Comprehending the mechanism behind human diseases with an established heritable component represents the forefront of personalized medicine. Nevertheless, numerous medically important genes are inaccurately represented in short-read sequencing data analysis due to their complexity and repetitiveness or the so-called "dark regions" of the human genome. The advent of PacBio as a long-read platform has provided new insights, yet HiFi whole-genome sequencing (WGS) cost remains frequently prohibitive. We introduce a targeted sequencing and analysis framework, Twist Alliance Dark Genes Panel (TADGP), designed to offer phased variants across 389 medically important yet complex autosomal genes. We highlight TADGP accuracy across eleven control samples and compare it to WGS. This demonstrates that TADGP achieves variant calling accuracy comparable to HiFi-WGS data, but at a fraction of the cost. Thus, enabling scalability and broad applicability for studying rare diseases or complementing previously sequenced samples to gain insights into these complex genes. TADGP revealed several candidate variants across all cases and provided insight into LPA diversity when tested on samples from rare disease and cardiovascular disease cohorts. In both cohorts, we identified novel variants affecting individual disease-associated genes (e.g., IKZF1, KCNE1). Nevertheless, the annotation of the variants across these 389 medically important genes remains challenging due to their underrepresentation in ClinVar and gnomAD. Consequently, we also offer an annotation resource to enhance the evaluation and prioritization of these variants. Overall, we can demonstrate that TADGP offers a cost-efficient and scalable approach to routinely assess the dark regions of the human genome with clinical relevance.

中文翻译：

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缩小差距：大规模解决复杂的医学相关基因

通过已确定的遗传成分来理解人类疾病背后的机制代表了个性化医疗的前沿。然而，由于其复杂性和重复性或人类基因组的所谓“黑暗区域”，许多医学上重要的基因在短读长测序数据分析中无法准确表示。PacBio 作为长读长平台的出现提供了新的见解，但 HiFi 全基因组测序 (WGS) 的成本仍然常常令人望而却步。我们推出了一种靶向测序和分析框架，即 Twist Alliance Dark Genes Panel (TADGP)，旨在提供 389 个医学上重要但复杂的常染色体基因的阶段性变异。我们强调了 11 个对照样本的 TADGP 准确性，并将其与 WGS 进行比较。这表明 TADGP 的变异检出精度可与 HiFi-WGS 数据相媲美，但成本仅为 HiFi-WGS 数据的一小部分。因此，为研究罕见疾病或补充先前测序的样本以深入了解这些复杂基因提供了可扩展性和广泛的适用性。TADGP 在所有病例中揭示了几种候选变异，并在对罕见疾病和心血管疾病队列的样本进行测试时提供了对 LPA 多样性的深入了解。在这两个队列中，我们发现了影响个体疾病相关基因的新变异（例如，IKZF1、KCNE1）。然而，这 389 个医学上重要的基因的变异注释仍然具有挑战性，因为它们在 ClinVar 和 gnomAD 中代表性不足。因此，我们还提供注释资源来增强对这些变体的评估和优先级排序。总体而言，我们可以证明 TADGP 提供了一种经济高效且可扩展的方法，可以定期评估具有临床相关性的人类基因组的黑暗区域。