu-KIR3DL08

Mamu-KIR3DL08*001:01

KIR3DL8

AY728189

(Sambrook et al. 2005)

Mamu-KIR3DL08

Mamu-KIR3DL08*001:02

KIR3DL8*002-BNB

EU419071

(Moreland et al. 2011)

Mamu-KIR3DL08

Mamu-KIR3DL08*002

KIR3DL17

AF361084, GU112306

(Blokhuis et al. 2010; Grendell et al. 2001)

Mamu-KIR3DL08

Mamu-KIR3DL08*003

KIR3DL17

AF361085

(Grendell et al. 2001)

Mamu-KIR3DL08

Mamu-KIR3DL08*004

KIR3DL-like_2

AY505477

(Andersen et al. 2004)

Mamu-KIR3DL08

Mamu-KIR3DL08*005

KIRDL8

AY728189

(Sambrook et al. 2005)

Mamu-KIR3DL08

Mamu-KIR3DL08*006

KIR3DL8*001-BNB

EU419070

(Moreland et al. 2011)

Mamu-KIR3DL08

Mamu-KIR3DL08*007

None

GU112268

(Blokhuis et al. 2010)

Mamu-KIR3DL08

Mamu-KIR3DL08*008

None

GU112285

(Blokhuis et al. 2010)

Mamu-KIR3DL08

Mamu-KIR3DL08*009

None

GU112290

(Blokhuis et al. 2010)

Mamu-KIR3DL08

Mamu-KIR3DL08*010

None

GU112330

(Blokhuis et al. 2010)

Mamu-KIR3DL08

Mamu-KIR3DL08*011

KIR3DL allele 8

FJ562115

(Bostik et al. 2009)

Mamu-KIR3DL10

Mamu-KIR3DL10*001

KIR3DL10

AY728183

(Sambrook et al. 2005)

Mamu-KIR3DL10

Mamu-KIR3DL10*002:01

KIR3DL9, KIR3DL allele 5

AF334624, GU112259, FJ562112

(Hershberger et al. 2001)(Blokhuis et al. 2010; Bostik et al. 2009)

Mamu-KIR3DL10

Mamu-KIR3DL10*002:02

3DL3NK

GU299486

(Colantonio et al. 2011)

Mamu-KIR3DL10

Mamu-KIR3DL10*003

KIR3DL10*001-BNB

EU419038

(Moreland et al. 2011)

Mamu-KIR3DL10

Mamu-KIR3DL10*004

KIR3DL10*002-BNB

EU419039

(Moreland et al. 2011)

Mamu-KIR3DL10

Mamu-KIR3DL10*005:01

3DL10-2DL501

GU014294

(Colantonio et al. 2011)

Mamu-KIR3DL10

Mamu-KIR3DL10*005:02

None

GU112295

(Blokhuis et al. 2010)

Mamu-KIR3DL10

Mamu-KIR3DL10*006

KIR3DL allele 6

FJ562113

(Bostik et al. 2009)

Mamu-KIR3DL11

Mamu-KIR3DL11*001

KIR3DL11

AF334626, GU112271

(Blokhuis et al. 2010; Hershberger et al. 2001)

Mamu-KIR3DL11

Mamu-KIR3DL11*002

KIR3DL-1

FN424250

(Kruse et al. 2010)

Mamu-KIR3DL11

Mamu-KIR3DL11*003

KIR3DL-6

FN424259

(Kruse et al. 2010)

Mamu-KIR3DL11

Mamu-KIR3DL11*004

KIR3DL-7

FN424261

(Kruse et al. 2010)

Mamu-KIR3DL11

Mamu-KIR3DL11*005

None

GU112276

(Blokhuis et al. 2010)

Mamu-KIR3DL11

Mamu-KIR3DL11*006

None

GU112296

(Blokhuis et al. 2010)

Mamu-KIR3DL11

Mamu-KIR3DL11*007

KIR3DL allele 9

FJ562116

(Bostik et al. 2009)

Mamu-KIR3DL20

Mamu-KIR3DL20*001

KIR3DL20*001-BNB

EU419047

(Moreland et al. 2011)

Mamu-KIR3DL20

Mamu-KIR3DL20*002

KIR3DL20

AY728184, GU112327

(Blokhuis et al. 2010; Sambrook et al. 2005)

Mamu-KIR3DL20

Mamu-KIR3DL20*003

KIR3DL20_variant_2

AY728186

(Sambrook et al. 2005)

Mamu-KIR3DL20

Mamu-KIR3DL20*004

KIR3DL20*003-BNB

EU419048

(Moreland et al. 2011)

Mamu-KIR3DL20

Mamu-KIR3DL20*005

KIR3DL20*004-BNB

EU419049

(Moreland et al. 2011)

