MUTATIONAL SIGNATURE(S) OF HUMAN GENOMIC REARRANGEMENT MECHANISMS

人类基因组重排机制的突变特征

• 批准号: 10363624
• 负责人: PHILIP John HASTINGS
• 金额: $ 36.97万
• 依托单位: BAYLOR COLLEGE OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-09-05 至 2024-02-29
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10363624
• 关键词: 17p11.2; Animal Model; Base Pairing; Cells; Chromosome 17; Chromosomes; Clinical; Complex; Confusion; Copy Number Polymorphism; DNA; DNA Repair; DNA Sequence; DNA Sequence Alteration; DNA Sequence Rearrangement; DNA biosynthesis; DNA replication fork; Data; Deamination; Dideoxy Chain Termination DNA Sequencing; Diploidy; Disease; Disease susceptibility; Event; Family; Fathers; Gene Conversion; Gene Dosage; Generations; Genes; Genetic; Genetic Crossing Over; Genome; Genomics; Goals; Health; Human; Hybrids; Intervention; Knowledge; Lead; Length; Link; Location; Malignant Neoplasms; Maps; Medical; Methods; Mismatch Repair; Modeling; Molecular; Mothers; Mutagenesis; Mutation; Parents; Patients; Pattern; Phase; Pilot Projects; Polymerase; Population; Positioning Attribute; Process; Property; Recurrence; Resolution; Rest; Sampling; Series; Side; Single Nucleotide Polymorphism; Single-Stranded DNA; Site; Somatic Mutation; Structure; Tail; Techniques; Technology; Testing; Validation; Variant; base; experimental study; falls; genome sequencing; genomic variation; homologous recombination; human DNA; human genomics; insertion/deletion mutation; nanopore; novel; novel sequencing technology; recruit; repaired; single molecule; trait; whole genome

PROJECT SUMMARY/ABSTRACT Copy number variation (CNV), too many or too few copies of a segment of the genome, underlies many important human medical issues. We had predicted that, based on our MMBIR model for the generation of much CNV by aberrant repair of broken replication forks, that there would be a unidirectional tract of hypermutation of considerable length extending from the junction of the CNV. We devised a series of techniques to analyze seven million base-pair tracts of DNA sequence surrounding CNVs on chromosome 17. With these techniques we were successful in determining the precise structure of, and mutations linked to, 26 CNVs. We also analyzed both parents' genomes. We discovered what we sought: there are tracts of hypermutation in one direction linked to the CNV extending for up to one million base-pairs from the CNV. This confirms that our postulated mechanism is responsible for at least half of these CNV events. For the other half that do not show hypermutation, we will obtain data from a larger sample of parents until we can say whether these arose by a different mechanism or whether it is the tail of the distribution of the same mechanism. Because of the very highly detailed resolution of our analyses, we are able to see into the mechanisms that generate the hypermutation tracts. We find two mechanisms that we can provisionally decipher and possibly a third whose cause we have not yet found. Near the CNV, a low processivity polymerase makes multiple template switches and slips on the template that is being replicated. Further away, we see evidence of processes acting on single-stranded DNA giving clustered mutations of a unique signature. The third signature might relate to the diminished mismatch repair that is expected when broken replication forks prime replication. The additional data will make the signatures clearer and allow us to determine the causes. The next step is to generalize the findings to the rest of the genome. We will do this by whole genome sequencing of CNVs at other sites. In a third project we are going to use new sequencing technology to decipher the recurrent CNVs that arise by crossing-over between repeated sequences. This has been an intractable problem with previous technology because of the numerous copies of the sequence present in the cell. We expect to find the precise positions of crossovers and gene conversion tracts, indicating the rules that govern where they will fall, and determine the extent and signature (and therefore the cause) of any new mutations. Together these Aims will extend understanding of DNA repair events gone wrong that lead to genomic disorders, and potentially suggest ways to control or avoid this happening.

项目总结/摘要 拷贝数变异（CNV），即基因组片段的拷贝过多或过少，是许多基因突变的基础。 重要的人类医学问题。我们预测，基于我们的MMBIR模型， 许多CNV通过异常修复断裂的复制叉，将有一个单向的 从CNV的连接处延伸的相当长的高度突变。我们设计了一系列 技术来分析17号染色体上CNVs周围的700万个碱基对的DNA序列。 利用这些技术，我们成功地确定了26的精确结构和与之相关的突变。 CNVs。我们还分析了父母双方的基因组。我们发现了我们所寻求的： 与CNV相关的一个方向的超突变从CNV延伸多达一百万个碱基对。这 证实了我们假设的机制是负责至少一半的这些CNV事件。对另一半 没有表现出超突变，我们将从更大的父母样本中获得数据，直到我们可以说是否 这些都是由不同的机制引起的，还是同一机制的尾部分布。 由于我们的分析非常详细，我们能够看到的机制， 产生超突变片段我们找到两种机制，我们可以暂时破译， 第三个我们尚未找到其原因。在CNV附近，低持续合成能力的聚合酶产生多个 模板开关和滑动的模板是被复制。在更远的地方，我们看到了 作用于单链DNA的过程，产生具有独特特征的成簇突变。第三签名 可能与当中断的复制分叉启动复制时预期的减少的错配修复有关。 额外的数据将使签名更清晰，并使我们能够确定原因。下一步是 将这些发现推广到基因组的其他部分。我们将通过CNV的全基因组测序来实现这一点， 其他网站.在第三个项目中，我们将使用新的测序技术来破译重复出现的CNVs 由重复序列之间的交叉产生。这一直是一个棘手的问题， 由于细胞中存在大量的序列拷贝，我们希望能找到 交叉和基因转换区域的位置，指示控制它们将落在哪里的规则，以及 确定任何新突变的程度和特征（从而确定原因）。这些目标将 扩展对导致基因组疾病的DNA修复事件的理解，并可能 提出控制或避免这种情况发生的方法。

项目成果

Persistent damaged bases in DNA allow mutagenic break repair in Escherichia coli.

• DOI: 10.1371/journal.pgen.1006733
• 发表时间: 2017-07
• 期刊: PLoS genetics
• 影响因子: 4.5
• 作者: Moore JM;Correa R;Rosenberg SM;Hastings PJ
• 通讯作者: Hastings PJ

Mechanisms for the Generation of Two Quadruplications Associated with Split-Hand Malformation.

• DOI: 10.1002/humu.22929
• 发表时间: 2016-02
• 期刊: Human mutation
• 影响因子: 3.9
• 作者: Gu S;Posey JE;Yuan B;Carvalho CM;Luk HM;Erikson K;Lo IF;Leung GK;Pickering CR;Chung BH;Lupski JR
• 通讯作者: Lupski JR

The role of combined SNV and CNV burden in patients with distal symmetric polyneuropathy.

• DOI: 10.1038/gim.2015.124
• 发表时间: 2016-05
• 期刊: Genetics in medicine : official journal of the American College of Medical Genetics
• 作者: Pehlivan D;Beck CR;Okamoto Y;Harel T;Akdemir ZH;Jhangiani SN;Withers MA;Goksungur MT;Carvalho CM;Czesnik D;Gonzaga-Jauregui C;Wiszniewski W;Muzny DM;Gibbs RA;Rautenstrauss B;Sereda MW;Lupski JR
• 通讯作者: Lupski JR

Mechanisms underlying structural variant formation in genomic disorders.

• DOI: 10.1038/nrg.2015.25
• 发表时间: 2016-04
• 期刊: Nature reviews. Genetics
• 作者: Carvalho CM;Lupski JR
• 通讯作者: Lupski JR