Fifth BoLA Workshop Tables

 

Table 1.
Information on class II probes used for RFLP typing.

^aTransmembrane domain probes.
^b References:

1. Muggli-Cockett & Stone, 1988
2. Groenen et al., 1990
3. Muggli-Cockett & Stone, 1991
4. van der Poel et al., 1990
5. Sigurdardóttir et al. (unpublished)
6. Xu et al., 1991
7. Stone & Muggli-Cockett, 1990
8. Auffray et al., 1982
9. Tonnelle et al., 1985, Stone & Muggli-Cockett, 1993.

 

Table 2.
Antisera used to define workshop class II specificities (r>0.65).

^a Serum name used in the laboratory which produced the serum. If multiple aliquots of the same serum clustered, the results for the aliquot with the highest r value are shown.
^b Absorbed with lymphocytes (Lymph) or platelets (Plat). Lymphocyte absorptions remove class I, class II and/or non-MHC activity while platelet absorptions only remove class I and/or non-MHC activity directed against antigens expressed on platelets.
^c Correlation coefficient between serum and specificity.
^d Clustered in both BER and WGN.
^e Data shown is for BER typing.
^f Data shown is for WGN typing.
^g Same serum used at two different dilutions.

Table 3.
Haplotypes carried by workshop animals.

^a For breed and parentage information see Table 1 of Davies et al. (1994).
^b Origin of haplotype if known.
^c Class I serotypes and IEF defined splits (F#).
^d Class IIa haplotype (DH) reference numbers.
^e Specificities expected but not detected (false negatives) are shown in round brackets (). Specificities assigned but not attributed to either haplotype (unknown linkage, cross reactions, tails and false positives) are shown in square brackets [].
^f Numbers by themselves are DRBF types, numbers preceded by a U are UDF types.
^g Linkage not determined, see Table 1 of Davies et al. (1994) for class I types.
^h Not determined because of inconsistent or incomplete data.
ⁱ Negative. Missing or inconsistent results due to weak hybridization.
^j Not typed.
^k Due to missing data the presence or absence of Dc5,6,7,9,11,12 and 13 could not be determined.
^l DRB*3G assigned by MLI and DRB*3E assigned by URB. As this was a unique haplotype, it could not be determined which pattern was correct.
^m This is a typing mistake. DQB-TM*12 expected and transmitted to daughter, WK5-46.
ⁿ The DBB*7D pattern found in WK5-47 was expected with this haplotype. The DRB*3F and DRB*7D patterns are identical except for the presence of a 6.4 kb TaqI fragment in the DRB*3F pattern. Both MLI and URB detected a 6.4 kb fragment in this animal.

Table 4.
Workshop IEF nomenclature and local equivalents.

Figure 1.
A schematic drawing of IEF defined DRB specific banding patterns based on immunoprecipitation with the mAbs IL-A21 and TH14B. Gels were run under workshop conditions with a gel size of 18 by 28cm and the anode at the bottom. Paterns DRBF1-12 were accepted as workshop IEF types, the UDF patterns are local UTN types that need confirmation and have not yet been accepted.

Table 5.
DRB RFLP patterns.

                                 Restriction fragments (kb)a
               ----------------------------------------------------------
                                      TaqI                          PvuII
               ---------------------------------------------------  -----
               1 1                                                       
               7 2 9 8 6 6 6 6 5 5 4 4 4 3 3 2 2 2 2 2 1 1 1 1 1 0   6 1 
               . . . . . . . . . . . . . . . . . . . . . . . . . .   . . 
 Allele        0 0 0 4 4 3 2 0 4 0 9 4 1 7 3 8 3 2 1 0 9 6 3 2 1 9   1 4 
-------------------------------------------------------------------------
  1Ab                +                 + +   +     +                     
  1Bb                                  + +               + +     +       
  1C               +                   +               + +               
  1D           +             + +       +                 +               
  1Ebc                 +                               + + +     +       
  1Fbc                       +         + +                 +     +       
  1Gbc                                 +       +       + +       +       
  2Ab                      +   +       +                 + +           + 
  2Bb                          +       +                 +               
  2C                   +               + +               +               
  3A                                   +               + +       +       
  3B                           +             +         + +               
  3Cbd           5   +                 +             5 5   5 4 4 4       
  3Dbc                 +     +         + + +         +                 + 
  3Ebc                       +         + +           :           +     + 
  3Fbc                 +     + +       +                 +       +       
  3Gbe                                 + + +       +                   + 
  3Hbc                 +     +     +                 +   + +     +       
  3Ibc                 :           +                   + + +     +       
  4Ab                          +         +   +     +                     
  4B                                   +                 +               
  5Ab                +       +         +                 +               
  5Bb                +                       +         + +           +   
  5Cbc               + +                               + +               
  5Dbc                       +       + + + + +                           
  6                                    +                 + +     +       
  7Ab          +             +         +                 + +           + 
  7B                                                   +     +       +      
  7Db                        + +       +                 +       +       
  7Eb                        +         +     +           +             + 
  8Ab                                  +               + + +     +       
  8B                         +         +                 +       +     + 
  8Cbc                 +     +         +       +         +       +       
  9A                         + +             +           +       +       
  9B                                     +   +           +               
  9C                         +         +                 + +     +       
 10b                         + +         + + +                           
 11Ab                                  + +   +     +                     
 11C                         +         +   +             +               
 11Eb                        +         +                 +       +       
 12A                                   + +                 +     +       
 12Bb                          +       + +                       +       
 13A                           +         +   +           +               
 13B                                       + +           + +             
 13Cb                        +                           +               
 14bc                  +     + +                 +                       
-----------------------------------------------------------------------------------------------------------------

