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Orphan human Mendelian recessive diseases are individually rare, but together constitute a major healthcare burden and cause significant childhood morbidity and mortality. 20-30% of all infant deaths and 11% of pediatric hospital admissions are related to genetic disorders. In collaboration with the Beyond Batten Disease Foundation, NCGR is developing a carrier screening test for 448 autosomal recessive (AR) and X-linked recessive (XLR) disorders caused by tens of thousands of mutations.The screening test will utilize target enrichment of genes, multiplexed deep, next-generation sequencing, and automated bioinformatic analysis to indentify carrier status for causal mutations for the 448 selected disorders.To identify the appropriate target enrichment technology for the carrier screening test, a total of 24 samples from carriers of 17 autosomal recessive diseases and 1 X-linked recessive disease were enriched for 437 genes using Agilent SureSelect, RainDance, febit, and Olink enrichment techniques and subjected to multiplexed deep sequencing using the Illumina GA IIx. The 24 samples contained 42 previously characterized mutations including 18 SNPs, 12 short in/dels, and 7 gross deletions impacting both coding and splicing elements. The four enrichment techniques were evaluated for % sequencing reads on target, fold enrichment and mutation detection, with a desired sequencing threshold of at least 20x coverage of at least 99% of targeted nucleotides based upon 500 Mb of aligned sequences, less than 1% of targeted nucleotides with zero coverage, and very high sensitivity and specificity for heterozygous variant detection.The results of the target enrichment comparison will be presented.The orphan disease carrier screening assessment will become available in early 2010 and is targeted to cost $500.