PCR amplicons identify widespread copy number variation in human centromeric arrays and instability in cancer

Abstract

SUMMARY Centromeric α-satellite repeats represent ~6% of the human genome, but their length and repetitive nature make sequencing and analysis of those regions challenging. However, centromeres are essential for the stable propagation of chromosomes, so tools are urgently needed to monitor centromere copy number and how it influences chromosome transmission and genome stability. We developed and benchmarked droplet digital PCR (ddPCR) assays that measure copy number for five human centromeric arrays. We applied them to characterize natural variation in centromeric array size, analyzing normal tissue from 37 individuals from China and 39 individuals from the US and UK. Each chromosome-specific array varies in size up to 10-fold across individuals and up to 50-fold across chromosomes, indicating a unique complement of arrays in each individual. We also used the ddPCR assays to analyze centromere copy number in 76 matched tumor-normal samples across four cancer types, representing the most-comprehensive quantitative analysis of centromeric array stability in cancer to date. In contrast to stable transmission in cultured cells, centromeric arrays show gain and loss events in each of the cancer types, suggesting centromeric α-satellite DNA represents a new category of genome instability in cancer. Our methodology for measuring human centromeric-array copy number will advance research on centromeres and genome integrity in normal and disease states.

Verkko: telomere-to-telomere assembly of diploid chromosomes

“…This enabled us to assess variability between centromeric regions in a diploid human genome. Consistent with prior studies 50-57 , we found that centromeric α-satellite higher-order repeat (HOR) arrays often vary in length by tens to hundreds of kilobases. For example, Figure 4 shows the centromeric HOR arrays from Chr19.…”

In-Depth Satellitome Analyses of 37 Drosophila Species Illuminate Repetitive DNA Evolution in the Drosophila Genus

“…Second, SatDNA sequences are a fast-evolving genomic feature, and studies are limited by the species present in the literature, which may display a limited snapshot of SatDNA sequence evolution in Drosophila . Finally, considerable intraspecific SatDNA variation is observed in eukaryotic genomes ( Arora et al 2021 ; de Lima et al 2021 ), thus future population surveys of genome size variation and repeat composition may be necessary to completely understand the evolution of SatDNA in Drosophila . Our results help reveal how SatDNA evolved and are evolving within the Drosophila genus and serve as an important resource to improve analysis of SatDNA in Drosophila genome assemblies, comparative genomic analyses, and future functional studies.…”

Satellite DNAs in Health and Disease

“…These satellite arrays are hypervariable in the human population and alterations in their activity have been linked to cancer [ 127 , 129 ]. The detection of copy number variation within long satellite DNA arrays is relatively complex and often requires development of new assays [ 130 ], such as nanoplate-based digital PCR. Further studies are necessary to reveal satellite DNAs and RNAs as potential diagnostic, prognostic or therapeutic cancer biomarkers.…”