                         SEQUENCE LISTING

<110>  WANG, Chunlin
       MINDRINOS, Michael N
       DAVIS, Mark M
       DAVIS, Ronald W
       KRISHNAKUMAR, Sujatha
 
<120>  HAPLOTYPING OF HLA LOCI WITH ULTRA-DEEP SHOTGUN SEQUENCING

<130>  STAN-759WO

<140>  PCT/US14/12585
<141>  2014-01-22

<150>  US 61/755,231
<151>  2013-01-22

<160>  84    

<170>  PatentIn version 3.5

<210>  1
<211>  22
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  1
tccccagacg ccgaggatgg cc                                                22


<210>  2
<211>  22
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  2
tccccagacc ccgaggatgg cc                                                22


<210>  3
<211>  25
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  3
ccttggggat tccccaactc cgcag                                             25


<210>  4
<211>  24
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  4
cacatcagag ccctgggcac tgtc                                              24


<210>  5
<211>  27
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  5
ttatgcctac acgaacacag acacatg                                           27


<210>  6
<211>  22
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  6
ctcctcagac gccgagatgc tg                                                22


<210>  7
<211>  22
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  7
ctcctcagac gccaagatgc tg                                                22


<210>  8
<211>  22
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  8
ctcctcagac accgagatgc tg                                                22


<210>  9
<211>  22
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  9
ctcctcagac gccgagatgc gg                                                22


<210>  10
<211>  22
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  10
ctcctcagac gccaagatgc gg                                                22


<210>  11
<211>  22
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  11
ctcctcagac accgagatgc gg                                                22


<210>  12
<211>  28
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  12
ccaacttgtg tcgggtcctt cttccagg                                          28


<210>  13
<211>  28
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  13
ccaacctatg tcgggtcctt cttccagg                                          28


<210>  14
<211>  24
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  14
cacatcagag ccctgggcac tgtc                                              24


<210>  15
<211>  26
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  15
catccctctt tctacagcaa ccccct                                            26


<210>  16
<211>  26
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  16
catccctctt tcgacagcaa ccccct                                            26


<210>  17
<211>  22
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  17
ctccccagac gccgagatgc gg                                                22


<210>  18
<211>  22
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  18
ctccccagag gccgagatgc gg                                                22


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

<220>
<223>  Synthetic nucleic acid sequence

<400>  19
gagtccaagg ggagaggtaa gtttcct                                           27


<210>  20
<211>  27
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  20
gagtccaagg ggagaggtaa gtgtcct                                           27


<210>  21
<211>  24
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  21
ctcatcagag ccctgggcac tgtt                                              24


<210>  22
<211>  24
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  22
ctatccctcc tcccacacca accg                                              24


<210>  23
<211>  31
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  23
gctcttaata caaactcttc agctagtaac t                                      31


<210>  24
<211>  31
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  24
gctcttaata caaactcttc agctagtaac t                                      31


<210>  25
<211>  31
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  25
gctcttaata gaaactcttc aactagtaac t                                      31


<210>  26
<211>  21
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  26
tcacaatggc ccttggtgtc t                                                 21


<210>  27
<211>  21
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  27
tcacaatggc ccctggtgtc t                                                 21


<210>  28
<211>  21
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  28
tcacaagggc ccttggtgtc t                                                 21


<210>  29
<211>  32
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  29
ccatcaggtc cgagctgtgt tgactaccac tt                                     32


<210>  30
<211>  32
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  30
ccatcaggtc cgagctgtgt tgactaccac ta                                     32


<210>  31
<211>  32
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  31
ccatcaggtc caagctgtgt tgactaccac ta                                     32


<210>  32
<211>  32
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  32
ccatcaggtc tgagctgtgt tgactaccac ta                                     32


<210>  33
<211>  32
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  33
ccatcaggtc cgagctgtgt tgactaccac tg                                     32


<210>  34
<211>  25
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  34
cctagggcag agcaggggga caagc                                             25


<210>  35
<211>  25
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  35
cctagggcag agcagggaga caagc                                             25


<210>  36
<211>  25
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  36
cctagggcag agcaggggga caagc                                             25


<210>  37
<211>  23
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  37
agtcttgatc ctcatagcag caa                                               23


<210>  38
<211>  28
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  38
atgcagcgga ccatgtgtca acttatgc                                          28


