                         SEQUENCE LISTING

<110>  CLINICAL GENOMICS PTY LTD
 
<120>  METHOD FOR METHYLATION ANALYSIS

<130>  P38974PCAU

<150>  2014902155
<151>  2014-06-05

<160>  86    

<170>  PatentIn version 3.5

<210>  1
<211>  95
<212>  DNA
<213>  human

<400>  1
gacgacgcac cctctccgtg tcccgctctg cgcccttctg cgcgccccgc tccctgtacc       60

ggagcagcga tccgggaggc ggccgagagg tgcgc                                  95


<210>  2
<211>  96
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  bisulfite converted and fully methylated version of diagnostic 
       IKZF1 amplicon

<400>  2
gacgacgtat ttttttcgtg tttcgttttg cgtttttttg cgcgtttcgc tttttgtatc       60

ggagtagcga ttcgggaggc ggtcgagagg tgcgcg                                 96


<210>  3
<211>  24
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to partially methylated diagnostic IKZF1 amplicon

<400>  3
gacgacgtat ttttttcgtg tttc                                              24


<210>  4
<211>  16
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to partially methylated diagnostic IKZF1 amplicon

<400>  4
gcgcacctct cgaccg                                                       16


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

<220>
<223>  probe directed to partially methylated diagnostic IKZF1 amplicon

<400>  5
tttgtatcgg agtagcgatt cgggagg                                           27


<210>  6
<211>  27
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe directed to partially methylated diagnostic IKZF1 amplicon

<400>  6
tttgtatcgg agtagcgatt tgggagg                                           27


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

<220>
<223>  probe directed to partially methylated diagnostic IKZF1 amplicon

<400>  7
tttgtatcgg agtagtgatt cgggagg                                           27


<210>  8
<211>  27
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe directed to partially methylated diagnostic IKZF1 amplicon

<400>  8
tttgtattgg agtagcgatt cgggagg                                           27


<210>  9
<211>  27
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe directed to partially methylated diagnostic IKZF1 amplicon

<400>  9
tttgtatcgg agtagtgatt tgggagg                                           27


<210>  10
<211>  27
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe directed to partially methylated diagnostic IKZF1 amplicon

<400>  10
tttgtattgg agtagcgatt tgggagg                                           27


<210>  11
<211>  27
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe directed to partially methylated diagnostic IKZF1 amplicon

<400>  11
tttgtattgg agtagtgatt cgggagg                                           27


<210>  12
<211>  27
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe directed to partially methylated diagnostic IKZF1 amplicon

<400>  12
tttgtattgg agtagtgatt tgggagg                                           27


<210>  13
<211>  29
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to BCAT1

<400>  13
gtttttttgt tgatgtaatt cgttaggtc                                         29


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

<220>
<223>  primer directed to BCAT1

<400>  14
caatacccga aacgacgacg                                                   20


<210>  15
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe directed to BCAT1

<400>  15
ttcgtcgcga gagggtcggt t                                                 21


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

<220>
<223>  primer directed to ACTB1

<400>  16
ggagtttttg ttttttggtt agttg                                             25


<210>  17
<211>  29
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to ACTB1

<400>  17
caaaataaaa tacaaaacaa acctaatcc                                         29


<210>  18
<211>  34
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe directed to ACTB1

<400>  18
atggaggttt agtggtaata taggttttgt ttgg                                   34


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

<220>
<223>  probe directed to partially methylated diagnostic IKZF1 amplicon


<220>
<221>  misc_feature
<222>  (8)..(8)
<223>  n is either inosine; an abasic spacer; or 
       6H,8H-3,4-dihydropyrimido[4,5-c][1,2]oxazin-7-one (or a 
       functional analogue thereof)

<220>
<221>  misc_feature
<222>  (16)..(16)
<223>  n is either inosine; an abasic spacer; or 
       6H,8H-3,4-dihydropyrimido[4,5-c][1,2]oxazin-7-one (or a 
       functional analogue thereof)

<220>
<221>  misc_feature
<222>  (21)..(21)
<223>  n is either inosine; an abasic spacer; or 
       6H,8H-3,4-dihydropyrimido[4,5-c][1,2]oxazin-7-one (or a 
       functional analogue thereof)

<400>  19
tttgtatngg agtagngatt ngggagg                                           27


<210>  20
<211>  29
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe directed to partially methylated diagnostic IKZF1 amplicon


