                         SEQUENCE LISTING

<110>  PACT PHARMA, INC.
 
<120>  METHODS FOR IMPROVED T CELL RECEPTOR SEQUENCING

<130>  087520.0254 PCT

<150>  US 63/212,286
<151>  2021-06-17

<160>  40    

<170>  PatentIn version 3.5

<210>  1
<211>  57
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic


<220>
<221>  misc_feature
<222>  (57)..(57)
<223>  n is a, c, g, or t

<400>  1
aagcagtggt atcaacgcag agtacttttt tttttttttt tttttttttt tttttvn          57


<210>  2
<211>  65
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic


<220>
<221>  misc_feature
<222>  (26)..(33)
<223>  n is a, c, g, or t

<220>
<221>  misc_feature
<222>  (65)..(65)
<223>  n is a, c, g, or t

<400>  2
aagcagtggt atcaacgcag agtacnnnnn nnnttttttt tttttttttt tttttttttt       60

tttvn                                                                   65


<210>  3
<211>  30
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic


<220>
<221>  rRNA
<222>  (28)..(29)
<223>  rG

<220>
<221>  misc_feature
<222>  (30)..(30)
<223>  locked nucleic acid (LNA) guanylate

<400>  3
aagcagtggt atcaacgcag agtacatggg                                        30


<210>  4
<211>  30
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic


<220>
<221>  modified_base
<222>  (1)..(1)
<223>  5Bios

<220>
<221>  rRNA
<222>  (28)..(29)
<223>  rG

<220>
<221>  misc_feature
<222>  (30)..(30)
<223>  locked nucleic acid (LNA) guanylate

<400>  4
ragcagtggt atcaacgcag agtacatggg                                        30


<210>  5
<211>  46
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic


<220>
<221>  misc_feature
<222>  (36)..(43)
<223>  n is a, c, g, or t

<220>
<221>  rRNA
<222>  (44)..(45)
<223>  rG

<220>
<221>  misc_feature
<222>  (46)..(46)
<223>  locked nucleic acid (LNA) guanylate

<400>  5
agagacagaa gcagtggtat caacgcagag tacatnnnnn nnnggg                      46


<210>  6
<211>  23
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: sP239

<400>  6
aagcagtggt atcaacgcag agt                                               23


<210>  7
<211>  27
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: a0001

<400>  7
gccacagcac tgttgctctt gaagtcc                                           27


<210>  8
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: a0003

<400>  8
ccaccagctc agctccacgt g                                                 21


<210>  9
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: S0009

<400>  9
ctcgccacgt cggctatcct g                                                 21


<210>  10
<211>  23
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: a0017

<400>  10
gaggtcgctg tagcttgctc acg                                               23


<210>  11
<211>  73
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: sP259


<220>
<221>  misc_feature
<222>  (21)..(50)
<223>  n at positions 21 - 24 must be present; and n at positions 25-50 
       can be present or absent

<220>
<221>  misc_feature
<222>  (21)..(50)
<223>  n, if present, is a, c, g, or t

<400>  11
actcgcgagg gacgtgaagc nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn aagcagtggt       60

atcaacgcag agt                                                          73


<210>  12
<211>  24
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: TRAC_Primer2

<400>  12
gacaaaactg tgctagacat gagg                                              24


<210>  13
<211>  23
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: aP0042

<400>  13
cagggaagaa gcctgtggcc agg                                               23


<210>  14
<211>  99
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: S0010


<220>
<221>  misc_feature
<222>  (23)..(52)
<223>  n at positions 23 - 26 must be present; and n at positions 27-52 
       can be present or absent

<220>
<221>  misc_feature
<222>  (23)..(52)
<223>  n, if present, is a, c, g, or t

<400>  14
ccagggtttt cccagtcacg acnnnnnnnn nnnnnnnnnn nnnnnnnnnn nncacgtcgg       60

ctatcctgat cggatgaagc agtggtatca acgcagagt                              99


<210>  15
<211>  77
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: aP0043


<220>
<221>  misc_feature
<222>  (25)..(54)
<223>  n at positions 25 - 28 must be present; and n at positions 29-54 
       can be present or absent

<220>
<221>  misc_feature
<222>  (25)..(54)
<223>  n, if present, is a, c, g, or t