<210>  39
<211>  29
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  39
acattcccac ctttacagta tttcacagg                                         29


<210>  40
<211>  23
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  40
cgccccctcc ccgcagagaa tta                                               23


<210>  41
<211>  28
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  41
acctttcttg ctcctcctgt gcatgaag                                          28


<210>  42
<211>  23
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  42
ttcgtgtccc cacagcacgt ttc                                               23


<210>  43
<211>  23
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  43
ttcgtgtacc cgcagcacgt ttc                                               23


<210>  44
<211>  23
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  44
ttcgtgtccc cacagcatgt ttc                                               23


<210>  45
<211>  23
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  45
ttcttgtccc cccagcacgt ttc                                               23


<210>  46
<211>  23
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  46
tttgtgcccc cacagcacgt ttc                                               23


<210>  47
<211>  26
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  47
acctgttggc tgaagtccag agtgtc                                            26


<210>  48
<211>  26
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  48
acctcttggc tgaagtccag agtgtc                                            26


<210>  49
<211>  26
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  49
acctgttggc tggagtccag agtgtc                                            26


<210>  50
<211>  26
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  50
acctgttggc ggaagtccag agtgtc                                            26


<210>  51
<211>  26
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  51
acctgttggg tgaagtccag agtgcc                                            26


<210>  52
<211>  25
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  52
tgtgcgttgg ggacaaggca attct                                             25


<210>  53
<211>  25
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  53
acacatcgga atcacctagg gaact                                             25


<210>  54
<211>  25
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  54
gggtagaaga tggtagatga cagct                                             25


<210>  55
<211>  25
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  55
gtggggaaag gaccccggtc cctgc                                             25


<210>  56
<211>  25
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  56
acccttacac tctctgccat gacca                                             25


<210>  57
<211>  25
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  57
aaacagggcc cagccagggt ccctc                                             25


<210>  58
<211>  25
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  58
gtgctgtgca acagataatg actgc                                             25


<210>  59
<211>  25
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  59
aggaagtgaa aagtggtcaa gctga                                             25


<210>  60
<211>  25
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  60
tgccaccgtc accactatct acttg                                             25


<210>  61
<211>  25
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  61
taccatcagg aaggttcaaa ccatg                                             25


<210>  62
<211>  25
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  62
ggtagaagat ggtaggtgat ggctg                                             25


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

<220>
<223>  Synthetic nucleic acid sequence

<400>  63
gaaatggaca cagttcctga tcctg                                             25


<210>  64
<211>  25
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  64
tctccctgaa accgcttcta aatgc                                             25


<210>  65
<211>  25
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  65
gttgagggga agccttctct gtcac                                             25


<210>  66
<211>  25
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  66
ctccacaccc ctctccagac actga                                             25


<210>  67
<211>  25
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  67
tttatgtggg gaagggaagc cttta                                             25


<210>  68
<211>  25
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  68
agtgaatggg gaaggaatga gagac                                             25


<210>  69
<211>  62
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  69
ttgtcttgtg gacaacatct ttcctcctgt ggtcaacatc acatggctga gcaatgggca       60

gt                                                                      62


<210>  70
<211>  62
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  70
ctgtcttgtg gacaacatct ttcctcctgt ggtcaacatc acatggctga gcaatgggca       60

gt                                                                      62


<210>  71
<211>  62
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  71
ctgtcttgtg gacaacatct ttcctcctgt ggtcaacatc acatggctga gcaatgggca       60

cg                                                                      62


<210>  72
<211>  103
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  72
ccggcccggc cgcggggagc cccgcttcat cgcagtgggc tacgtggacg acacgcagtt       60

cgtgcggttc gacagcgacg ccgcgagcca gaggatggag ccg                        103


<210>  73
<211>  108
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  73
ccggcccggc cgcggggagc cccgcttcat cgcagtgggc tacgtggact ggacgacacg       60

cagttcgtgc ggttcgacag cgacgccgcg agccagagga tggagccg                   108


<210>  74
<211>  102
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  74
aggagccgcg ggcgccatgg atagagcagg aggggccgga gtattgggac cgggagacac       60

agatctccaa gaccaacaca cagacttacc gagagagcct gc                         102


<210>  75
<211>  110
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  75
aggagccgcg ggcgccatgg atagagcagg aggggccgga gtattgggac cgggagacac       60