^a Fragments detected with the DRB2 and A1 exon 3 probes (+); fragments for which data is equivocal (:).
^b Present in workshop animals.
^c New patterns.
^d DRB*3C was defined in the Fourth BoLA Workshop and a member of the same Brown Swiss family was included in the Fifth workshop. However, the fragments assigned to this haplotype were significantly different: assigned in both workshops (+); assigned in Fourth Workshop (4); assigned in Fifth Workshop (5).
^e This haplotype was called DRB*3C by Joosten et al. (1990). However, two different DRB*3C patterns have been defined.

Table 6.
DRB2-TM RFLP patterns.

                  Fragments (kb)
           --------------------
              TaqI       BglII 
           -----------  -------
                            1      
           5 5 4 4 3 1  0 9 7 5
           . . . . . .  . . . .
 Allele    9 4 2 0 7 6  3 0 5 9
---------------------------------------
   11      +            +      
   13          +        +      
   21      +              +    
   23          +          +    
   24            +        +    
   25              +      +    
   26                +    +    
   31      +                +  
   32        +              +  
   44            +            +
   46                +        +
---------------------------------------

Table 7.
DQA RFLP patterns.

                                   Restriction fragments (kb)a                       
           --------------------------------------------------------------------------
                                     TaqI                                  PvuII         
           -------------------------------------------------  -----------------------
                                                              1                      
           8 8 8 8 8 7 7 7 7 7 6 6 6 6 5 5 4 4 4 4 3 2 1 1 0  0 9 9 9 8 7 6 5 4 4 2 2
           . . . . . . . . . . . . . . . . . . . . . . . . .  . . . . . . . . . . . .
Allele     9 7 6 4 2 6 5 4 2 0 9 7 1 0 9 4 7 4 3 1 8 9 7 3 9  5 9 5 0 5 2 3 6 8 6 8 5
--------------------------------------------------------------------------------------

 1Ab                         +                                  +                    
 1Bb                                     2               +      +                    
 1C              +                                              +                    
 1Dbc                  +                                 +      +                    
 1Ebc        +                                                  +                    
 2b                                +                                                +
 3Ab           +                                                                    +
 3Bb         +                                                                      +
 3Cbc                                      +                                        +
 4B                                                      +                          +
 5b                                  3       3                3     3                
 6A                            3             3                3               3      
 6B                            3                     3                      3 3      
 7Ab                         +                     3 3 +        +         3          
 7B                                                3 3 2 +                3         +
 7Cb       +                                       3 3 2                  3         +
 7Db         +                                     3 3          +         3          
 7Fbc        +                                     3 3            3           3     +
 8b              +                                 3 3 2          3       3       +  
 9Ab                         2         3                   +  +       3              
 9Bb                 +                 3                      +       3              
10b              +                     3                      +     3                
11Ab                 +     3                                  +     3                
11Bb             +         3                                  +     3                
11Db                     +       3                            +     3                
11E                +         3                                +     3                
11Fbc                +                 3                      +     3                
12b              +                     3                            3   +            
13A                                            3   3              3             3    
13Bb                                             3 3              3             3    
14b          +                                                                    +  

^a Fragments detected with the W1 exon 2, W1 exon 3, DQA5 exon 2+3 and pII-alpha-5 cDNA probes (+); fragments detected with the W1 exon 2 probe (2), the TaqI 1.7 kb fragment hybridizes with the pII-alpha-5 cDNA probe and weakly with the DQA5 exon 2+3 probe; fragments detected with the W1 exon 3, DQA5 exon 2+3 and pII-alpha-5 cDNA probes (3).
^b Present in workshop animals.
^c New patterns.

 

Table 8.
DQB RFLP patterns.

