CN116218976A - 一种检测人类胚胎染色体罗氏易位的引物组合以及方法 - Google Patents
一种检测人类胚胎染色体罗氏易位的引物组合以及方法 Download PDFInfo
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Abstract
本发明公开了检测人类胚胎染色体罗氏易位的引物组合及方法,检测人类胚胎染色体罗氏易位的引物组合,包括第13号染色体SNP位点的引物组合、第14号染色体SNP位点的引物组合、第15号染色体SNP位点的引物组合、第21号染色体SNP位点的引物组合和第22号染色体SNP位点的引物组合中的一组或两组以上。本发明的方法实用、简便、通用性强,并且结合了高通量测序技术,有着成本低、灵敏度高、特异性强、准确性高的优点。
Description
技术领域
本发明涉及基因检测领域,具体涉及一种检测人类胚胎染色体罗氏易位的引物组合以及方法。
背景技术
罗氏易位(Robertsoniantranslocation,ROB)是人类常见的一种染色体结构异常,当人类的两个近端着丝粒染色体(13、14、15、21、22号染色体)在着丝处或其附近断裂后融合成为1个染色体,导致染色体数减少,长臂数不变,短臂数减少两条,这种易位就被称为罗氏易位。在一般人群中,罗氏易位的发生率为1/1000(Therman E,Susman B,DennistonC.The nonrandom participation of human acrocentric chromosomes inRobertsonian translocations[J].Annals ofHuman Genetics,2012,53(1):49-65),罗氏易位携带者只有45条染色体,其携带者不仅流产、不育发生率高,也容易生育唐氏综合征及染色体不平衡易位的患儿,罗氏易位携带者在临床表现上除反复流产和胚胎停止发育外,还表现为原发或继发性闭经、不孕、第二性征发育差、智力低下、无精子症等。(赵晓,孙晓纲,沈国民,等.中国人群罗伯逊易位携带者的核型分布与生育情况分析[J].中国妇幼保健,2011,026(011):1672-1676)。理论上非同源罗氏易位携带者只有1/3的可能产生染色体正常(或)平衡易位的后代。目前发现罗氏易位共有15种,其中包含10种非同源的罗氏易位,和5种同源罗氏易位。同源的罗氏易位无法生出正常后代(形成的胚胎为单体或三体);而非同源罗氏易位中以13和14染色体易位最为常见,约为75%以上,14和21染色体次之。罗氏易位携带者的生殖细胞在第1次减数分裂中正常的二价体结构将被三价体(非同源罗氏易位)或单价体(同源罗氏易位)取代,进而产生多种类型不同染色体组成的配子,理论上非同源罗氏易位可产生6种配子,1种正常配子,1种平衡易位配子,其余均为不平衡配子;而同源罗氏易位携带者几乎没有正常配子形成。
罗氏易位的携带者因没有重要基因丢失,不会对个体发育产生严重影响,表型正常,但由于染色体短臂的丢失,在第1次减数分裂过程中罗氏易位携带者生殖细胞易位染色体和相应2个正常染色体配对形成3价染色体,这种结构会导致交替、邻式和不常见的3∶0三种分裂方式的出现。只有交替可产生正常或平衡的配子,其他2种方式产生非平衡的配子,一旦罗氏易位携带者与健康者婚配,这种占大部分的非平衡配子可能会导致易位携带者出现妊娠困难或妊娠过程中反复流产,甚至会导致21-三体综合征、13-三体综合征等先天缺陷患儿的出生。罗氏易位目前没有根治方法,目前越来越多的罗氏易位携带者寻求试管婴儿技术对胚胎进行植入前诊断。
已被报道的可用于罗氏易位携带者的胚胎的检测技术主要包括荧光原位杂交技术(FISH)、微阵列比较基因组杂交(aCGH)及NGS(张雯珂,徐晓菲,李敏,等.染色体易位携带者胚胎植入前遗传学诊断进展[J].国际生殖健康/计划生育杂志,2015,34(4):4),FISH技术曾是PGD主要的遗传学方法之一,用以筛查染色体臂间倒位及易位,判定是否存在嵌合以及染色体异常。其局限性主要表现在由于探针数量或染料种类的限制,FISH技术无法全面检测23对染色体的结构异常;波兰学者LUKASZUK博士利用FISH技术和NGS分别对一对男方携带罗氏易位衍生染色体的夫妇进行PGD检测,2012年1月进行FISH检测挑选后移植的胚胎在第10个孕周时流产。
发明内容
本发明的目的在于提供检测人类胚胎染色体罗氏易位的引物组合,对人类胚胎染色体罗氏易位具有较高特异性,可进行有效鉴定。
本发明的技术方案为:检测人类胚胎染色体罗氏易位的引物组合,包括第13号染色体引物组合、第14号染色体引物组合、第15号染色体引物组合、第21号染色体引物组合和第22号染色体引物组合中的一组或两组以上。
第13号染色体引物组合包括表1中至少一组引物组。第14号染色体引物组合包括表2中至少一组引物组。第15号染色体引物组合包括表3中至少一组引物组。第21号染色体引物组合包括表4中至少一组引物组。第22号染色体引物组合包括表5中至少一组引物组。
表1:第13号染色体引物表
表2:第14号染色体引物表
表3:第15号染色体引物表
表4:第21号染色体引物表
表5:第22号染色体引物表
本发明的目的之二在于提供所述检测人类胚胎染色体罗氏易位的引物组合作为检测染色体罗氏易位的诊断试剂的应用。
本发明的目的之三在于提供所述检测人类胚胎染色体罗氏易位的引物组合在制备检测染色体罗氏易位的试剂盒的应用。
本发明的目的之四在于提供检测人类胚胎染色体罗氏易位的方法。
具体地,检测人类胚胎染色体罗氏易位的方法,包括以下步骤:
(1)获取亲代双方和胚胎的DNA样本;
(2)根据染色体近端着丝粒区域筛选高频突变SNP位点作为标记;
(3)检测胚胎DNA样本的染色体拷贝数;
(4)根据筛选的SNP位点,确定亲代双方和胚胎目标位点的基因型;
(5)基于亲代双方和胚胎的基因型及家系关系,分析亲代双方和胚胎的单体型;
(6)根据子代的染色体拷贝数检测结果、亲代双方携带染色体罗氏易位的核型以及亲代双方和胚胎的单体型,分析胚胎染色体罗氏易位的情况;
其中,所述步骤(4)中,取第13号染色体、第14号染色体、第15号染色体、第21号染色体和第22号染色体中任意两条染色体的表1-5中的所述的引物组合扩增亲代双方和胚胎的DNA,然后建库测序,然后根据测序结果对亲代双方和胚胎染色体发生易位的SNP位点进行分析,确定亲代双方和胚胎目标位点的基因型。
所述SNP位点包括以下位点或其任意组合:
Chr13:rs9581127,rs4441121,rs9581196,rs7327770,rs9319224,rs4770840,rs4770842,rs11616593,rs1022917,rs7993967,rs504544,rs638773,rs912872,rs2774494,rs491873,rs1475325,rs577178,rs2611308,rs2611310,rs9512327,rs9319331,rs661471,rs1888312,rs1806658,rs7985257,rs1330731,rs7325950,rs9509098,rs877098,rs9315400,rs945370,rs1537787,rs1537791,rs945372,rs9509107,rs9509109,rs6490533,rs7321990,rs7324573,rs12322993,rs2313854,rs1335872,rs4335644,rs9509194,rs9509195,rs9509209,rs7323298,rs9315569,rs953957,rs2183207,rs4578496,rs9552175,rs4770027,rs9509211,rs3936015,rs79475914,rs12428869,rs115135024,rs9509247,rs9509441,rs572640,rs9316060,rs2585890,rs9509488,rs9509497,rs57961085,rs9552361,rs144534964,rs17278868,rs1327178,rs3783152,rs11616