Confirming genes influencing risk to cleft lip with/without cleft palate in a case-parent trio study.

A collection of 1,108 case-parent trios ascertained through an isolated, nonsyndromic cleft lip with or without cleft palate (CL/P) was used to replicate the findings from a genome-wide association study (GWAS) conducted by Beaty et al. (Nat Genet 42:525-529, 2010), where four different genes/regions were identified as influencing risk to CL/P. Tagging SNPs for 33 different genes were genotyped (1,269 SNPs). All four of the genes originally identified as showing genome-wide significance (IRF6, ABCA4 and MAF, plus the 8q24 region) were confirmed in this independent sample of trios (who were primarily of European and Southeast Asian ancestry). In addition, eight genes classified as 'second tier' hits in the original study (PAX7, THADA, COL8A1/FILIP1L, DCAF4L2, GADD45G, NTN1, RBFOX3 and FOXE1) showed evidence of linkage and association in this replication sample. Meta-analysis between the original GWAS trios and these replication trios showed PAX7, COL8A1/FILIP1L and NTN1 achieved genome-wide significance. Tests for gene-environment interaction between these 33 genes and maternal smoking found evidence for interaction with two additional genes: GRID2 and ELAVL2 among European mothers (who had a higher rate of smoking than Asian mothers). Formal tests for gene-gene interaction (epistasis) failed to show evidence of statistical interaction in any simple fashion. This study confirms that many different genes influence risk to CL/P.

Jackson-Weiss and Crouzon syndromes are allelic with mutations in fibroblast growth factor receptor 2.

Jackson-Weiss syndrome is an autosomal dominant condition characterized by craniosynostosis, foot anomalies and great phenotypic variability. Recently mutations in fibroblast growth factor receptor 2 (FGFR2) have been found in patients with another craniosynostotic syndrome, Crouzon syndrome. FGFR2 is a member of the tyrosine kinase receptor superfamily, having a high affinity for peptides that signal the transduction pathways for mitogenesis, cellular differentiation and embryogenesis. We now report an FGFR2 mutation in the conserved region of the immunoglobulin IIIc domain in the Jackson-Weiss syndrome family in which the syndrome was originally described. In addition, in four of 12 Crouzon syndrome cases, we identified two new mutations and found two previously described mutations in the same region.

Reverse transcriptase encoded by a human transposable element.

L1 elements are highly repeated mammalian DNA sequences whose structure suggests dispersal by retrotransposition. A consensus L1 element encodes a protein with sequence similarity to known reverse transcriptases. The second open reading frame from the human L1 element L1.2A was expressed as a fusion protein targeted to Ty1 virus-like particles in Saccharomyces cerevisiae and shown to have reverse transcriptase activity. This activity was eliminated by a missense mutation in the highly conserved amino acid motif Y/F-X-D-D. Thus, L1 represents a potential source of the reverse transcriptase activity necessary for dispersion of the many classes of mammalian retroelements.

Isolation of an active human transposable element.

Two de novo insertions of truncated L1 elements into the factor VIII gene on the X chromosome have been identified that produced hemophilia A. A full-length L1 element that is the likely progenitor of one of these insertions was isolated by its sequence identity to the factor VIII insertion. This L1 element contains two open-reading frames and is one of at least four alleles of a locus on chromosome 22 that has been occupied by an L1 element for at least 6 million years.

An in vivo assay for the reverse transcriptase of human retrotransposon L1 in Saccharomyces cerevisiae.

