title: Rare copy number variations in congenital heart disease patients identify unique genes in left-right patterning.
abstract: Dominant human genetic diseases that impair reproductive fitness and have high locus heterogeneity constitute a problem for gene discovery because the usual criterion of finding more mutations in specific genes than expected by chance may require extremely large populations. Heterotaxy (Htx), a congenital heart disease resulting from abnormalities in left-right (LR) body patterning, has features suggesting that many cases fall into this category. In this setting, appropriate model systems may provide a means to support implication of specific genes. By high-resolution genotyping of 262 Htx subjects and 991 controls, we identify a twofold excess of subjects with rare genic copy number variations in Htx (14.5% vs. 7.4%, P = 1.5 × 10(-4)). Although 7 of 45 Htx copy number variations were large chromosomal abnormalities, 38 smaller copy number variations altered a total of 61 genes, 22 of which had Xenopus orthologs. In situ hybridization identified 7 of these 22 genes with expression in the ciliated LR organizer (gastrocoel roof plate), a marked enrichment compared with 40 of 845 previously studied genes (sevenfold enrichment, P < 10(-6)). Morpholino knockdown in Xenopus of Htx candidates demonstrated that five (NEK2, ROCK2, TGFBR2, GALNT11, and NUP188) strongly disrupted both morphological LR development and expression of pitx2, a molecular marker of LR patterning. These effects were specific, because 0 of 13 control genes from rare Htx or control copy number variations produced significant LR abnormalities (P = 0.001). These findings identify genes not previously implicated in LR patterning.
authors.affiliation: Department of Genetics, The Howard Hughes Medical Institute,Yale University School of Medicine, New Haven, CT 06520, USA.
authors.forename: Khalid A
authors.initials: KA
authors.lastname: Fakhro
authors.forename: Murim
authors.initials: M
authors.lastname: Choi
authors.forename: Stephanie M
authors.initials: SM
authors.lastname: Ware
authors.forename: John W
authors.initials: JW
authors.lastname: Belmont
authors.forename: Jeffrey A
authors.initials: JA
authors.lastname: Towbin
authors.forename: Richard P
authors.initials: RP
authors.lastname: Lifton
authors.forename: Mustafa K
authors.initials: MK
authors.lastname: Khokha
authors.forename: Martina
authors.initials: M
authors.lastname: Brueckner
mesh_terms: D000818:Animals; D019521:Body Patterning / Q000235:genetics*; D002869:Chromosome Aberrations; D056915:DNA Copy Number Variations / Q000235:genetics*; D005775:Gastrula / Q000196:embryology / Q000378:metabolism; D055785:Gene Knockdown Techniques; D005838:Genotype; D006330:Heart Defects, Congenital / Q000235:genetics*; D018398:Homeodomain Proteins / Q000235:genetics / Q000378:metabolism; D006801:Humans; D017403:In Situ Hybridization; D017350:N-Acetylgalactosaminyltransferases / Q000235:genetics; D028861:Nuclear Pore Complex Proteins / Q000235:genetics; D017346:Protein Serine-Threonine Kinases / Q000235:genetics; D018125:Receptors, Transforming Growth Factor beta / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D014981:Xenopus / Q000235:genetics*; D029867:Xenopus Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D018398:Homeodomain Proteins; D028861:Nuclear Pore Complex Proteins; C416234:Nup188 protein, Xenopus; C438619:Pitx2b protein, Xenopus; D018125:Receptors, Transforming Growth Factor beta; D014157:Transcription Factors; D029867:Xenopus Proteins; D017350:N-Acetylgalactosaminyltransferases; C490316:NEK2 protein, Xenopus; D017346:Protein Serine-Threonine Kinases