379,rs78730531,rs1199938,rs2761909,rs1886861,rs9550757,rs9316506,rs9509833,rs9506722,rs4770189,rs9580189,rs749170,rs7999069,rs9506746,rs9509921,rs7333403,rs4769179,rs1570733,rs942231,rs9506758,rs12865369,rs9509948,rs3129596,rs9316741,rs9552601,rs2320809,rs7994054,rs9510058,rs6490715,rs9317008,rs9550843,rs9510308,rs4770302,rs9510340,rs2114224,rs9552733,rs9506980,rs4770371,rs872271,rs9510597,rs3794371,rs9552867,rs518727,rs4770437,rs9578586,rs9552937,rs7489602,rs4143617,rs2274928,rs9510750,rs9580642,rs9510770,rs3794350,rs9553022,rs7993131,rs3794334,rs9318086,rs9580769;
Chr14:rs28609794,rs28671467,rs2251143,rs2489770,rs1686549,rs1892239,rs937025,rs1630546,rs1686594,rs11621796,rs2792146,rs8021956,rs10142989,rs3850313,rs10141228,rs8010858,rs10873109,rs12587697,rs2775236,rs1959641,rs2775233,rs962479,rs2775234,rs979798,rs1959636,rs1958715,rs1959629,rs944399,rs1958718,rs1952820,rs12588910,rs4981728,rs12433363,rs4144240,rs2210191,rs17277088,rs8005245,rs9323534,rs2039235,rs17097307,rs10147184,rs1958698,rs10141836,rs8021846,rs4981088,rs1953555,rs11624675,rs8014956,rs8003958,rs1953552,rs1760904,rs1760903,rs1713423,rs6575809,rs7154662,rs4982086,rs7150924,rs938881,rs2275007,rs1760944,rs1130409,rs12147458,rs7149433,rs4981223,rs1009310,rs28460579,rs4981259,rs12372906,rs891299,rs12587456,rs1010461,rs8004382,rs1888562,rs8003578,rs6571363,rs8010867,rs75545359,rs6571394,rs11156743,rs11156753,rs10138807,rs1243459,rs12432962,rs943991,rs1952151,rs1958395,rs7149011,rs11629332,rs12432043,rs7154575,rs3736824,rs11157019,rs926027,rs12590415,rs8017132,rs1569287,rs7160973,rs2075477,rs2075478,rs4982495,rs12879132,rs12432727,rs28583314,rs8007442,rs7157624,rs8022682,rs3827932,rs7147975,rs12431534,rs4982588,rs10047934,rs8007403,rs2293732,rs227866,rs226998,rs1263639,rs1263640,rs5742803,rs8005354,rs970348,rs4982648,rs7151103,rs12433985,rs8019656,rs2073345,rs743257,rs3811182,rs4982727,rs77828441,rs8003631;
Chr15:rs71464574,rs7179358,rs4932079,rs4038410,rs60615788,rs3817032,rs1818080,rs28657025,rs11857633,rs6422230,rs6600022,rs7496540,rs6600034,rs6600041,rs75255127,rs12442259,rs12441699,rs7496888,rs12437683,rs11248795,rs12916204,rs1814945,rs6600085,rs9635445,rs1908936,rs56401292,rs4778566,rs12592629,rs3812924,rs7181789,rs34324428,rs7170784,rs17137384,rs6606817,rs11263678,rs999842,rs1545060,rs67278742,rs11638659,rs7182936,rs7167687,rs57848577,rs4778298,rs59413773,rs45464395,rs1109036,rs2346695,rs17137226,rs76194208,rs61388954,rs2044372,rs11853131,rs12439364,rs8042352,rs1562203,rs12900257,rs3890107,rs4257175,rs11857798,rs4778536,rs12903906,rs4778558,rs12439354,rs12373002,rs28544508,rs11639077,rs6576483,rs4480754,rs850817,rs850813,rs850812,rs699329,rs699330,rs12914458,rs878247,rs67664694,rs1722802,rs61999926,rs1524845,rs12440861,rs1903251,rs11636636,rs8037816,rs12902723,rs35174852,rs7172367,rs2017497,rs11635083,rs2061505,rs12908063,rs67663858,rs12916148,rs2085738,rs2169118,rs898368,rs1380547,rs11633562,rs17759506,rs17117862,rs4778358,rs12437807,rs12914082,rs17760092,rs8033044,rs7164093,rs980634,rs17760249,rs1903247,rs4778266,rs12905098;