Mamu-KIR3DL20

Mamu-KIR3DL20*006

None

GU112255

(Blokhuis et al. 2010)

Mamu-KIR3DL20

Mamu-KIR3DL20*007

None

GU112256

(Blokhuis et al. 2010)

Mamu-KIR3DL20

Mamu-KIR3DL20*008

None

GU112264

(Blokhuis et al. 2010)

Mamu-KIR3DL20

Mamu-KIR3DL20*009

None

GU112270

(Blokhuis et al. 2010)

Mamu-KIR3DL20

Mamu-KIR3DL20*010

None

GU112275

(Blokhuis et al. 2010)

Mamu-KIR3DL20

Mamu-KIR3DL20*011

None

GU112289

(Blokhuis et al. 2010)

Mamu-KIR3DL20

Mamu-KIR3DL20*012

None

GU112299

(Blokhuis et al. 2010)

Mamu-KIR3DL20

Mamu-KIR3DL20*013

None

GU112304, GU112317

(Blokhuis et al. 2010)

Mamu-KIR3DL20

Mamu-KIR3DL20*014

None

GU112308

(Blokhuis et al. 2010)

Mamu-KIR3DL20

Mamu-KIR3DL20*015

None

GU134802

(Blokhuis et al. 2010)

Mamu-KIR3DS01

Mamu-KIR3DS01*001:01

KIR3DH5

AF361087

(Grendell et al. 2001)

Mamu-KIR3DS01

Mamu-KIR3DS01*001:02

None

GU112307

(Blokhuis et al. 2010)

Mamu-KIR3DS01

Mamu-KIR3DS01*002

KIR3DH1

AY728190

(Sambrook et al. 2005)

Mamu-KIR3DS01

Mamu-KIR3DS01*003

KIR3DH-7

GU564161

(Chaichompoo et al. 2010)

Mamu-KIR3DS02

Mamu-KIR3DS02*001

KIR3DH2

AF334649

(Hershberger et al. 2001)

Mamu-KIR3DS02

Mamu-KIR3DS02*002

KIR3DH-like_5

AY505483

(Andersen et al. 2004)

Mamu-KIR3DS02

Mamu-KIR3DS02*003

KIR3DH-like_6

AY505484

(Andersen et al. 2004)

Mamu-KIR3DS02

Mamu-KIR3DS02*004:01

KIR3DH2*001-BNB, KIR3DH14

EU419026, EU702460

(Blokhuis et al. 2009a; Moreland et al. 2011)

Mamu-KIR3DS02

Mamu-KIR3DS02*004:02

KIR3DH13, 3DH42

EU702459, GU014296

(Blokhuis et al. 2009a) (Colantonio et al. 2011)

Mamu-KIR3DS02

Mamu-KIR3DS02*004:03

KIR3DH12

EU702458

(Blokhuis et al. 2009a)

Mamu-KIR3DS02

Mamu-KIR3DS02*005

KIR3DH2*002-BNB

EU419027

(Moreland et al. 2011)

Mamu-KIR3DS02

Mamu-KIR3DS02*006

KIR3DH16

EU702462

(Blokhuis et al. 2009a)

Mamu-KIR3DS02

Mamu-KIR3DS02*007

KIR3DH15

EU702461

(Blokhuis et al. 2009a)

Mamu-KIR3DS02

Mamu-KIR3DS02*008

KIR3DH10

EU702456, GU112278

(Blokhuis et al. 2009a; Blokhuis et al. 2010)

Mamu-KIR3DS02

Mamu-KIR3DS02*009

None

GU112261, GU112315

(Blokhuis et al. 2010)

Mamu-KIR3DS02

Mamu-KIR3DS02*010

None

GU112297

(Blokhuis et al. 2010)

Mamu-KIR3DS02

Mamu-KIR3DS02*011

None

GU112323

(Blokhuis et al. 2010)

Mamu-KIR3DS02

Mamu-KIR3DS02*012

3DH2*NEW1

JN613291

(Hellmann et al. 2011)

Mamu-KIR3DS02

Mamu-KIR3DS02*013

3DH2*NEW1

JN613299

(Hellmann et al. 2011)

Mamu-KIR3DS03

Mamu-KIR3DS03*001:01

KIR3DH3

AF334650, GU112312

(Hershberger et al. 2001) (Blokhuis et al. 2010)

Mamu-KIR3DS03

Mamu-KIR3DS03*001:02

None

GU112294

(Blokhuis et al. 2010)

Mamu-KIR3DS03

Mamu-KIR3DS03*002

KIR3DH9

EU702455, GU112269

(Blokhuis et al. 2009a; Blokhuis et al. 2010)

