Frog-
Yes or No, the goal of genetic analysis is the discovery of the cause and effect relationships between gene variants and the traits they control?
In your narrow context, no. The GOAL of genetic analysis is multifaceted. For example, phylogenetic reconstruction depends more strongly on variations within the non-coding regions and therefore does not depend on the relationship between gene variants and traits.
From the very beginning with Mendel's observations the goal has been the same. The genome project was undertaken for the same reason. To identify the variations within and between individual DNA patterns that lead to the traits and characteristics that define us.
No, again. Mendel's work was motivated by the desire to understand the mechanism of inheritance, not disease.
The human genome project was sold to congress on the PROMISE of understanding and curing disease, but was always understood to be only a prerequisite first step. The real work of began only after sequencing was "completed". Plus, with the understanding that the genome was intended to be an average genome (a combination of approximately 12 individuals, not a specific individual) it makes the type of comparisons you are referring to, impossible.
Eric Lander is often credited with this analogy. Completing the human genome project is similar to having the "parts list" to a complex machine (a Boeing 747). But the "parts list" will not tell you how it works, or worse, how to repair it. But a logical first step to ever understanding disease is to, at least, know the parts that may be involved.
I'm sure you have read the Nature article.
I have not. Please provide the reference. But to answer your question (blindly) are you asking for a proximate or ultimate interpretation of that "discovery"? Ultimately, it may mean that Homo sapiens have a larger, founding population that previously thought, or has undergone more recombination events than predicted. Proximately, for understanding disease, it means very little. The larger than expected amount of genetic variation is more than adequately handled with the myriad of statistical methods available. In fact, with more variation among individuals, any similarities between disease individuals would "flag" more strongly.
even when your evidence agrees with me you try to make it look otherwise.
You've made this claim before. What exactly are you referring to?
Good Luck.