Chr21:rs1295228677,rs2775054,rs13050604,rs7278737,rs13048561,rs926880,rs447420,rs454215,rs2822526,rs4816274,rs2822529,rs2822537,rs2254297,rs980268,rs2822582,rs2822587,rs2142242,rs2822618,rs2822625,rs13050350,rs2822647,rs2142239,rs1882884,rs2822657,rs2822659,rs11088040,rs6516781,rs3761320,rs2822716,rs760345,rs9636587,rs466541,rs461853,rs1000728,rs2822809,rs439328,rs1037807,rs28431355,rs461309,rs466557,rs9983503,rs2822858,rs2822860,rs2822861,rs8127644,rs8134250,rs62218098,rs2822908,rs2822909,rs4817370,rs964035,rs2822975,rs2256417,rs2039239,rs975336,rs2823054,rs2403877,rs1556286,rs2823056,rs2823061,rs9978683,rs7282412,rs2823066,rs2256038,rs9974193,rs7279893,rs1014526,rs965098,rs2823141,rs2823158,rs2823165,rs2823177,rs2823245,rs2205532,rs2205533,rs2823252,rs427761,rs1786007,rs9305765,rs11088585,rs11911959,rs8126683,rs9979472,rs2823795,rs1375625,rs9636653,rs7275493,rs7276173,rs2823981,rs2150381,rs62221673,rs2823989,rs2823990,rs1475860,rs2178914,rs2824157,rs1014604,rs11088604,rs1319427,rs56260038,rs969905,rs11700487,rs4818324,rs4143391,rs6517737,rs2824246,rs8133027,rs182174,rs202873,rs1999288,rs208898,rs11702664,rs2824292,rs2251967,rs764657,rs2846881,rs2249100,rs2249449,rs2250305,rs2824376,rs2824397;
Chr22:rs1981533,rs174289,rs7284169,rs174345,rs174348,rs174371,rs5992838,rs5992841,rs369081,rs436590,rs448184,rs390745,rs437633,rs399757,rs2111546,rs1003361,rs2016042,rs5992884,rs1867353,rs5746489,rs3747031,rs3213927,rs431071,rs439712,rs1077543,rs448680,rs5747948,rs11089247,rs9618453,rs2073775,rs6518515,rs2074003,rs2238739,rs2238743,rs2238745,rs5993488,rs1557844,rs2238752,rs2238755,rs2800958,rs2800970,rs2189491,rs2800981,rs807759,rs2240110,rs5747997,rs712959,rs5746671,rs698422,rs11704250,rs756652,rs2283652,rs5748219,rs5993647,rs2073758,rs5748232,rs5993650,rs2073759,rs2073761,rs885985,rs5993709,rs1476445,rs5748391,rs747226,rs6518580,rs4819519,rs737869,rs713675,rs2073762,rs3087869,rs5746849,rs740603,rs165849,rs1990249,rs5761392,rs1005640,rs1035239,rs8137132,rs62219029,rs165630,rs2269830,rs2269831,rs165846,rs2329483,rs2329583,rs165764,rs165730,rs165680,rs165862,rs4675,rs2236643,rs6928,rs13943,rs743409,rs5999550,rs9607287,rs4821402,rs4821629,rs2213141,rs762471,rs5756751,rs1894250,rs5750601,rs2073454,rs1543779,rs5757568,rs5757569。
所述SNP位点包括每条染色体的至少1个SNP位点,最优选的是,上述所有SNP位点。
所述步骤(3)和(4)中,独立地分别选择高通量测序方法。所述高通量测序平台为Ion Torrent。
与现有技术相比,本发明具有以下有益效果:
1.先证者缺失的情况,直接以胚胎的结果作为先证者进行分析(缺失特异性区间的分析可以直接判定胚胎的表型);胚胎的直接判定结果可以作为连锁分析结果的验证。
2.实用性:本发明可以解决目前常规方法无法区分胚胎、胎儿或流产组织罗氏易位携带者检测问题。
3.简便性:本发明基于细胞染色体拷贝数分析结果和单体型分析不同细胞的染色体易位情况,不需要对细胞进行观察,可以快速地区分正常和易位携带胚胎。
4.通用性:本发明采用了多SNP进行分析,可用于不同配偶的胚胎移植前诊断、胎儿诊断或流产组织诊断。
5.高通量:基于高通量测序技术,本发明可以分析染色体的易位,通过在每个样品上加上不同的标签序列,可以一次地对大量样品进行分析。
6.成本低:随着测序技术的不断发展和测序成本的不断降低,本发明对染色体易位检测的成本也在不断下降。
7.高灵敏度:可用于3~5个细胞的分析。因此除了流产组织、宫颈来源的滋养层细胞外,尤其适合于试管婴儿技术中胚胎移植前的检测。
8.引物组使用灵活:本发明选取罗氏易位染色体上下游2M区域位点,选取等位基因频率大于0.20的高频突变位点,进行引物设计。所得的引物具有较高的特异性,在目标染色体上序列唯一,能特异扩增罗氏易位13、14、15、21、22号染色体紧密连锁的单核苷酸多态性(SNP)位点。不同染色体引物池可以随意两两组合,组合后的引物池不影响PCR反应体系。这些引物在位置特异的寡核苷酸具有相同的退火温度,能进行多重反应;而且扩增后,通过高通量测序分析能通过SNP连锁分析判断胚胎是否携带罗氏易位衍生染色体。
9.准确性:根据易位染色体拷贝数的变化,及携带对应染色体的样本,可以推测易位的染色体中各自的衍生染色体单体型,进而作相互验证,准确性更高。
附图说明
图1是13号染色体单体型结果。
图2是13号染色体单体型结果。
图3是14号染色体单体型结果。
图4是14号染色体单体型结果。
图5是本发明的方法的流程图。
图6是本发明的方法的胚胎易位染色体分析图。
具体实施方式
下面将更详细地描述本申请的具体实施例。提供这些实施例是为了能够更透彻地理解本申请,并且能够将本申请的范围完整的传达给本领域的技术人员。一、12例胚胎基于Ion Torrent测序平台检测
1.全基因组扩增获得胚胎的DNA样本:获取此实施例家系的12枚胚胎活检样本,将体外培养的3-6天的囊胚期滋养层细胞。胚胎细胞样本按照Fapon single Cell geneme-Ampli Kit(厂家:Fapon;货号:NK023)标准操作流程对12个胚胎样本进行全基因组扩增,获得胚胎样本DNA。将细胞裂解后的基因组跟特殊的随机引物随机结合、延伸,这些引物末端带有一段特殊的通用序列,可以使扩增子的尾端互补,自身成环,防止DNA过度拷贝,扩增产物无法作为新模板,从而很大程度上防止DNA复制后的指数性扩增,增加了全基因组扩增的均一性。预扩增的产物用一对引物进行指数扩增,增加扩增产物产量。
获得的胚胎样本DNA采用dsDNAHSAssay Kit试剂盒(厂家:翌圣生物;货号:12642ES76)进行Qubit 4.0浓度测定,按照试剂盒说明书操作步骤进行检测。
2.通过高通量测序检测胚胎DNA样本的的染色体拷贝数变异(CNV)
本步骤采用的文库构建试剂盒为Fapon Two-Step Library Prep Kit for IonTorrent(厂家:Fapon;货号:NK012)。
1)末端补平:将得到的胚胎样本DNA片段中加入可与黏性末端结合的引物,与末端补平试剂混合经过孵育,得到平末端的样本。
末端补平反应体系为50μL体系,反应体系的组成成分具体为:
