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Background  Our genomewide studies support targeted testing the most frequent genetic diseases by patient category: (1) pregnant patients, (2) at-risk conceptuses, (3) affected children, and (4) abnormal adults. This approach not only identifies most reported disease causing sequences accurately, but also minimizes incorrectly identified additional disease causing loci.    Methods  Diseases were grouped in descending order of occurrence from four data sets: (1) GeneTests 534 listed population prevalences, (2) 4129 high risk prenatal karyotypes, (3) 1265 affected patient microarrays, and (4) reanalysis of 25,452 asymptomatic patient results screened prenatally for 108 genetic diseases. These most frequent diseases are categorized by transmission: (A) autosomal recessive, (B) X-linked, (C) autosomal dominant, (D) microscopic chromosome rearrangements, (E) submicroscopic copy number changes, and (F) frequent ethnic diseases.    Results  Among affected and carrier patients worldwide, most reported mutant genes would be identified correctly according to one of four patient categories from at-risk couples with <64 tested genes to affected adults with 314 tested loci.  Three clinically reported patient series  confirmed this approach.  First, only 54 targeted chromosomal sites  would have detected  all  938 microscopically visible  unbalanced  karyotypes among 4129 karyotyped POC, CVS, and amniocentesis samples.  Second ,  37 of 48 reported aneuploid regions  were found among our 1265 clinical microarrays confirming the locations of  8 schizophrenia loci  and  20 aneuploidies altering intellectual ability , while also  identifying 9 of the most frequent deletion syndromes. Third,  testing  15 frequent genes  would have identified 124 couples with a 1 in 4 risk of a fetus with a recessive disease compared to the 127 couples identified by testing all 108 genes, while testing all mutations in 15 genes could have identified more couples.    Conclusion  Testing the  most frequent disease causing abnormalities in 1 of 8 reported disease loci [~1 of 84 total genes]  will identify   ~   7 of 8 reported abnormal Caucasian newborn genotypes . This would eliminate ~8 to 10 of ~10 Caucasian newborn gene sequences selected as abnormal that are actually normal variants identified when testing all ~2500 diseases looking for the remaining 1 of 8 disease causing genes. This approach enables more accurate testing within available laboratory and reimbursement resources.    Electronic supplementary material  The online version of this article (doi:10.1186/s12967-014-0333-8) contains supplementary material, which is available to authorized users.

Analyzing the most frequent disease loci in targeted patient categories optimizes disease gene identification and test accuracy worldwide