Application of a PCR sequencing method, based on DNA barcoding technique and DNA incomplete shearing strategy, in HLA genotyping
The invention provides a PCR sequencing method, wherein the combination of primer indexes, DNA incomplete shearing strategy and the second generation sequencing technique (Paired-End sequencing technique) can make the length of PCR products that can be sequenced by a sequencer longer than the maximum sequencing length of the sequencer while making full use of the characteristics of the second generation sequencing technique such as high throughput and low cost, thereby greatly broadening its applicable scope. In addition, the present invention also provides primer indexes for the PCR sequencing method and the use of the method in genotyping, particularly in HLA analysis, and also provides the PCR primers used, particularly the PCR primers for HLA-A, B, HLA-C and HLA-DQB1 gene.
1. A method for determining the nucleotide sequence of a nucleic acid of interest, comprising:
a) providing n samples, wherein n is an integer of ≥1;
b) optionally dividing the n samples into m groups, wherein m is an integer and n≥m≥1;
c) performing PCR amplification on the samples under conditions suitable for amplifying the nucleic acid of interest when templates from the samples are available, wherein a pair or multiple pairs of index primers are used for each sample, each pair of index primers consists of a forward index primer and a reverse index primer, and each index primer consists of a PCR primer and a primer index added to the 5′-end of the PCR primer, wherein the primer index of the forward index primer and the primer index of the reverse index primer in each pair of index primers are identical or different, and wherein the primer indexes in the pair of index primers used for different samples are different;
d) pooling products of the PCR amplification from each of the samples together;
e) subjecting the amplified products to incomplete shearing to obtain a mixture of intact un-sheared PCR products and partially sheared PCR products, and purifying and recovering said mixture of intact un-sheared PCR products and partially sheared PCR products;
f) constructing a PCR-free sequencing library based on the mixture of intact un-sheared PCR products and partially sheared PCR products recovered in e), wherein different library adapters are added to distinguish different PCR-Free sequencing libraries;
g) purifying and recovering DNA bands between the maximum read length and the maximum applicable DNA length of a sequencer using the second generation sequencing technique;
h) subjecting the recovered DNA mixture to the sequencer to obtain sequences of the sheared DNA; and
i) matching obtained sequencing data to corresponding samples based on a unique primer index for each sample, aligning obtained sequences of the sheared DNA against DNA reference sequences corresponding to the PCR products, and assembling a complete sequence of the nucleic acid of interest from the obtained sequences of the sheared DNA based on sequence overlap and linkage relationship, whereby a length of the complete sequence of the nucleic acid of interest exceeds a maximum read length of a sequencer used for said sequencing.
2. The method of claim 1 , wherein:
a) said PCR primers are PCR primers for amplification of HLA gene, HLA-A/B gene, Exons 2, 3 and 4 of HLA-A/B, or Exon 2 of HLA-DRB1;
b) said PCR primers are PCR primers for amplification of Exons 2, 3 and 4 of HLA-A/B as shown in SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 and 12;
c) said PCR primers are PCR primers for amplification of Exons 2, 3 and 4 of HLA-A/B as shown in SEQ ID NO: 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23 and 24;
d) said PCR primers are PCR primers for amplification of Exon 2 of HLA-DRB1 as shown in SEQ ID NO: 231, 232, 233, 234, 235, 236, 237 and 238;
e) said PCR primers are PCR primers for amplification of HLA gene, HLA-C gene, or Exons 2, 3 and/or 4 of HLA-C;
f) said PCR primers are PCR primers for amplification of Exons 2, 3 and/or 4 of HLA-C as shown in SEQ ID NO: 25, 26, 27, 28, 29 and 30;
g) said PCR primers are PCR primers for amplification of Exons 2, 3 and/or 4 of HLA-C as shown in SEQ ID NO: 31, 32, 33, 34, 35 and 36;
h) said PCR primers are PCR primers for amplification of HLA gene, HLA-DQB1 gene, or Exon 2 and/3 of HLA-DQB1 gene; or
i) said PCR primers are PCR primers for amplification of Exon 2 and/3 of HLA-DQB1 gene as shown in SEQ ID NO: 37, 38, 39 and 40.
