Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Av. Getúlio Vargas, 333, Quitandinha CEP: 25651-075, Petrópolis, Rio de Janeiro, Brazil.
Allergy and Immunology Service of Institute of Women, Children and Adolescents' Health Fernandes Figueira (IFF/FIOCRUZ), Rio de Janeiro, RJ, Brazil.
BMC Genom Data. 2023 Aug 17;24(1):47. doi: 10.1186/s12863-023-01148-z.
Inherited genetic defects in immune system-related genes can result in Inborn Errors of Immunity (IEI), also known as Primary Immunodeficiencies (PID). Diagnosis of IEI disorders is challenging due to overlapping clinical manifestations. Accurate identification of disease-causing germline variants is crucial for appropriate treatment, prognosis, and genetic counseling. However, genetic sequencing is challenging in low-income countries like Brazil. This study aimed to perform genetic screening on patients treated within Brazil's public Unified Health System to identify candidate genetic variants associated with the patient's phenotype.
Thirteen singleton unrelated patients from three hospitals in Rio de Janeiro were enrolled in this study. Genomic DNA was extracted from the peripheral blood lymphocytes of each patient, and whole exome sequencing (WES) analyses were conducted using Illumina NextSeq. Germline genetic variants in IEI-related genes were prioritized using a computational framework considering their molecular consequence in coding regions; minor allele frequency ≤ 0.01; pathogenicity classification based on American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) guidelines gathered from the VarSome clinical database; and IEI-related phenotype using the Franklin tool. The genes classification into IEI categories follows internationally recognized guidelines informed by the International Union of Immunological Societies Expert Committee. Additional methods for confirmation of the variant included Sanger sequencing, phasing analysis, and splice site prediction.
A total of 16 disease-causing variants in nine genes, encompassing six different IEI categories, were identified. X-Linked Agammaglobulinemia, caused by BTK variations, emerged as the most prevalent IEI disorder in the cohort. However, pathogenic and likely pathogenic variants were also reported in other known IEI-related genes, namely CD40LG, CARD11, WAS, CYBB, C6, and LRBA. Interestingly, two patients with suspected IEI exhibited pathogenic variants in non-IEI-related genes, ABCA12 and SLC25A13, potentially explaining their phenotypes.
Genetic screening through WES enabled the detection of potentially harmful variants associated with IEI disorders. These findings contribute to a better understanding of patients' clinical manifestations by elucidating the genetic basis underlying their phenotypes.
免疫系统相关基因的遗传缺陷可导致先天性免疫缺陷（IEI），也称为原发性免疫缺陷（PID）。由于临床表现重叠，IEI 疾病的诊断具有挑战性。准确识别致病种系变异对于适当的治疗、预后和遗传咨询至关重要。然而，在像巴西这样的低收入国家，基因测序具有挑战性。本研究旨在对在巴西公立统一卫生系统接受治疗的患者进行基因筛查，以鉴定与患者表型相关的候选遗传变异。
本研究纳入了来自里约热内卢三家医院的 13 名单倍体无关患者。从每位患者的外周血淋巴细胞中提取基因组 DNA，并使用 Illumina NextSeq 进行全外显子组测序（WES）分析。使用考虑编码区域中分子后果的计算框架、等位基因频率≤0.01、基于美国医学遗传学与基因组学学院和分子病理学协会（ACMG/AMP）指南的致病性分类、以及 Franklin 工具中的 IEI 相关表型，对 IEI 相关基因中的种系遗传变异进行优先级排序。根据国际免疫学会联合会专家委员会的建议，对基因进行分类，归入国际公认的 IEI 类别。变体确认的其他方法包括 Sanger 测序、相位分析和剪接位点预测。
在 9 个基因中发现了 16 个致病变异，涵盖了 6 个不同的 IEI 类别。X 连锁无丙种球蛋白血症，由 BTK 变异引起，是该队列中最常见的 IEI 疾病。然而，其他已知的 IEI 相关基因（CD40LG、CARD11、WAS、CYBB、C6 和 LRBA）也报告了致病性和可能致病性变异。有趣的是，两名疑似 IEI 的患者表现出非 IEI 相关基因 ABCA12 和 SLC25A13 的致病性变异，这可能解释了他们的表型。
通过 WES 进行基因筛查可检测与 IEI 疾病相关的潜在有害变异。这些发现通过阐明表型背后的遗传基础，有助于更好地理解患者的临床表现。
