Targeted Resequencing of the Pericentromere of Chromosome 2 Linked to Constitutional Delay of Growth and Puberty

Constitutional delay of growth and puberty (CDGP) is the most common cause of pubertal delay. CDGP is defined as the proportion of the normal population who experience pubertal onset at least 2 SD later than the population mean, representing 2.3% of all adolescents. While adolescents with CDGP spontaneously enter puberty, they are at risk for short stature, decreased bone mineral density, and psychosocial problems. Genetic factors contribute heavily to the timing of puberty, but the vast majority of CDGP cases remain biologically unexplained, and there is no definitive test to distinguish CDGP from pathological absence of puberty during adolescence. Recently, we published a study identifying significant linkage between a locus at the pericentromeric region of chromosome 2 (chr 2) and CDGP in Finnish families. To investigate this region for causal variation, we sequenced chr 2 between the genomic coordinates of 79–124 Mb (genome build GRCh37) in the proband and affected parent of the 13 families contributing most to this linkage signal. One gene, DNAH6, harbored 6 protein-altering low-frequency variants (< 6% in the Finnish population) in 10 of the CDGP probands. We sequenced an additional 135 unrelated Finnish CDGP subjects and utilized the unique Sequencing Initiative Suomi (SISu) population reference exome set to show that while 5 of these variants were present in the CDGP set, they were also present in the Finnish population at similar frequencies. Additional variants in the targeted region could not be prioritized for follow-up, possibly due to gaps in sequencing coverage or lack of functional knowledge of non-genic genomic regions. Thus, despite having a well-characterized sample collection from a genetically homogeneous population with a large population-based reference sequence dataset, we were unable to pinpoint variation in the linked region predisposing delayed puberty. This study highlights the difficulties of detecting genetic variants under linkage regions for complex traits and suggests that advancements in annotation of gene function and regulatory regions of the genome will be critical for solving the genetic background of complex phenotypes like CDGP.

生长发育与青春期发育延迟（Constitutional delay of growth and puberty, CDGP）是引发青春期延迟最常见的病因。CDGP被定义为正常人群中青春期启动时间较群体均值晚至少2个标准差的个体，占所有青少年群体的2.3%。尽管CDGP青少年可自发性进入青春期，但他们面临身材矮小、骨密度降低以及社会心理问题的风险。遗传因素对青春期启动时间影响显著，但绝大多数CDGP病例仍无法从生物学层面得到解释，且目前尚无明确检测手段可在青少年时期区分CDGP与病理性青春期缺如。近期，我们发表了一项研究，证实芬兰家系中2号染色体着丝粒旁区域（chr 2）的位点与CDGP存在显著连锁关联。为探究该区域的致病变异，我们对13个对该连锁信号贡献最大的家系的先证者及受累亲本，进行了基因组坐标79–124 Mb区间（基因组版本GRCh37）内的2号染色体测序。其中，DNAH6基因在10名CDGP先证者中携带6个会改变蛋白质序列的低频变异（芬兰人群中频率<6%）。我们额外对135名无关芬兰CDGP受试者进行了测序，并借助独特的芬兰测序计划（Sequencing Initiative Suomi, SISu）人群参考外显子组数据集，结果显示：尽管其中5个变异在CDGP组中存在，但其在芬兰人群中的出现频率与之相近。靶向区域内的其他变异无法被优先选为后续研究对象，这可能源于测序覆盖度存在缺口，或是目前对非编码基因组区域的功能认知不足。因此，尽管我们依托遗传同源性较高的人群建立了经过良好表征的样本库，并搭配了大规模人群参考测序数据集，仍无法定位到连锁区域内与青春期延迟易感性相关的变异。本研究凸显了针对复杂性状的连锁区域内遗传变异检测的难点，并提示，对基因功能及基因组调控区域的注释进展，将是解析CDGP这类复杂表型遗传基础的关键所在。