PCR反应条件如下:20℃30min;70℃10min,4℃保持。
2)接头连接:将步骤1)得到的DNA片段与P1接头、特异性接头(A)、接头连接反应试剂混合进行连接反应,得到具有识别性接头的DNA片段。
本步骤中使用的P1接头为:
CCACTACGCCTCCGCTTTCCTCTCTATGGGCAGTCGGTGAT
ATCACCGACTGCCCATAGAGAGGAAAGCGGAGGCGTAGTGG-s-T-s-T。
本步骤中使用的特异性接头(A)是由如下正反两个序列组成的96个Barcode x,Barcode x代表的具体序列如下所示:
接头连接反应体系为100μL体系,反应体系的组成成分具体为:
接头连接PCR反应条件如下:20℃15min;4℃保持。
3)磁珠纯化:将步骤2)中得到的DNA片段进行磁珠纯化,去除多余的小片段和接头二聚体及多余的引物等,得到纯化的DNA片段。
本步骤采用DNAClean Beads Kit(厂家:翌圣生物;货号:12601ES56),样本:磁珠=1:0.9;获得25μL接头连接的文库片段。
4)指数性扩增:将步骤3)中得到的DNA片段加入文库扩增引物及文库扩增反应试剂进行PCR扩增,得到将目的片段放大后的DNA片段。并将这些DNA片段采用磁珠进行纯化,得到目的片段的DNA文库。
a文库片段PCR扩增
此中文库扩增引物序列如下:
Primer-1:CCACTACGCCTCCGCTTTCCTCTCTATG;
Primer-2:CCATCTCATCCCTGCGTGTC。
扩增反应体系为50μL体系,反应体系的组成成分具体为:
PCR扩增反应条件如下:72℃10min;98℃45s,(98℃20s,65℃30s,72℃30s)6个循环;72℃5min;4℃保持。
b扩增产物纯化
采用DNAClean Beads Kit(厂家:翌圣生物;货号:12601ES56),样本:磁珠=1:1;获得25μL接头连接后指数性扩增的文库片段。
获得的DNA文库采用1×dsDNAHS Assay Kit试剂盒(厂家:翌圣生物;货号:12642ES76)进行浓度测定,按照试剂盒说明书操作步骤进行检测。
5)文库质控:将步骤4)中得到的DNA文库用Qubit4.0定量设备检测文库浓度。
将文库产物均一化,混合至100pM
a)将ng/ul浓度换算成nM浓度,如图
b)根据以下公式进行取样
Volume ofsamples=V(f)*C(f)/#*C(i)
注:其中,
V(f):混合后的样本终体积;
C(f):混合后的所有样本的终浓度;
#:混合Mix的所有样本数目;
C(i):每一个样本的初始浓度(nM);
最终用EB补足终体积。
按照Ion P1 Hi-Q OT2200试剂盒(厂家:Life Technologies;货号A26434)的标准操作说明进行模板制备和模板富集。
6)CNV-seq:将步骤5)中得到的DNA文库基于Ion Torrent测序平台对样本DNA进行低深度全基因组测序。使用已知的正常样本构建基准数据库,将测序结果与人类参考基因组碱基序列进行比对,通过生物信息分析以发现受检样本存在的CNVs。
本步骤按照Ion P1 Hi-Q测序200试剂盒(厂家:Life Technologies;货号A26772)标准操作说明进行上机测序。
7)数据分析:使用已知的正常样本构建基准数据库,将测序结果与人类参考基因组碱基序列进行比对,通过生物信息分析以发现受检样本存在的CNVs。
8)此实施例家系CNV分析结果显示,见表7。
生物信息学方法包括以下方法:
①下机数据分析方法:将制作好的测序文库体系在Ion Torrent Proton平台中进行高通量测序,测序结束后,采用Torrent_Server_5.0_VM软件对生成的原始测序下机数据进行预处理,去除了下机数据中的接头序列。并用Tmap比对工具将处理过后的测序数据比对到GRCh37(hg19)人类参考基因组上。
②生信分析的方法:通过Torrent Suite(v5.4.0)分析套件中的“CoverageAnalysis和“Variant Caller”等插件对预处理后的测序数据进行基因型分析,分析目标区域chr13,chr14,chr15,chr21以及chr22中每个基因位点的单体型多态性位点(SNP)的覆盖深度和基因型情况。利用父母和先验者与紧密连锁SNP染色体上的位置和基因型构建单体型。通过已经建好的单体型对胚胎是否携带异常染色体进行判断。
③IonAmpliSeq靶向区域拷贝数分析方法:使用已知的正常样本构建基准数据库,计算每个样本chr13,chr14,chr15,chr21以及chr22染色体的相对序列值(RC),并利用不同样本的平均值,通过统计分析,确定了参考值的范围。接下来,通过利用参考值对每个样本进行缺失判定。
④根据SNP位点,确定亲代双方和子代目标位点的基因型:选择与父母有区别的SNP位点,再判断其后代是否携带罗氏易位衍生染色体。
5.根据步骤4的SNP位点,确定亲代和子代目标位点的基因型,再判断其后代是否携带罗氏易位衍生染色体,获得亲代双方和胚胎的单体型。
6.根据胚胎的染色体拷贝数变异(CNV)检测结果、亲代双方携带染色体罗氏易位的核型、以及亲代双方和胚胎的单体型,分析胚胎染色体罗氏易位的情况。步骤4的SNP位点选自以下组合:
二、12例胚胎遗传诊断主要实验步骤
(1)全血基因组DNA提取
获取2例父母和1例女儿的样本,夫妻双方及女儿样本来自外周血样本,采用MagPure Fast BloodDNA LQ Kit(厂家:美基生物,货号:MD5111-03)提取试剂盒,按照试剂盒说明书操作步骤提取。对获得的样本DNA进行Qubit 4.0浓度测定。
DNA样本采用dsDNA HS Assay Kit试剂盒(厂家:翌圣生物;货号:12642ES76)进行浓度测定,按照试剂盒说明书操作步骤进行检测。
(2)多重PCR扩增
使用表1-表2中的第13号染色体和第14号染色体引物表合成引物,并根据上述一的步骤2的6)中的CNV结果即表7,对其中结果非嵌合的5例胚胎样本即CML-07,CML-08,CML-09,CML-11,CML-12进行下一步检测。将定量后的5例胚胎和3例外周血产物按照多重扩增体系(厂家:Fapon;货号:MDT131)按照以下体系加入试剂进行多重PCR扩增:
反应条件:
多重扩增产物质检:取1.5μL的扩增产物进行电泳质检,琼脂糖凝胶浓度(2%),确认目标片段扩增成功。
纯化扩增产物:磁珠纯化扩增产物,本步骤采用DNA Clean Beads Kit(厂家:翌圣生物;货号:12601ES56),补42μL无核酸酶水,样本:磁珠=1:1.2;获得20μL多重产物。
纯化好的PCR产物,用Qubit4.0测定浓度,采用dsDNAHS Assay Kit试剂盒(厂家:翌圣生物;货号:12642ES76)进行浓度测定,按照试剂盒说明书操作步骤进行检测。
(3)文库构建
本步骤采用的文库构建试剂盒为Fapon Two-Step Library Prep Kit for IonTorrent(厂家:Fapon;货号:NK012),其步骤与一中的步骤2-3操作一致。
(4)模板制备
将文库产物均一化,混合至100pM
1)将ng/ul浓度换算成nM浓度,如图
2)根据以下公式进行取样
Volume ofsamples=V(f)*C(f)/#*C(i)
注:其中,
V(f):混合后的样本终体积;
C(f):混合后的所有样本的终浓度;
#:混合Mix的所有样本数目;
C(i):每一个样本的初始浓度(nM);
最终用EB补足终体积。
按照Ion P1 Hi-Q OT2200试剂盒(厂家:Life Technologies;货号A26434)的标准操作说明进行模板制备和模板富集。
(5)高通量测序:将步骤(4)中得到的DNA文库基于Ion Torrent测序平台进行高通量测序,得到测序结果。
按照Ion P1 Hi-Q测序200试剂盒(厂家:Life Technologies;货号A26772)标准操作说明进行上机测序。
(6)数据分析
使用已知的正常样本构建基准数据库,计算每个样本13号及14号染色体的相对序列值(RC),并利用CMLNE的单体型结果确定父母双方的染色体单体。
