黑龙江地区人群HLA-A、B、DRB1高分辨等位基因及单体型多态性研究①
2016-02-24李鑫丁镌王鑫侯玲刘颖刘杰
李 鑫 丁 镌 王 鑫 侯 玲 刘 颖 刘 杰
(哈尔滨市血液中心,哈尔滨150056)
黑龙江地区人群HLA-A、B、DRB1高分辨等位基因及单体型多态性研究①
李鑫丁镌王鑫侯玲刘颖②刘杰②
(哈尔滨市血液中心,哈尔滨150056)
[摘要]目的:研究中国造血干细胞捐献者资料库黑龙江分库无关捐献者HLA-A、B、DRB1高分辨等位基因和单体型频率分布特征。方法:采用PCR-测序分型技术(SBT)对13 670名随机、无血缘关系、健康的中华骨髓库黑龙江分库造血干细胞捐献者进行HLA-A、B、DRB1高分辨基因分型,利用计数法和最大似然性原理方法分别计算HLA-A、B、DRB1等位基因及单体型频率。结果:共观察到286个HLA等位基因,其中频率>0.1的A、B、DRB1座位特异性分别为A* 02∶01、A*24∶02、A*11∶01、DR*07∶01、DR*09∶01、DR*15∶01。1 087条A-B单体型中,22条单体型的频率高于0.01,267条单体型呈现显著的正连锁不平衡(ALD>0,HF≥1.09×10-4,χ2>3.84),12条表现为强连锁不平衡(RLD>0.80);1 329条B-DRB1单体型中,19条单体型的频率高于0.01,357条单体型呈现显著的正连锁不平衡,18条表现为强连锁不平衡(RLD>0.80);4 428条A-B-DRB1单体型中,1 348条单体型有意义(频率≥1.09×10-4),17条单体型频率高于0.005。结论:获得黑龙江地区人群HLA-A、B、DRB1高分辨等位基因频率和单体型分布数据及相关遗传参数,等位基因和单体型的分布特征接近北方汉族人群,但具有其自身分布特征。
HLA系统是迄今所知人类基因中多态性最复杂的遗传系统,其等位基因频率及其连锁不平衡特点在不同种族、民族、地域存在明显差异。其多态性及分布差异是自然选择造成的,它保证了种群能产生对各种病原体特异的免疫应答,以维持群体的稳定性。因此,一个群体高分辨水平的HLA多态性的研究对组织器官移植寻找合适供者、群体遗传学、人类学和法医学至关重要。目前有关用骨髓库样本检测HLA基因多态性在中国人群中的报道尽管已有很多,但大部分或是小样本数据调查,或是低分辨分型数据的研究。我们采用SBT分型技术对2009年至2014年13 670例中国干细胞库黑龙江地区自愿捐献者进行HLA-A、B、DRB1高分辨分型,得到了较为可靠、完整的大样本HLA群体分型数据,统计分析了HLA等位基因频率、单体型频率以及连锁不平衡结果等相关遗传参数资料,现报道如下。
1材料与方法
1.1材料
1.1.1标本来源13 670份标本全部来自2009年至2014年黑龙江地区健康、无血缘关系、18~55周岁造血干细胞捐献者。
1.1.2主要试剂和仪器TIANamp Blood DNA Kit血液基因组DNA提取试剂(美国 Tiangen公司),PCR-SBT 基因分型试剂盒(德国ROSE公司),9 700 PCR 扩增仪,Bio-Rad PCR 扩增仪,3730xl DNA Analyzer测序仪。
1.2实验方法外周静脉血样(EDTA抗凝)5 ml,应用TIANamp Blood DNA Kit血液基因组DNA提取试剂(美国 Tiangen公司)提取基因组DNA,检测DNA浓度在40~100 ng/μl,OD260/280比值为1.6~1.8。采用PCR-SBT方法对HLA-A、B、DRB1 进行常规测序分型,操作步骤严格按试剂说明书进行。其中对属于HLAⅠ类基因的A、B位点进行第2、3和4外显子双向测序,而对于HLAⅡ类基因的DRB1进行第2外显子双向测序.对无法确定高分辨分型结果的样本,则选择序列特异性测序引物(Sequence specific sequencing primer,SSSP)对该样本再次测序,获得相应的高分辨结果。测序反应纯化后的产物置于3730xl DNA Analyzer测序仪上进行电泳分析,导出的结果采用序列分析软件ATF-loader进行分析。
1.3统计学处理
1.3.1等位基因频率和单体型频率采用直接计数法和最大数学预期值算法(expectation-maximization,EM)通过Arlequin3.1软件分别计算等位基因频率和单体型频率,同时对各基因位点作Hardy-Weinberg平衡检验[1]。
1.3.2最小群体数量的估计在由n个个体组成的群体中,某单体型只出现一次,该单体型频率HP=1/2n,但并非所有频率≥1/2n的单体型都是可靠的。由此在随机人群中,如果要求有P的把握在群体中检测到该单体型,所需要的群体最少数量为N,n= log(1-P)/log(1-2 hP+HP2)。如果把P设置在95%区间,则n=-1.3010/log(1-2 hP+HP2)[2]。
1.3.3连锁不平衡参数计算两座位HLA单体型连锁不平衡参数的计算采用标准表格法,包括绝对△值(ALD)、最大△值(mlD)和相对△值(RLD),计算公式:△ij=fij-fi×fj;△max=fij(△ij<0),△max=fi×(1-fj)(△ij≥0且fi 1.3.4频率分布的熵值(Entropy)计算在信息学理论中,频率分布的熵值是对包括多个子项的项目所含信息量的度量,具体到HLA领域,是对1个或1组紧密连锁的HLA基因座位多态性高低的度量[3],计算公式:E=-∑fi×log2fi(fi为HLA基因或单体型的频率)。 2结果 2.1HLA-A、B、DRB1等位基因频率13670份标本共检测到HLA-A、B、DRB1基因座位上286种HLA编码基因(见表1)。HLA-A、B、DRB1基因座分别检出等位基因80、136和70个基因。A、B、DRB1基因座HW吻合度的检验结果均为P>0.05,表明本研究来源群体的基因分布符合Hardy-Weinberg平衡定律。各座位上等位基因频率的分布情况显示,E(B)>E(DRB1)>E(A),表明HLA基因座位B、DRB1、A的多态性程度依次降低(见表2)。 2.2最小群体数量的估计在调查的群体样本中,有95%可信度的单体型频率≥1.09×10-4认为是可靠的,小于此数值的单体型频率,则需要在更大样本的群体资料中进行估计。 