Not only may agencies select for genetic traits, some fear parents may start to(select for genetic traits省略) as well in what might be considered the most extreme application of genetic information-designing children.
参考译文：在被认为是发挥最极致的应用方面——即设计孩子,不仅许多机构开始选择基因的特点，许多担忧的父母也开始选择基因信息。

句子整体结构解析：Not only may+主语+其它，主语+谓语+(as well)

(1)以上句子的主干结构是not only......(but also),因为用了as well, but also省略了。start to 后省略了select for genetic traits。这一句倒装是因为not only 放在了句首。

(2)In what might be considered the most extreme application of genetic information是状语，

(3)in表示在......方面。in+what引导宾语从句，构成介词短语