(7)单体型分析
(1)样本检测结果显示,见表6。
(2)CNV分析结果显示,见表7。
(3)13号染色体单体型结果见图1,图2。
(4)14号染色体单体型结果见图3,图4。
(5)13号染色体单体型分析结果显示,见表8。
(6)14号染色体单体型分析结果显示,见表9。
表6样本检测结果显示
表7CNV分析结果显示
表8 13号染色体单体型分析结果显示
表9 14号染色体单体型分析结果
Claims (10)
1.检测人类胚胎染色体罗氏易位的引物组合,包括第13号染色体SNP位点的引物组合、第14号染色体SNP位点的引物组合、第15号染色体SNP位点的引物组合、第21号染色体SNP位点的引物组合和第22号染色体SNP位点的引物组合中的一组或两组以上;其特征是,
(1)所述第13号染色体SNP位点的引物组合包括至少一组引物组:正向引物序列SEQIDNO:2n-1,反向引物序列SEQ ID NO:2n,n为选自1-129的自然数;
(2)所述第14号染色体SNP位点的引物组合为以下至少一组引物组:正向引物序列SEQID NO:2n-1,反向引物序列SEQ ID NO:2n,n为选自130-259的自然数;
(3)所述第15号染色体SNP位点的引物组合为以下至少一组引物组:正向引物序列SEQID NO:2n-1,反向引物序列SEQ ID NO:2n,n为选自260-369的自然数;
(4)所述第21号染色体SNP位点的引物组合为以下至少一组引物组:正向引物序列SEQID NO:2n-1,反向引物序列SEQ ID NO:2n,n为选自370-490的自然数;
(5)所述第22号染色体SNP位点的引物组合为以下至少一组引物组:正向引物序列SEQID NO:2n-1,反向引物序列SEQ ID NO:2n,n为选自491-597的自然数。
2.根据权利要求1所述的检测人类胚胎染色体罗氏易位的引物组合,其特征是,所述SNP位点包括以下位点或其任意组合:
Chr13:rs9581127,rs4441121,rs9581196,rs7327770,rs9319224,rs4770840,rs4770842,rs11616593,rs1022917,rs7993967,rs504544,rs638773,rs912872,rs2774494,rs491873,rs1475325,rs577178,rs2611308,rs2611310,rs9512327,rs9319331,rs661471,rs1888312,rs1806658,rs7985257,rs1330731,rs7325950,rs9509098,rs877098,rs9315400,rs945370,rs1537787,rs1537791,rs945372,rs9509107,rs9509109,rs6490533,rs7321990,rs7324573,rs12322993,rs2313854,rs1335872,rs4335644,rs9509194,rs9509195,rs9509209,rs7323298,rs9315569,rs953957,rs2183207,rs4578496,rs9552175,rs4770027,rs9509211,rs3936015,rs79475914,rs12428869,rs115135024,rs9509247,rs9509441,rs572640,rs9316060,rs2585890,rs9509488,rs9509497,rs57961085,rs9552361,rs144534964,rs17278868,rs1327178,rs3783152,rs11616379,rs78730531,rs1199938,rs2761909,rs1886861,rs9550757,rs9316506,rs9509833,rs9506722,rs4770189,rs9580189,rs749170,rs7999069,rs9506746,rs9509921,rs7333403,rs4769179,rs1570733,rs942231,rs9506758,rs12865369,rs9509948,rs3129596,rs9316741,rs9552601,rs2320809,rs7994054,rs9510058,rs6490715,rs9317008,rs9550843,rs9510308,rs4770302,rs9510340,rs2114224,rs9552733,rs9506980,rs4770371,rs872271,rs9510597,rs3794371,rs9552867,rs518727,rs4770437,rs9578586,rs9552937,rs7489602,rs4143617,rs2274928,rs9510750,rs9580642,rs9510770,rs3794350,rs9553022,rs7993131,rs3794334,rs9318086,rs9580769;
Chr14:rs28609794,rs28671467,rs2251143,rs2489770,rs1686549,rs1892239,rs937025,rs1630546,rs1686594,rs11621796,rs2792146,rs8021956,rs10142989,rs3850313,rs10141228,rs8010858,rs10873109,rs12587697,rs2775236,rs1959641,rs2775233,rs962479,rs2775234,rs979798,rs1959636,rs1958715,rs1959629,rs944399,rs1958718,rs1952820,rs12588910,rs4981728,rs12433363,rs4144240,rs2210191,rs17277088,rs8005245,rs9323534,rs2039235,rs17097307,rs10147184,rs1958698,rs10141836,rs8021846,rs4981088,rs1953555,rs11624675,rs8014956,rs8003958,rs1953552,rs1760904,rs1760903,rs1713423,rs6575809,rs7154662,rs4982086,rs7150924,rs938881,rs2275007,rs1760944,rs1130409,rs12147458,rs7149433,rs4981223,rs1009310,rs28460579,rs4981259,rs12372906,rs891299,rs12587456,rs1010461,rs8004382,rs1888562,rs8003578,rs6571363,rs8010867,rs75545359,rs6571394,rs11156743,rs11156753,rs10138807,rs1243459,rs12432962,rs943991,rs1952151,rs1958395,rs7149011,rs11629332,rs12432043,rs7154575,rs3736824,rs11157019,rs926027,rs12590415,rs8017132,rs1569287,rs7160973,rs2075477,rs2075478,rs4982495,rs12879132,rs12432727,rs28583314,rs8007442,rs7157624,rs8022682,rs3827932,rs7147975,rs12431534,rs4982588,rs10047934,rs8007403,rs2293732,rs227866,rs226998,rs1263639,rs1263640,rs5742803,rs8005354,rs970348,rs4982648,rs7151103,rs12433985,rs8019656,rs2073345,rs743257,rs3811182,rs4982727,rs77828441,rs8003631;
