[Show abstract][Hide abstract] ABSTRACT: Scoring the correlation between two genes by their shared properties is a common and basic work in biological study. A prospective way to score this correlation is to quantify the overlap between the two sets of homogeneous properties of the two genes. However the proper model has not been decided, here we focused on studying the quantification of overlap and proposed a more effective model after theoretically compared 7 existing models. We defined three characteristic parameters (d, R, r) of an overlap, which highlight essential differences among the 7 models and grouped them into two classes. Then the pros and cons of the two groups of model were fully examined by their solution space in the (d, R, r) coordinate system. Finally we proposed a new model called OScal (Overlap Score calculator), which was modified on Poisson distribution (one of 7 models) to avoid its disadvantages. Tested in assessing gene relation using different data, OScal performs better than existing models. In addition, OScal is a basic mathematic model, with very low computation cost and few restrictive conditions, so it can be used in a wide-range of research areas to measure the overlap or similarity of two entities.
[Show abstract][Hide abstract] ABSTRACT: Coronary artery disease (CAD) is the leading cause of death worldwide. It has been established that internal mammary arteries
(IMA) are resistant to the development of atherosclerosis, whereas left anterior descending (LAD) coronary arteries are athero-prone.
The contrasting properties of these two arteries provide an innovative strategy to identify the genes that play important
roles in the development of atherosclerosis. We carried out microarray analysis to identify genes differentially expressed
between IMA and LAD. Twenty-nine genes showed significant differences in their expression levels between IMA and LAD, which
included the TES gene encoding Testin. The role of TES in the cardiovascular system is unknown. Here we show that TES is involved in endothelial cell (EC) functions relevant to atherosclerosis. Western blot analysis showed higher TES expression in IMA than in LAD. Reverse transcription polymerase chain reaction and western blot analyses showed that TES was consistently and markedly down-regulated by more than 6-fold at both mRNA and protein levels in patients with CAD compared
with controls without CAD (P= 0.000049). The data suggest that reduced TES expression is associated with the development of CAD. Knockdown of TES expression by small-interfering RNA promoted oxidized-LDL-mediated monocyte adhesion to ECs, EC migration and the transendothelial
migration of monocytes, while the over-expression of TES in ECs blunted these processes. These results demonstrate association between reduced TES expression and CAD, establish a novel role for TES in EC functions and raise the possibility that reduced TES expression increases susceptibility to the development of CAD.
Preview · Article · Dec 2011 · Human Molecular Genetics
[Show abstract][Hide abstract] ABSTRACT: A genome-wide association study (GWAS) identified significant association between variants in MEIS1, BTBD9, and MAP2K5/SKOR1 and restless legs syndrome (RLS). However, many independent replication studies are needed to unequivocally establish a valid genotype-phenotype association across various populations. To further validate the GWAS findings, we investigated three variants, rs2300478 in MEIS1, rs9357271 in BTBD9, and rs1026732 in MAP2K5/SKOR1 in 38 RLS families and 189 RLS patients/560 controls from the US for their association with RLS.
Both family-based and population-based case-control association studies were carried out.
The family-based study showed that SNP rs1026732 in MAP2K5/SKOR1 was significantly associated with RLS (P=0.01). Case-control association studies showed significant association between all three variants and RLS (P=0.0001/OR=1.65, P=0.0021/OR=1.59, and P=0.0011/OR=1.55 for rs2300478, rs9357271, and rs1026732, respectively).
Variants in MEIS1, BTBD9, and MAP2K5/SKOR1 confer a significant risk of RLS in a US population.
[Show abstract][Hide abstract] ABSTRACT: Osteogenesis imperfecta (OI, also known as brittle bone disease) is caused mostly by mutations in two type I collagen genes, COL1A1 and COL1A2 encoding the pro-α1 (I) and pro-α2 (I) chains of type I collagen, respectively. Two Chinese families with autosomal dominant OI were identified and characterized. Linkage analysis revealed linkage of both families to COL1A2 on chromosome 7q21.3-q22.1. Mutational analysis was carried out using direct DNA sequence analysis. Two novel missense mutations, c.3350A>G and c.3305G>C, were identified in exon 49 of COL1A2 in the two families, respectively. The c.3305G>C mutation resulted in substitution of a glycine residue (G) by an alanine residue (A) at codon 1102 (p.G1102A), which was found to be mutated into serine (S), argine (R), aspartic acid (D), or valine (V) in other families. The c.3350A>G variant may be a de novo mutation resulting in p.Y1117C. Both mutations co-segregated with OI in respective families, and were not found in 100 normal controls. The G1102 and Y1117 residues were evolutionarily highly conserved from zebrafish to humans. Mutational analysis did not identify any mutation in the COX-2 gene (a modifier gene of OI). This study identifies two novel mutations p.G1102A and p.Y1117C that cause OI, significantly expands the spectrum of COL1A2 mutations causing OI, and has a significant implication in prenatal diagnosis of OI.