L1 elements constitute a highly repetitive human DNA family (50,000 to 100,000 copies) lacking long terminal repeats and ending in a poly(A) tail. Some L1 elements are capable of retrotransposition in the human genome (Kazazian, H. H., Jr., C. Wong, H. Youssoufian, A. F. Scott, D. G. Phillips, and S.E. Antonarakis, Nature (London) 332:164-166, 1988). Although most are 5' truncated, a consensus sequence of complete L1 elements is 6 kb long and contains two open reading frames (ORFs) (Scott, A. F., B. J. Schmeckpeper, M. Abdelrazik, C. T. Comey, B. O'Hara, J. P. Rossiter, T. Cooley, P. Health, K. D. Smith, and L. Margolet, Genomics 1:113-125, 1987). The protein encoded by ORF2 has reverse transcriptase (RT) activity in vitro (Mathias, S. L., A. F. Scott, H. H. Kazazian, Jr., J. D. Boeke, and A. Gabriel, Science 254:1808-1810, 1991). Because L1 elements are so numerous, efficient methods for identifying active copies are required. We have developed a simple in vivo assay for the activity of L1 RT based on the system developed by Derr et al. (Derr, L. K., J. N. Strathern, and D. J. Garfinkel, Cell 67:355-364, 1991) for yeast HIS3 pseudogene formation. L1 ORF2 displays an in vivo RT activity similar to that of yeast Ty1 RT in this system and generates pseudogenes with unusual structures. Like the HIS3 pseudogenes whose formation depends on Ty1 RT, the HIS3 pseudogenes generated by L1 RT are joined to Ty1 sequences and often are part of complex arrays of Ty1 elements, multiple HIS3 pseudogenes, and hybrid Ty1/L1 elements. These pseudogenes differ from those previously described in that there are base pairs of unknown origin inserted at several of the junctions. In two of three HIS3 pseudogenes studied, the L1 RT appears to have jumped from the 5' end of a Ty1/L1 transcript to the poly(A) tract of the HIS3 RNA.

High throughput SNP and expression analyses of candidate genes for non-syndromic oral clefts.

BACKGROUND: Recent work suggests that multiple genes and several environmental risk factors influence risk for non-syndromic oral clefts, one of the most common birth defects in humans. Advances in high-throughput genotyping technology now make it possible to test multiple markers in many candidate genes simultaneously. METHODS: We present findings from family based association tests of single nucleotide polymorphism (SNP) markers in 64 candidate genes genotyped using the BeadArray approach in 58 case-parent trios from Maryland (USA) to illustrate how multiple markers in multiple genes can be analysed. To assess whether these genes were expressed in human craniofacial structures relevant to palate and lip development, we also analysed data from the Craniofacial and Oral Gene Expression Network (COGENE) consortium, and searched public databases for expression profiles of these genes. RESULTS: Thirteen candidate genes showed significant evidence of linkage in the presence of disequilibrium, and ten of these were found to be expressed in relevant embryonic tissues: SP100, MLPH, HDAC4, LEF1, C6orf105, CD44, ALX4, ZNF202, CRHR1, and MAPT. Three other genes showing statistical evidence (ADH1C, SCN3B, and IMP5) were not expressed in the embryonic tissues examined here. CONCLUSIONS: This approach demonstrates how statistical evidence on large numbers of SNP markers typed in case-parent trios can be combined with expression data to identify candidate genes for complex disorders. Many of the genes reported here have not been previously studied as candidates for oral clefts and warrant further investigation.

Haplotype diversity in 11 candidate genes across four populations.

Analysis of haplotypes based on multiple single-nucleotide polymorphisms (SNP) is becoming common for both candidate gene and fine-mapping studies. Before embarking on studies of haplotypes from genetically distinct populations, however, it is important to consider variation both in linkage disequilibrium (LD) and in haplotype frequencies within and across populations, as both vary. Such diversity will influence the choice of "tagging" SNPs for candidate gene or whole-genome association studies because some markers will not be polymorphic in all samples and some haplotypes will be poorly represented or completely absent. Here we analyze 11 genes, originally chosen as candidate genes for oral clefts, where multiple markers were genotyped on individuals from four populations. Estimated haplotype frequencies, measures of pairwise LD, and genetic diversity were computed for 135 European-Americans, 57 Chinese-Singaporeans, 45 Malay-Singaporeans, and 46 Indian-Singaporeans. Patterns of pairwise LD were compared across these four populations and haplotype frequencies were used to assess genetic variation. Although these populations are fairly similar in allele frequencies and overall patterns of LD, both haplotype frequencies and genetic diversity varied significantly across populations. Such haplotype diversity has implications for designing studies of association involving samples from genetically distinct populations.

A paternally derived inverted duplication of 7q with evidence of a telomeric deletion.

