颜林林
(2022-09-21 07:48):
#paper doi:10.1002/humu.24458 Human Mutation, 2022, A survey of current methods to detect and genotype inversions. 倒位(inversion)是基因组上一类特殊的变异,越来越多的技术方法可以对其进行发现和鉴定,也因此发现该事件广泛存在于不同物种的基因组中。这篇综述从技术角度,分别介绍了PCR、NGS序列比对、单倍体型识别、模板链测序(template‐strand sequencing,Strand‐seq)、光学图谱(optical mapping,Bionano)及基因组组装这六类方法对倒位的鉴定,以及相应方法所取得的研究进展。
A survey of current methods to detect and genotype inversions
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Abstract:
Polymorphic inversions are ubiquitous in humans and they have been linked to both adaptation and disease. Following their discovery in Drosophila more than a century ago, inversions have proved to be more elusive than other structural variants. A wide variety of methods for the detection and genotyping of inversions have recently been developed: multiple techniques based on selective amplification by PCR, short- and long-read sequencing approaches, principal component analysis of small variant haplotypes, template strand sequencing, optical mapping, and various genome assembly methods. Many methods apply complex wet lab protocols or increasingly refined bioinformatic analyses. This review is an attempt to provide a practical summary and comparison of the methods that are in current use, with a focus on metrics such as the maximum size of segmental duplications at inversion breakpoints that each method can tolerate, the size range of inversions that they recover, their throughput, and whether the locations of putative inversions must be known beforehand.
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