                                SEQUENCE LISTING

<110> Robinson, William
      Rahman, Amena
      King, Robert
      Garren, Hideki
      Bayhill Therapeutics, Inc.

<120> Methods of Selecting MS Patients for
  Antigen Specific Therapy
  

<130> 021686-002310PC

<140> WO PCT/US11/20345   
<141> 2011-01-06  

<150> US 61/293,544       
<151> 2010-01-08  

<160> 53

<170> FastSEQ for Windows Version 4.0

<210> 1
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin basic protein peptide MBP 1-20

<400> 1
Met Ala Ser Gln Lys Arg Pro Ser Gln Arg His Gly Ser Lys Tyr Leu
 1               5                  10                  15      
Ala Thr Ala Ser
            20  


<210> 2
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin basic protein peptide MBP 11-30

<400> 2
His Gly Ser Lys Tyr Leu Ala Thr Ala Ser Thr Met Asp His Ala Arg
 1               5                  10                  15      
His Gly Phe Leu
            20  


<210> 3
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin basic protein peptide MBP 21-40

<400> 3
Thr Met Asp His Ala Arg His Gly Phe Leu Pro Arg His Arg Asp Thr
 1               5                  10                  15      
Gly Ile Leu Asp
            20  


<210> 4
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin basic protein peptide MBP 31-50

<400> 4
Pro Arg His Arg Asp Thr Gly Ile Leu Asp Ser Ile Gly Arg Phe Phe
 1               5                  10                  15      
Gly Gly Asp Arg
            20  


<210> 5
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin basic protein peptide MBP 41-60

<400> 5
Ser Ile Gly Arg Phe Phe Gly Gly Asp Arg Gly Ala Pro Lys Arg Gly
 1               5                  10                  15      
Ser Gly Lys Val
            20  


<210> 6
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin basic protein peptide MBP 51-70

<400> 6
Gly Ala Pro Lys Arg Gly Ser Gly Lys Val Pro Trp Leu Lys Pro Gly
 1               5                  10                  15      
Arg Ser Pro Leu
            20  


<210> 7
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin basic protein peptide MBP 61-80

<400> 7
Pro Trp Leu Lys Pro Gly Arg Ser Pro Leu Pro Ser His Ala Arg Ser
 1               5                  10                  15      
Gln Pro Gly Leu
            20  


<210> 8
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin basic protein peptide MBP 71-90

<400> 8
Pro Ser His Ala Arg Ser Gln Pro Gly Leu Cys Asn Met Tyr Lys Asp
 1               5                  10                  15      
Ser His His Pro
            20  


<210> 9
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin basic protein peptide MBP 81-100

<400> 9
Cys Asn Met Tyr Lys Asp Ser His His Pro Ala Arg Thr Ala His Tyr
 1               5                  10                  15      
Gly Ser Leu Pro
            20  


<210> 10
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin basic protein peptide MBP 91-110

<400> 10
Ala Arg Thr Ala His Tyr Gly Ser Leu Pro Gln Lys Ser His Gly Arg
 1               5                  10                  15      
Thr Gln Asp Glu
            20  


<210> 11
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin basic protein peptide MBP 101-120

<400> 11
Gln Lys Ser His Gly Arg Thr Gln Asp Glu Asn Pro Val Val His Phe
 1               5                  10                  15      
Phe Lys Asn Ile
            20  


<210> 12
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin basic protein peptide MBP 110-131

<400> 12
Asn Pro Val Val His Phe Phe Lys Asn Ile Val Thr Pro Arg Thr Pro
 1               5                  10                  15      
Pro Pro Ser Gln
            20  


<210> 13
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin basic protein peptide MBP 120-141

<400> 13
Val Thr Pro Arg Thr Pro Pro Pro Ser Gln Gly Lys Gly Arg Gly Leu
 1               5                  10                  15      
Ser Leu Ser Arg
            20  


<210> 14
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin basic protein peptide MBP 130-151

