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全基因组定序

本页使用了标题或全文手工转换
维基百科，自由的百科全书
霰弹枪定序法的流程图
显示基因定序结果的电泳图谱（英语：Electropherogram）[1]

全基因组定序（Whole genome sequencing，WGS）是将一个生物的基因组完整（或接近完整）定序的流程。1990年代起陆续有生物的基因组被完整定序，最早被定序完成的生物为流感嗜血杆菌（1995年），1996年首次有真核生物（酿酒酵母）被完整定序。2014年以后全基因组定序逐渐开始被用于临床用途[2][3][4]，以病人基因组资讯决定其疗法，即个人化医疗[5]。2000年全基因体定序技术获《科学》期刊选为该年的年度突破（英语：Breakthrough of the Year）[6]。

历史

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流感嗜血杆菌为第一个被全基因组定序的生物
秀丽隐杆线虫为第一个被全基因组定序的多细胞生物（动物）
阿拉伯芥为第一个被全基因组定序的植物

1977年，弗雷德里克·桑格的团队将ΦX174噬菌体（英语：Phi X 174）的基因组完整定序，长5368bp，是第一个被完整定序的基因组[7][8][9]。1990年代起测序技术逐渐成熟，开始被用于定序生物的完整基因组[10]。第一个被完整定序的生物为流感嗜血杆菌，共长183万bp，于1995年由霰弹枪定序法完成[11]，随后有其他细菌与古菌的基因组陆续被以相同方法定序。真核生物的基因组大小则大的多，因此定序较为困难，1996年酿酒酵母的基因组定序完成，约长1200万bp，为第一个被完整定序的真核生物[12]；1998年秀丽隐杆线虫的基因组被完整定序，为第一个完成定序的多细胞真核生物[13]。真核生物定序的方式除使用霰弹枪定序法外，还用到了细菌人工染色体（BAC）、酵母菌人工染色体（YAC）等基因文库[14]。



1999年人类22号染色体（最短的体染色体）被定序发表[15]；2000年黑腹果蝇的基因组被完整定序，为第二种被完整定序的动物[16]，同年阿拉伯芥的基因组定序也告完成，是第一个被完整定序的植物[17]。2001年人类基因组计划发表人类基因组的定序草图（draft）[18]，2003年宣告真染色质的序列皆定序完成[19][20]，2021年发表定序程度达“完整”的基因组[21][22]；2002年小鼠的基因组也被定序发表[23]。目前已有上千种生物的基因组被完整定序。2005年起桑格测序等传统的定序方法逐渐被Illumina染料定序（英语：Illumina dye sequencing）、焦磷酸测序、SMRT定序（英语：Single-molecule real-time sequencing）与奈米孔洞测序等次世代定序（英语：Massive parallel sequencing）（NGS）技术取代（但仍使用霰弹枪定序法的策略，将基因组打碎成许多片段后分别完成定序，再进行组装）。[24][25]

商业化

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2001年至2019年一次人类全基因组定序的费用变化

已有许多公司尝试将全基因组定序商业化以作研究或临床用途[26]，包括Illumina[27]、Knome（英语：Knome）[28]、Sequenom（英语：Sequenom）[29]、454生物科学[30]、Pacific Biosciences（英语：Pacific Biosciences）[31]、Complete Genomics（英语：Complete Genomics）[32]、Helicos Biosciences（英语：Helicos Biosciences）[33]、GE Global Research（英语：GE Global Research）（通用电气的研发部门）、Affymetrix（英语：Affymetrix）、IBM、Intelligent Bio-Systems[34]、Life Technologies、Oxford Nanopore Technologies（英语：Oxford Nanopore Technologies）[35]与华大基因等[36][37][38]。2010年代晚期全基因组定序一次约要价1000美元，许多公司正试图将成本进一步降低[39]，2017年华大基因的全基因组定序收费已降为一人600美元[40]，2019年Veritas Genetics（英语：Veritas Genetics）也将费用降至一人599美元[41]

应用

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全基因组关联分析（GWAS）的结果（曼哈顿图（英语：Manhattan plot））示意图

在生医研究中，全基因组定序可被用于全基因组关联分析（GWAS）以寻找基因组中与特定疾病相关的单核苷酸多态性（SNP）位点[42]。

全基因组定序在医疗上也有很大的应用价值，2009年Illumina即推出了用于临床医疗的全基因组分析套件，供医师在不知病人病因、传统疗法均效果不彰时使用[43]。因近年来全基因组定序的费用大幅下降，其应用潜力也大幅增加。2011年布莱根妇女医院与哈佛医学院创立了Genomes2People（G2P）计画，旨在将基因定序整合进临床医疗[44]。

伦理争议

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人类全基因组定序可能伴随一些伦理议题，此技术虽有诊断出疾病的潜力[45]，但也有造成基因歧视（英语：Genetic discrimination）、隐私外泄（特别是未成年人的隐私[46]）与心理上负面影响之风险[47]。另外当一个人接受全基因组定序时，除了自己基因组的资讯外，还可能得知其近亲的基因组资讯，进而推得他们过去、现在或未来的健康状况[48]，因此接受定序者是否应与近亲分享定序的结果也是一伦理议题，若其带有一与某疾病相关的突变，却不愿与近亲分享此资讯，则医疗人员可能面临预防医疗与病人隐私的两难[45]。科学研究中的全基因组定序也可能有隐私外泄的疑虑，因学术研究发表时通常需要将病人的基因型的资讯发表到公开资料库，此资讯虽为匿名，但在疾病或突变相当罕见的情况下仍有可能使病人被认出[45]。

被全基因组定序的名人

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最早被全基因组定序完成的人是克莱格·凡特[49][50][51]与詹姆斯·杜威·沃森[52][53][54]，于2007年完成（覆盖度（英语：Coverage (genetics)）分别为7.5与7.4），2008年又有一名匿名的中国汉族人（覆盖度为36）[55]、奈及利亚约鲁巴人（覆盖度为30）[56]、荷兰的女性遗传学家玛乔琳·克里克（为首位基因组被完整定序的女性，覆盖度7至8）[57][58]与一高加索人种的白血病女性患者基因组被定序完成[59]。史蒂夫·贾伯斯为最早被全基因组定序的20人之一，有消息指其花费高达10万美元[60]。截至2012年6月共有69个人接近完整的基因组序列资料向大众公开[61]。2013年11月有一西班牙家庭在接受23andMe与华大基因定序后，将全家的全基因组序列以创用CC公有领域授权条款公开，是第一个公开的家族全基因组序列资料[62]。

参见

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参考文献

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