Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “SNP analysis”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,441 records · Page 80Linked to original sources
PubMed1999

Re-sequencing of DNA from a diverse panel of cattle reveals a high level of polymorphism in both intron and exon.

In order to assess the extent of DNA sequence variation in cattle, introns and exons from both the leptin and Amyloid Precursor Protein (APP) genes have been sequenced in a panel of DNAs derived from 22 diverse animals. Direct DNA sequencing of PCR products was used; thus, 44 chromosomes were studied. Polymorphisms were identified by manual scanning of sequence chromatograms and computerized sequence analysis. Twenty Single Nucleotide Polymorphisms (SNPs) were detected in 1788 bp sequenced from the leptin gene, giving a frequency of 1 SNP per 89 bp. Twenty-four SNPs were detected in a 458-bp fragment of the APP gene; 23 of the polymorphisms were contained in a 302-bp intron 16 fragment. This equates to an SNP frequency of 1 per 13 bp for the intron. We can thus conclude that this portion of the bovine APP gene constitutes a hypermutable region. Nucleotide sequence diversity values of 0.019 and 0.0026 were obtained for APP and leptin respectively.

Amino Acid Substitution↗
PubMed2007

Low molecular weight phenotype of Apo(a) is a risk factor of corticosteroid-induced osteonecrosis of the femoral head after renal transplant.

OBJECTIVE: Osteonecrosis of the femoral head (ONF) is a necrosis due to disruption of the blood flow. The disease often occurs in association with corticosteroid treatment. The pathology of corticosteroid-induced ONF is unclear, although abnormalities in the coagulation and fibrinolytic systems or in the lipid metabolism have been reported to be involved. We examined the relationships between development of ONF and genetic variations and plasma level of lipoprotein(a) (Lp(a)), which is closely involved in the coagulation and fibrinolytic systems and lipid metabolism. METHODS: The study population consisted of 112 renal transplant patients undergoing corticosteroid treatment. Their apolipoprotein (a) [apo(a)] isoform was determined by Western blotting, and patients were classified into low molecular weight (LMW) or high molecular weight (HMW) groups. The plasma Lp(a) level was measured. Patients were also examined for 3 single-nucleotide polymorphisms (SNP), -773 (G/A), +93 (C/T), and +121 (G/A). Relationships between these 3 genetic factors of Lp(a) and ONF development were examined using statistical methods including multivariate analysis. RESULTS: A strong relationship was observed between the apo(a) molecular weight phenotype and ONF development, with an increased risk of ONF development for the LMW group (adjusted odds ratio 5.75, 95% CI 1.76-18.74, p = 0.0038). No significant relationships were observed between ONF and plasma Lp(a) level and SNP. CONCLUSION: Apo(a) molecular weight phenotype would be a useful predictor of ONF that develops after corticosteroid treatment.

Apoprotein(a)↗
PubMed2005

Genetic analysis of adiponectin and obesity in Hispanic families: the IRAS Family Study.

Adiponectin, coded for by the APM1 gene, is a novel adipocyte-derived hormone implicated in energy homeostasis and obesity. Several genetic studies have observed evidence of association between APM1 gene polymorphisms and features of the metabolic syndrome, such as insulin resistance and obesity. As part of a comprehensive genetic analysis of the APM1 gene, we have screened 96 unrelated individuals for polymorphisms in the promoter, coding regions, and 3'untranslated region (UTR). Three promoter single-nucleotide polymorphisms (SNPs), two rare coding SNPs (G113A and T1233C), and 13 SNPs in the 3'UTR were identified. Eighteen SNPs were genotyped in 811 Hispanic individuals from 45 families in the IRAS Family Study (IRASFS). SNPs were tested for association with six obesity quantitative traits (body mass index, waist, waist:hip ratio, subcutaneous adipose tissue, visceral adipose tissue, and visceral:subcutaneous ratio). Significant evidence of association to at least one of the obesity traits was identified in seven of the 18 SNPs (<0.001-0.05). The promoter SNP INS CA-11156 was the most consistently associated SNP and was associated significantly with all measures of obesity, except the visceral:subcutaneous ratio (P-values 0.009-0.03). Haplotype analysis supported this evidence of association, with haplotypes containing an insertion of one CA repeat at position -11156 consistently being associated with lower obesity values (P-value <0.001-0.05). The adiponectin polymorphisms, in particular those in the promoter region, thus show significant association with obesity measures in the Hispanic population. Additional studies are needed to confirm our findings and determine which polymorphism causes the functional effect.