2.3HLA单体型频率分布情况见表3,观察到1087条HLA-A-B、1329条HLA-B-DRB1和4428条HLA-A-B-DRB1单体型,分别占单体型理论总数的9.99%(1 087/10 880)、13.96%(1 329/9 520)、0.58%(4 428/761 600)。4428条A-B-DRB1单体型中“可靠”的(频率≥1.09×10-4)有1 348条,占单体型总数的30.44%(1 348/4 428),但累计频率高达85.17%,其中频率>0.001有158条,频率最高的10条HLA-A-B、B-DRB1和A-B-DRB1单体型及其频率数值见表4。 2.4连锁不平衡参数本组资料仅选取频率≥1.09×10-4的有意义单体型计算连锁不平衡参数。结果显示,分别有267条HLA-A-B单体型和357条HLA-B-DRB1单体型呈现显著的正连锁不平衡(ALD>0,HF≥1.09×10-4,χ2>3.84),其中A*02∶53N-B*27∶04、A*25∶01-B*18∶01等12条A-B单体型和B*42∶01-DR*13∶02、B*27∶24-DR*04∶05等18条B-DRB1单体型表现为强连锁不平衡(RLD>0.80)。见表5。表1黑龙江地区HLA-A、B、DRB1高分辨等位基因频率 Tab.1High resolution allele frequencies of HLA-A,B,DRB1 in population from Heilongjiang region HLA-AGeneFrequecyHLA-BGeneFrequecyHLA-BGeneFrequecyHLA-DRB1GeneFrequecy02∶010.16550813∶020.09513527∶250.00021907∶010.14239224∶020.15032946∶010.07092251∶070.00021909∶010.14074611∶010.14312440∶010.05746253∶010.00021915∶010.13668630∶010.08953915∶010.05665756∶030.00021912∶020.07849333∶030.07867651∶010.05665739∶090.00018311∶010.05449902∶060.07183640∶060.05193944∶050.00018308∶030.05193902∶070.05775413∶010.04758655∶120.00014613∶020.04319701∶010.04890358∶010.04718415∶1980.00011003∶010.03939331∶010.04151444∶030.04019815∶680.00011004∶050.03924703∶010.03628452∶010.03675935∶040.00011015∶020.0339826∶010.02673748∶010.03511340∶110.00011014∶050.02717632∶010.01784954∶010.03120042∶020.00011012∶01∶01G0.02633502∶030.01554515∶110.02904251∶060.00011001∶010.01964268∶010.00716935∶01∶01G0.02699307∶100.00007304∶060.01938602∶050.00669340∶020.02509115∶100.00007313∶010.01806929∶010.0066207∶020.02275115∶190.00007316∶020.01572811∶020.00621815∶180.02110539∶310.00007310∶010.01547202∶100.00508457∶010.01799640∶780.00007304∶010.01269203∶020.00292615∶020.01682544∶270.00007304∶030.01225333∶010.00248738∶020.01667951∶220.00007314∶01∶01G0.01152223∶010.00234155∶020.01620351∶360.00007308∶020.00771824∶200.00226837∶010.01525273∶010.00007314∶030.00720624∶080.001539∶010.01422807∶480.00003711∶040.00636430∶040.00131735∶030.01393613∶160.00003714∶040.00625569∶010.00106167∶010.01075315∶090.00003704∶040.00592566∶010.00095150∶010.01027815∶150.00003701∶020.00303668∶020.00087851∶020.01013215∶1520.00003714∶070.00274324∶070.00076808∶010.00991215∶1780.00003704∶100.00259729∶020.00076815∶270.00888815∶340.00003704∶070.00234102∶53N0.00069544∶02∶01G0.00735215∶660.00003704∶080.00201224∶040.00058527∶040.00596215∶860.00003704∶020.00186511∶030.00054938∶010.00585227∶360.00003713∶120.00179226∶030.00051227∶050.00566927∶400.00003711∶060.0013930∶020.00043907∶05∶01G0.00563335∶110.00003715∶040.0013924∶030.00040214∶020.00398735∶120.00003708∶010.00102402∶480.00036615∶070.00369435∶140.00003714∶120.00087824∶100.00036640∶030.00354837∶020.00003716∶010.00084102∶090.00032918∶010.00292639∶040.00003708∶040.00080526∶020.00021915∶170.00281639∶060.00003713∶070.00076834∶010.00021956∶010.00245139∶240.00003713∶030.000695 (转下页) (续表1) HLA-AGeneFrequecyHLA-BGeneFrequecyHLA-BGeneFrequecyHLA-DRB1GeneFrequecy02∶110.00018335∶080.00230440∶1250.00003708∶090.00062225∶010.00018349∶010.00215840∶250.00003711∶030.00043902∶020.00014615∶050.00212140∶430.00003714∶020.00040202∶420.00014635∶020.00201240∶480.00003714∶180.00032968∶240.00014627∶070.00190240∶550.00003715∶060.00021902∶900.00011015∶250.00182940∶590.00003714∶060.00018324∶300.00011041∶010.00153640∶840.00003711∶280.00011030∶180.00011039∶050.00135346∶160.00003713∶500.00011074∶01∶01G0.00011045∶010.0012851∶040.00003715∶030.00011002∶170.00007315∶320.00124451∶090.00003703∶270.00007303∶080.00007359∶010.00106152∶110.00003711∶190.00007311∶060.00007348∶030.00102454∶160.00003713∶050.00007323∶260.00007355∶010.00102454∶170.00003714∶100.00007333∶080.00007314∶010.00095156∶150.00003714∶250.00007368∶380.00007315∶580.00084157∶020.00003714∶490.00007374∶030.00007340∶400.00080557∶030.00003703∶350.00003792∶890.00007355∶040.00080554∶160.00003704∶130.00003701∶030.00003735∶050.00076854∶170.00003711∶200.00003702∶040.00003751∶080.00073256∶150.00003711∶570.00003702∶1450.00003715∶460.00065857∶020.00003712∶030.00003702∶200.00003742∶010.00054957∶030.00003712∶050.00003702∶360.00003781∶01∶01G0.00054981∶010.00003712∶160.00003702∶930.00003715∶130.00051212∶200.00003711∶040.00003747∶010.00043913∶060.00003711∶190.00003755∶070.00043913∶130.00003711∶360.00003727∶020.00040213∶190.00003711∶390.00003781∶020.00040214∶220.00003711∶880.00003715∶120.00036614∶290.00003724∶1210.00003715∶350.00036615∶050.00003724∶170.00003715∶080.00032915∶310.00003724∶210.00003727∶240.00032915∶050.00003724∶280.00003715∶030.00029315∶310.00003724∶320.00003715∶290.00025624∶680.00003727∶060.00025626∶080.00003741∶020.00025626∶180.00003756∶040.00025626∶200.00003715∶210.00021929∶100.00003715∶380.00021932∶030.00003718∶020.00021974∶020.00003727∶030.000219 Note:HLA-A*74∶01∶01G includes 74∶01,74∶02;HLA-B*07∶05∶01G includes 07∶05,07∶06;HLA-B*35∶01∶01G includes 35∶01,35∶42;HLA-B*81∶01∶01G includes 81∶01,81∶02;HLA-B*44∶02∶01G includes 44∶02,44∶19N;HLA-DRB1*12∶01∶01G includes 12∶01,12∶06,12∶10,12∶17;HLA-DRB1*14∶01∶01G includes 14∶01,14∶54. 