agatctccaa gaccaacaca cagacttacc gagttaccga gagagcctgc                 110


<210>  76
<211>  108
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  76
gtgcgtggag tggctccgca gacacctgga gaacgggaag gagacgctgc agcgcgcggg       60

taccaggggc agtggggagc cttccccatc tcctataggt cgccgggg                   108


<210>  77
<211>  107
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  77
gtgcgtggag tggctccgca gacacctgga gaacgggaag gagacgctgc agcgcgcggg       60

taccggggca gtggggagcc ttccccatct cctataggtc gccgggg                    107


<210>  78
<211>  174
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  78
ggacctcctg gagcagaggc gggccgcggt ggacacctac tgcagacaca actacggggt       60

tggtgagagc ttcacagtgc agcggcgagg tgagcgcggc gcggggcggg gcctgagtcc      120

ctgtaagcgg agaatctgag tgtgtgtgtg tgtgtgtgtg tgtgtgtgtg taag            174


<210>  79
<211>  179
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  79
ggacttcctg gaagacaggc gggccgcggt ggacacctac tgcagacaca actacggggt       60

tggtgagagc ttcacagtgc agcggcgagg tgagcgcggc gcggggcggg gcctgagtcc      120

ctgtgagctg ggaatctgag tgtgtgtgtg tgtgtgtgtg tgtgtgtgtg tgtgtgtgt       179


<210>  80
<211>  179
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  80
ggacttcctg gaagacaggc gggccgcggt ggacacctac tgcagacaca actacggggt       60

tggtgagagc ttcacggtgc agcggcgagg tgagcgcggc gcggggcggg gcctgagtcc      120

ctgtgagctg ggaatctgag tgtgtgtgtg tgtgtgtgtg tgtgtgtgtg tgtgtgtgt       179


<210>  81
<211>  180
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  81
cgacagccga cgccgcgagt ccgaggatgg cgccccgggc gccatggata gagcaggagg       60

ggccggagta ttgggaccgg aacacacaga tctgcaagac caacacacag acttaccgag      120

agagcctgcg gaacctgcgc ggctactaca accagagcga ggccgggtct cacatcatcc      180


<210>  82
<211>  180
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  82
cgacagccga cgccgcgagt ccgaggatgg cgccccgggc gccatggata gagcaggagg       60

ggccggagta ttgggaccgg gagacacaga tctccaagac caacacacag acttaccgag      120

agagcctgcg gaacctgcgc ggctactaca accagagcga ggccgggtct cacaccctcc      180


<210>  83
<211>  448
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  83
atgcgggtca cggcgccccg aaccgtcctc ctgctgctct cgggagccct ggccctgacc       60

gagacctggg ccggctccca ctccatgagg tatttctaca ccgccatgtc ccggcccggc      120

cgcggggagc cccgcttcat cgcagtgggc tacgtggacg acacccagtt cgtgaggttc      180

gacagcgacg ccgcgagtcc gaggatggcg ccccgggcgc catggataga gcaggagggg      240

ccggagtatt gggaccggga gacacagatc tccaagacca acacacagac ttaccgagag      300

agcctgcgga acctgcgcgg ctactacaac cagagcgagg ccgggtctca caccctccag      360

aggatgtacg gctgcgacgt ggggccggac gggcgcctcc tccgcgggca tgaccagtcc      420

gcctacgacg gcaaggatta catcgccc                                         448


<210>  84
<211>  448
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic nucleic acid sequence

<400>  84
atgcgggtca tggcgccccg aaccgtcctc ctgctgctct cgggagccct ggccctgacc       60

gagacctggg ccggctccca ctccatgagg tatttctaca ccgccatgtc ccggcccggc      120

cgcggggagc cccgcttcat cgcagtgggc tacgtggacg acacccagtt cgtgaggttc      180

gacagcgacg ccgcgagtcc gaggatggcg ccccgggcgc catggataga gcaggagggg      240

ccggagtatt gggaccggga gacacagatc tccaagacca acacacagac ttaccgagag      300

agcctgcgga acctgcgcgg ctactacaac cagagcgagg ccgggtctca caccctccag      360

aggatgtaag gctgcgacgt ggggccggac gggcgcctcc tccgcgggca tgaccagtcc      420

gcctacgacg gcaaggatta catcgccc                                         448