<400>  15
agcggataac aatttcacac aggannnnnn nnnnnnnnnn nnnnnnnnnn nnnncgctgt       60

agcttgctca cgtccag                                                      77


<210>  16
<211>  112
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: Reverse primer for TCR-alpha constant region


<220>
<221>  misc_feature
<222>  (29)..(30)
<223>  location of i5 barcode

<220>
<221>  misc_feature
<222>  (63)..(92)
<223>  n at positions 63 - 66 must be present; and n at positions 67-92 
       can be present or absent

<220>
<221>  misc_feature
<222>  (63)..(92)
<223>  n, if present, is a, c, g, or t

<400>  16
aatgatacgg cgaccaccga gatctacact cgtcggcagc gtcagatgtg tataagagac       60

agnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnacggcagg gtcagggttc tg              112


<210>  17
<211>  112
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: Reverse primer for TCR-beta constant region


<220>
<221>  misc_feature
<222>  (29)..(30)
<223>  location of i5 barcode

<220>
<221>  misc_feature
<222>  (63)..(92)
<223>  n at positions 63 - 66 must be present; and n at positions 67-92 
       can be present or absent

<220>
<221>  misc_feature
<222>  (63)..(92)
<223>  n, if present, is a, c, g, or t

<220>
<221>  misc_feature
<222>  (93)..(93)
<223>  n is a, c, g, or t

<400>  17
aatgatacgg cgaccaccga gatctacact cgtcggcagc gtcagatgtg tataagagac       60

agnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnagcgacc tcgggtggga ac              112


<210>  18
<211>  108
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: Forward primer for TCR-alpha and TCR-beta


<220>
<221>  misc_feature
<222>  (24)..(25)
<223>  location of i7 barcode

<220>
<221>  misc_feature
<222>  (59)..(88)
<223>  n at positions 59 - 62 must be present; and n at positions 63 - 
       88 can be present or absent

<220>
<221>  misc_feature
<222>  (59)..(88)
<223>  n, if present, is a, c, g, or t

<400>  18
caagcagaag acggcatacg agatgtctcg tgggctcgga gatgtgtata agagacagnn       60

nnnnnnnnnn nnnnnnnnnn nnnnnnnnac tcgcgaggga cgtgaagc                   108


<210>  19
<211>  110
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: Forward primer for NeoID


<220>
<221>  misc_feature
<222>  (24)..(25)
<223>  location of i7 barcode

<220>
<221>  misc_feature
<222>  (59)..(88)
<223>  n at positions 59 - 62 must be present; and n at positions 63 - 
       88 can be present or absent

<220>
<221>  misc_feature
<222>  (59)..(88)
<223>  n, if present, is a, c, g, or t

<400>  19
caagcagaag acggcatacg agatgtctcg tgggctcgga gatgtgtata agagacagnn       60

nnnnnnnnnn nnnnnnnnnn nnnnnnnncc agggttttcc cagtcacgac                 110


<210>  20
<211>  116
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: Reverse primer for NeoID


<220>
<221>  misc_feature
<222>  (29)..(30)
<223>  location of i5 barcode

<220>
<221>  misc_feature
<222>  (63)..(92)
<223>  n at positions 63 - 66 must be present; and n at positions 67-92 
       can be present or absent

<220>
<221>  misc_feature
<222>  (63)..(92)
<223>  n, if present, is a, c, g, or t

<400>  20
aatgatacgg cgaccaccga gatctacact cgtcggcagc gtcagatgtg tataagagac       60

agnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnagcggata acaatttcac acagga          116


<210>  21
<211>  53
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: S-oligo-dT


<220>
<221>  misc_feature
<222>  (53)..(53)
<223>  n is a, c, g, or t

<400>  21
acgagcatca gcagcatacg attttttttt tttttttttt tttttttttt tvn              53


<210>  22
<211>  67
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: W-oligo-dT


<220>
<221>  misc_feature
<222>  (28)..(35)
<223>  n is a, c, g, or t

<220>
<221>  misc_feature
<222>  (67)..(67)
<223>  n is a, c, g, or t

<400>  22
attctagagg ccgaggcggc cgacatgnnn nnnnnttttt tttttttttt tttttttttt       60

tttttvn                                                                 67


<210>  23
<211>  58
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: N-oligo-dT