<400> 14
Gly Lys Gly Arg Gly Leu Ser Leu Ser Arg Phe Ser Trp Gly Ala Glu
 1               5                  10                  15      
Gly Gln Arg Pro
            20  


<210> 15
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin basic protein peptide MBP 140-161

<400> 15
Phe Ser Trp Gly Ala Glu Gly Gln Arg Pro Gly Phe Gly Tyr Gly Gly
 1               5                  10                  15      
Arg Ala Ser Asp
            20  


<210> 16
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin basic protein peptide MBP 150-171

<400> 16
Gly Phe Gly Tyr Gly Gly Arg Ala Ser Asp Tyr Lys Ser Ala His Lys
 1               5                  10                  15      
Gly Phe Lys Gly
            20  


<210> 17
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin basic protein peptide MBP 160-181

<400> 17
Tyr Lys Ser Ala His Lys Gly Phe Lys Gly Val Asp Ala Gln Gly Thr
 1               5                  10                  15      
Leu Ser Lys Ile
            20  


<210> 18
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin basic protein peptide MBP 170-191

<400> 18
Val Asp Ala Gln Gly Thr Leu Ser Lys Ile Phe Lys Leu Gly Gly Arg
 1               5                  10                  15      
Asp Ser Arg Ser
            20  


<210> 19
<211> 17
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin basic protein peptide MBP 180-198

<400> 19
Phe Lys Leu Gly Gly Arg Asp Ser Arg Ser Gly Ser Pro Met Ala Arg
 1               5                  10                  15      
Arg
    

<210> 20
<211> 17
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin basic protein peptide MBP 83-99 RM

<400> 20
Glu Asn Pro Val Val His Phe Phe Lys Asn Ile Val Thr Pro Arg Thr
 1               5                  10                  15      
Pro
    

<210> 21
<211> 19
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin basic protein peptide MBP 111-129 RM

<400> 21
Leu Ser Arg Phe Ser Trp Gly Ala Glu Gly Gln Arg Pro Gly Phe Gly
 1               5                  10                  15      
Tyr Gly Gly
            

<210> 22
<211> 25
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin basic protein peptide MBP 131-155 RM

<400> 22
Ala Ser Asp Tyr Lys Ser Ala His Lys Gly Leu Lys Gly Val Asp Ala
 1               5                  10                  15      
Gln Gly Thr Leu Ser Lys Ile Phe Lys
            20                  25  


<210> 23
<211> 25
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin basic protein peptide MBP 146-170 RM

<400> 23
Ala Gln Gly Thr Leu Ser Lys Ile Phe Lys Leu Gly Gly Arg Asp Ser
 1               5                  10                  15      
Arg Ser Gly Ser Pro Met Ala Arg Arg
            20                  25  


<210> 24
<211> 17
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic HIV normalization peptide
      HIVgp41(597-613)/3D6

<400> 24
Gly Cys Ser Gly Lys Leu Ile Cys Thr Thr Ala Val Pro Trp Asn Ala
 1               5                  10                  15      
Ser
    

<210> 25
<211> 16
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic HIV normalization peptide
      HIVgp41(656-671)/2F5

<400> 25
Asn Glu Gln Glu Leu Leu Glu Leu Asp Lys Trp Ala Ser Leu Trp Asn
 1               5                  10                  15      


<210> 26
<211> 14
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic HIV normalization peptide
      HIVgp41(667-680)/4E10

<400> 26
Ala Ser Leu Trp Asn Trp Phe Asn Ile Thr Asn Trp Leu Trp
 1               5                  10                  


<210> 27
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin oligodendrocyte protein peptide MOG N term

<400> 27
Met Arg Gly Ser Gly Gln Phe Arg Val Ile Gly Pro Arg His Pro Ile
 1               5                  10                  15      
Arg Ala Leu Val
            20  


<210> 28
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin oligodendrocyte protein peptide MOG 21-40