No preview · Article · Apr 2011 · Journal of Genetics and Genomics
[Show abstract][Hide abstract] ABSTRACT: Recent genome-wide single nucleotide polymorphism (SNP) association studies (GWAS) have identified a number of SNPs that were significantly associated with coronary artery disease and myocardial infarction (MI). However, many independent replication studies in other populations are needed to unequivocally confirm the GWAS association. To assess GWAS association, we have established a case-control cohort consisting of 1231 well-characterised MI patients and 560 controls without detectable coronary stenosis, all selected from the Cleveland Genebank population. The Genebank cohort has sufficient power to detect the association between MI and four GWAS SNPs, including rs17465637 within the MIA3 gene, rs2943634 (intergenic), rs6922269 in MTHFD1L, and rs599839 near SORT1. SNPs were genotyped by TaqMan assays and follow-up multivariate logistic regression analysis with incorporation of significant covariates showed significant association with MI for MIA3 SNP rs17465637 (P-adj= 0.0034) and SORT1 SNP rs599839 (P-adj= 0.009). The minor allele G of rs599839 was also associated with a decreased LDL-C level of 5-9 mg/dL per allele, but not with HDL-C or triglyceride levels. No association for MI or lipid levels was found for SNPs rs2943634 and rs6922269 (P-adj > 0.05). Our results establish two SNPs, rs17465637 in MIA3 and rs599839 near SORT1 as significant risk factors for MI in the American Genebank Caucasian population.
Preview · Article · Apr 2011 · Annals of Human Genetics
[Show abstract][Hide abstract] ABSTRACT: We previously mapped a genetic locus for restless legs syndrome (RLS) to chromosome 9p22-24 (RLS3) and a later genome-wide association study (GWAS) implicated the PTPRD gene at the RLS3 locus as a susceptibility gene for RLS. However, from the standpoint of genetics, the GWAS association needs to be validated by independent studies. In this study, we used both family-based and population-based association studies to assess the association between PTPRD and RLS in an American Caucasian population.
We genotyped two intronic SNPs rs1975197 and rs4626664 in PTPRD in 144 family members from 15 families and a case control cohort of 189 patients and 560 controls. Direct DNA sequence analysis was used to screen coding exons and exon-intron boundaries of PTPRD for rare mutations.
A family-based sibling transmission disequilibrium test showed association of RLS with SNP rs1975197 (P = 0.015), but not with rs4626664 (P = 0.622). The association with rs1975197 was significantly replicated by a population-based case control association study (allelic P = 0.0004, odds ratio = 1.68; genotypic P = 0.0013 and 0.0003 for an additive and dominant model, respectively). One rare p.E1639D variant was identified in exon 39 in kindred RLS40005. The rare D1639 allele did not co-segregate with RLS in the family, suggesting that p.E1639D variant is not a causative mutation.
This represents the first independent study to validate the association between PTPRD variants and RLS. Both family-based and population-based association studies suggest that PTPRD variant rs1975197 confers risk of RLS.
No preview · Article · Feb 2011 · Movement Disorders
[Show abstract][Hide abstract] ABSTRACT: Coronary artery disease (CAD) is a complex, multifactorial disease and a leading cause of mortality world wide. Over the past
decades, great efforts have been made to elucidate the underlying genetic basis of CAD and massive data have been accumulated.
To integrate these data together and to provide a useful resource for researchers, we developed the CADgene, a comprehensive
database for CAD genes. We manually extracted CAD-related evidence for more than 300 candidate genes for CAD from over 1300
publications of genetic studies. We classified these candidate genes into 12 functional categories based on their roles in
CAD. For each gene, we extracted detailed information from related studies (e.g. the size of case–control, population, SNP,
odds ratio, P-value, etc.) and made useful annotations, which include general gene information, Gene Ontology annotations, KEGG pathways,
protein–protein interactions and others. Besides the statistical number of studies for each gene, CADgene also provides tools
to search and show the most frequently studied candidate genes. In addition, CADgene provides cumulative data from 11 publications
of CAD-related genome-wide association studies. CADgene has a user-friendly web interface with multiple browse and search
functions. It is freely available at http://www.bioguo.org/CADgene/.
