美国国家癌症研究所Shyam K. Sharan课题组，实现了基于饱和基因组编辑的BRCA2变体临床分类。相关论文于2025年1月8日在线发表在《自然》杂志上。

研究人员利用CRISPR–Cas9基因组编辑技术，在人源化小鼠胚胎干细胞系中确定了不确定意义的变异（VUS）的功能效应。研究人员对编码BRCA2羧基末端DNA结合域的区域内几乎所有可能的单核苷酸变异（SNV）进行了分类。研究人员为6551个SNV生成了功能评分，覆盖了BRCA2残基2479–3216的外显子15–26区间内96.4%的可能SNV。

这些变异包括1282个在临床变异数据库ClinVar中被分类为错义VUS的SNV，依据研究人员提出的功能评分，其中77.2%被归类为良性，20.4%被归类为致病性。检测结果表明，区域内3384个SNV是良性的，776个是致病性的。

研究人员的分类与ClinVar的致病性数据、正交功能检测和计算元预测结果高度一致。研究人员将基于胚胎干细胞的BRCA2饱和基因组编辑数据集与其他可用证据结合，并利用美国医学遗传学会（ACMG）/分子病理学协会（AMP）指南对所有可能的SNV进行了临床分类。该分类以序列-功能图的形式提供，是解读人群中未知变异以及为医生和遗传咨询师评估BRCA2 VUS的宝贵资源。

据悉，基于测序的遗传检测揭示了大量BRCA2序列变异。由于临床、家族和流行病学数据的限制，成千上万的变异被视为VUS。

附：英文原文

Title: Saturation genome editing-based clinical classification of BRCA2 variants

Author: Sahu, Sounak, Galloux, Melissa, Southon, Eileen, Caylor, Dylan, Sullivan, Teresa, Arnaudi, Matteo, Zanti, Maria, Geh, Josephine, Chari, Raj, Michailidou, Kyriaki, Papaleo, Elena, Sharan, Shyam K.

Issue&Volume: 2025-01-08

Abstract: Sequencing-based genetic tests have uncovered a vast array of BRCA2 sequence variants1. Owing to limited clinical, familial and epidemiological data, thousands of variants are considered to be variants of uncertain significance2,3,4 (VUS). Here we have utilized CRISPR–Cas9-based saturation genome editing in a humanized mouse embryonic stem cell line to determine the functional effect of VUS. We have categorized nearly all possible single nucleotide variants (SNVs) in the region that encodes the carboxylate-terminal DNA-binding domain of BRCA2. We have generated function scores for 6,551 SNVs, covering 96.4% of possible SNVs in exons 15–26 spanning BRCA2 residues 2479–3216. These variants include 1,282 SNVs that are categorized as missense VUS in the clinical variant database ClinVar, with 77.2% of these classified as benign and 20.4% classified as pathogenic using our functional score. Our assay provides evidence that 3,384 of the SNVs in the region are benign and 776 are pathogenic. Our classification aligns closely with pathogenicity data from ClinVar, orthogonal functional assays and computational meta predictors. We have integrated our embryonic stem cell-based BRCA2-saturation genome editing dataset with other available evidence and utilized the American College of Medical Genetics and Genomics/Association for Molecular Pathology guidelines for clinical classification of all possible SNVs. This classification is available as a sequence–function map and serves as a valuable resource for interpreting unidentified variants in the population and for physicians and genetic counsellors to assess BRCA2 VUS in patients.

DOI: 10.1038/s41586-024-08349-1

Source: https://www.nature.com/articles/s41586-024-08349-1