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Genome reconstruction and haplotype phasing using chromosome conformation capture methodologies.
Briefings in Functional Genomics ( IF 2.5 ) Pub Date : 2019-12-26 , DOI: 10.1093/bfgp/elz026
Zhichao Xu , Jesse R Dixon

Genomic analysis of individuals or organisms is predicated on the availability of high-quality reference and genotype information. With the rapidly dropping costs of high-throughput DNA sequencing, this is becoming readily available for diverse organisms and for increasingly large populations of individuals. Despite these advances, there are still aspects of genome sequencing that remain challenging for existing sequencing methods. This includes the generation of long-range contiguity during genome assembly, identification of structural variants in both germline and somatic tissues, the phasing of haplotypes in diploid organisms and the resolution of genome sequence for organisms derived from complex samples. These types of information are valuable for understanding the role of genome sequence and genetic variation on genome function, and numerous approaches have been developed to address them. Recently, chromosome conformation capture (3C) experiments, such as the Hi-C assay, have emerged as powerful tools to aid in these challenges for genome reconstruction. We will review the current use of Hi-C as a tool for aiding in genome sequencing, addressing the applications, strengths, limitations and potential future directions for the use of 3C data in genome analysis. We argue that unique features of Hi-C experiments make this data type a powerful tool to address challenges in genome sequencing, and that future integration of Hi-C data with alternative sequencing assays will facilitate the continuing revolution in genomic analysis and genome sequencing.

中文翻译:

使用染色体构象捕获方法进行基因组重建和单倍型定相。

对个人或有机体的基因组分析取决于高质量参考和基因型信息的可用性。随着高通量DNA测序成本的快速下降,这种方法已变得可用于多种生物以及越来越多的个体。尽管取得了这些进步,但是基因组测序的某些方面仍然对现有测序方法具有挑战性。这包括在基因组组装过程中产生远距离连续性,鉴定种系和体细胞组织中的结构变异,二倍体生物中单倍型的定相以及来自复杂样品的生物的基因组序列解析。这些类型的信息对于了解基因组序列和遗传变异对基因组功能的作用非常有价值,并且已经开发出许多方法来解决它们。最近,染色体构象捕获(3C)实验(例如Hi-C分析)已成为强大的工具,可以帮助应对这些挑战,实现基因组重建。我们将回顾Hi-C作为一种辅助基因组测序的工具的当前用途,解决在基因组分析中使用3C数据的应用,优势,局限性和潜在的未来方向。我们认为,Hi-C实验的独特功能使该数据类型成为解决基因组测序挑战的强大工具,并且将来将Hi-C数据与替代测序测定法整合在一起将促进基因组分析和基因组测序的不断发展。诸如Hi-C分析之类的工具已经成为强大的工具,可以帮助应对基因组重建的这些挑战。我们将回顾Hi-C作为一种辅助基因组测序的工具的当前用途,解决在基因组分析中使用3C数据的应用,优势,局限性和潜在的未来方向。我们认为,Hi-C实验的独特功能使该数据类型成为解决基因组测序挑战的强大工具,并且将来将Hi-C数据与替代测序测定结合起来将促进基因组分析和基因组测序的不断发展。诸如Hi-C分析之类的工具已经成为强大的工具,可以帮助应对基因组重建的这些挑战。我们将回顾一下Hi-C作为一种辅助基因组测序的工具的当前用途,探讨在基因组分析中使用3C数据的应用,优势,局限性和潜在的未来方向。我们认为,Hi-C实验的独特功能使该数据类型成为解决基因组测序挑战的强大工具,并且将来将Hi-C数据与替代测序测定结合起来将促进基因组分析和基因组测序的不断发展。在基因组分析中使用3C数据的局限性和潜在的未来方向。我们认为,Hi-C实验的独特功能使该数据类型成为解决基因组测序挑战的强大工具,并且将来将Hi-C数据与替代测序测定法整合在一起将促进基因组分析和基因组测序的不断发展。在基因组分析中使用3C数据的局限性和潜在的未来方向。我们认为,Hi-C实验的独特功能使该数据类型成为解决基因组测序挑战的强大工具,并且将来将Hi-C数据与替代测序测定法整合在一起将促进基因组分析和基因组测序的不断发展。
更新日期:2020-04-17
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