We report on a de novo constitutional rearrangement involving the long arm of chromosome 7 in a second trimester fetus with the karyotype of 46,XX, inv dup del (7)(pter-q36::q36-q21.2:) pat. Both a large duplication (q21.2-q36) and a small deletion (within q36) were confirmed by FISH studies. DNA analysis on the family showed that the abnormal chromosome was derived from a single paternal homolog. A mechanism is proposed in light of this finding. The phenotype at autopsy was consistent with reported cases of similar duplications in chromosome 7 in that hydrocephalus, a depressed nasal bridge, low set ears, microretrognathia and a short neck were present.

Influence of coating bath chemistry on the deposition of 3-mercaptopropyl trimethoxysilane films deposited on magnesium alloy.

Magnesium alloys have a low specific density and a high strength to weight ratio. This makes them sought after light weight construction materials for automotive and aerospace applications. These materials have also recently become of interest for biomedical applications. Unfortunately, the use of magnesium alloys in many applications has been limited due to its high susceptibility to corrosion. One way to improve the corrosion resistance of magnesium alloys is through the deposition of protective coatings. Many of the current pretreatments/coatings available use toxic chemicals such as chromates and hydrofluoric acid. One possible environmentally friendly alternative is organosilane coatings which have been shown to offer significant corrosion protection to both aluminum alloys and steels. Organosilanes are ambifunctional molecules that are capable of covalent bonding to metal hydroxide surfaces. In order for covalent bonding to occur, the organosilane must undergo hydrolysis in the coating bath followed by a condensation reaction with the surface. There are a number of factors that influence the rates of these reactions such as pH and concentration of reactants. These factors can also influence competing reactions in solution such as oligomerization. The rates of hydrolysis and condensation of 3-mercaptopropyltrimethoxy silane in methanol have been analyzed with (1)H NMR and ATR-FTIR. The results indicate that organosilane oligomers begin to form in solution before the molecules are fully hydrolyzed. The organosilane films deposited on magnesium alloy AZ91 at a variety of concentrations and pre-hydrolysis times were characterized with a combination of ATR-FTIR, ellipsometry and SEM/EDS. The results show that both organosilane film thickness and uniformity are affected by the chemistry occurring in the coating bath prior to deposition.

Variants in the gene encoding C3 are associated with asthma and related phenotypes among African Caribbean families.

Proinflammatory and immunoregulatory products from C3 play a major role in phagocytosis, respiratory burst, and airways inflammation. C3 is critical in adaptive immunity; studies in mice deficient in C3 demonstrate that features of asthma are significantly attenuated in the absence of C3. To test the hypothesis that the C3 gene on chromosome 19p13.3-p13.2 contains variants associated with asthma and related phenotypes, we genotyped 25 single nucleotide polymorphism (SNP) markers distributed at intervals of approximately 1.9 kb within the C3 gene in 852 African Caribbean subjects from 125 nuclear and extended pedigrees. We used the multiallelic test in the family-based association test program to examine sliding windows comprised of 2-6 SNPs. A five-SNP window between markers rs10402876 and rs366510 provided strongest evidence for linkage in the presence of linkage disequilibrium for asthma, high log[total IgE], and high log[IL-13]/[log[IFN-gamma] in terms of global P-values (P = 0.00027, 0.00013, and 0.003, respectively). A three-SNP haplotype GGC for the first three of these markers showed best overall significance for the three phenotypes (P = 0.003, 0.007, 0.018, respectively) considering haplotype-specific tests. Taken together, these results implicate the C3 gene as a priority candidate controlling risk for asthma and allergic disease in this population of African descent.

Analysis of candidate genes on chromosome 2 in oral cleft case-parent trios from three populations.