3. The method of claim 1 , wherein said primer indexes are designed for:
a) PCR primers for amplification of a specific gene of HLA;
b) PCR primers for amplification of Exons 2, 3 and 4 of HLA-A/B and Exon 2 of HLA-DRB1;
c) PCR primers shown in SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 and 12;
d) PCR primers shown in SEQ ID NO: 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23 and 24; or
e) PCR primers shown in SEQ ID NO: 231, 232, 233, 234, 235, 236, 237 and 238.
4. The method of claim 1 , wherein at least 10 pairs of primer indexes selected from the group consisting of primer index Nos. PI-1 to PI-95 as set forth in the table below are used
Primer
Forward
Reverse
index No.
primer index
primer index
PI-1
SEQ ID NO: 41
SEQ ID NO: 42
PI-2
SEQ ID NO: 43
SEQ ID NO: 44
PI-3
SEQ ID NO: 45
SEQ ID NO: 46
PI-4
SEQ ID NO: 47
SEQ ID NO: 48
PI-5
SEQ ID NO: 49
SEQ ID NO: 50
PI-6
SEQ ID NO: 51
SEQ ID NO: 52
PI-7
SEQ ID NO: 53
SEQ ID NO: 54
PI-8
SEQ ID NO: 55
SEQ ID NO: 56
PI-9
SEQ ID NO: 57
SEQ ID NO: 58
PI-10
SEQ ID NO: 59
SEQ ID NO: 60
PI-11
SEQ ID NO: 61
SEQ ID NO: 62
PI-12
SEQ ID NO: 63
SEQ ID NO: 64
PI-13
SEQ ID NO: 65
SEQ ID NO: 66
PI-14
SEQ ID NO: 67
SEQ ID NO: 68
PI-15
SEQ ID NO: 69
SEQ ID NO: 70
PI-16
SEQ ID NO: 71
SEQ ID NO: 72
PI-17
SEQ ID NO: 73
SEQ ID NO: 74
PI-18
SEQ ID NO: 75
SEQ ID NO: 76
PI-19
SEQ ID NO: 77
SEQ ID NO: 78
PI-20
SEQ ID NO: 79
SEQ ID NO: 80
PI-21
SEQ ID NO: 81)
SEQ ID NO: 82
PI-22
SEQ ID NO: 83
SEQ ID NO: 84
PI-23
SEQ ID NO: 85
SEQ ID NO: 86
PI-24
SEP ID NO: 87
SEQ ID NO: 88
PI-25
SEQ ID NO: 89
SEQ ID NO: 90
PI-26
SEQ ID NO: 91
SEQ ID NO: 92
PI-27
SEQ ID NO: 93
SEQ ID NO: 94
PI-28
SEQ ID NO: 95
SEQ ID NO: 96
PI-29
SEQ ID NO: 97
SEQ ID NO: 98
PI-30
SEQ ID NO: 99
SEQ ID NO: 100
PI-31
SEQ ID NO: 101
SEQ ID NO: 102
PI-32
SEQ ID NO: 103
SEQ ID NO: 104
PI-33
SEQ ID NO: 105
SEQ ID NO: 106
PI-34
SEQ ID NO: 107
SEQ ID NO: 108
PI-35
SEQ ID NO: 109
SEQ ID NO: 110
PI-36
SEQ ID NO: 111
SEQ ID NO: 112
PI-37
SEQ ID NO: 113
SEQ ID NO: 114
PI-38
SEQ ID NO: 115
SEQ ID NO: 116
PI-39
SEQ ID NO: 117
SEQ ID NO: 118
PI-40
SEQ ID NO: 119
SEQ ID NO: 120
PI-41
SEQ ID NO: 121
SEQ ID NO: 122
PI-42
SEQ ID NO: 123
SEQ ID NO: 124
PI-43
SEQ ID NO: 125
SEQ ID NO: 126
PI-44
SEQ ID NO: 127
SEQ ID NO: 128
PI-45
SEQ ID NO: 129
SEQ ID NO: 130
PI-46
SEQ ID NO: 131
SEQ ID NO: 132
PI-47
SEQ ID NO: 133
SEQ ID NO: 134
PI-48
SEQ ID NO: 135
SEQ ID NO: 136
PI-49
SEQ ID NO: 137
SEQ ID NO: 138
PI-50
SEQ ID NO: 139
SEQ ID NO: 140
PI-51
SEQ ID NO: 141
SEQ ID NO: 142
PI-52
SEQ ID NO: 143
SEQ ID NO: 144
PI-53
SEQ ID NO: 145
SEQ ID NO: 146
PI-54
SEQ ID NO: 147