<220>
<221>  misc_feature
<222>  (6)..(6)
<223>  n is either inosine; an abasic spacer; or 
       N6-methoxy-2,6-diaminopurine (or a functional analogue thereof)

<220>
<221>  misc_feature
<222>  (11)..(11)
<223>  n is either inosine; an abasic spacer; or 
       N6-methoxy-2,6-diaminopurine (or a functional analogue thereof)

<220>
<221>  misc_feature
<222>  (19)..(19)
<223>  n is either inosine; an abasic spacer; or 
       N6-methoxy-2,6-diaminopurine (or a functional analogue thereof)

<400>  20
ctcccnaatc nctactccna tacaaaaag                                         29


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

<220>
<223>  probe directed to partially methylated diagnostic IKZF1 amplicon


<220>
<221>  misc_feature
<222>  (6)..(6)
<223>  n is either inosine; an abasic spacer; or 
       6H,8H-3,4-dihydropyrimido[4,5-c][1,2]oxazin-7-one (or a 
       functional analogue thereof)

<220>
<221>  misc_feature
<222>  (11)..(11)
<223>  n is either inosine; an abasic spacer; or 
       6H,8H-3,4-dihydropyrimido[4,5-c][1,2]oxazin-7-one (or a 
       functional analogue thereof)

<220>
<221>  misc_feature
<222>  (19)..(19)
<223>  n is either inosine; an abasic spacer; or 
       6H,8H-3,4-dihydropyrimido[4,5-c][1,2]oxazin-7-one (or a 
       functional analogue thereof)

<400>  21
tttttnggat ngttgtttng gtataggg                                          28


<210>  22
<211>  28
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe directed to partially methylated diagnostic IKZF1 amplicon


<220>
<221>  misc_feature
<222>  (10)..(10)
<223>  n is either inosine; an abasic spacer; or 
       N6-methoxy-2,6-diaminopurine (or a functional analogue thereof)

<220>
<221>  misc_feature
<222>  (18)..(18)
<223>  n is either inosine; an abasic spacer; or 
       N6-methoxy-2,6-diaminopurine (or a functional analogue thereof)

<220>
<221>  misc_feature
<222>  (23)..(23)
<223>  n is either inosine; an abasic spacer; or 
       N6-methoxy-2,6-diaminopurine (or a functional analogue thereof)

<400>  22
ccctataccn aaacaacnat ccnaaaaa                                          28


<210>  23
<211>  29
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe for detection of the sense strand of SEQ ID NO:2

<400>  23
ctcccgaatc gctactccga tacaaaaag                                         29


<210>  24
<211>  29
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe for detection of the sense strand of SEQ ID NO:2

<400>  24
ctcccaaatc gctactccga tacaaaaag                                         29


<210>  25
<211>  29
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe for detection of the sense strand of SEQ ID NO:2

<400>  25
ctcccgaatc actactccga tacaaaaag                                         29


<210>  26
<211>  29
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe for detection of the sense strand of SEQ ID NO:2

<400>  26
ctcccgaatc gctactccaa tacaaaaag                                         29


<210>  27
<211>  29
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe for detection of the sense strand of SEQ ID NO:2

<400>  27
ctcccaaatc actactccga tacaaaaag                                         29


<210>  28
<211>  29
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe for detection of the sense strand of SEQ ID NO:2

<400>  28
ctcccaaatc gctactccaa tacaaaaag                                         29


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

<220>
<223>  probe for detection of the sense strand of SEQ ID NO:2

<400>  29
ctcccgaatc actactccaa tacaaaaag                                         29


<210>  30
<211>  29
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe for detection of the sense strand of SEQ ID NO:2

<400>  30
ctcccaaatc actactccaa tacaaaaag                                         29


<210>  31
<211>  28
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe for detection of the bisulfite converted version of the 
       complementary strand of SEQ ID NO:1

<400>  31
tttttcggat cgttgtttcg gtataggg                                          28


<210>  32
<211>  28
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe for detection of the bisulfite converted version of the 
       complementary strand of SEQ ID NO:1

<400>  32
tttttcggat cgttgttttg gtataggg                                          28


<210>  33
<211>  28
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe for detection of the bisulfite converted version of the 
       complementary strand of SEQ ID NO:1

<400>  33
tttttcggat tgttgtttcg gtataggg                                          28


<210>  34
<211>  28
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe for detection of the bisulfite converted version of the 
       complementary strand of SEQ ID NO:1

<400>  34
ttttttggat cgttgtttcg gtataggg                                          28