Full-text · Article · Nov 2010 · Nucleic Acids Research
[Show abstract][Hide abstract] ABSTRACT: Plasma HDL cholesterol levels (HDL-C) are an independent predictor of coronary artery disease (CAD). We have completed a genome-wide linkage scan for HDL-C in a US cohort consisting of 388 multiplex families with premature CAD (GeneQuest). The heritability of HDL-C in GeneQuest was 0.37 with gender and age as covariates (P = 5.1 x 10(-4)). Two major quantitative trait loci (QTL) for log-transformed HDL-C adjusted for age and gender were identified onto chromosomes 7p22 and 15q25 with maximum multipoint logarithm of odds (LOD) scores of 3.76 and 6.69, respectively. Fine mapping decreased the 7p22 LOD score to a nonsignificant level of 3.09 and split the 15q25 QTL into two loci, one minor QTL on 15q22 (LOD = 2.73) that spanned the LIPC gene, and the other at 15q25 (LOD = 5.63). A family-based quantitative transmission disequilibrium test (QTDT) revealed significant association between variant rs1800588 in LIPC and HDL-C in the GeneQuest population (P = 0.0067), which may account for the minor QTL on 15q22. The 15q25 QTL is the most significant locus identified for HDL-C to date, and these results provide a framework for the ultimate identification of the underlying HDL-C variant and gene on chromosomes 15q25, which will provide insights into novel regulatory mechanisms of HDL-C metabolism.
Full-text · Article · Jun 2010 · The Journal of Lipid Research
[Show abstract][Hide abstract] ABSTRACT: A frameshift mutation in the NPPA gene was identified in 1 family with atrial fibrillation (AF), however, further studies are needed to establish unequivocally the genetic association between NPPA and AF.
A case control association study and mutational analysis of NPPA were performed with 384 sporadic AF patients and 844 controls from a Chinese GeneID population. Genotyping was performed using High-Resolution Melt analysis. Mutational analysis was performed using direct DNA sequencing analysis.
Significant allelic association was detected between single nucleotide polymorphism (SNP) rs5063 and lone AF (p=0.015, OR=1.63; adjusted p=0.003). Genotypic association was significant assuming an additive or dominant model (adjusted p=0.005 and 0.007, respectively). Six new variants were identified in NPPA, including 2 in the 5'-UTR, 2 in the 3'-UTR, and 2 missense substitutions. Variants c.413T>C, c.*48G>A and c.*133G>T were not present in 844 controls, and the others were identified in controls.
Variants in NPPA confer risk of lone AF in a Chinese population. Thus, in addition to being a disease-causing gene with mutations identified in familial AF cases, NPPA is a susceptibility gene for lone AF.
No preview · Article · Apr 2010 · Clinica chimica acta; international journal of clinical chemistry
[Show abstract][Hide abstract] ABSTRACT: Mutations in the cardiac sodium channel gene SCN5A cause long QT syndrome (LQTS). We previously generated an LQTS mouse model (TG-NS) that overexpresses the LQTS mutation N1325S in SCN5A. The TG-NS mice manifested the clinical features of LQTS including spontaneous VT, syncope and sudden death. However, the long-term prognosis of LQTS on the structure of the heart has not been investigated in this or any other LQTS models and human patients.
Impaired systolic function and reduced left ventricular fractional shortening were detected by echocardiography, morphological and histological examination in two lines of adult mutant transgenic mice. Histological and TUNEL analyses of heart sections revealed fibrosis lesions and increased apoptosis in an age-dependent manner. Cardiomyocyte apoptosis was associated with the increased activation of caspases 3 and 9 in TG-NS hearts. Western blot analysis showed a significantly increased expression of the key Ca(2+) handling proteins L-type Ca(2+) channel, RYR2 and NCX in TG-NS hearts. Increased apoptosis and an altered expression of Ca(2+) handling proteins could be detected as early as 3months of age when echocardiography showed little or no alterations in TG-NS mice.
