Here is some information you might be after:

https://www.ncbi.nlm.nih.gov/pubmed/21881504

http://www.nature.com/articles/npjgenmed201512

In very simple words, if you just want to see chromosomal aberrations then go for Array CGH, if you want to see point mutations in some selected group of genes then you may go for NGS gene panel sequencing, if you want to do exome for diagnostics then its OK. If you are still unable to identify your gene of choice then last option is whole genome sequencing.

The target gene sequencing ie. Sanger sequencing, arrayCGH and whole exome sequencing we have successfully used for our cases. 

Best of luck

I second Dr.Musharaf Jelani....!!!

WES: only exons

WGS: whole genome

WES is easier to analyze while WGS is difficult to alalyze.

Go for WES for diagnostic samples, its one of the best method to identify the causitive variant in a known or novel gene.

Thankx