Mateo Robertino Karlo, Johnson Royce, Lehmann Ordan J
Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada.
Mol Vis. 2012;18:1301-11. Epub 2012 May 30.
Manitoba Oculotrichoanal (MOTA) syndrome is an autosomal recessive disorder present in First Nations families that is characterized by ocular (cryptophthalmos), facial, and genital anomalies. At the commencement of this study, its genetic basis was undefined.
Homozygosity analysis was employed to map the causative locus using DNA samples from four probands of Cree ancestry. After single nucleotide polymorphism (SNP) genotyping, data were analyzed and exported to PLINK to identify regions identical by descent (IBD) and common to the probands. Candidate genes within and adjacent to the IBD interval were sequenced to identify pathogenic variants, with analyses of potential deletions or duplications undertaken using the B-allele frequency and log(2) ratio of SNP signal intensity.
Although no shared IBD region >1 Mb was evident on preliminary analysis, adjusting the criteria to permit the detection of smaller homozygous IBD regions revealed one 330 Kb segment on chromosome 9p22.3 present in all 4 probands. This interval comprising 152 SNPs, lies 16 Kb downstream of FRAS1-related extracellular matrix protein 1 (FREM1), and no copy number variations were detected either in the IBD region or FREM1. Subsequent sequencing of both genes in the IBD region, followed by FREM1, did not reveal any mutations.
This study illustrates the utility of studying geographically isolated populations to identify genomic regions responsible for disease through analysis of small numbers of affected individuals. The location of the IBD region 16 kb from FREM1 suggests the phenotype in these patients is attributable to a variant outside of FREM1, potentially in a regulatory element, whose identification may prove tractable to next generation sequencing. In the context of recent identification of FREM1 coding mutations in a proportion of MOTA cases, characterization of such additional variants offers scope both to enhance understanding of FREM1's role in cranio-facial biology and may facilitate genetic counselling in populations with high prevalences of MOTA to reduce the incidence of this disorder.
曼尼托巴眼鼻肛（MOTA）综合征是一种常染色体隐性疾病，存在于原住民家庭中，其特征为眼部（隐眼畸形）、面部和生殖器异常。在本研究开始时，其遗传基础尚不明确。
采用纯合性分析，利用来自4名克里族血统先证者的DNA样本对致病基因座进行定位。在进行单核苷酸多态性（SNP）基因分型后，对数据进行分析并导出至PLINK，以识别先证者共有的同源区域（IBD）。对IBD区间内及相邻的候选基因进行测序，以识别致病变异，并利用SNP信号强度的B等位基因频率和log(2)比值对潜在的缺失或重复进行分析。
尽管在初步分析中未发现大于1 Mb的共享IBD区域，但调整标准以允许检测较小的纯合IBD区域后，发现所有4名先证者的9号染色体p22.3上均存在一个330 Kb的片段。该区间包含152个SNP，位于FRAS1相关细胞外基质蛋白1（FREM1）下游16 Kb处，在IBD区域或FREM1中均未检测到拷贝数变异。随后对IBD区域内的两个基因以及FREM1进行测序，未发现任何突变。
本研究说明了研究地理上隔离的人群以通过分析少量受影响个体来识别疾病相关基因组区域的实用性。IBD区域距FREM1 16 kb的位置表明，这些患者的表型归因于FREM1之外的一个变异，可能存在于一个调控元件中，其识别可能通过下一代测序得以实现。鉴于最近在部分MOTA病例中发现了FREM1编码突变，对这类其他变异的表征既有助于加深对FREM1在颅面生物学中作用的理解，也可能有助于在MOTA高发人群中进行遗传咨询，以降低该疾病的发病率。