Mamu-KIR3DS03

Mamu-KIR3DS03*003

KIR3DH8

EU702454

(Blokhuis et al. 2009a)

Mamu-KIR3DS04

Mamu-KIR3DS04*001

KIR3DH4

AF334651

(Hershberger et al. 2001)

Mamu-KIR3DS04

Mamu-KIR3DS04*002

KIR3DH4*001-BNB

EU419028

(Moreland et al. 2011)

Mamu-KIR3DS04

Mamu-KIR3DS04*003

KIR3DH4*002-BNB, KIR3DH4

EU419029, JN613296

(Hellmann et al. 2011; Moreland et al. 2011)

Mamu-KIR3DS04

Mamu-KIR3DS04*004

KIR3DH6

EU702452

(Blokhuis et al. 2009a)

Mamu-KIR3DS04

Mamu-KIR3DS04*005

KIR3DH4

JN613300

(Hellmann et al. 2011)

Mamu-KIR3DS04

Mamu-KIR3DS04*006

KIR3DH-1

GU564157

(Chaichompoo et al. 2010)

Mamu-KIR3DS05

Mamu-KIR3DS05*001

KIR3DH1*001-BNB

EU419024, EU419025, EU702468, AY505487, GU112262

(Moreland et al. 2011)

Mamu-KIR3DS05

Mamu-KIR3DS05*002:01

KIR3DH1*002-BNB, KIR3DM1, KIR_Partial_Sequence_1

EU419025, EU702468, AY505487, GU112262

(Andersen et al. 2004; Blokhuis et al. 2009a; Blokhuis et al. 2010; Moreland et al. 2011)

Mamu-KIR3DS05

Mamu-KIR3DS05*002:02

KIR3DM6

EU702473

(Blokhuis et al. 2009a)

Mamu-KIR3DS05

Mamu-KIR3DS05*003

KIR3DM-1

FN424260

(Kruse et al. 2010)

Mamu-KIR3DS06

Mamu-KIR3DS06*001

KIR3DH-like_7

AY505485

(Andersen et al. 2004)

Mamu-KIR3DS06

Mamu-KIR3DS06*002:01

KIR3DH-like8

EU688985

(Moreland et al. 2011)

Mamu-KIR3DS06

Mamu-KIR3DS06*002:02

None

GU112298

(Blokhuis et al. 2010)

Mamu-KIR3DS06

Mamu-KIR3DS06*003

KIR3DH18

EU702464

(Blokhuis et al. 2009a)

Mamu-KIR3DS06

Mamu-KIR3DS06*004

KIR3DH-4

FN424257

(Kruse et al. 2010)

Mamu-KIR3DS06

Mamu-KIR3DS06*005

None

GU112260

(Blokhuis et al. 2010)

Mamu-KIR3DS06

Mamu-KIR3DS06*006

None

GU112314

(Blokhuis et al. 2010)

Mamu-KIR3DSW07

Mamu-KIR3DSW07*001

KIR3DH7

EU702453, GU112272

(Blokhuis et al. 2009a; Blokhuis et al. 2010)

Mamu-KIR3DSW07

Mamu-KIR3DSW07*002

KIR3DH-5

FN424258

(Kruse et al. 2010)

Mamu-KIR3DSW08

Mamu-KIR3DSW08*001

KIR3DH-like_1

AY505479

(Andersen et al. 2004)

Mamu-KIR3DSW08

Mamu-KIR3DSW08*002

KIR3DH-like_2

AY505480

(Andersen et al. 2004)

Mamu-KIR3DSW08

Mamu-KIR3DSW08*003

KIR3DH-like_3

AY505481

(Andersen et al. 2004)

Mamu-KIR3DSW08

Mamu-KIR3DSW08*004

KIR3DH-like_4

AY505482

(Andersen et al. 2004)

Mamu-KIR3DSW08

Mamu-KIR3DSW08*005

KIR3DH21

EU702467

(Blokhuis et al. 2009a)

Mamu-KIR3DSW08

Mamu-KIR3DSW08*006

KIR3DH-2

FN424254

(Kruse et al. 2010)

Mamu-KIR3DSW08

Mamu-KIR3DSW08*007

KIR3DH-3

FN424255

(Kruse et al. 2010)

Mamu-KIR3DSW08

Mamu-KIR3DSW08*008

None

GU112325

(Blokhuis et al. 2010)

Mamu-KIR3DSW08

Mamu-KIR3DSW08*009

None

GU112328

(Blokhuis et al. 2010)

Mamu-KIR3DSW08

Mamu-KIR3DSW08*010

KIR3DSW08

JN613297

(Hellmann et al. 2011)