Chr15:rs71464574,rs7179358,rs4932079,rs4038410,rs60615788,rs3817032,rs1818080,rs28657025,rs11857633,rs6422230,rs6600022,rs7496540,rs6600034,rs6600041,rs75255127,rs12442259,rs12441699,rs7496888,rs12437683,rs11248795,rs12916204,rs1814945,rs6600085,rs9635445,rs1908936,rs56401292,rs4778566,rs12592629,rs3812924,rs7181789,rs34324428,rs7170784,rs17137384,rs6606817,rs11263678,rs999842,rs1545060,rs67278742,rs11638659,rs7182936,rs7167687,rs57848577,rs4778298,rs59413773,rs45464395,rs1109036,rs2346695,rs17137226,rs76194208,rs61388954,rs2044372,rs11853131,rs12439364,rs8042352,rs1562203,rs12900257,rs3890107,rs4257175,rs11857798,rs4778536,rs12903906,rs4778558,rs12439354,rs12373002,rs28544508,rs11639077,rs6576483,rs4480754,rs850817,rs850813,rs850812,rs699329,rs699330,rs12914458,rs878247,rs67664694,rs1722802,rs61999926,rs1524845,rs12440861,rs1903251,rs11636636,rs8037816,rs12902723,rs35174852,rs7172367,rs2017497,rs11635083,rs2061505,rs12908063,rs67663858,rs12916148,rs2085738,rs2169118,rs898368,rs1380547,rs11633562,rs17759506,rs17117862,rs4778358,rs12437807,rs12914082,rs17760092,rs8033044,rs7164093,rs980634,rs17760249,rs1903247,rs4778266,rs12905098;
Chr21:rs1295228677,rs2775054,rs13050604,rs7278737,rs13048561,rs926880,rs447420,rs454215,rs2822526,rs4816274,rs2822529,rs2822537,rs2254297,rs980268,rs2822582,rs2822587,rs2142242,rs2822618,rs2822625,rs13050350,rs2822647,rs2142239,rs1882884,rs2822657,rs2822659,rs11088040,rs6516781,rs3761320,rs2822716,rs760345,rs9636587,rs466541,rs461853,rs1000728,rs2822809,rs439328,rs1037807,rs28431355,rs461309,rs466557,rs9983503,rs2822858,rs2822860,rs2822861,rs8127644,rs8134250,rs62218098,rs2822908,rs2822909,rs4817370,rs964035,rs2822975,rs2256417,rs2039239,rs975336,rs2823054,rs2403877,rs1556286,rs2823056,rs2823061,rs9978683,rs7282412,rs2823066,rs2256038,rs9974193,rs7279893,rs1014526,rs965098,rs2823141,rs2823158,rs2823165,rs2823177,rs2823245,rs2205532,rs2205533,rs2823252,rs427761,rs1786007,rs9305765,rs11088585,rs11911959,rs8126683,rs9979472,rs2823795,rs1375625,rs9636653,rs7275493,rs7276173,rs2823981,rs2150381,rs62221673,rs2823989,rs2823990,rs1475860,rs2178914,rs2824157,rs1014604,rs11088604,rs1319427,rs56260038,rs969905,rs11700487,rs4818324,rs4143391,rs6517737,rs2824246,rs8133027,rs182174,rs202873,rs1999288,rs208898,rs11702664,rs2824292,rs2251967,rs764657,rs2846881,rs2249100,rs2249449,rs2250305,rs2824376,rs2824397;
Chr22:rs1981533,rs174289,rs7284169,rs174345,rs174348,rs174371,rs5992838,rs5992841,rs369081,rs436590,rs448184,rs390745,rs437633,rs399757,rs2111546,rs1003361,rs2016042,rs5992884,rs1867353,rs5746489,rs3747031,rs3213927,rs431071,rs439712,rs1077543,rs448680,rs5747948,rs11089247,rs9618453,rs2073775,rs6518515,rs2074003,rs2238739,rs2238743,rs2238745,rs5993488,rs1557844,rs2238752,rs2238755,rs2800958,rs2800970,rs2189491,rs2800981,rs807759,rs2240110,rs5747997,rs712959,rs5746671,rs698422,rs11704250,rs756652,rs2283652,rs5748219,rs5993647,rs2073758,rs5748232,rs5993650,rs2073759,rs2073761,rs885985,rs5993709,rs1476445,rs5748391,rs747226,rs6518580,rs4819519,rs737869,rs713675,rs2073762,rs3087869,rs5746849,rs740603,rs165849,rs1990249,rs5761392,rs1005640,rs1035239,rs8137132,rs62219029,rs165630,rs2269830,rs2269831,rs165846,rs2329483,rs2329583,rs165764,rs165730,rs165680,rs165862,rs4675,rs2236643,rs6928,rs13943,rs743409,rs5999550,rs9607287,rs4821402,rs4821629,rs2213141,rs762471,rs5756751,rs1894250,rs5750601,rs2073454,rs1543779,rs5757568,rs5757569。
3.权利要求1所述检测人类胚胎染色体罗氏易位的引物组合作为检测染色体罗氏易位的诊断试剂的应用。