Our findings revealed for the first time that the LQTS mutation N1325S in SCN5A causes cardiac fibrosis and contractile dysfunction in mice, possibly through cellular mechanisms involving aberrant cardiomyocyte apoptosis. Therefore, we provide the experimental evidence supporting the notion that some LQTS patients have an increased risk of structural and functional cardiac damage in a prolonged disease course.
Full-text · Article · Sep 2009 · International journal of cardiology
[Show abstract][Hide abstract] ABSTRACT: Hypokalaemic periodic paralysis (HypoPP) is an autosomal dominant disorder, which is characterized by periodic attacks of muscle weakness associated with a decrease in the serum potassium level. A major disease-causing gene for HypoPP has been identified as CACNA1S, which encodes the skeletal muscle calcium channel alpha-subunit with four transmembrane domains (I-IV), each with six transmembrane segments (S1-S6). To date, all CACNA1S mutations identified in HypoPP patients are located within the voltage-sensor S4 segment. In this study we report a novel CACNA1S mutation in a new region of the protein, the S3 segment of domain III. We characterized a four-generation South American family with HypoPP. Genetic analysis identified a novel V876E mutation in all HypoPP patients in the family, but not in normal family members or 160 control people. Clinical analysis indicates that mutation V876E is associated with a severe outcome as characterized by a very early age of onset, complete penetrance and a severe prognosis including death. These results identify a new mutation in CACNA1S and expand the spectrum of CACNA1S mutations associated with HypoPP.
Full-text · Article · Sep 2009 · Journal of Human Genetics
[Show abstract][Hide abstract] ABSTRACT: Atrial fibrillation (AF) is the most common arrhythmia in the clinical setting and an independent risk factor for stroke. Approximately 10 million Chinese people are affected by AF, but the genetic basis is largely unknown. A recent genome-wide association study in Iceland identified association between SNP rs2200733 on 4q25 and AF; however, many independent replication studies are essential to unequivocally validate this association. To assess the association between rs2200733 and AF as well as that between rs2200733 and ischemic stroke in a mainland Chinese Han population, we carried out case-control association studies with 383 AF patients versus 851 non-AF controls and 811 ischemic stroke patients versus 688 non-stroke controls. Highly significant association was detected between rs2200733 and AF in a Chinese Han population (allelic P = 3.7 × 10(-11) with OR = 1.81; genotypic P = 4.1 × 10(-12) with a dominant model). When the AF cases were divided into lone AF (32.6%) and other types of AF (67.4%), significantly stronger association was found with lone AF (OR = 2.40, P = 1.3 × 10(-9) compared to OR = 1.59, P = 6.2 × 10(-7) for other types of AF; P = 0.02 for two ORs). No significant association was found between rs2200733 and ischemic stroke. Our results suggest that SNP rs2200733 confers a highly significant risk of AF, but not ischemic stroke, in a more representative Chinese Han population in the mainland China.
[Show abstract][Hide abstract] ABSTRACT: TBX5 is a T-box transcriptional factor required for cardiogenesis and limb development. TBX5 mutations cause Holt-Oram syndrome characterized by congenital heart defects and upper limb deformations. Here we establish a novel function for TBX5 in pre-mRNA splicing, and we show that this function is relevant to the pathogenesis of Holt-Oram syndrome, providing a novel pathogenic mechanism for the disease. Proteomics in combination with affinity purification identifies splicing factor SC35 as a candidate TBX5-associating protein. Co-immunoprecipitation and glutathione S-transferase pulldown assays confirm the complex formation between TBX5 and SC35. TBX5 can bind to RNA homopolymers (polyribonucleotides) and to the 5'-splice site, which overrides the binding of SC35 to the same RNA. Overexpression of TBX5 increases the efficiency of pre-mRNA splicing and regulates alternative splice site selection. However, co-expression of TBX5 and SC35 antagonizes each other's positive effect on splicing. The most severe TBX5 mutation, G80R, with complete penetrance of the cardiac phenotype, strongly affects pre-mRNA splicing, whereas other mutations with incomplete penetrance of the cardiac phenotype, including R237Q, do not alter the splicing activity of TBX5. This study establishes TBX5 as the first cardiac gene and the first human disease gene with dual roles in both transcriptional activation and pre-mRNA splicing.