Mamu-KIR3DSW08

Mamu-KIR3DSW08*011

KIR3DH-4

GU564158

(Chaichompoo et al. 2010)

Mamu-KIR3DSW08

Mamu-KIR3DSW08*012

KIR3DH-5

GU564159

(Chaichompoo et al. 2010)

Mamu-KIR3DSW09

Mamu-KIR3DSW09*001

KIR3DH5*001-BNB

EU419030

(Moreland et al. 2011)

Mamu-KIR3DSW09

Mamu-KIR3DSW09*002

KIR3DH5-like1

EU688986

(Moreland et al. 2011)

Mamu-KIR3DSW09

Mamu-KIR3DSW09*003

None

GU112301

(Blokhuis et al. 2010)

Mamu-KIR3DSW09

Mamu-KIR3DSW09*004

KIR3DH20

EU702466, GU112273

(Blokhuis et al. 2009a), (Blokhuis et al. 2010)

Mamu-KIR3DSW09

Mamu-KIR3DSW09*005

mmKIR3DH-1

FN424249

(Kruse et al. 2010)

Mamu-KIR3DSW09

Mamu-KIR3DSW09*006

KIR3DH-8

GU564162

(Chaichompoo et al. 2010)

Mamu-KIR3DLX1

Mamu-KIR3DLX1*001

KIR3DL0

DQ157756

(Sambrook et al. 2006)

Table 5

Allele designations and their previous names

Gene

Allele designation

Previous designations

Accession number

Reference

Patr-KIR2DL4

Patr-KIR2DL4*001

None

HM068617

(Abi-Rached et al. 2010)

Patr-KIR2DL4

Patr-KIR2DL4*002

None

AC155174, AF258804

(Khakoo et al. 2000)

Patr-KIR2DL4

Patr-KIR2DL4*003

None

BX842589

(Sambrook et al. 2005)

Patr-KIR2DL5

Patr-KIR2DL5*001

None

HM068617

(Abi-Rached et al. 2010)

Patr-KIR2DL5

Patr-KIR2DL5*002

None

AF274005

(Rajalingam et al. 2001)

Patr-KIR2DL5

Patr-KIR2DL5*003

None

AC155174

 

Patr-KIR2DL5

Patr-KIR2DL5*004

None

BX842589

(Sambrook et al. 2005)

Patr-KIR2DL5

Patr-KIR2DL5*005

None

AF258805

(Khakoo et al. 2000)

Patr-KIR2DL6

Patr-KIR2DL6*001

None

BX842589, AM292662

(Sambrook et al. 2005)

Patr-KIR2DL6

Patr-KIR2DL6*002

None

AF258806

 

Patr-KIR2DL6

Patr-KIR2DL6*003

None

AM292661

 

Patr-KIR2DL7

Patr-KIR2DL7*001

None

HM068617

(Abi-Rached et al. 2010)

Patr-KIR2DL8

Patr-KIR2DL8*001

None

HM068617

(Abi-Rached et al. 2010)

Patr-KIR2DL8

Patr-KIR2DL8*002

None

AC155174, AM279149

Biassoni, unpublished

Patr-KIR2DL8

Patr-KIR2DL8*003

None

BX842589

(Sambrook et al. 2005)

Patr-KIR2DL9

Patr-KIR2DL9*001

None

AC155174

 

Patr-KIR2DL9

Patr-KIR2DL9*002

None

AM292657

Biassoni, unpublished

Patr-KIR2DL9

Patr-KIR2DL9*003

None

AM400233

Biassoni, unpublished

Patr-KIR2DS4

Patr-KIR2DS4*001

None

HM068617

 

Patr-KIR2DS4

Patr-KIR2DS4*002

None

AF258807

 

Patr-KIR3DL1

Patr-KIR3DL1*001:01

None

AC155174

 

Patr-KIR3DL1

Patr-KIR3DL1*001:02

None

AF266729

(Rajalingam et al. 2001)

Patr-KIR3DL1

Patr-KIR3DL1*002

None

BX842589, AF258798

(Sambrook et al. 2005)

Patr-KIR3DL1

Patr-KIR3DL1*003

None

AF266730

(Rajalingam et al. 2001)

Patr-KIR3DL1

Patr-KIR3DL1*004

None

AF258799

 

Patr-KIR3DL1

Patr-KIR3DL1*005

None

HM068617

 

Patr-KIR3DL3

Patr-KIR3DL3*001

None

HM068617

 

Patr-KIR3DL3

Patr-KIR3DL3*002

None

BX842589

 

Patr-KIR3DL3

Patr-KIR3DL3*003

None

AC155174

 

Patr-KIR3DL3

Patr-KIR3DL3*004

None

AY327500

 

