We developed a bacterial artificial chromosome/phage artifical chromosome (BAC/PAC) contig covering a ∼2.5-cM SCIDA region defined by linkage disequilibrium analysis, from which we isolated over 30 microsatellite markers and further refined the region to a ∼500-kb interval by haplotype analysis ( 21).

In an attempt to identify the SCIDA gene, we conducted a combined positional candidate and positional cloning approach. To date, no human SCID cases have been associated with mutations in the above factors, which have also been excluded from causing RS-SCID or SCIDA ( 8, 11). The resolution of the coding and signal ends depends on several ubiquitously expressed proteins, including DNA-protein kinase catalytic subunit (PKcs), Ku 80/70 complex, XRCC4, and DNA ligase IV, which are essential factors for the general nonhomologous end joining machinery. The functional significance of RAG proteins has been well demonstrated in RAG-deficient mice and also in T −B −NK + SCID cases found to have RAG mutations ( 4, 5, 6). The cleavage leaves blunt signal ends (with RSSs at the ends) that can be directly ligated, and covalently sealed hairpinned coding ends, which require further processing before the rejoining of different V, (D), and J segments into various exon-encoding Ag recognition sites. It has been well established that V(D)J recombination is initiated by the RAG1/2 complex, which recognizes the recombination signal sequences (RSSs) that flank the V, D, and J segments and introduce DNA double-strand breaks (DSBs) between the RSSs and the coding sequences ( 19, 20). V(D)J recombination is the mechanism by which V, D, and J gene segments of Igs and TCRs are rearranged and assembled in the germline into the exon-encoding Ag recognition receptors in lymphoid cells ( 18). Finally, we found that the SCIDA primary transcript (Artemis) encodes a nuclear protein. We also discovered three additional alternative exons and detected at least six alternatively spliced SCIDA variants (SCIDA-V1, 2, 3, 4, 5, and 6) coexisting with the primary transcript in trace amounts. The above results indicate that this SNM1-like gene (Artemis) is the gene responsible for SCIDA. The wild-type construct of the primary transcript can effectively complement the defective coding joint and reduced signal joint formation in SCIDA fibroblasts. This nonsense founder mutation results in the truncation of the deduced protein product. In our evaluation of this gene, we have identified a unique nonsense mutation in 21 SCIDA patients that is closely correlated to the founder haplotypes that we had previously identified. One of the transcripts showed significant homology with the mouse and yeast SNM1/PSO 2 and was recently reported (Artemis) to be responsible for another T −B −NK + SCID condition (radiation sensitive SCID) in 13 patients of primarily European origin.

After excluding potential candidate genes, we conducted a combined positional candidate and positional cloning approach leading to the identification of nine novel transcripts in the refined SCIDA region. SCIDA fibroblasts were found to have defective coding joint and reduced, but precise signal joint formation during V(D)J recombination. We previously mapped the SCIDA gene to a 6.5-cM interval on chromosome 10p. Athabascan SCID (SCIDA) is an autosomal recessive disorder found among Athabascan-speaking Native Americans and is manifested by the absence of both T and B cells (T −B −NK + SCID).

What mutation causes SCIDS