研究人员报道了Giraffe，一个泛基因组短读映射器，它可以有效地映射到通过序列图串联起来的单倍型的集合。Giraffe将测序读数映射到数以千计的人类基因组上，其速度可与映射到单一参考基因组的标准方法相比。绘图精度的提高使全基因组的基因分型管线在下游得到了改善，既适用于小变体，也适用于较大的结构变体。研究人员用Giraffe对5,202个不同的人类基因组中的167,000个结构性变体进行了基因分型，这些变体是在长读研究中发现的，而长读研究是用短读进行测序的。研究人员认为，泛组学有助于更全面地描述变异的特征，因此有可能改善许多基因组学分析。
附：英文原文
Title: Pangenomics enables genotyping of known structural variants in 5202 diverse genomes
Author: Jouni Sirén, Jean Monlong, Xian Chang, Adam M. Novak, Jordan M. Eizenga, Charles Markello, Jonas A. Sibbesen, Glenn Hickey, Pi-Chuan Chang, Andrew Carroll, Namrata Gupta, Stacey Gabriel, Thomas W. Blackwell, Aakrosh Ratan, Kent D. Taylor, Stephen S. Rich, Jerome I. Rotter, David Haussler, Erik Garrison, Benedict Paten
Issue&Volume: 2021-12-17
Abstract: We introduce Giraffe, a pangenome short-read mapper that can efficiently map to a collection of haplotypes threaded through a sequence graph. Giraffe maps sequencing reads to thousands of human genomes at a speed comparable to that of standard methods mapping to a single reference genome. The increased mapping accuracy enables downstream improvements in genome-wide genotyping pipelines for both small variants and larger structural variants. We used Giraffe to genotype 167,000 structural variants, discovered in long-read studies, in 5202 diverse human genomes that were sequenced using short reads. We conclude that pangenomics facilitates a more comprehensive characterization of variation and, as a result, has the potential to improve many genomic analyses.
DOI: abg8871
Source: https://www.science.org/doi/10.1126/science.abg8871