Patr-KIR3DL4

Patr-KIR3DL4*001:01

None

AM400232

Biassoni, unpublished

Patr-KIR3DL4

Patr-KIR3DL4*001:02

None

AF258800

(Khakoo et al. 2000)

Patr-KIR3DL4

Patr-KIR3DL4*002

None

HM068617

(Abi-Rached et al. 2010)

Patr-KIR3DL5

Patr-KIR3DL5*001

None

AM400235

Biassoni, unpublished

Patr-KIR3DL5

Patr-KIR3DL5*003:01

None

AF258801

(Khakoo et al. 2000)

Patr-KIR3DL5

Patr-KIR3DL5*004

None

AC155174, AM292659

Biassoni, unpublished

Patr-KIR3DS2

Patr-KIR3DS2*001

None

AC155174

 

Patr-KIR3DS2

Patr-KIR3DS2*002

None

AF258803

 

Patr-KIR3DS6

Patr-KIR3DS6*001

None

AM396937

Biassoni, unpublished

Table 6

Allele designations and their previous names

Gene

Allele designation

Previous designations

Accession number

Reference

Poab-KIR2DL10

Poab-KIR2DL10*001

2DLA

AF470358

(Guethlein et al. 2002)

Poab-KIR2DL11

Poab-KIR2DL11*001

2DLB

EF014479

(Guethlein et al. 2007b)

Poab-KIR2DL12

Poab-KIR2DL12*001

2DLC

AC200148

 

Poab-KIR2DL5

Poab-KIR2DL5*001

2DL5

AC200148

 

Poab-KIR2DS10

Poab-KIR2DS10*001

None

AF470364

(Guethlein et al. 2002)

Poab-KIR2DS13

Poab-KIR2DS13*001

2DSC1/2DSB

AF470362

(Guethlein et al. 2002)

Poab-KIR2DS14

Poab-KIR2DS14*001

2DSB/2DSD2

AF470361

(Guethlein et al. 2002)

Poab-KIR2DS14

Poab-KIR2DS14*002

2DSA/2DSD1

AF470360

(Guethlein et al. 2002)

Poab-KIR3DL1

Poab-KIR3DL1*001:01

3DLH

AF470373

(Guethlein et al. 2002)

Poab-KIR3DL1

Poab-KIR3DL1*001:02

None

AC200148

 

Poab-KIR3DL1

Poab-KIR3DL1*002

3DLC

AF470367

(Guethlein et al. 2002)

Poab-KIR3DL1

Poab-KIR3DL1*003

None

AF470372

(Guethlein et al. 2002)

Poab-KIR3DL1

Poab-KIR3DL1*004:01

3DLD2

AF470369

(Guethlein et al. 2002)

Poab-KIR3DL1

Poab-KIR3DL1*004:02

3DLD1

EF014479

(Guethlein et al. 2007b)

Poab-KIR3DL1

Poab-KIR3DL1*005

3DLA

AF470365

(Guethlein et al. 2002)

Poab-KIR3DL1

Poab-KIR3DL1*006

3DLI

AF470374

(Guethlein et al. 2002)

Poab-KIR3DL1

Poab-KIR3DL1*007

3DLB

AF470366

(Guethlein et al. 2002)

Poab-KIR3DL3

Poab-KIR3DL3*001

3DL3

AC200148

 

Poab-KIR3DS1

Poab-KIR3DS1*001

3DS1

AF470375

(Guethlein et al. 2002)

Poab-KIRDP

Poab-KIRDP*001

DP

AC200148

 

Popy-KIR2DS10

Popy-KIR2DS10*001

2DSD/2DSA

AF470364

(Guethlein et al. 2002)

Popy-KIR2DS13

Popy-KIR2DS13*001

2DSC2/2DSB

AF470363

(Guethlein et al. 2002)

Popy-KIR3DL1

Popy-KIR3DL1*001

3DLF

AF470372

(Guethlein et al. 2002)

Popy-KIR3DL1

Popy-KIR3DL1*002:01

3DLE2

AF470371

(Guethlein et al. 2002)

Popy-KIR3DL1

Popy-KIR3DL1*002:02

3DLE1

AF470370

(Guethlein et al. 2002)

Table 7

Allele designations and their previous names

Gene

Allele designation

Previous designations

Accession number

Breed

Reference

Bota-KIR2DL1

Bota-KIR2DL1*001

KIR2DL1

AY075102,AF490399

UnknownHolstein

(McQueen et al. 2002; Storset et al. 2003; Zimin et al. 2009)

Bota-KIR2DL1

Bota-KIR2DL1*002

None

JX848327

Holstein-Freisian

(Sanderson et al. 2014)

Bota-KIR2DS1

Bota-KIR2DS1*001N

KIR2DS1

JX848328

Holstein-Freisian

(Sanderson et al. 2014)