Isolated oral clefts, including cleft lip with/without cleft palate (CL/P) and cleft palate (CP), have a complex and heterogeneous etiology. Case-parent trios from three populations were used to study genes spanning chromosome 2, where single nucleotide polymorphic (SNP) markers were analyzed individually and as haplotypes. Case-parent trios from three populations (74 from Maryland, 64 from Singapore and 95 from Taiwan) were genotyped for 962 SNPs in 104 genes on chromosome 2, including two well-recognized candidate genes: TGFA and SATB2. Individual SNPs and haplotypes (in sliding windows of 2-5 SNPs) were used to test for linkage and disequilibrium separately in CL/P and CP trios. A novel candidate gene (ZNF533) showed consistent evidence of linkage and disequilibrium in all three populations for both CL/P and CP. SNPs in key regions of ZNF533 showed considerable variability in estimated genotypic odds ratios and their significance, suggesting allelic heterogeneity. Haplotype frequencies for regions of ZNF533 were estimated and used to partition genetic variance into among-and within-population components. Wright's fixation index, a measure of genetic diversity, showed little difference between Singapore and Taiwan compared with Maryland. The tensin-1 gene (TNS1) also showed evidence of linkage and disequilibrium among both CL/P and CP trios in all three populations, albeit at a lower level of significance. Additional genes (VAX2, GLI2, ZHFX1B on 2p; WNT6-WNT10A and COL4A3-COL4A4 on 2q) showed consistent evidence of linkage and disequilibrium only among CL/P trios in all three populations, and TGFA showed significant evidence in two of three populations.

Promoter binding proteins of an active human L1 retrotransposon.

Human Long Interspersed elements (LINEs or L1Hs elements) are a highly repetitive class of DNA sequences which are dispersed by retrotransposition. Full length L1Hs transcripts and L1-encoded proteins have been shown by others to be present in NTera2D1 and other related teratocarcinoma cell lines. Using standard methods for the identification of DNA binding proteins we identified two proteins or complexes of proteins which specifically bind to the L1Hs promoter region and are qualitatively different between NTera2D1 and HeLa cell nuclear extracts. These proteins represent candidates for the factors controlling the differential expression of L1 sequences.

Transcripts homologous to a long repeated DNA element in the human genome.

Using three cloned DNA fragments from a 6.4-kb (kilobase pair) DNA element repeated several thousand times in the human genome (Adams, J. W., Kaufman, R. E., Kretschmer, P. J., Harrison, M. and Nienhuis, A. W. (1980) Nucleic Acids Res. 8, 6113-6128) and DNA/RNA hybridization, we show that transcripts homologous to this DNA family exist in total cellular RNA from human blood cells and from a mouse-human hybrid cell line with one human chromosome, the X. No such transcripts were detected in RNA from rabbit blood or a mouse cell line. For each DNA fragment studied, we found that blood transcripts and X-chromosome transcripts were indistinguishable in electrophoretic mobility and very heterogeneous in length; in addition, prominent hybridization bands were seen at 4.7 and 1.9 kb. Transcription from this DNA family likely occurs from heterogeneous templates. The existence of RNAs smaller than 6.4 kb suggests that part of the repeat unit can be transcribed and/or there exists a cellular mechanism to make these short RNAs from longer precursors. The vast majority of the RNAs homologous to the long repeat are not polyadenylated. In blood RNA there are a few hundred copies of beta-globin mRNA for every transcript homologous to this 6.4 kb repeat.

DNA restriction endonuclease analysis for localization of human beta- and delta-globin genes on chromosome 11.

DNA from a clone of a mouse-human hybrid that retained a human chromosome consisting of the major part of chromosome 11 and region q25-26-qter of the X chromosome was digested with various restriction endonucleases, subjected to electrophoresis in agarose gels, and transferred to nitrocellulose filters. The restriction digest pattern of the clone, when hybridized with a 32P-labeled plasmid fragment containing human beta-globin gene sequences, was a composite of the normal human and mouse (A9) patterns. When back-selected in 6-thioguanine to eliminate the 11 translocation chromosome, the hybrid cells showed only the A9 restriction pattern. These results substantiate the localization of beta- and delta-globin genes to human chromosome 11 and exclude the region 11q23-qter as the site.

Two additional potential retrotransposons isolated from a human L1 subfamily that contains an active retrotransposable element.

We have previously reported the isolation of a human retrotransposable L1 element. This element, allele L1.2B at the LRE-1 locus of chromosome 22, was shown by nucleotide sequence identity to be the direct precursor of a de novo retrotransposition event into the factor VIII gene on the X chromosome, resulting in hemophilia A in patient JH-27. We now report the isolation of the two remaining full-length members of the subfamily of L1 elements closely related to L1.2B present in the genome of the mother of JH-27. Since these elements, L1.3 and L1.4, are very similar in sequence to L1.2B and contain both open reading frames 1 and 2 intact, they are also likely to be active retrotransposable elements. This suggests that certain L1 subfamilies may contain multiple active elements.