4.权利要求1所述检测人类胚胎染色体罗氏易位的引物组合在制备检测染色体罗氏易位的试剂盒的应用。
5.检测人类胚胎染色体罗氏易位的方法,包括以下步骤:
(1)获取亲代双方和胚胎的DNA样本;
(2)根据染色体近端着丝粒区域筛选高频突变SNP位点作为标记;
(3)检测胚胎DNA样本的染色体拷贝数;
(4)根据筛选的SNP位点,确定亲代双方和胚胎目标位点的基因型;
(5)基于亲代双方和胚胎的基因型及家系关系,分析亲代双方和胚胎的单体型;
(6)根据子代的染色体拷贝数检测结果、亲代双方携带染色体罗氏易位的核型以及亲代双方和胚胎的单体型,分析胚胎染色体罗氏易位的情况;
其特征是,所述步骤(4)中,取第13号染色体、第14号染色体、第15号染色体、第21号染色体和第22号染色体中任意两条染色体的权利要求1所述的引物组合扩增亲代双方和胚胎的DNA,然后建库测序,然后根据测序结果对亲代双方和胚胎染色体发生易位的SNP位点进行分析,确定亲代双方和胚胎目标位点的基因型。
6.根据权利要求5所述的检测人类胚胎染色体罗氏易位的方法,其特征是,所述SNP位点包括以下位点或其任意组合:
Chr13:rs9581127,rs4441121,rs9581196,rs7327770,rs9319224,rs4770840,rs4770842,rs11616593,rs1022917,rs7993967,rs504544,rs638773,rs912872,rs2774494,rs491873,rs1475325,rs577178,rs2611308,rs2611310,rs9512327,rs9319331,rs661471,rs1888312,rs1806658,rs7985257,rs1330731,rs7325950,rs9509098,rs877098,rs9315400,rs945370,rs1537787,rs1537791,rs945372,rs9509107,rs9509109,rs6490533,rs7321990,rs7324573,rs12322993,rs2313854,rs1335872,rs4335644,rs9509194,rs9509195,rs9509209,rs7323298,rs9315569,rs953957,rs2183207,rs4578496,rs9552175,rs4770027,rs9509211,rs3936015,rs79475914,rs12428869,rs115135024,rs9509247,rs9509441,rs572640,rs9316060,rs2585890,rs9509488,rs9509497,rs57961085,rs9552361,rs144534964,rs17278868,rs1327178,rs3783152,rs11616379,rs78730531,rs1199938,rs2761909,rs1886861,rs9550757,rs9316506,rs9509833,rs9506722,rs4770189,rs9580189,rs749170,rs7999069,rs9506746,rs9509921,rs7333403,rs4769179,rs1570733,rs942231,rs9506758,rs12865369,rs9509948,rs3129596,rs9316741,rs9552601,rs2320809,rs7994054,rs9510058,rs6490715,rs9317008,rs9550843,rs9510308,rs4770302,rs9510340,rs2114224,rs9552733,rs9506980,rs4770371,rs872271,rs9510597,rs3794371,rs9552867,rs518727,rs4770437,rs9578586,rs9552937,rs7489602,rs4143617,rs2274928,rs9510750,rs9580642,rs9510770,rs3794350,rs9553022,rs7993131,rs3794334,rs9318086,rs9580769;
Chr14:rs28609794,rs28671467,rs2251143,rs2489770,rs1686549,rs1892239,rs937025,rs1630546,rs1686594,rs11621796,rs2792146,rs8021956,rs10142989,rs3850313,rs10141228,rs8010858,rs10873109,rs12587697,rs2775236,rs1959641,rs2775233,rs962479,rs2775234,rs979798,rs1959636,rs1958715,rs1959629,rs944399,rs1958718,rs1952820,rs12588910,rs4981728,rs12433363,rs4144240,rs2210191,rs17277088,rs8005245,rs9323534,rs2039235,rs17097307,rs10147184,rs1958698,rs10141836,rs8021846,rs4981088,rs1953555,rs11624675,rs8014956,rs8003958,rs1953552,rs1760904,rs1760903,rs1713423,rs6575809,rs7154662,rs4982086,rs7150924,rs938881,rs2275007,rs1760944,rs1130409,rs12147458,rs7149433,rs4981223,rs1009310,rs28460579,rs4981259,rs12372906,rs891299,rs12587456,rs1010461,rs8004382,rs1888562,rs8003578,rs6571363,rs8010867,rs75545359,rs6571394,rs11156743,rs11156753,rs10138807,rs1243459,rs12432962,rs943991,rs1952151,rs1958395,rs7149011,rs11629332,rs12432043,rs7154575,rs3736824,rs11157019,rs926027,rs12590415,rs8017132,rs1569287,rs7160973,rs2075477,rs2075478,rs4982495,rs12879132,rs12432727,rs28583314,rs8007442,rs7157624,rs8022682,rs3827932,rs7147975,rs12431534,rs4982588,rs10047934,rs8007403,rs2293732,rs227866,rs226998,rs1263639,rs1263640,rs5742803,rs8005354,rs970348,rs4982648,rs7151103,rs12433985,rs8019656,rs2073345,rs743257,rs3811182,rs4982727,rs77828441,rs8003631;