SEQ ID NO: 148
PI-55
SEQ ID NO: 149
SEQ ID NO: 150
PI-56
SEQ ID NO: 151
SEQ ID NO: 152
PI-57
SEQ ID NO: 153
SEQ ID NO: 154
PI-58
SEQ ID NO: 155
SEQ ID NO: 156
PI-59
SEQ ID NO: 157
SEQ ID NO: 158
PI-60
SEQ ID NO: 159
SEQ ID NO: 160
PI-61
SEQ ID NO: 161
SEQ ID NO: 162
PI-62
SEQ ID NO: 163
SEQ ID NO: 164
PI-63
SEQ ID NO: 165
SEQ ID NO: 166
PI-64
SEQ ID NO: 167
SEQ ID NO: 168
PI-65
SEQ ID NO: 169
SEQ ID NO: 170
PI-66
SEQ ID NO: 171
SEQ ID NO: 172
PI-67
SEQ ID NO: 173
SEQ ID NO: 174
PI-68
SEQ ID NO: 175
SEQ ID NO: 176
PI-69
SEQ ID NO: 177
SEQ ID NO: 178
PI-70
SEQ ID NO: 179
SEQ ID NO: 180
PI-71
SEQ ID NO: 181
SEQ ID NO: 182
PI-72
SEQ ID NO: 183
SEQ ID NO: 184
PI-73
SEQ ID NO: 185
SEQ ID NO: 186
PI-74
SEQ ID NO: 187
SEQ ID NO: 188
PI-75
SEQ ID NO: 189
SEQ ID NO: 190
PI-76
SEQ ID NO: 191
SEQ ID NO: 192
PI-77
SEQ ID NO: 193
SEQ ID NO: 194
PI-78
SEQ ID NO: 195
SEQ ID NO: 196
PI-79
SEQ ID NO: 197
SEQ ID NO: 198
PI-80
SEQ ID NO: 199
SEQ ID NO: 200
PI-81
SEQ ID NO: 201
SEQ ID NO: 202
PI-82
SEQ ID NO: 203
SEQ ID NO: 204
PI-83
SEQ ID NO: 205
SEQ ID NO: 206
PI-84
SEQ ID NO: 207
SEQ ID NO: 208
PI-85
SEQ ID NO: 209
SEQ ID NO: 210
PI-86
SEQ ID NO: 211
SEQ ID NO: 212
PI-87
SEQ ID NO: 213
SEQ ID NO: 214
PI-88
SEQ ID NO: 215
SEQ ID NO: 216
PI-89
SEQ ID NO: 217
SEQ ID NO: 218
PI-90
(SEQ ID NO: 219
SEQ ID NO: 220
PI-91
(SEQ ID NO: 221
SEQ ID NO: 222
PI-92
SEQ ID NO: 223
SEQ ID NO: 224
PI-93
SEQ ID NO: 225
SEQ ID NO: 226
PI-94
SEQ ID NO: 227
SEQ ID NO: 228
PI-95
SEQ ID NO: 229
SEQ ID NO: 230.
5. The method of claim 1 , wherein said DNA shearing is performed by chemical shearing and/or physical shearing.
6. The method of claim 5 , wherein said chemical shearing comprises enzymatic digestion.
7. The method of claim 5 , wherein said physical shearing comprises ultrasonic shearing or mechanical shearing.
8. The method of claim 1 , wherein, in step g), the DNA bands between the maximum read length and the maximum applicable DNA length of the second generation sequencer are purified and recovered by electrophoresis and gel slicing, or by magnetic beads.
9. The method of claim 1 , wherein the sample is from human.
10. The method of claim 9 , wherein the sample is human blood.
11. The method of claim 1 , wherein the sequencer uses Paired-End technique.
12. The method of claim 1 , wherein the sequencer is a Hiseq 2000 sequencer, an Illumina GA sequencer, an Illumina Solexa sequencer, or a Roche454 sequencer.
13. The method of claim 1 , wherein the DNA bands purified and recovered in step g) have a length ranging from 450 bp to 700 bp, and wherein the sequencer is an Illumina GA sequencer.