<400> 28
Glu Leu Pro Cys Arg Ile Ser Pro Gly Lys Asn Ala Thr Gly Met Glu
 1               5                  10                  15      
Val Gly Trp Tyr
            20  


<210> 29
<211> 21
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated protein
      antigen element, MS autoantigen peptide, myelin
      oligodendrocyte protein peptide MOG 35-55 RM

<400> 29
Met Glu Val Gly Trp Tyr Arg Pro Pro Phe Ser Arg Val Val His Leu
 1               5                  10                  15      
Tyr Arg Asn Gly Lys
            20      


<210> 30
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin 71-90

<400> 30
Leu Leu Lys Asp Ala Ile Gly Glu Gly Lys Val Thr Leu Arg Ile Arg
 1               5                  10                  15      
Asn Val Arg Phe
            20  


<210> 31
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin oligodendrocyte protein peptide MOG 81-100

<400> 31
Val Thr Leu Arg Ile Arg Asn Val Arg Phe Ser Asp Glu Gly Gly Phe
 1               5                  10                  15      
Thr Cys Phe Phe
            20  


<210> 32
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated protein
      antigen element, MS autoantigen peptide, cyclic nucleotide
      phosphodiesterase peptide CNPase 343-362 RM

<220> 
<221> ACETYLATION    
<222> (1)...(1)
<223> N-acetyl-glutamic acid

<400> 32
Glu Val Gly Glu Leu Ser Arg Gly Lys Leu Tyr Ser Leu Gly Asn Gly
 1               5                  10                  15      
Arg Trp Met Leu
            20  


<210> 33
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated protein
      antigen element, MS autoantigen peptide, oligodendrocyte
      specific protein peptide OSP 101-120

<400> 33
Thr Val Leu Pro Cys Ile Arg Met Gly Gln Glu Pro Gly Val Ala Lys
 1               5                  10                  15      
Tyr Arg Arg Ala
            20  


<210> 34
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated protein
      antigen element, MS autoantigen peptide, oligodendrocyte
      specific protein peptide OSP 132-151

<400> 34
Leu Cys Ala Leu Val Ala Thr Ile Trp Phe Pro Val Cys Ala His Arg
 1               5                  10                  15      
Glu Thr Thr Ile
            20  


<210> 35
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated protein
      antigen element, MS autoantigen peptide, oligodendrocyte
      specific protein peptide OSP 182-201

<400> 35
Ala Gln Ala Phe Gly Glu Asn Val Ser Thr Thr Leu Arg Ala Leu Ala
 1               5                  10                  15      
Pro Arg Leu Met
            20  


<210> 36
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin-associated oligodendrocytic basic protein
      peptide MOBP 1-20

<400> 36
Met Ser Gln Lys Pro Ala Lys Glu Gly Pro Arg Leu Ser Lys Asn Gln
 1               5                  10                  15      
Lys Tyr Ser Glu
            20  


<210> 37
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin-associated oligodendrocytic basic protein
      peptide MOBP 31-50

<400> 37
Thr Phe Leu Asn Ser Lys Lys Glu Ile Val Asp Arg Lys Tyr Ser Ile
 1               5                  10                  15      
Cys Lys Ser Gly
            20  


<210> 38
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin-associated oligodendrocytic basic protein
      peptide MOBP 41-60

<400> 38
Asp Arg Lys Tyr Ser Ile Cys Lys Ser Gly Cys Phe Tyr Gln Lys Lys
 1               5                  10                  15      
Glu Glu Asp Trp
            20  


<210> 39
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin-associated oligodendrocytic basic protein
      peptide MOBP 61-80

<400> 39
Ile Cys Cys Ala Cys Gln Lys Thr Arg Thr Ser Arg Arg Ala Lys Pro
 1               5                  10                  15      
Pro Gln Arg Pro
            20  


<210> 40
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin-associated oligodendrocytic basic protein
      peptide MOBP 91-110

<400> 40
Val Arg Ala Pro Ala Lys Pro Arg Ser Pro Pro Arg Ser Glu Arg Gln
 1               5                  10                  15      
Pro Arg Ser Pro
            20  


