Gem stones are used by many of us for some reason or other. Why we use these stones, is known to few of us. As a matter of fact, when we were born, our body physiology was more or less affected by the prevailing ambience, the materials surrounding us, the influence of the celestial bodies, like Sun, Moon, other planets, stars etc. Our nerve centres, our circulatory system, our digestive system all have been influenced by such elements. As for an example, you can note that when a man is born in USA at the same time let us say aanother man is born in India. They will differ in their physiology for the reasons already stated above. In addition this, the genetical influence also matters. 

A gem stone is prescribed, to bestow beneficial results  to the native. So we have to really examine the various astrological parameters of the person and then only prescribe. The basic and simple logic is to recommend a gem stone, which is beneficial for the native. For example, the lord of the nineth house and the lord of the fifth house are always beneficial to any person. So we need to prescribe gem stones accordingly. Let us say a person's ascendant is Cancer. Then Jupitor is its nineth house. So prescribe yellow saphire for such native. Again his 5th house lord is Mars. Red Coral or Moonga is the stone for Mars. You can prescribe this stone for this native. If you examine in detail, you can know that, Mars is yoga karaka for this native, because Mars is the lord of 10th and 5th i.e. the lord of quadrant and trine. Hence for such natives, Red Coral or Moonga stone is prescribed.