14. A method of determining HLA genotype of a sample, comprising:
a) sequencing a sample from a patient by the method of claim 2 ;
b) aligning the sequencing results against sequence data of Exons of HLA, Exons 2, 3 and 4 of HLA-A/B, Exons 2, 3 and/or Exon 4 of HLA-C, Exon 2 and/or 3 of HLA-DQB1 gene and/or Exon 2 of HLA-DRB1 in HLA database; and
c) determine the HLA genotype of the sample if the result of sequence alignment shows 100% match.
15. The method of claim 14 , wherein said primer indexes are designed for:
a) PCR primers for amplification of a specific gene of HLA;
b) PCR primers for amplification of Exons 2, 3 and 4 of HLA-A/B and Exon 2 of HLA-DRB1;
c) PCR primers shown in SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 and 12;
d) PCR primers shown in SEQ ID NO: 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23 and 24; or
e) PCR primers shown in SEQ ID NO: 231, 232, 233, 234, 235, 236, 237 and 238.
16. The method of claim 14 , wherein at least 10 pairs of primer indexes selected from the group consisting of primer index Nos. PI-1 to PI-95 as set forth in the table below are used
Primer
Forward
Reverse
index No.
primer index
primer index
PI-1
SEQ ID NO: 41
SEQ ID NO: 42
PI-2
SEQ ID NO: 43
SEQ ID NO: 44
PI-3
SEQ ID NO: 45
SEQ ID NO: 46
PI-4
SEQ ID NO: 47
SEQ ID NO: 48
PI-5
SEQ ID NO: 49
SEQ ID NO: 50
PI-6
SEQ ID NO: 51
SEQ ID NO: 52
PI-7
SEQ ID NO: 53
SEQ ID NO: 54
PI-8
SEQ ID NO: 55
SEQ ID NO: 56
PI-9
SEQ ID NO: 57
SEQ ID NO: 58
PI-10
SEQ ID NO: 59
SEQ ID NO: 60
PI-11
SEQ ID NO: 61
SEQ ID NO: 62
PI-12
SEQ ID NO: 63
SEQ ID NO: 64
PI-13
SEQ ID NO: 65
SEQ ID NO: 66
PI-14
SEQ ID NO: 67
SEQ ID NO: 68
PI-15
SEQ ID NO: 69
SEQ ID NO: 70
PI-16
SEQ ID NO: 71
SEQ ID NO: 72
PI-17
SEQ ID NO: 73
SEQ ID NO: 74
PI-18
SEQ ID NO: 75
SEQ ID NO: 76
PI-19
SEQ ID NO: 77
SEQ ID NO: 78
PI-20
SEQ ID NO: 79
SEQ ID NO: 80
PI-21
SEQ ID NO: 81)
SEQ ID NO: 82
PI-22
SEQ ID NO: 83
SEQ ID NO: 84
PI-23
SEQ ID NO: 85
SEQ ID NO: 86
PI-24
SEQ ID NO: 87
SEQ ID NO: 88
PI-25
SEQ ID NO: 89
SEQ ID NO: 90
PI-26
SEQ ID NO: 91
SEQ ID NO: 92
PI-27
SEQ ID NO: 93
SEQ ID NO: 94
PI-28
SEQ ID NO: 95
SEQ ID NO: 96
PI-29
SEQ ID NO: 97
SEQ ID NO: 98
PI-30
SEQ ID NO: 99
SEQ ID NO: 100
PI-31
SEQ ID NO: 101
SEQ ID NO: 102
PI-32
SEQ ID NO: 103
SEQ ID NO: 104
PI-33
SEQ ID NO: 105
SEQ ID NO: 106
PI-34
SEQ ID NO: 107
SEQ ID NO: 108
PI-35
SEQ ID NO: 109
SEQ ID NO: 110
PI-36
SEQ ID NO: 111
SEQ ID NO: 112
PI-37
SEQ ID NO: 113
SEQ ID NO: 114
PI-38
SEQ ID NO: 115
SEQ ID NO: 116
PI-39
SEQ ID NO: 117
SEQ ID NO: 118
PI-40
SEQ ID NO: 119
SEQ ID NO: 120
PI-41
SEQ ID NO: 121