<210>  35
<211>  28
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe for detection of the bisulfite converted version of the 
       complementary strand of SEQ ID NO:1

<400>  35
tttttcggat tgttgttttg gtataggg                                          28


<210>  36
<211>  28
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe for detection of the bisulfite converted version of the 
       complementary strand of SEQ ID NO:1

<400>  36
ttttttggat cgttgttttg gtataggg                                          28


<210>  37
<211>  28
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe for detection of the bisulfite converted version of the 
       complementary strand of SEQ ID NO:1

<400>  37
ttttttggat tgttgtttcg gtataggg                                          28


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

<220>
<223>  probe for detection of the bisulfite converted version of the 
       complementary strand of SEQ ID NO:1

<400>  38
ttttttggat tgttgttttg gtataggg                                          28


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

<220>
<223>  probe for detection of the bisulfite converted version of the 
       complementary strand of SEQ ID NO:1

<400>  39
ccctataccg aaacaacgat ccgaaaaa                                          28


<210>  40
<211>  28
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe for detection of the bisulfite converted version of the 
       complementary strand of SEQ ID NO:1

<400>  40
ccctatacca aaacaacgat ccgaaaaa                                          28


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

<220>
<223>  probe for detection of the bisulfite converted version of the 
       complementary strand of SEQ ID NO:1

<400>  41
ccctataccg aaacaacaat ccgaaaaa                                          28


<210>  42
<211>  28
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe for detection of the bisulfite converted version of the 
       complementary strand of SEQ ID NO:1

<400>  42
ccctataccg aaacaacgat ccaaaaaa                                          28


<210>  43
<211>  28
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe for detection of the bisulfite converted version of the 
       complementary strand of SEQ ID NO:1

<400>  43
ccctatacca aaacaacaat ccgaaaaa                                          28


<210>  44
<211>  28
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe for detection of the bisulfite converted version of the 
       complementary strand of SEQ ID NO:1

<400>  44
ccctatacca aaacaacgat ccaaaaaa                                          28


<210>  45
<211>  28
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe for detection of the bisulfite converted version of the 
       complementary strand of SEQ ID NO:1

<400>  45
ccctataccg aaacaacaat ccaaaaaa                                          28


<210>  46
<211>  28
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe for detection of the bisulfite converted version of the 
       complementary strand of SEQ ID NO:1

<400>  46
ccctatacca aaacaacaat ccaaaaaa                                          28


<210>  47
<211>  16
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe for detection of the bisulfite converted version of the 
       complementary strand of SEQ ID NO:1

<400>  47
cgcgtatttt tcggtc                                                       16


<210>  48
<211>  16
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  probe for detection of the bisulfite converted version of the 
       complementary strand of SEQ ID NO:1

<400>  48
cgacgcaccc tctccg                                                       16


<210>  49
<211>  24
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to partially methylated IKZF1

<400>  49
gatgacgtat ttttttcgtg tttc                                              24


<210>  50
<211>  24
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to partially methylated IKZF1

<400>  50
gacgatgtat ttttttcgtg tttc                                              24


<210>  51
<211>  24
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to partially methylated IKZF1

<400>  51
gacgacgtat tttttttgtg tttc                                              24


<210>  52
<211>  24
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to partially methylated IKZF1

<400>  52
gacgacgtat ttttttcgtg tttt                                              24


<210>  53
<211>  24
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to partially methylated IKZF1

<400>  53
gatgatgtat ttttttcgtg tttc                                              24


<210>  54
<211>  24
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to partially methylated IKZF1

<400>  54
gacgatgtat tttttttgtg tttc                                              24


<210>  55
<211>  24
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to partially methylated IKZF1

<400>  55
gacgacgtat tttttttgtg tttt                                              24


<210>  56
<211>  24
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to partially methylated IKZF1

<400>  56
gatgacgtat tttttttgtg tttc                                              24


<210>  57
<211>  24
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to partially methylated IKZF1

<400>  57
gacgatgtat ttttttcgtg tttt                                              24


<210>  58
<211>  24
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to partially methylated IKZF1

<400>  58
gatgacgtat ttttttcgtg tttt                                              24


<210>  59
<211>  24
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to partially methylated IKZF1

<400>  59
gatgatgtat tttttttgtg tttc                                              24


<210>  60
<211>  24
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to partially methylated IKZF1

<400>  60
gatgatgtat ttttttcgtg tttt                                              24


