Large-scale medical resequencing for X-linked mental retardation.

Severe intellectual disability (ID), commonly referred to as mental retardation (MR), comprises a large collection of clinical conditions whose associated phenotypes include substantially below-average intelligence test scores and limited abilities in socially adaptive behaviors, such as communication, self-care, social interaction, and school functioning. ID/MR affects 1%–3% of the worldwide population with variable severity, is a frequent cause of pediatric, genetic, neurologic, and developmental medicine referrals, and poses huge social and economic burdens. Genetic factors, such as trisomy 21 in Down syndrome, and environmental risk factors, such as fetal alcohol syndrome, contribute to the pathogenesis of ID/MR. Although the genetic causes are heterogeneous and complex, a 30%– 40% excess of males vs females and the existence in many families of an evident X-linked inheritance pattern suggest a major role for inactivating mutations in X-chromosome genes. The notion is that these mutations cause ID/MR predominantly in males, in whom, unlike females, there is no second X chromosome present to complement the defect and thereby inhibit its phenotypic expression. Consequently, a variety of molecular genetic strategies have been applied to the X chromosome, including candidate gene analysis, linkage mapping followed by location cloning, and precise delineation of chromosomal anomalies (balanced translocation, inversion, and microdeletion/duplication). These efforts have led to the discovery of a trinucleotide expansion in the 5 untranslated region of the FMR1 (fragile X mental retardation 1) gene as the cause of fragile X syndrome, the most frequent form of X-linked ID/MR, and mutations in approximately 90 other genes in rarer families (1, 2 ). Because known genes account for less than half of the 200 delineated X-linked ID/MR conditions (http://xlmr.interfree.it/ home.htm), many novel X-linked genetic factors have yet to be identified. To address this issue, Tarpey et al. recently undertook a “drain the pond” approach in which they systematically examined the sequences of coding exons for 718 X-chromosome genes in 208 X-linked ID/MR individuals prescreened for known X-linked ID/MR gene mutations (3 ). Although this project successfully identified a number of new ID/MR-associated genes, it demonstrated the challenge of the direct-sequencing approach and presaged, for both the X chromosome and autosomes, the complexity of interpreting the genomic sequence data that are expected to accumulate rapidly with the advent of next-generation sequencing technologies (4 ). The global X-chromosome exon-sequencing approach used by Tarpey et al. offers a strategy unbiased by assumptions concerning the nature of the genes involved in ID/MR. The positive outcome of the screen was the identification of 9 X-linked ID/MR genes: AP1S2 (adaptor-related protein complex 1, sigma 2 subunit), CUL4B (cullin 4B), BRWD3 (bromodomain and WD repeat domain containing 3), UPF3B [UPF3 regulator of nonsense transcripts homolog B (yeast)], ZDHHC9 (zinc finger, DHHC-type containing 9), SLC9A6 [solute carrier family 9 (sodium/hydrogen exchanger), member 6], SYP (synaptophysin), ZNF711 (zinc finger protein 711), and CASK [calcium/calmodulindependent serine protein kinase (MAGUK family)]. These results were based on both the occurrence of one or more truncating mutations in cases but not controls and confirmation by family-based segregation with the ID phenotype. In some cases, targeted follow-up sequencing was carried out in 914 additional individuals and 1129 unaffected control individuals. Although these findings raised to approximately 11% the proportion of X-chromosome genes in which inactivating mutations are associated with ID/MR, they left nearly 75% of the X-linked ID/MR families studied without an identified mutation. Although some of these lesions could lie in gene-coding sequences on the X chromosome not assessed in this study (approximately 35% of 1 Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA; 2 Department of Laboratory Medicine, Children’s Hospital Boston, Boston, MA; Departments of 3 Neurology, 4 Pathology, and 5 Genetics, Harvard Medical School, Boston, MA. * Address correspondence to this author at: Massachusetts General Hospital/ Harvard Medical School, 185 Cambridge St., Boston, MA 02114. Fax 617-7265735; e-mail [email protected]. Received October 6, 2009; accepted December 11, 2009. Previously published online at DOI: 10.1373/clinchem.2009.135020 6 Nonstandard abbreviations: ID, intellectual disability; MR, mental retardation. 7 Human genes: FMR1, fragile X mental retardation 1; AP1S2, adaptor-related protein complex 1, sigma 2 subunit; CUL4B, cullin 4B; BRWD3, bromodomain and WD repeat domain containing 3; UPF3B, UPF3 regulator of nonsense transcripts homolog B (yeast); ZDHHC9, zinc finger, DHHC-type containing 9; SLC9A6, solute carrier family 9 (sodium/hydrogen exchanger), member 6; SYP, synaptophysin; ZNF711, zinc finger protein 711; CASK, calcium/calmodulindependent serine protein kinase (MAGUK family). Clinical Chemistry 56:3 339–341 (2010) Perspectives