Population-scale genotyping of structural variation in the era of long-read sequencing

Chimera: The spoiler in multiple displacement amplification

“…Long-read sequencing [79] using DNA products amplified by phi29 DNA polymerase-based MDA has become a popular choice. This technology has been utilized to perform more detailed analyses of single-cell genomes [80] , [81] and has led to the discovery of novel somatic variations, structural variations [82] , [83] , and repeat regions of genomes [12] , [13] , which were hard to study in single cells before [84] , [85] . As a result, there is a better understanding [86] of somatic variation, mutation rates, and the functional effects of these genomic elements.…”

Recent advances and current challenges in population genomics of structural variation in animals and plants

“…Consequently, not many population genomic studies based on long reads have emerged so far ( Audano et al, 2019 ; Weissensteiner et al, 2020 ; Beyter et al, 2021 ; Quan et al, 2021 ; Yan et al, 2021 ; Rech et al, 2022 ). Majority of these studies employ a hybrid strategy which involves sequencing a smaller number of genomes by using long reads while the remaining samples are sequenced with short-read technology ( Ho et al, 2020 ; De Coster et al, 2021 ; Quan et al, 2022 ). Structural variants identified by LRS in representative genomes can then be genotyped from SRS data in all other samples.…”

“…Structural variants identified by LRS in representative genomes can then be genotyped from SRS data in all other samples. This approach combines the advantages of both read-sequencing technologies: the power of LRS to discover multiple types and a wider size range of SVs ( Quan et al, 2022 ), and the generally high genotyping precision of SRS-based algorithms ( Kosugi et al, 2019 ). Even so, not all SVs that are detected from long reads can be accurately genotyped from short-read data, and as much as half remain invisible to it ( Huddleston et al, 2017 ; Chakraborty et al, 2019 ; Ebert et al, 2021 ).…”

“…Pangenomes are superior to single reference genomes because they combine genomes from multiple individuals and thus better incorporate genomic polymorphism within a population, and they are becoming increasingly used for SV studies in humans and other species ( Beyter et al, 2021 ; Ebert et al, 2021 ; Qin et al, 2021 ; Yan et al, 2021 ; Zhou et al, 2022 ; for a list of studies based on plant pan-genomes see Yuan et al, 2021 ). Instead of being represented as a linear sequence, pangenomes are constructed as graphs to which sequencing reads are aligned ( De Coster et al, 2021 ; Quan et al, 2022 ), enabling reliable genotyping of SVs by short reads in thousands of samples, which facilitates large population studies. However, approaches for graph-based genotyping are in their infancy, and tools for more efficient construction of complex graphs and alignment of reads to graphs are still under development ( Quan et al, 2022 ).…”

“…Instead of being represented as a linear sequence, pangenomes are constructed as graphs to which sequencing reads are aligned ( De Coster et al, 2021 ; Quan et al, 2022 ), enabling reliable genotyping of SVs by short reads in thousands of samples, which facilitates large population studies. However, approaches for graph-based genotyping are in their infancy, and tools for more efficient construction of complex graphs and alignment of reads to graphs are still under development ( Quan et al, 2022 ).…”