SEQ ID NO: 122
PI-42
SEQ ID NO: 123
SEQ ID NO: 124
PI-43
SEQ ID NO: 125
SEQ ID NO: 126
PI-44
SEQ ID NO: 127
SEQ ID NO: 128
PI-45
SEQ ID NO: 129
SEQ ID NO: 130
PI-46
SEQ ID NO: 131
SEQ ID NO: 132
PI-47
SEQ ID NO: 133
SEQ ID NO: 134
PI-48
SEQ ID NO: 135
SEQ ID NO: 136
PI-49
SEQ ID NO: 137
SEQ ID NO: 138
PI-50
SEQ ID NO: 139
SEQ ID NO: 140
PI-51
SEQ ID NO: 141
SEQ ID NO: 142
PI-52
SEQ ID NO: 143
SEQ ID NO: 144
PI-53
SEQ ID NO: 145
SEQ ID NO: 146
PI-54
SEQ ID NO: 147
SEQ ID NO: 148
PI-55
SEQ ID NO: 149
SEQ ID NO: 150
PI-56
SEQ ID NO: 151
SEQ ID NO: 152
PI-57
SEQ ID NO: 153
SEQ ID NO: 154
PI-58
SEQ ID NO: 155
SEQ ID NO: 156
PI-59
SEQ ID NO: 157
SEQ ID NO: 158
PI-60
SEQ ID NO: 159
SEQ ID NO: 160
PI-61
SEQ ID NO: 161
SEQ ID NO: 162
PI-62
SEQ ID NO: 163
SEQ ID NO: 164
PI-63
SEQ ID NO: 165
SEQ ID NO: 166
PI-64
SEQ ID NO: 167
SEQ ID NO: 168
PI-65
SEQ ID NO: 169
SEQ ID NO: 170
PI-66
SEQ ID NO: 171
SEQ ID NO: 172
PI-67
SEQ ID NO: 173
SEQ ID NO: 174
PI-68
SEQ ID NO: 175
SEQ ID NO: 176
PI-69
SEQ ID NO: 177
SEQ ID NO: 178
PI-70
SEQ ID NO: 179
SEQ ID NO: 180
PI-71
SEQ ID NO: 181
SEQ ID NO: 182
PI-72
SEQ ID NO: 183
SEQ ID NO: 184
PI-73
SEQ ID NO: 185
SEQ ID NO: 186
PI-74
SEQ ID NO: 187
SEQ ID NO: 188
PI-75
SEQ ID NO: 189
SEQ ID NO: 190
PI-76
SEQ ID NO: 191
SEQ ID NO: 192
PI-77
SEQ ID NO: 193
SEQ ID NO: 194
PI-78
SEQ ID NO: 195
SEQ ID NO: 196
PI-79
SEQ ID NO: 197
SEQ ID NO: 198
PI-80
SEQ ID NO: 199
SEQ ID NO: 200
PI-81
SEQ ID NO: 201
SEQ ID NO: 202
PI-82
SEQ ID NO: 203
SEQ ID NO: 204
PI-83
SEQ ID NO: 205
SEQ ID NO: 206
PI-84
SEQ ID NO: 207
SEQ ID NO: 208
PI-85
SEQ ID NO: 209
SEQ ID NO: 210
PI-86
SEQ ID NO: 211
SEQ ID NO: 212
PI-87
SEQ ID NO: 213
SEQ ID NO: 214
PI-88
SEQ ID NO: 215
SEQ ID NO: 216
PI-89
SEQ ID NO: 217
SEQ ID NO: 218
PI-90
(SEQ ID NO: 219
SEQ ID NO: 220
PI-91
(SEQ ID NO: 221
SEQ ID NO: 222
PI-92
SEQ ID NO: 223
SEQ ID NO: 224
PI-93
SEQ ID NO: 225
SEQ ID NO: 226
PI-94
SEQ ID NO: 227
SEQ ID NO: 228
PI-95
SEQ ID NO: 229
SEQ ID NO: 230.
17. The method of claim 14 , wherein said DNA shearing is performed by chemical shearing and/or physical shearing, wherein said chemical shearing comprises enzymatic digestion, and wherein said physical shearing comprises ultrasonic shearing or mechanical shearing.
18. The method of claim 14 , wherein the sample is from human.
19. The method of claim 18 , wherein the sample is human blood.
20. The method of claim 14 , wherein the DNA bands purified and recovered for sequencing have a length ranging from 450 bp to 700 bp, and wherein the second generation sequencer is an Illumina GA sequencer.