                                 Restriction fragments (kb)a
           ------------------------------------------------------------------------
                            TaqI                                PvuII
           -------------------------------------  ---------------------------------
           2 1                                                                     
           0 0 9 8 8 7 7 7 5 5 4 4 3 3 3 3 1 1 1  9 8 8 7 7 6 5 5 4 4 3 2 2 1 1 1 1
           . . . . . . . . . . . . . . . . . . .  . . . . . . . . . . . . . . . . .
           0 2 3 6 3 5 4 0 8 4 5 2 7 6 2 0 5 4 1  2 3 0 6 2 9 5 3 1 0 4 6 0 8 7 7 3
Allele     0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0  0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0
------------------------------------------------------------------------------------
 1b                      3                                            2   3     3  
 2b                      3                                    +                    
 3Ab             3                                        +                        
 3Bb           3                                          +                        
 3Cbc        3                                            +                        
 4b                                  3                    +                        
 5b                                3       3   c      +             3     2 3      
 6A        3                               3   c    + +             3              
 6B        3                           3 3          +                              
 7Ab                     3 2 3                                3       2   3     3  
 7B                        2 3       3                      3 3       2            
 7C              3         2 3                            +   3                    
 7Eb           3           2 3                            3   3                    
 8b                        2 3                 3              3   3     2          
 9Ab         2                 3   3         2            + 2                     3
 9Bb         2         3       3                        3   2                      
10b          2                 3   3         2              2 +               3   3
11Ab         2     3               3                  +                   2 3      
11Cb         2                 3   3                      +               2 3      
11D          :                 3   3                  +                   2 3      
11Eb               3               3                  + 2                   3      
12b              2     3       3                  +       +                        
13A                              3                              +                  
13Bb                           3                                +                  
13C                  3                                          +                  
14b                                            3                  3     3          

^a Fragments detected with the Y1 exon 2, Y1 exon 3 and DQbeta-1 cDNA probes (+); fragments detected with the Y1 exon 2 and DQbeta-1 cDNA probes (2); fragments detected with the Y1 exon 3 and DQbeta-1 cDNA probes (3); fragments detected with the DQbeta-1 cDNA probe but not with the genomic probes (c); fragments for which data remains equivocal (:).
^b Present in workshop animals.
^c New patterns.

Table 9.
DQB-TM RFLP patterns.

               Fragments (kb)
           ----------------------
              TaqI        PvuII  
           ---------  -----------
           9 8 4 4 1  8 7 7 5 3 2
           . . . . .  . . . . . .
 Allele    3 3 5 3 8  0 5 1 6 3 5
 -------------------------------------
   11      +          +          
   12      +            +        
   13      +              +      
   14      +                +    
  213        +        +   +      
   33          +          +      
   42            +      +        
   43            +        +      
   44            +          +    
   45            +            +  
   46            +              +
   53              +      +      

Table 10.
Class IIa haplotypes sorted by DRB3 PCR-RFLP.

^a Class IIa haplotype (DH) reference numbers.
^b Number by themselves are DRBF types, numbers preceded by a U are UDF types.
^c Breeds: AY=Ayrshire; BF=British Friesian; BS=Brown Swiss; DB=Danish Black Pied; DR=Danish Red; HE=Hereford; HF=Holstein Friesian; JE=Jersey; LM=Limousin. Number of animals with haplotype shown in brackets. Results for 59 animals, WK5-47 was omitted because her haplotypes could not be defined.
^d Not determined.
^e Haplotype may express Dw1 and/or Dw8.
^f Cow, WK5-45, was assigned DRB3-MS*179 rather than DRB3-MS*175 (see results).
^g URB and MLI assigned different patterns to this animal.
^h WK5-59 was assigned a 6.4 kb TaqI fragment by both MLI and URB. Consequently, this animal apparently had the DRB*3F rather than the DRB*7D pattern. However, as the two animals were of the same breed and had the same class I serotype the data was not deemed conclusive enough to split this haplotype.
ⁱ Negative. Missing or inconsistent results due to weak hybridization.
^j Confirmed by segregation in this breed.
^k Occurred opposite a segregating haplotype in this breed.
^l Includes one class IIa homozygote.

 

Table 11.
Class IIa haplotypes sorted by serological specificities.

^a Class IIa haplotype (DH) reference numbers.
^b Specificities that appear to correspond to DR or DQ molecular motifs are indicated by fine and bold boxes, respectively. Dc12 which reacts with DH8A and DH22B is not shown because although it is probably a DQ specificity it is not associated with a molecular motif.
^c Number of animals with haplotype for which serological data was available.
^d Not determined.
^e Negative. Missing or inconsistent results due to weak hybridization.
^f Haplotype may express Dw1 and/or Dw8.
^g Supported by data from Fourth BoLA Workshop (Bernoco et al., 1991).
^h Supported by data from Davies et al., 1992a.

 

Table 12.
Segregating and inferred class I - Class IIa haplotypes.

^a Class I serotype and IEF defined splits (Davies et al., 1994).
^b Class IIa (DH) haplotypes as defined in Table 10. Breeds and number of cattle per breed are shown in brackets.
^c A15(A8)F1 and A15(A8)F2 have been combined because despite apparently having different IEF patterns there is no other evidence to support the conclusion that these are distinct haplotypes (Davies et al., 1994).
^d Confirmed by segregation in this breed.
^e Occurred opposite a segregating haplotype in this breed.
^f Statistically significant association (r=0.65).
^g Occurred opposite a haplotype showing a statistically significant association. Only shown in absence of more conclusive evidence.
^h Segregating or inferred in URB cattle of this breed in the Fourth BoLA Workshop (Bernoco et al., 1991).
ⁱ Found in a class IIa homozygote.

 

 Table 13.
Class IIb haplotypes (n=54).