Chr15:rs71464574,rs7179358,rs4932079,rs4038410,rs60615788,rs3817032,rs1818080,rs28657025,rs11857633,rs6422230,rs6600022,rs7496540,rs6600034,rs6600041,rs75255127,rs12442259,rs12441699,rs7496888,rs12437683,rs11248795,rs12916204,rs1814945,rs6600085,rs9635445,rs1908936,rs56401292,rs4778566,rs12592629,rs3812924,rs7181789,rs34324428,rs7170784,rs17137384,rs6606817,rs11263678,rs999842,rs1545060,rs67278742,rs11638659,rs7182936,rs7167687,rs57848577,rs4778298,rs59413773,rs45464395,rs1109036,rs2346695,rs17137226,rs76194208,rs61388954,rs2044372,rs11853131,rs12439364,rs8042352,rs1562203,rs12900257,rs3890107,rs4257175,rs11857798,rs4778536,rs12903906,rs4778558,rs12439354,rs12373002,rs28544508,rs11639077,rs6576483,rs4480754,rs850817,rs850813,rs850812,rs699329,rs699330,rs12914458,rs878247,rs67664694,rs1722802,rs61999926,rs1524845,rs12440861,rs1903251,rs11636636,rs8037816,rs12902723,rs35174852,rs7172367,rs2017497,rs11635083,rs2061505,rs12908063,rs67663858,rs12916148,rs2085738,rs2169118,rs898368,rs1380547,rs11633562,rs17759506,rs17117862,rs4778358,rs12437807,rs12914082,rs17760092,rs8033044,rs7164093,rs980634,rs17760249,rs1903247,rs4778266,rs12905098;
Chr21:rs1295228677,rs2775054,rs13050604,rs7278737,rs13048561,rs926880,rs447420,rs454215,rs2822526,rs4816274,rs2822529,rs2822537,rs2254297,rs980268,rs2822582,rs2822587,rs2142242,rs2822618,rs2822625,rs13050350,rs2822647,rs2142239,rs1882884,rs2822657,rs2822659,rs11088040,rs6516781,rs3761320,rs2822716,rs760345,rs9636587,rs466541,rs461853,rs1000728,rs2822809,rs439328,rs1037807,rs28431355,rs461309,rs466557,rs9983503,rs2822858,rs2822860,rs2822861,rs8127644,rs8134250,rs62218098,rs2822908,rs2822909,rs4817370,rs964035,rs2822975,rs2256417,rs2039239,rs975336,rs2823054,rs2403877,rs1556286,rs2823056,rs2823061,rs9978683,rs7282412,rs2823066,rs2256038,rs9974193,rs7279893,rs1014526,rs965098,rs2823141,rs2823158,rs2823165,rs2823177,rs2823245,rs2205532,rs2205533,rs2823252,rs427761,rs1786007,rs9305765,rs11088585,rs11911959,rs8126683,rs9979472,rs2823795,rs1375625,rs9636653,rs7275493,rs7276173,rs2823981,rs2150381,rs62221673,rs2823989,rs2823990,rs1475860,rs2178914,rs2824157,rs1014604,rs11088604,rs1319427,rs56260038,rs969905,rs11700487,rs4818324,rs4143391,rs6517737,rs2824246,rs8133027,rs182174,rs202873,rs1999288,rs208898,rs11702664,rs2824292,rs2251967,rs764657,rs2846881,rs2249100,rs2249449,rs2250305,rs2824376,rs2824397;
Chr22:rs1981533,rs174289,rs7284169,rs174345,rs174348,rs174371,rs5992838,rs5992841,rs369081,rs436590,rs448184,rs390745,rs437633,rs399757,rs2111546,rs1003361,rs2016042,rs5992884,rs1867353,rs5746489,rs3747031,rs3213927,rs431071,rs439712,rs1077543,rs448680,rs5747948,rs11089247,rs9618453,rs2073775,rs6518515,rs2074003,rs2238739,rs2238743,rs2238745,rs5993488,rs1557844,rs2238752,rs2238755,rs2800958,rs2800970,rs2189491,rs2800981,rs807759,rs2240110,rs5747997,rs712959,rs5746671,rs698422,rs11704250,rs756652,rs2283652,rs5748219,rs5993647,rs2073758,rs5748232,rs5993650,rs2073759,rs2073761,rs885985,rs5993709,rs1476445,rs5748391,rs747226,rs6518580,rs4819519,rs737869,rs713675,rs2073762,rs3087869,rs5746849,rs740603,rs165849,rs1990249,rs5761392,rs1005640,rs1035239,rs8137132,rs62219029,rs165630,rs2269830,rs2269831,rs165846,rs2329483,rs2329583,rs165764,rs165730,rs165680,rs165862,rs4675,rs2236643,rs6928,rs13943,rs743409,rs5999550,rs9607287,rs4821402,rs4821629,rs2213141,rs762471,rs5756751,rs1894250,rs5750601,rs2073454,rs1543779,rs5757568,rs5757569。
7.根据权利要求6所述的检测人类胚胎染色体罗氏易位的方法,其特征是,所述SNP位点包括每条染色体的至少1个SNP位点。
8.根据权利要求6所述的检测人类胚胎染色体罗氏易位的方法,其特征是,所述步骤(3)和(4)中,独立地分别选择高通量测序方法。
9.根据权利要求8所述的检测人类胚胎染色体罗氏易位的方法,其特征是,所述高通量测序平台为Ion Torrent。
10.根据权利要求9所述的检测人类胚胎染色体罗氏易位的方法,其特征是,在高通量测序方法中采用P1接头和特异性接头A对DNA进行接头连接,其中,
所述P1接头为:
CCACTACGCCTCCGCTTTCCTCTCTATGGGCAGTCGGTGAT
ATCACCGACTGCCCATAGAGAGGAAAGCGGAGGCGTAGTGG-s-T-s-T;
所述特异性接头A为SEQ ID NO1197至SEQ ID NO.1388的所示的序列。
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