3' Untranslated Regions↗
PubMed1999

Single nucleotide polymorphism determination using primer extension and time-of-flight mass spectrometry.

The high frequency of single nucleotide polymorphisms (SNPs) in the human genome makes them a valuable source of genetic markers for identity testing, genome mapping, and medical diagnostics. Conventional technologies for detecting SNPs are laborious and time-consuming, often prohibiting large-scale analysis. A rapid, accurate, and cost-effective method is needed to meet the demands of a high-throughput DNA assay. We demonstrate here that analysis of these genetic markers can now be performed routinely in a rapid, automated, and high-throughput fashion using time-of-flight mass spectrometry and a primer extension assay with a novel cleavable primer. SNP genotyping by mass spectrometry involves detection of single-base extension products of a primer immediately adjacent to the SNP site. Measurement of the mass difference between the SNP primer and the extension peak reveals which nucleotide is present at the polymorphic site. The primer is designed such that its extension products can be purified and chemically released from the primer in an automated format. The reduction in size of the products as a result of this chemical cleavage allows more accurate identification of the polymorphic base, especially in samples from a heterozygotic population. All six possible heterozygotes are resolved unambiguously, including an A/T heterozygote with extension products differing by only 9 Da. Multiplex SNP determination is demonstrated by simultaneously probing multiple SNP sites from a single polymerase chain reaction (PCR) product as well as from multiplexed PCR amplicons. Samples are processed in parallel on a robotic workstation, and analyzed serially in an automated mass spectrometer with analysis times of only a few seconds per sample, making it possible to process thousands of samples per day.

DNA Primers↗
PubMed1999

Release of endogenous ascorbic acid preserves extracellular dopamine in the mammalian retina.

PURPOSE: To investigate whether the inhibitory effect of nitric oxide (NO) on dopamine release from the retina is due to chemical oxidation of dopamine in the extracellular medium rather than to an inhibitory effect on dopamine release from retinal neurons. METHODS: Dopamine was incubated in Krebs bicarbonate medium and its rate of chemical degradation measured by high-performance liquid chromatography (HPLC). The effects of NO donors and antioxidants on dopamine were assessed by comparing dopamine degradation in the presence and absence of drug. The effects of NO donors on the K-evoked release of [3H]dopamine were measured from isolated superfused rabbit retinas. The release of ascorbic acid from the isolated rat retina and from an eyecup preparation in anesthetized rabbits was measured by HPLC. RESULTS: After 10 minutes' incubation in Krebs bicarbonate medium, the dopamine concentration decreased by 20%. This decline increased to 80% in the presence of S-nitroso-N-acetyl-DL-penicillamine (SNAP) or sodium nitroprusside (SNP). The increased rate of dopamine degradation was abolished if retina was incubated in the medium and then removed before the incubation of dopamine. The protective effect of preincubation with tissue was lost in the presence of ascorbate oxidase suggesting the release of ascorbic acid. HPLC analysis confirmed a substantial release of ascorbic acid from both rabbit and rat retinas. The K-evoked release of [3H]dopamine from the rabbit retina was inhibited by SNP. CONCLUSIONS: NO can rapidly, oxidize dopamine in physiological medium, but in the presence of retina, sufficient endogenous antioxidants (mainly ascorbate) are released to prevent this chemical reaction. Thus, the inhibitory action of NO on dopamine release results from an action on retinal neurons. Ascorbate release in the retina may have an important physiological role in prolonging the life of dopamine, which often has to diffuse long distances from axons in the inner plexiform layer to receptors in other retinal layers.

Animals↗
PubMed2006

Molecular approaches in the diagnosis of primary immunodeficiency diseases.

Over 120 inherited primary immunodeficiency diseases (PIDs) are known to exist. The genes responsible for many of these diseases have also been identified. Recent advances in diagnostic procedures have enabled these to be identified earlier and appropriately treated. While a number of approaches are available to identify mutations, direct sequencing remains the gold standard. This approach identifies the exact genetic change with substantial precision. We suggest that a sensitive and economical approach to mutation detection could be the direct sequencing of cDNA followed by the confirmatory sequencing of the corresponding exon. While screening techniques such as single-stranded conformation polymorphism (SSCP), heteroduplex analysis (HA), denaturing gradient gel electrophoresis (DGGE), and denaturing high-performance liquid chromatography (dHPLC) have proven useful, each has inherent advantages and disadvantages. We discuss these advantages and disadvantages and also discuss the potential of future sequencing technologies such as pyrosequencing, combinatorial sequencing-by-hybridization, multiplex polymerase colony (polony), and resequencing arrays as tools for future mutation detection. In addition we briefly discuss several high-throughput SNP detection technologies.

