Identification of the gene defect underlying ICF2 syndrome

描述(申请人提供)：ICF(免疫缺陷、着丝粒不稳定和面部畸形)综合征患者由于B细胞无丙种球蛋白血症和各种先天性畸形而反复发作，通常是致命的呼吸道和胃肠道感染。在大约一半的患者中，DNA甲基转移酶3B(Dnmt3b)基因的突变已被确定为ICF综合征(ICF1)的潜在原因，而在其余患者中，基因缺陷尚不清楚。这些无Dnmt3b缺陷的ICF2患者的临床表型与ICF1患者相同。所有ICF患者，包括ICF1和ICF2，都患有B细胞无丙球蛋白血症。在植物血凝素刺激下，所有ICF患者都可以识别出多辐射染色体。此外，特定的DNA重复序列显示出明显的低甲基化。这两个观察结果都被认为是ICF综合征的分子标志。由于所有ICF2患者都表现出α-卫星重复低甲基化，这是他们与ICF1患者的不同之处，因此ICF2综合征可能涉及第二个疾病位点(基因缺陷)。基因研究排除了Dnmt3b基因的三个ICF2病例的鉴定进一步证实了这一点。这一应用的中心前提是确定ICF2综合征的基因缺陷和主要致病机制。首先，使用纯合性作图的方法，在五个血缘关系良好的ICF2患者中确定表现纯合性的候选基因座。还提供了其他ICF2病例，以协助地图研究。其次，通过使用Illumina/Solexa基因组分析仪对两名近亲ICF2患者的整个人类外显子组进行测序，将识别出这些患者所有纯合子区域的所有纯合子DNA变体。携带纯合子DNA变异体的候选基因将根据SNP数据库中没有已识别的序列变异体、基因功能和密码子变化而优先考虑它们与ICF2的因果关系。最后，通过对其余患者优先候选基因的所有外显子和外显子-内含子边界的直接测序，结合对ICF2患者细胞培养中候选基因的表达研究，将识别出ICF2综合征的基因缺陷。 公共卫生相关性：这一应用的中心前提是确定ICF2综合征的基因缺陷，ICF2综合征是一种原发免疫缺陷。这将增加我们对ICF2综合征分子机制的理解，并可能为治疗提供新的线索。此外，它还将改善对这种疾病的产前和出生后诊断，并促进遗传咨询。

DESCRIPTION (provided by applicant): Patients with ICF (Immunodeficiency, Centromeric instability, and Facial anomalies) syndrome suffer from recurrent and often fatal respiratory and gastrointestinal infections due to agammaglobulinemia with B cells as well as a variety of congenital malformations. In approximately half of the patients mutations in the DNA methyltransferase 3B (DNMT3B) gene have been identified as the underlying cause of ICF syndrome (ICF1), while in the remainder of patients the gene defect is unknown. These ICF2 patients without DNMT3B defect show a clinical phenotype identical to ICF1 patients. All patients with ICF, both ICF1 and ICF2, suffer from agammaglobulinemia with B cells. Upon phytohaemagglutinin stimulation, multiradiate chromosomes can be identified in all ICF patients. In addition, specific DNA repeats show pronounced hypomethylation. Both observations are considered molecular hallmarks for ICF syndrome. Since all ICF2 patients show alpha-satellite repeat hypomethylation, which distinguishes them from ICF1 patients, the involvement of a second disease locus (gene defect) in ICF2 syndrome is expected. This is further substantiated by the identification of three ICF2 cases in which the DNMT3B gene is excluded by genetic studies. The central premise of this application is to identify the gene defect and primary pathogenic mechanism underlying ICF2 syndrome. First, using the method of homozygosity mapping, candidate loci that show homozygosity by descent in five consanguineous ICF2 patients will be identified. Additional ICF2 cases are available to aid the mapping study. Second, by sequence determination of the whole human exome in two consanguineous ICF2 patients using the Illumina/Solexa Genome Analyzer, all homozygous DNA variants in these patients in all regions of homozygosity will be identified. Candidate genes carrying homozygous DNA variants will be prioritized for their causal involvement in ICF2 based on the absence of the identified sequence variants in SNP databases, gene function and codon change. Finally, by direct sequencing of all exons and exon-intron boundaries of the prioritized candidate genes in the remaining patients in combination with expression studies of the candidate genes in cell cultures of ICF2 patients, the gene defect underlying ICF2 syndrome will be identified. PUBLIC HEALTH RELEVANCE: The central premise of this application is to identify the gene defect in ICF2 syndrome, a primary immune deficiency. This will increase our understanding of the molecular mechanism underlying ICF2 syndrome, and may provide new clues for therapy. Additionally, it will improve prenatal and postnatal diagnosis of the disease and facilitate genetic counseling.