<210>  61
<211>  24
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to partially methylated IKZF1

<400>  61
gatgacgtat tttttttgtg tttt                                              24


<210>  62
<211>  24
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to partially methylated IKZF1

<400>  62
gacgatgtat tttttttgtg tttt                                              24


<210>  63
<211>  16
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to partially methylated IKZF1

<400>  63
acgcacctct cgaccg                                                       16


<210>  64
<211>  16
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to partially methylated IKZF1

<400>  64
gcacacctct cgaccg                                                       16


<210>  65
<211>  16
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to partially methylated IKZF1

<400>  65
gcgcacctct caaccg                                                       16


<210>  66
<211>  16
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to partially methylated IKZF1

<400>  66
gcgcacctct cgacca                                                       16


<210>  67
<211>  16
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to partially methylated IKZF1

<400>  67
acacacctct cgaccg                                                       16


<210>  68
<211>  16
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to partially methylated IKZF1

<400>  68
gcacacctct caaccg                                                       16


<210>  69
<211>  16
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to partially methylated IKZF1

<400>  69
gcacacctct caaccg                                                       16


<210>  70
<211>  16
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to partially methylated IKZF1

<400>  70
acgcacctct caaccg                                                       16


<210>  71
<211>  16
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to partially methylated IKZF1

<400>  71
acgcacctct cgacca                                                       16


<210>  72
<211>  16
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to partially methylated IKZF1

<400>  72
gcacacctct cgacca                                                       16


<210>  73
<211>  16
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to partially methylated IKZF1

<400>  73
acacacctct caaccg                                                       16


<210>  74
<211>  16
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to partially methylated IKZF1

<400>  74
acacacctct cgacca                                                       16


<210>  75
<211>  16
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to partially methylated IKZF1

<400>  75
acgcacctct caacca                                                       16


<210>  76
<211>  16
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer directed to partially methylated IKZF1

<400>  76
gcacacctct caacca                                                       16


<210>  77
<211>  24
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  fully unmethylated primer

<400>  77
gatgatgtat tttttttgtg tttt                                              24


<210>  78
<211>  16
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  fully unmethylated primer

<400>  78
acacacctct caacca                                                       16


<210>  79
<211>  27
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  IKZF1


<220>
<221>  misc_feature
<222>  (8)..(8)
<223>  n represents a methylated cytosine

<220>
<221>  misc_feature
<222>  (16)..(16)
<223>  n represents a methylated cytosine

<220>
<221>  misc_feature
<222>  (21)..(21)
<223>  n represents a methylated cytosine

<400>  79
cctgtacngg agcagngatc ngggagg                                           27


<210>  80
<211>  27
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  IKZF1


<220>
<221>  misc_feature
<222>  (16)..(16)
<223>  n represents a methylated cytosine

<220>
<221>  misc_feature
<222>  (21)..(21)
<223>  n represents a methylated cytosine

<400>  80
cctgtaccgg agcagngatc ngggagg                                           27


<210>  81
<211>  27
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  IKZF1


<220>
<221>  misc_feature
<222>  (8)..(8)
<223>  n represents a methylated cytosine

<220>
<221>  misc_feature
<222>  (21)..(21)
<223>  n represents a methylated cytosine

<400>  81
cctgtacngg agcagcgatc ngggagg                                           27


<210>  82
<211>  27
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  IKZF1


<220>
<221>  misc_feature
<222>  (8)..(8)
<223>  n represents a methylated cytosine

<220>
<221>  misc_feature
<222>  (16)..(16)
<223>  n represents a methylated cytosine

<400>  82
cctgtacngg agcagngatc cgggagg                                           27


<210>  83
<211>  27
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  IKZF1


<220>
<221>  misc_feature
<222>  (21)..(21)
<223>  n represents a methylated cytosine

<400>  83
cctgtaccgg agcagcgatc ngggagg                                           27


<210>  84
<211>  27
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  IKZF1


<220>
<221>  misc_feature
<222>  (16)..(16)
<223>  n represents a methylated cytosine

<400>  84
cctgtaccgg agcagngatc cgggagg                                           27


<210>  85
<211>  27
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  IKZF1


<220>
<221>  misc_feature
<222>  (8)..(8)
<223>  n represents a methylated cytosine

<400>  85
cctgtacngg agcagcgatc cgggagg                                           27


<210>  86
<211>  27
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  IKZF1

<400>  86
cctgtaccgg agcagcgatc cgggagg                                           27


