Interpreting Genetic Variants of Uncertain Significance

描述（由申请人提供）：人类个体基因组测序可能很快就会在某些临床环境中成为常规——例如，诊断儿科患者的疑似孟德尔疾病，或指导癌症治疗的治疗决策。然而，即使其成本降至1000美元或更低，“个人基因组”的价值仍将受到个体遗传变异的低可解释性的高度限制。例如，尽管BRCA1和BRCA2在存在功能丧失突变时具有临床可操作性，尽管在过去十年中，这两个基因已在50万例患者中进行了测序，但返回给患者的结果往往仍然是“意义不确定的变体”。随着临床测序的加速和临床可操作基因列表的增长，这一挑战将深刻深化。为了解决这个问题，我们建议开发一种新的方法，在前所未有的规模上实验测量这种“不确定意义的变异”的功能后果，以及用于估计整个人类基因组中任何可能变异的相对致病性的创新计算方法。对于临床相关基因，我们将利用大量并行技术进行核酸合成和测序，以达到饱和分辨率解剖功能的新范式。该范例的应用将对所有可能的单一残基变异的功能后果产生实验基础预测，从而为解释在患者中新观察到的变异提供信息。对于人类基因组的其余部分，我们将开发一个框架，将不断增加的编码和非编码注释的多样性整合到一个单一的度量。然后，我们将计算人类基因组中所有可能的单核苷酸变异的相对致病性度量。我们预计，这些方法和由此产生的致病性“预计算”将广泛地使人类基因组序列在不同的临床和研究环境中得到解释。

DESCRIPTION (provided by applicant): The sequencing of individual human genomes may soon be routine in certain clinical contexts - for example, to diagnose suspected Mendelian disorders in pediatric patients, or to guide therapeutic decisions in cancer treatment. However, even as its cost plummets to $1,000 or less, the value of a "personal genome" will remain highly constrained by the poor interpretability of individual genetic variants. For example, although BRCA1 and BRCA2 are clinically actionable when loss-of-function mutations are present, and although both genes have been sequenced in >50,000 patients over the past decade, the result returned to patients is often still "variant of uncertain significance". This challenge will profoudly deepen as clinical sequencing accelerates and as the list of clinically actionable genes grows. To address this, we propose to develop a novel approach for experimentally measuring the functional consequences of such "variants of uncertain significance" at an unprecedented scale, as well as innovative computational approaches for estimating the relative pathogenicity of any possible variant in the entire human genome. For clinically relevant genes, we will exploit massively parallel technologies for nucleic acid synthesis and sequencing towards a new paradigm for dissecting function at saturating resolution. The application of this paradigm will yield experimentally grounded predictions for the functional consequences of all possible single residue variants, thereby informing the interpretation of variants newly observed in patients. For the remainder of the human genome, we will develop a framework for integrating a proliferating diversity of coding and non-coding annotations to a single metric. We will then calculate this metric of relative pathogenicity for all possible single nucleotide variants in the human genome. We anticipate that these methods and the resulting "pre-computations" of pathogenicity will broadly enable the interpretation of human genome sequences in diverse clinical and research settings.