Algorithms↗
PubMed2001

Sequence analysis using logic regression.

Logic Regression is a new adaptive regression methodology that attempts to construct predictors as Boolean combinations of (binary) covariates. In this paper we use this algorithm to deal with single-nucleotide polymorphism (SNP) sequence data. The predictors that are found are interpretable as risk factors of the disease. Significance of these risk factors is assessed using techniques like cross-validation, permutation tests, and independent test sets. These model selection techniques remain valid when data is dependent, as is the case for the family data used here. In our analysis of the Genetic Analysis Workshop 12 data we identify the exact locations of mutations on gene 1 and gene 6 and a number of mutations on gene 2 that are associated with the affected status, without selecting any false positives.

Algorithms↗
PubMed2005

Exo+ proofreading polymerases mediate genetic analysis and its application in biomedical studies.

Polymerases with a proofreading function in their internal 3' to 5' exonuclease possess high fidelity for DNA replication both in vivo and in vitro. The obstacle facing Exo+ polymerases for single nucleotide polymorphism (SNP) detection could be bypassed by using primer-3'-termini modification. This hypothesis has been well tested using three types of modified allele specific primers with: 3' labeling, 3' to 5' exonuclease resistance, and 3' dehydroxylation. Accordingly, three new SNP assaying methods have been developed to carry out genome-wide genotyping, taking advantage of the enzymatic properties of Exo+ polymerases. These new mutation detection assays are widely adaptable to a variety of platforms, including multi-well plate and microarray technologies. Application of Exo+ polymerases to genetic analysis, including genotyping that is mostly relevant to pharma-cogenetics, high-fidelity gene expression profiling, rare mutation detection and mutation load assay, will help to accelerate the pace of personalized medicine. In this review paper, we will first introduce three new assays that we have recently developed, and then describe a number of their applications in pharmacogenetics and in other biomedical studies.

DNA Primers↗
PubMed2000

Expression-based genetic/physical maps of single-nucleotide polymorphisms identified by the cancer genome anatomy project.

SNPs (Single-Nucleotide Polymorphisms), the most common DNA variant in humans, represent a valuable resource for the genetic analysis of cancer and other illnesses. These markers may be used in a variety of ways to investigate the genetic underpinnings of disease. In gene-based studies, the correlations between allelic variants of genes of interest and particular disease states are assessed. An extensive collection of SNP markers may enable entire molecular pathways regulating cell metabolism, growth, or differentiation to be analyzed by this approach. In addition, high-resolution genetic maps based on SNPs will greatly facilitate linkage analysis and positional cloning. The National Cancer Institute's CGAP-GAI (Cancer Genome Anatomy Project Genetic Annotation Initiative) group has identified 10,243 SNPs by examining publicly available EST (Expressed Sequence Tag) chromatograms. More than 6800 of these polymorphisms have been placed on expression-based integrated genetic/physical maps. In addition to a set of comprehensive SNP maps, we have produced maps containing single nucleotide polymorphisms in genes expressed in breast, colon, kidney, liver, lung, or prostate tissue. The integrated maps, a SNP search engine, and a Java-based tool for viewing candidate SNPs in the context of EST assemblies can be accessed via the CGAP-GAI web site (http://cgap.nci.nih.gov/GAI/). Our SNP detection tools are available to the public for noncommercial use.

Chromosome Mapping↗
PubMed1996

Baroreflex gain: characterization using autoregressive moving average analysis.