Bota-KIR2DS2

Bota-KIR2DS2*001N

None

JX848329

Holstein-Freisian

(Sanderson et al. 2014)

Bota-KIR2DS3

Bota-KIR2DS3*001N

None

JX848330

Holstein-Freisian

(Sanderson et al. 2014)

Bota-KIR2DXS1

Bota-KIR2DXS1*001

None

AF490400

Holstein

(Storset et al. 2003)

Bota-KIR2DXP1

Bota-KIR2DXP1*001

None

JX848331

Holstein-Freisian

(Sanderson et al. 2014)

Bota-KIR2DXP2

Bota-KIR2DXP2*001

None

JX848332

Holstein-Freisian

(Sanderson et al. 2014)

Bota-KIR3DXL1

Bota-KIR3DXL1*001

KIR3DL1

AF490402

Holstein

(Storset et al. 2003; Zimin et al. 2009)

Bota-KIR3DXL1

Bota-KIR3DXL1*002

None

JX848333

Holstein-Freisian

(Sanderson et al. 2014)

Bota-KIR3DXL2

Bota-KIR3DXL2*001

None

JX848334

Holstein-Freisian

(Sanderson et al. 2014)

Bota-KIR3DXL3

Bota-KIR3DXL3*001

None

JX848335

Holstein-Freisian

(Sanderson et al. 2014)

Bota-KIR3DXL4

Bota-KIR3DXL4*001

KIR3DL2–001

EF197118

Holstein-Freisian

(Dobromylskyj and Ellis 2007; Zimin et al. 2009)

Bota-KIR3DXL4

Bota-KIR3DXL4*002

None

JX848336

Holstein-Freisian

(Sanderson et al. 2014)

Bota-KIR3DXL5

Bota-KIR3DXL5*001

None

JX848337

Holstein-Freisian

(Sanderson et al. 2014)

Bota-KIR3DXL6

Bota-KIR3DXL6*001N

KIR3DL1P

AY075103JX848338

UnknownHolstein-Freisian

(McQueen et al. 2002) (Sanderson et al. 2014)

Bota-KIR3DXL6

Bota-KIR3DXL6*002

KIR3DL3

EF197119

Holstein-Freisian

(Dobromylskyj and Ellis 2007; Zimin et al. 2009)

Bota-KIR3DXL7

Bota-KIR3DXL7*001

None

JX848339

Holstein-Freisian

(Sanderson et al. 2014)

Bota-KIR3DXS1

Bota-KIR3DXS1*001

KIR3DS1

AF490401

Holstein

(Storset et al. 2003; Zimin et al. 2009)

Bota-KIR3DXS1

Bota-KIR3DXS1*002

KIR3DS1–002

EF197120

Holstein-Freisian

(Dobromylskyj and Ellis 2007)

Bota-KIR3DXS1

Bota-KIR3DXS1*003

None

JX848340

Holstein-Freisian

(Sanderson et al. 2014)

Bota-KIR3DXS2

Bota-KIR3DXS2*001N

None

JX848341

Holstein-Freisian

(Sanderson et al. 2014)

Bota-KIR3DXS3

Bota-KIR3DXS3*001N

None

JX848342

Holstein-Freisian

(Sanderson et al. 2014)

Each KIR allele name includes a unique number corresponding to up to three sets of digits separated by colons. All alleles are given a three-digit name, which corresponds to the first set of digits; longer names are assigned only when necessary.

The digits placed before the first colon describe the alleles that differ at non-synonymous substitutions (also called coding substitutions). Alleles that differ only by synonymous nucleotide substitutions (also called silent or non-coding substitutions) but are within the coding sequence are distinguished by their second sets of digits. Alleles that only differ by sequence polymorphisms in the introns, or in the 5′ or 3′ untranslated regions that flank the exons and introns, are distinguished by their third sets of digits.

In addition to the unique allele number, optional suffixes can be added to an allele name to indicate the expression status of the gene and/or its encoded protein. Alleles known not to be expressed—so called “Null” alleles—have been given the suffix “N.” Alleles that have been shown to be alternatively expressed may have the suffix “L,” “S,” “C,” “A,” or “Q.”

The suffix “L” is used to indicate an allele that has been shown to have “Low” cell surface expression when compared to normal levels. The “S” suffix is used to denote an allele specifying a protein which is expressed as a soluble, “Secreted” molecule and is not present on the cell surface. The “C” suffix is assigned to alleles producing proteins that are present in the “Cytoplasm” and not on the cell surface. An “A” suffix indicates an “Aberrant” expression, where there is doubt as to whether a protein is actually expressed. A “Q” suffix is used when the expression of an allele is “Questionable,” given that the mutation seen in the allele has been shown to affect normal expression levels in other alleles and other KIR genes.