<220>
<221>  misc_feature
<222>  (19)..(26)
<223>  n is a, c, g, or t

<220>
<221>  misc_feature
<222>  (58)..(58)
<223>  n is a, c, g, or t

<400>  23
actatctaga gcggccgcnn nnnnnntttt tttttttttt tttttttttt ttttttvn         58


<210>  24
<211>  73
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: B-oligo-dT


<220>
<221>  misc_feature
<222>  (34)..(41)
<223>  n is a, c, g, or t

<220>
<221>  misc_feature
<222>  (73)..(73)
<223>  n is a, c, g, or t

<400>  24
acactctttc cctacacgac gctcttccga tctnnnnnnn nttttttttt tttttttttt       60

tttttttttt tvn                                                          73


<210>  25
<211>  63
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: K-oligo-dT


<220>
<221>  misc_feature
<222>  (24)..(31)
<223>  n is a, c, g, or t

<220>
<221>  misc_feature
<222>  (63)..(63)
<223>  n is a, c, g, or t

<400>  25
tagaggccga ggcggccgac atgnnnnnnn nttttttttt tttttttttt tttttttttt       60

tvn                                                                     63


<210>  26
<211>  33
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: S-TSO


<220>
<221>  modified_base
<222>  (1)..(1)
<223>  5Bios

<220>
<221>  misc_feature
<222>  (20)..(27)
<223>  n is a, c, g, or t

<400>  26
rgagacagat tgcgcaatgn nnnnnnnrgr grg                                    33


<210>  27
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: S3-PCR1-forward primer

<400>  27
agagacagat tgcgcaatg                                                    19


<210>  28
<211>  39
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: S3-PCR2-forward primer

<400>  28
actcgcgagg gacgtgaagc agagacagat tgcgcaatg                              39


<210>  29
<211>  33
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: W-TSO


<220>
<221>  modified_base
<222>  (1)..(1)
<223>  5Bios

<400>  29
rttctagagg ccgaggcggc cgacatgrgr grg                                    33


<210>  30
<211>  27
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: W-PCR1-forward primer

<400>  30
attctagagg ccgaggcggc cgacatg                                           27


<210>  31
<211>  77
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: W-PCR2-forward primer


<220>
<221>  misc_feature
<222>  (21)..(50)
<223>  n at positions 21 - 24 must be present; and n at positions 25 - 
       50 can be present or absent

<220>
<221>  misc_feature
<222>  (21)..(50)
<223>  n, if present, is a, c, g, or t

<400>  31
actcgcgagg gacgtgaagc nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn attctagagg       60

ccgaggcggc cgacatg                                                      77


<210>  32
<211>  24
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: N-TSO


<220>
<221>  modified_base
<222>  (1)..(1)
<223>  5Bios

<400>  32
rctatctaga gcggccgcrg rgrg                                              24


<210>  33
<211>  18
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: N-PCR1-forward primer

<400>  33
actatctaga gcggccgc                                                     18


<210>  34
<211>  68
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: N-PCR2-forward primer


<220>
<221>  misc_feature
<222>  (21)..(50)
<223>  n at positions 21 - 24 must be present; and n at positions 25 - 
       50 can be present or absent

<220>
<221>  misc_feature
<222>  (21)..(50)
<223>  n, if present, is a, c, g, or t

<400>  34
actcgcgagg gacgtgaagc nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn actatctaga       60

gcggccgc                                                                68


<210>  35
<211>  39
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: B-TSO


<220>
<221>  modified_base
<222>  (1)..(1)
<223>  5Bios

<400>  35
rcactctttc cctacacgac gctcttccga tctrgrgrg                              39


<210>  36
<211>  33
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: B-PCR1-forward primer

<400>  36
acactctttc cctacacgac gctcttccga tct                                    33


<210>  37
<211>  53
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: B-PCR2-forward primer

<400>  37
actcgcgagg gacgtgaagc acactctttc cctacacgac gctcttccga tct              53


<210>  38
<211>  29
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: K-TSO


<220>
<221>  modified_base
<222>  (1)..(1)
<223>  5Bios

<400>  38
kagaggccga ggcggccgac atgrgrgrg                                         29


<210>  39
<211>  23
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: K-PCR1-forward primer

<400>  39
tagaggccga ggcggccgac atg                                               23


<210>  40
<211>  43
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic: K-PCR2-forward primer

<400>  40
actcgcgagg gacgtgaagc tagaggccga ggcggccgac atg                         43


