Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76, Stockholm, Sweden.
Department of Clinical Genetics and Genomics, Karolinska University Hospital, 171 76, Stockholm, Sweden.
Sci Rep. 2024 Apr 18;14(1):9000. doi: 10.1038/s41598-024-59683-3.
Long-read genome sequencing (lrGS) is a promising method in genetic diagnostics. Here we investigate the potential of lrGS to detect a disease-associated chromosomal translocation between 17p13 and the 19 centromere. We constructed two sets of phased and non-phased de novo assemblies; (i) based on lrGS only and (ii) hybrid assemblies combining lrGS with optical mapping using lrGS reads with a median coverage of 34X. Variant calling detected both structural variants (SVs) and small variants and the accuracy of the small variant calling was compared with those called with short-read genome sequencing (srGS). The de novo and hybrid assemblies had high quality and contiguity with N50 of 62.85 Mb, enabling a near telomere to telomere assembly with less than a 100 contigs per haplotype. Notably, we successfully identified the centromeric breakpoint of the translocation. A concordance of 92% was observed when comparing small variant calling between srGS and lrGS. In summary, our findings underscore the remarkable potential of lrGS as a comprehensive and accurate solution for the analysis of SVs and small variants. Thus, lrGS could replace a large battery of genetic tests that were used for the diagnosis of a single symptomatic translocation carrier, highlighting the potential of lrGS in the realm of digital karyotyping.
长读长测序（lrGS）是一种很有前途的遗传诊断方法。在这里，我们研究了 lrGS 检测 17p13 和 19 号染色体着丝粒之间与疾病相关的染色体易位的潜力。我们构建了两组相和非相从头组装；（i）仅基于 lrGS，（ii）将 lrGS 与光学图谱相结合的混合组装，使用 lrGS 读数的中位覆盖度为 34X。变体调用检测到结构变体（SVs）和小变体，并且比较了小变体调用的准确性与短读长基因组测序（srGS）调用的准确性。从头和混合组装具有高质量和连续性，N50 为 62.85 Mb，能够实现近端粒到端粒的组装，每个单倍型的连续体少于 100 个。值得注意的是，我们成功地确定了易位的着丝粒断点。当比较 srGS 和 lrGS 之间的小变体调用时，观察到 92%的一致性。总之，我们的研究结果强调了 lrGS 作为分析 SVs 和小变体的全面和准确解决方案的巨大潜力。因此，lrGS 可以替代用于诊断单个症状性易位携带者的大量基因测试，突出了 lrGS 在数字核型分析领域的潜力。