表2黑龙江地区HLA-A、B、DRB1基因频率分布 Tab.2Frequency distribution for the alleles of HLA-A,B,DRB1 Frequencyrange(×10-2)HLA-AnCumfre(%)HLA-BnCumfre(%)HLA-DRnCumfre(%)>10345.900341.981-101048.462789.411751.90.1-1124.57268.95155.37<0.1551.07831.64350.75Total8013670100EntropyE=3.74E=5.05E=4.19 表3黑龙江地区HLA-A-B、B-DRB1、A-B-DRB1单体型频率分布 Tab.3Haplotype frequency distribution of HLA-A,B,DRB1 in population from Heilongjiang region Frequencyrange(×10-4)HLA-A-BnCumfre(%)HLA-B-DRB1nCumfre(%)HLA-A-B-DRB1nCumfre(%)100-10002241.161938.38614.4410-10013542.4714640.3715235.6<1093016.37116421.25427049.96Notobserved97930819107571720Total108809520761600EntropyE=7.55E=7.84E=9.86 表5高度连锁不平衡的HLA-A-B、HLA-B-DRB1单体型 Tab.5Positive linkage disequilibrium of HLA-A-B,B-DRB1 haplotypes ABDRHF(×10-6)ALDmlDRLDχ202∶53N27∶040.0001100.0000940.0000941.0018.0125∶0118∶010.0001100.0001000.0001001.0030.5833∶0114∶020.0024510.0024410.0024770.9916537.0730∶0113∶020.0789720.0704540.0810210.8719337.8629∶0245∶010.0006580.0006340.0007440.85473.8230∶0414∶010.0008050.0008040.0009500.8514133.7429∶0107∶05∶01G0.0047170.0046800.0055960.8416254.6102∶4851∶010.0001830.0001830.0002190.8411419.5502∶4867∶010.0001830.0001830.0002190.8411419.5568∶0227∶030.0001830.0001830.0002190.844756.9202∶0550∶010.0055910.0055220.0066240.8312328.1534∶0115∶210.0001830.0001740.0002100.8398.2142∶0113∶020.0005490.0005250.0005251.00332.6427∶2404∶050.0003290.0003160.0003161.00220.2615∶2115∶020.0002190.0002190.0002191.0013635.8635∶0308∶010.0001100.0000950.0000951.0018.3640∶0208∶040.0001100.0001100.0001101.006848.3254∶0110∶010.0001100.0001070.0001071.0093.3915∶1312∶020.0005010.0004610.0004720.98156.8415∶3215∶040.0010970.0010950.0012420.8819017.4014∶0201∶020.002670.0026580.0030240.8816068.7437∶0108∶020.0001610.0001580.0001800.88249.0235∶0211∶040.0017550.0017420.0019990.876535.5415∶4615∶010.0005740.0004840.0005680.8582.5615∶1713∶020.0024060.0022840.0026940.851229.2681∶01∶01G15∶010.0004750.0004000.0004740.8467.5515∶2915∶010.0002190.0001840.0002210.8330.6508∶0103∶010.0082870.0078970.0095220.834590.6315∶3811∶010.0001830.0001710.0002070.8370.9113∶0207∶010.0808780.0673320.0815890.8311790.63 表4黑龙江地区10条最常见HLA-A-B、B-DRB1、A-B-DRB1单体型频率(×10-6) Tab.4Major 10 HLA-A-B,B-DRB1,A-B-DRB1 haplotypes and their haplotype frequencies(×10-6) HLA-A-BHFB-DRB1HFA-B-DRB1HFA*30∶01-B*13∶0278972B*13∶02-DR*07∶0180878A*30∶01-B*13∶02-DR*07∶0167302A*02∶07-B*46∶0140870B*46∶01-DR*09∶0134388A*02∶07-B*46∶01-DR*09∶0120284A*33∶03-B*58∶0136686B*13∶01-DR*12∶0230201A*33∶03-B*58∶01-DR*03∶0115901A*33∶03-B*44∶0324780B*52∶01-DR*15∶0221468A*02∶01-B*13∶01-DR*12∶0214796A*02∶01-B*13∶0118857B*40∶06-DR*09∶0120889A*33∶03-B*44∶03-DR*13∶0213491A*11∶01-B*40∶0116878B*58∶01-DR*03∶0120855A*33∶03-B*58∶01-DR*13∶0212696A*02∶01-B*15∶1116026B*15∶01-DR*15∶0117280A*02∶07-B*46∶01-DR*08∶039679A*24∶02-B*40∶0115502B*44∶03-DR*07∶0116892A*01∶01-B*57∶01-DR*07∶019612A*02∶01-B*15∶0115405B*44∶03-DR*13∶0215977A*01∶01-B*37∶01-DR*10∶018017A*24∶02-B*40∶0613122B*46∶01-DR*08∶0315954A*33∶03-B*44∶03-DR*07∶017483 3讨论