全基因组测序

全基因组测序（Whole genome sequencing，WGS）是将一个生物的基因组完整（或接近完整）测序的流程。1990年代起陆续有生物的基因组被完整测序，最早被测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）被完整测序。2014年以后全基因组测序逐渐开始被用于临床用途^[2][3][4]，以病人基因组信息决定其疗法，即个性化医疗^[5]。2000年全基因体测序技术获《科学》期刊选为该年的年度突破（英语：Breakthrough of the Year）^[6]。

霰弹枪测序法的流程图

显示基因测序结果的电泳图谱（英语：Electropherogram）^[1]

历史

流感嗜血杆菌为第一个被全基因组测序的生物

秀丽隐杆线虫为第一个被全基因组测序的多细胞生物（动物）

拟南芥为第一个被全基因组测序的植物

1977年，弗雷德里克·桑格的团队将ΦX174噬菌体（英语：Phi X 174）的基因组完整测序，长5368bp，是第一个被完整测序的基因组^[7][8][9]。1990年代起测序技术逐渐成熟，开始被用于测序生物的完整基因组^[10]。第一个被完整测序的生物为流感嗜血杆菌，共长183万bp，于1995年由霰弹枪测序法完成^[11]，随后有其他细菌与古菌的基因组陆续被以相同方法测序。真核生物的基因组大小则大的多，因此测序较为困难，1996年酿酒酵母的基因组测序完成，约长1200万bp，为第一个被完整测序的真核生物^[12]；1998年秀丽隐杆线虫的基因组被完整测序，为第一个完成测序的多细胞真核生物^[13]。真核生物测序的方式除使用霰弹枪测序法外，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（最短的常染色体）被测序发表^[15]；2000年黑腹果蝇的基因组被完整测序，为第二种被完整测序的动物^[16]，同年拟南芥的基因组测序也告完成，是第一个被完整测序的植物^[17]。2001年人类基因组计划发表人类基因组的测序草图（draft）^[18]，2003年宣告真染色质的序列皆测序完成^[19][20]，2021年发表测序程度达“完整”的基因组^[21][22]；2002年小鼠的基因组也被测序发表^[23]。目前已有上千种生物的基因组被完整测序。2005年起桑格测序等传统的测序方法逐渐被Illumina染料测序（英语：Illumina dye sequencing）、焦磷酸测序、SMRT测序（英语：Single-molecule real-time sequencing）与奈米孔洞测序等次世代测序（英语：Massive parallel sequencing）（NGS）技术取代（但仍使用霰弹枪测序法的策略，将基因组打碎成许多片段后分别完成测序，再进行组装）。^[24][25]

商业化

2001年至2019年一次人类全基因组测序的费用变化

已有许多公司尝试将全基因组测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年代晚期全基因组测序一次约要价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测序收费已降为一人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

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，全基因组测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]。

全基因组测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]。因近年来全基因组测序的费用大幅下降，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）计划，旨在将基因测序整合进临床医疗^[44]。

伦理争议

人类全基因组测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测序时，除了自己基因组的信息外，还可能得知其近亲的基因组信息，进而推得他们过去、现在或未来的健康状况^[48]，因此接受测序者是否应与近亲分享测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信息，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测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信息发表到公开数据库，此信息虽为匿名，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]。

被全基因组测序的名人

最早被全基因组测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]、尼日利亚约鲁巴人（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测序的女性，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测序完成^[59]。史蒂夫·乔布斯为最早被全基因组测序的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数据向大众公开^[61]。2013年11月有一西班牙家庭在接受23andMe与华大基因测序后，将全家的全基因组序列以知识共享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数据^[62]。

参见

• 覆盖度（英语：Coverage (genetics)）
• DNA测序
• DNA微阵列
• 遗传指纹分析
• 医学遗传学
• 核酸序列
• 人类基因组计划
• 个人基因组计划（英语：Personal Genome Project）
• 预测性医疗（英语：Predictive medicine）
• 个性化医疗
• 罕见功能性变异（英语：Rare functional variant）
• SNP比对分析（英语：SNP annotation）
• 外显子测序（英语：Exome Sequencing）

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外部链接

• James Watson's Personal Genome Sequence
• AAAS/Science: Genome Sequencing Poster