To study heart rate baroreflex gain, autoregressive moving average (ARMA) analysis, a multivariate method that allows evaluation of the dynamic ("beat-to-beat") interactions between changes in biological signals, was used to evaluate the relationships between R-R interval and arterial blood pressure (BP) during random-interval breathing. Parameters obtained by ARMA analysis of spontaneous fluctuations in BP and R-R interval in 17 volunteers were used to model the response of R-R interval to a transient 1-mmHg increase in BP; the resulting impulse-response and step-response curves were compared with baroreflex gain measured using bolus injections of phenylephrine (PE) and sodium nitroprusside (SNP). Impulse-response curves for the systolic BP-R-R relationship showed an early (0-1 s) sharp maximum of 5.5 +/- 4.2 ms/mmHg, which was smaller in magnitude but linearly correlated with baroreflex gain derived from SNP (14.5 +/- 9.7 ms/mmHg; r = 0.80, P < 0.002) and PE (31.6 +/- 26.7 ms/mmHg; r = 0.53, P < 0.05) injections. A similar relationship was also found between the one-beat ARMA step response and SNP injection (r = 0.70, P = 0.01). The integrated step response of the BP-R-R relationship over 6 s was 6.4 +/- 4.1 ms/mmHg, with no correlation to baroreflex gain determined by SNP (r = 0.33, P = 0.20) or PE (r = -0.15, P = 0.57). In conclusion, quantification of baroreflex gain consistent with other techniques may be achieved by ARMA analysis without perturbing mean BP. Correlation of baroreflex gain obtained by bolus injection to early measures of baroreflex gain obtained from the ARMA maximum impulse and early step responses, but not the late step response, suggests that the ARMA method may provide additional information regarding the frequency dependent effects of BP on R-R-interval.

Adolescent↗
PubMed2005

Potentiometric Detection of Single Nucleotide Polymorphism by Using a Genetic Field-effect transistor.

Potentiometric measurement of allele-specific oligonucleotide hybridization based on the principle of detection of charge-density change at the surface of a gate insulator by using of a genetic field-effect transistor has been demonstrated. Since DNA molecules are negatively charged in aqueous solution, a hybridization event at the gate surface leads to a charge-density change in the channel of the FET and can be directly transduced into an electrical signal without any labeling of target DNA molecules. One of the unique features of our method is to utilize DNA binders such as intercalators as charged species for double-stranded DNA after hybridization, since these are ionized and carry positive charges in aqueous solution. Single-base mismatch of the target DNA could be successfully detected both with the wild-type and with the mutant genetic FETs by controlling the hybridization temperatures and introducing Hoechst 33258 as DNA binder. The genetic FET platform is suitable as a simple, accurate, and inexpensive system for SNP typing in clinical diagnostics.

DNA↗
PubMed2005

A common haplotype at the 5' end of the RET proto-oncogene, overrepresented in Hirschsprung patients, is associated with reduced gene expression.

Hirschsprung disease (HSCR) is a complex genetic defect of intestinal innervation mainly ascribed to loss of function mutations of the RET gene. Although RETcoding mutations account for only 15% of HSCR sporadic cases, several linkage and association studies still indicate RET as a major HSCR gene, suggesting the existence of noncoding RET variants or common polymorphisms which can act in HSCR pathogenesis. We previously described a predisposing RET haplotype (A-C-A) composed of alleles at three SNPs (-1 bp and -5 bp from the RET transcription start site, NT_033985.6:g.975824G>A and NT_033985.6:g.975820C>A, respectively, and silent polymorphism c.135G>A), which was present in 62% of chromosomes from HSCR patients but only in 22% of control chromosomes. Here we address the question of how this 5' ACA haplotype may functionally act as a predisposing factor in HSCR pathogenesis by performing functional analysis of the same three SNPs. We demonstrate that neither the two promoter variants nor the exon 2 SNP interfere with reporter gene transcription or RET mRNA splicing, respectively. However, real-time RT-PCR, performed in RNA obtained from lymphoblasts of selected individuals, has shown that homozygosity for the whole ACA haplotype is associated with reduced RET gene expression. We propose that a yet unidentified variant in linkage disequilibrium with the ACA haplotype, rather than the single characterizing SNPs, acts as a HSCR susceptibility allele by affecting the normal amount of RET receptor on the cell surface.

5' Flanking Region↗
PubMed2007

Macrophage migration inhibitory factor (MIF) -173G/C promoter polymorphism influences upper gastrointestinal tract involvement and disease activity in patients with Crohn's disease.