As of May 2018, no alleles have been named with the “C,” “A,” “Q,” or “S” suffixes.

A schematic representation of the syntax for the non-human KIR allele designation is shown in Fig. 1.
Fig. 1

Non-human KIR nomenclature.

Details the syntax and structure of a non-human KIR allele designation

Species-specific guidelines

Naming rhesus macaque KIR genes

The Mamu-KIR sequences fall into a number of distinct lineages based on phylogenetic analysis. Most sequences correspond to lineage II KIR and are further divided into those encoding KIR that have long cytoplamic tails or short cytoplasmic tails. The genes have been numbered sequentially and where possible the gene name has the same the same number as the first reported allele for that gene. For example, the Mamu-KIR3DL1 gene (Hershberger et al. 2001) was renamed Mamu-KIR3DL01*001.

The nomenclature uses a two-digit numbering of individual genes for the macaque sequences as seen with the naming of Mamu-KIR3DL01*001. This renaming aims to avoid confusion with previous sequence names. Subsequent analysis has shown that some of the proposed sequences of different genes are actually allelic variants of the same gene. Rather than skipping numbers to avoid confusion, it was thought better to introduce the two-digit numbering system.

Recombinant alleles are named according to the locus, which provide the majority of the sequence. For example, the sequence originally named Mamu-KIR3DL5 (Hershberger et al. 2001) is a recombinant of Mamu-KIR3DL01 and Mamu-KIR3DL07. As such, it has been renamed as an allele of Mamu-KIR3DL01, Mamu-KIR3DL01*005. This principal has also been applied to recombinant alleles in other species.

Along with the lineage II KIR genes, rhesus macaques have KIR genes for lineage I, III, and V KIR. The lineage I KIR gene in rhesus macaques is orthologous to other primate lineage 1 KIR, referred to as 2DL4 and has been named Mamu-KIR2DL04. A single lineage III KIR is also present on some Mamu-KIR haplotypes and in all cases appears to be expressed as a one Ig domain KIR. It has been named Mamu-KIR1D. Finally, there is a lineage V KIR gene that is expressed as either a two Ig or three Ig domain KIR. The published genomic sequence shows the gene to contain three Ig domain encoding exons; however, due to splicing out of exon 4, also two Ig domain KIR variants are expressed. The majority of the rhesus macaque gene sequence appears orthologous to hominoid KIR3DL3 sequences, the exception being exon 3 [encoding the D0 domain] which appears more like the hominoid KIR2DL5 sequences. This sequence relationship coupled with the presence of splice variants that lacked exon 4 led to the naming of some of these sequences as Mamu-KIR2DL5. The presence of the intact gene as evidenced by the published genomic sequence, as well as the existence of full-length [three Ig domain containing] sequences has led us to propose naming this gene as Mamu-KIR3DL20. This distinguishes this gene from the remaining Mamu-KIR3DL as well as retaining the name of one of the first mRNA sequences that included all three Ig domain encoding exons, see Table 1 for further details. A full list of Mamu-KIR sequences is described in Table 4.

The identification of sequences in other Macaque species will follow the same rules, and use the species prefix (Mafa-KIR, Mane-KIR), and that genes would be named to match the closest rhesus gene.

Naming chimpanzee KIR genes

Three studies (Abi-Rached et al. 2010; Khakoo et al. 2000; Sambrook et al. 2005) have described complete sequences of three chimpanzee haplotypes. In addition, the analysis of chimpanzee KIR genotypes has inferred the organization of genes infers the existence of another 17 chimpanzee KIR haplotypes. These analyses have defined 13 different Patr-KIR genes.

In all chimpanzee KIR haplotypes, the framework gene at the telomeric end is a lineage II KIR gene. Formerly, two variants, now known to occupy this position, were named Pt-KIR3DL1/2 and Pt-KIR3DL3. The name Pt-KIR3DL1/2 was given to reflect its close relationship to both human KIR3DL1 and KIR3DL2. Although segregation analysis showed that Pt-KIR3DL3 and KIR3DL1/2 were never present on the same haplotype, Pt-KIR3DL3 was given a different name because it has a distinctive sequence. We are renaming the Pt-KIRDl1/2 and Pt-KIR3DL3 as allelic variants of Patr-KIR3DL1, the new name for the framework gene at the telomeric end of the chimpanzee KIR locus. This will allow the Patr-KIR3DL3 name to be given to the gene previously known as Patr-KIRC1, and which is orthologous to human KIR3DL3, the framework gene at the centromeric end of the KIR locus. See Table 2 for further details. A full list of Patr-KIR sequences is described in Table 5.