<210> 41
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin-associated oligodendrocytic basic protein
      peptide MOBP 151-170

<400> 41
Arg Pro Pro Gln Lys Ser Lys Gln Gln Pro Arg Ser Ser Pro Leu Arg
 1               5                  10                  15      
Gly Pro Gly Ala
            20  


<210> 42
<211> 13
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      myelin-associated oligodendrocytic basic protein
      peptide MOBP 171-183

<400> 42
Ser Arg Gly Gly Ser Pro Val Lys Ala Ser Arg Phe Trp
 1               5                  10              


<210> 43
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      heat shock protein alpha-B-crystallin peptide
      abCrys 1-20

<400> 43
Met Asp Ile Ala Ile His His Pro Trp Ile Arg Arg Pro Phe Phe Pro
 1               5                  10                  15      
Phe His Ser Pro
            20  


<210> 44
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      heat shock protein alpha-B-crystallin peptide
      abCrys 11-30

<400> 44
Arg Arg Pro Phe Phe Pro Phe His Ser Pro Ser Arg Leu Phe Asp Gln
 1               5                  10                  15      
Phe Phe Gly Glu
            20  


<210> 45
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      heat shock protein alpha-B-crystallin peptide
      abCrys 41-60

<400> 45
Ser Thr Ser Leu Ser Pro Phe Tyr Leu Arg Pro Pro Ser Phe Leu Arg
 1               5                  10                  15      
Ala Pro Ser Trp
            20  


<210> 46
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      heat shock protein alpha-B-crystallin peptide
      abCrys 100-120

<400> 46
His Gly Lys His Glu Glu Arg Gln Asp Glu His Gly Phe Ile Ser Arg
 1               5                  10                  15      
Glu Phe His Arg
            20  


<210> 47
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      heat shock protein alpha-B-crystallin peptide
      abCrys 110-131

<400> 47
His Gly Phe Ile Ser Arg Glu Phe His Arg Lys Tyr Arg Ile Pro Ala
 1               5                  10                  15      
Asp Val Asp Pro
            20  


<210> 48
<211> 15
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      heat shock protein alpha-B-crystallin peptide
      abCrys 161-176

<400> 48
Ile Thr Arg Glu Glu Lys Pro Ala Val Thr Ala Ala Pro Lys Lys
 1               5                  10                  15  


<210> 49
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      proteolipid protein peptide PLP 131-150

<400> 49
Gln Ala His Ser Leu Glu Arg Val Cys His Cys Leu Gly Lys Trp Leu
 1               5                  10                  15      
Gly His Pro Asp
            20  


<210> 50
<211> 20
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      proteolipid protein peptide PLP 201-220

<400> 50
Cys Ala Asp Ala Arg Met Tyr Gly Val Leu Pro Trp Asn Ala Phe Pro
 1               5                  10                  15      
Gly Lys Val Cys
            20  


<210> 51
<211> 17
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic multiple sclerosis (MS) associated
      protein antigen element, MS autoantigen peptide,
      proteolipid protein peptide PLP 261-277

<400> 51
Ala Thr Tyr Asn Phe Ala Val Leu Lys Leu Met Gly Arg Gly Thr Lys
 1               5                  10                  15      
Phe
    

<210> 52
<211> 22
<212> DNA
<213> Artificial Sequence

<220> 
<223> synthetic immunoinhibitory sequence (IIS) with
      core hexamer and flanking sequences

<221> misc_feature   
<222> (11)...(12)
<223> n = any naturally occurring or synthetic nucleotide,
      except positions 11 and 12 cannot be cg

<400> 52
tgactgtgrr nnyyagagat ga                                          22

<210> 53
<211> 4
<212> PRT
<213> Artificial Sequence

<220> 
<223> synthetic dominant target of T and B cell
      autoimmune response, myelin basic protein MBP
      87-99 motif

<400> 53
His Phe Phe Lys
 1              