BACKGROUND: Macrophage migration inhibitory factor (MIF) is a proinflammatory cytokine with increased expression in inflammatory bowel disease. The aim of the study was to analyze the role of the MIF -173G/C single nucleotide polymorphism in Crohn's disease (CD). METHODS: Using restriction fragment length polymorphism analysis, genomic DNA of 198 patients with CD and 159 unrelated controls was analyzed for the -173G/C SNP in the MIF promoter region. Colonic MIF mRNA expression was measured by quantitative polymerase chain reaction (PCR), serum MIF levels by enzyme-linked immunosorbent assay (ELISA). RESULTS: Thirty-six of the 146 G/G wildtype carriers (24.7%) but only 3 of the 45 G/C heterozygotes (6.7%) and only 1 of the C/C homozygotes (14.3%) were diagnosed with upper gastrointestinal tract involvement (P = 0.009, odds ratio [OR] = 0.22, 95% confidence interval [CI], 0.06-0.75 for wildtype versus hetero- and homozygous carriers). This result was confirmed in a second prospective study, in which all patients diagnosed with upper gastrointestinal involvement (n = 13) were G/G wildtype carriers (P = 0.01 versus controls). All patients (n = 12; 100%) with a Crohn's disease activity index (CDAI) > 300 were G/G wildtype carriers compared to only 65.6% wildtype carriers in the group with a CDAI < 150 (P = 0.016). MIF is expressed in the colonic mucosa of CD patients and intestinal epithelial cells but its mRNA expression does not correlate with the degree of inflammation and is not upregulated by proinflammatory cytokines. In CD, MIF serum levels are not influenced by the MIF -173G/C polymorphism. CONCLUSIONS: The MIF -173G/C polymorphism appears to be a factor contributing to a particular CD phenotype characterized by protection against upper gastrointestinal tract involvement and severe disease activity.

Adolescent↗
PubMed2001

TASK-5, a new member of the tandem-pore K(+) channel family.

TASKs are members of the recently identified K(+) channel family (KCNKx). Four TASKs (TASK1-4) identified so far form functional K(+) channels and encode background K(+) channels in various cell types. Recently, another member (TASK-5) was identified in the human genome. We cloned it and studied its tissue expression and functional properties. TASK-5 shares 51% amino acid identity with TASK-1 and TASK-3. Northern blot analysis showed that TASK-4 mRNA was expressed primarily in the adrenal gland and pancreas. Single nucleotide polymorphism (SNP) was found at amino acid position 95 that normally forms part of the K(+) channel selectivity filter. Neither form of TASK-5 showed channel activity when transfected in COS-7 cells. Exchange of C-termini of TASK-3 and TASK-5 failed to generate whole-cell currents. Thus, TASK-5 is a new member of the tandem-pore K(+) channel family but does not produce a functional plasma membrane K(+) current by itself.

Amino Acid Sequence↗
PubMed2006

Characterisation of single nucleotide polymorphisms in sugarcane ESTs.

Commercial sugarcane cultivars (Saccharum spp. hybrids) are both polyploid and aneuploid with chromosome numbers in excess of 100; these chromosomes can be assigned to 8 homology groups. To determine the utility of single nucleotide polymorphisms (SNPs) as a means of improving our understanding of the complex sugarcane genome, we developed markers to a suite of SNPs identified in a list of sugarcane ESTs. Analysis of 69 EST contigs showed a median of 9 SNPs per EST and an average of 1 SNP per 50 bp of coding sequence. The quantitative presence of each base at 58 SNP loci within 19 contiguous sequence sets was accurately and reliably determined for 9 sugarcane genotypes, including both commercial cultivars and ancestral species, through the use of quantitative light emission technology in pyrophosphate sequencing. Across the 9 genotypes tested, 47 SNP loci were polymorphic and 11 monomorphic. Base frequency at individual SNP loci was found to vary approximately twofold between Australian sugarcane cultivars and more widely between cultivars and wild species. Base quantity was shown to segregate as expected in the IJ76-514 x Q165 sugarcane mapping population, indicating that SNPs that occur on one or two sugarcane chromosomes have the potential to be mapped. The use of SNP base frequencies from five of the developed markers was able to clearly distinguish all genotypes in the population. The use of SNP base frequencies from a further six markers within an EST contig was able to help establish the likely copy number of the locus in two genotypes tested. This is the first instance of a technology that has been able to provide an insight into the copy number of a specific gene locus in hybrid sugarcane. The identification of specific and numerous haplotypes/alleles present in a genotype by pyrophosphate sequencing or alternative techniques ultimately will provide the basis for identifying associations between specific alleles and phenotype and between allele dosage and phenotype in sugarcane.

Alleles↗
PubMed2005

Peptidoglycan recognition proteins Pglyrp3 and Pglyrp4 are encoded from the epidermal differentiation complex and are candidate genes for the Psors4 locus on chromosome 1q21.