Naming orangutan KIR genes

In the initial description of orangutan KIR cDNA (Guethlein et al. 2002), the sequences were given letter designations because their relationships, either alleles or genes, were uncertain. Subsequent studies (Guethlein et al. 2007a; Guethlein et al. 2017; Locke et al. 2011; Mager et al. 2001) have provided complete sequences of three orangutan KIR haplotypes, as well as genotyping data that has allowed the structures of two additional KIR haplotypes to be inferred. These genomic data, in combination with the cDNA sequences, defined 11 KIR genes and 1 KIR pseudogene in the orangutan. At first, all orangutan KIR were named as “Popy” (Guethlein et al. 2007b). The orangutan KIR is now divided into two series corresponding to the two species of orangutan: Popy for Pongo pygmaeus and Poab for Pongo abelii depending on species of origin. Some KIR alleles are present in both orangutan species. These alleles shared have been given a different name in each species (Guethlein et al. 2017; Guethlein et al. 2015), see Table 3: for further details. A full list of Popy-KIR and Poab-KIR sequences is given in Table 6.

Naming cattle KIR genes

Assembly of the first cattle KIR haplotype allowed previously known cDNA sequences to be assigned to particular genes and allelic relationships to be defined (Dobromylskyj and Ellis 2007; Guethlein et al. 2007a; Hammond et al. 2016; Mager et al. 2001; Sanderson et al. 2014). This presents the opportunity to adopt an accurate and logical nomenclature system. Cattle KIR cDNA sequences were previously named using the established convention of Ig domain number and tail length. However, these alleles were annotated prior to the discovery of a second deeply divergent KIR lineage, the KIR3DX lineage (Guethlein et al. 2007a). The majority of the expanded cattle KIR belong to this second lineage. In developing a nomenclature system for the cattle KIR, we have incorporate their lineage ancestry within the name. Cattle KIR have been prefixed with a four-letter species designation “Bota” (Bos taurus) in line with non-human primates. Where possible previously named Bota-KIR has retained the same name with only the addition of an “X” after the domain number if from the KIR3DX lineage. There are three exceptions; Bota-KIR3DL1P and Bota-KIR3DL3, which are allelic, and Bota-KIR3DL2. These previously described cDNA sequences are all members of the KIR3DX lineage. Based on their position in the cattle haplotype and their relationships to other genes, Bota-KIR3DL1P was renamed Bota-KIR3DXL6*001N, Bota-KIR3DL3 was renamed Bota-KIR3DXL6*002, and Bota-KIR3DL2 was renamed Bota-KIR3DXL4. We have identified 16 cattle KIR genes. The proposed nomenclature for cattle KIR is given in Table 7.

Future guidelines

The sequences described in this report will be included in the Immuno Polymorphism Database (IPD) (Robinson et al. 2013). They will be maintained as a component of the IPD and be accessible at https://www.ebi.ac.uk/ipd/nhkir/. New sequences for any of the above species can be submitted using the current submission tool. As with the other databases, there are requirements that should be met before formal names can be given and the submitted KIR are included in the database. First, submission of full-length sequences is encouraged and for some species like rhesus macaque is already mandatory. Second, novel sequences must be confirmed, either through their replication in multiple individuals or at a minimum by coming from multiple independent PCR/cloning experiments. Full guidelines for submission of non-human KIR sequences to IPD can be found at https://www.ebi.ac.uk/ipd/nhkir/submission/help.

As KIR sequence data from other species reaches the level of the species included in this report, those species can be included in the database. The inclusion of a species will be at the discretion of the Nomenclature Committee and IPD and will be based on the number of sequences available as well as evidence of identified genes and haplotype structure.

Notes

Funding

JAH and NDS were supported by the United Kingdom Biotechnology and Biological Sciences Research Council (BBSRC) through projects BBS/E/I/00001410 and BBS/E/I/00001710.

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Copyright information

© The Author(s) 2018

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

Authors and Affiliations

  1. 1.Anthony Nolan Research InstituteLondonUK
  2. 2.UCL Cancer InstituteUniversity College LondonLondonUK
  3. 3.Department of Structural Biology and Department of Microbiology & Immunology, School of MedicineStanford UniversityStanfordUSA
  4. 4.The Pirbright InstituteWokingUK
  5. 5.Biomedical Primate Research CentreRijswijkNetherlands
  6. 6.Parker Institute for Cancer ImmunotherapySan FranciscoUSA
  7. 7.Oregon National Primate Research CentreOregon Health and Science UniversityBeavertonUSA
  8. 8.Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUK
  9. 9.Aix-Marseille II UniversityMarseilleFrance
  10. 10.German Primate CentreGottingenGermany

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