Psoriasis is a common inflammatory skin disease caused by genetic and environmental factors, including bacterial and viral infections. Since the skin is in constant contact with commensal and pathogenic microorganisms, we examined well-supported psoriasis genetic linkage intervals to identify genes encoding innate immune pattern recognition proteins that may play a role in pathogenesis. Two peptidoglycan recognition proteins, Pglyrp3 and Pglyrp4, are localized to the Psors4 locus on chromosome 1q21 in a gene cluster known as the epidermal differentiation complex (EDC). We show that these genes are expressed in the skin as well as in germinal centers in the tonsil. We tested 13 SNPs in or near these genes for association with psoriasis in two independent patient collections: a family-based patient set comprised of 375 individuals from 101 families, and a case-control patient collection of 282 patients with moderate to severe psoriasis and 192 healthy controls. In the family-based analysis, several SNPs in the Pglyrp3-Pglyrp4 locus show association with psoriasis (0.01 < P < 0.05). Multiple-SNP haplotypes incorporating Pglyrp3 and Pglyrp4 SNPs also show significant association in the transmission disequilibrium test (TDT; P < 0.01). In the case-control test, none of the SNPs that we tested show association with psoriasis when analyzed in single-SNP or haplotype-based tests. The discordance between the TDT and case-control results suggests that the two populations are significantly different in disease etiology, that the polymorphism responsible for the Psors4 linkage is elsewhere in the Pglyrp locus, or that the causative Psors4 polymorphism is in a location near but not in the Pglyrp locus. These data are consistent with previous reports of association of psoriasis with genes on 1q21, and suggest a role for Pglyrps in skin biology.

Carrier Proteins↗
PubMed2006

Identification of functional single nucleotide polymorphism haplotypes in the cytidine deaminase promoter.

Cytidine deaminase (CDA) hydrolytically deaminates and irreversibly deactivates the chemotherapeutic agent cytosine arabinoside (Ara-C), a deoxycytidine analog used for treatment of acute leukemias and lymphomas. To determine if single nucleotide polymorphisms (SNPs) in the promoter region of CDA affected gene expression, we sequenced approximately 1.6 Kb upstream of the CDA translation initiation site and containing the proximal promoter of CDA. We identified 6 SNPs; -92A>G, -205C>G, -451C>T, -897C>A, -1075A>G and -1181G>A. Based on predicted changes in transcription factor binding sites, three SNPs (-92A>G, -451C>T and -897C>A) were chosen for further investigation. The five haplotypes segregating in the population were cloned into a luciferase expression plasmid, transfected into Cos-1 cells and reporter activity measured at 24 and 48 h. Four haplotypes showed an average expression which was 2.5-fold higher at 24 h (P<0.0001) and 3.3-fold higher at 48 h (P<0.0001) than the lowest expressing haplotype. When reanalyzed as single SNP genotypes, the differences in expression were significant, except for -897 C/A, at 24 h, but the magnitude of difference was reduced, suggesting that no single SNP completely accounts for the expression differences observed at the haplotype level. As predicted from the in vitro analysis, individuals homozygous for common haplotype (ACC/ACC) showed higher levels of CDA enzymatic activity as individuals heterozygous for the wild type and low expressing haplotype (ACC/ATC). As CDA promoter region haplotypes may influence Ara-C chemosensitivity, shown here in in vitro and in vivo studies, the clinical relevance of these findings should be examined.

Animals↗
PubMed2005

PAX9 and TGFB3 are linked to susceptibility to nonsyndromic cleft lip with or without cleft palate in the Japanese: population-based and family-based candidate gene analyses.

The prevalence of nonsyndromic cleft lip with or without cleft palate (CL/P) and cleft palate only (CPO) are believed to be higher in the Japanese than in Americans, Europeans or Africans. The purpose of this study was to investigate, in a Japanese population, relationships between CL/P or CPO and seven candidate genes (TGFB3, DLX3, PAX9, CLPTM1, TBX10, PVRL1, TBX22) that showed positive associations in other populations and are expressed in the oral/lip region in developing mice. We first searched for mutations in these genes among 112 CL/P and 16 CPO patients, and found a heterozygous missense mutation (640A > G, S214G) in exon 3 of PAX9 in two sibs with CL/P and their phenotypically normal mother from a Japanese family. A population-based case-control analysis and a family-based transmission disequilibrium test (TDT), using single nucleotide polymorphisms (SNPs), and two-SNP haplotypes of the genes, between the 112 CL/P cases with their parents and 192 controls indicated a significant association at one SNP site, IVS1 + 5321, in TGFB3 with a P-value of 0.0016. Population-based haplotyping revealed that the association was most significant for haplotype "A/A" consisting of IVS1 + 5321 and IVS1 - 1572; TDT also gave a P-value of 0.0252 in this haplotype.

Amino Acid Sequence↗