No preview · Article · Aug 2009 · Journal of Biological Chemistry
[Show abstract][Hide abstract] ABSTRACT: The R952Q variant in the low density lipoprotein receptor-related protein 8 (LRP8)/apolipoprotein E receptor 2 (ApoER2) gene has been recently associated with familial and premature myocardial infarction (MI) by means of genome-wide linkage scan/association studies. We were interested in the possible interaction of the R952Q variant with another established cardiovascular genetic risk factor belonging to the same pathway, namely apolipoprotein E (APOE) epsilon2/epsilon3/epsilon4 genotype, in modulating apolipoprotein E (ApoE) plasma levels and risk of MI.
In the Italian cohort used to confirm the association of the R952Q variant with MI, we assessed lipid profile, apolipoprotein concentrations, and APOE epsilon2/epsilon3/epsilon4 genotype. Complete data were available for a total of 681 subjects in a case-control setting (287 controls and 394 patients with MI).
Plasma ApoE levels decreased progressively across R952Q genotypes (mean levels +/- SD = RR: 0.045 +/- 0.020, RQ: 0.044 +/- 0.014, QQ: 0.040 +/- 0.008 g/l; P for trend = 0.047). Combination with APOE genotypes revealed an additive effect on ApoE levels, with the highest level observed in RR/non-carriers of the E4 allele (0.046 +/- 0.021 g/l), and the lowest level in QQ/E4 carriers (0.035 +/- 0.009 g/l; P for trend = 0.010). QQ/E4 was also the combined genotype with the most significant association with MI (OR 3.88 with 95%CI 1.08-13.9 as compared with RR/non-carriers E4).
Our data suggest that LRP8 R952Q variant may have an additive effect to APOE epsilon2/epsilon3/epsilon4 genotype in determining ApoE concentrations and risk of MI in an Italian population.
Full-text · Article · Jun 2009 · BMC Medical Genetics
[Show abstract][Hide abstract] ABSTRACT: To clinically characterize and map the disease-associated locus in a five-generation Chinese family with autosomal dominant early-onset hereditary gingival fibromatosis (HGF).
A complete oral examination was conducted. Genomic DNA samples were obtained from 14 individuals. Short tandem repeats markers, which encompass four previously known loci related to HGF, were genotyped. Two-point log of the odds (LOD) scores were calculated using MLINK program of the LINKAGE software, multipoint and non-parametric linkage (NPL) analysis were performed using the GENEHUNTER software.
Clinical evaluation and histological examination of this family suggested typical features of HGF. The onset age was early in the generations, ranging between 1 and 2 years. None of the tested markers showed cosegregation among affected individuals. Genotyping data from four putative regions yielded significant negative two-point LOD scores (<-2.0) at theta=0. The maximum multipoint LOD scores and NPL analysis revealed exclusion of these loci as well.
Exclusion of linkage in this family to any of the known HGF loci proved the existence of a novel locus for autosomal dominant HGF and showed that this rare disorder is far more heterogeneous than previously expected.
No preview · Article · Jun 2009 · Journal Of Clinical Periodontology
[Show abstract][Hide abstract] ABSTRACT: AGGF1 is an angiogenic factor, and its deregulation is associated with a vascular malformation consistent with Klippel-Trenaunay
syndrome (KTS). This study defines the molecular mechanism for transcriptional regulation of AGGF1 expression. Transcription of AGGF1 starts at two nearby sites, −367 and −364 bp upstream of the translation start site. Analyses of 5′- and 3′-serial promoter
deletions defined the core promoter/regulatory elements, including two repressor sites (from −1971 to −3990 and from −7521
to −8391, respectively) and two activator sites (a GATA1 consensus binding site from −295 to −300 and a second activator site from −129 to −159). Both the GATA1 site and the second activator site are essential for AGGF1 expression. A similar expression profile was found for GATA1 and
AGGF1 in cells (including various endothelial cells) and tissues. Electrophoretic mobility shift assay and chromatin immunoprecipitation
assays demonstrated that GATA1 was able to bind to the AGGF1 DNA in vitro and in vivo. Overexpression of GATA1 increased expression of AGGF1. We identified one rare polymorphism −294C>T in a sporadic KTS patient,
which is located in the GATA1 site, disrupts binding of GATA1 to DNA, and abolishes the GATA1 stimulatory effect on transcription
of AGGF1. Knockdown of GATA1 expression by siRNA reduced expression of AGGF1, and resulted in endothelial cell apoptosis and inhibition
of endothelial capillary vessel formation and cell migration, which was rescued by purified recombinant human AGGF1 protein.
These results demonstrate that GATA1 regulates expression of AGGF1 and reveal a novel role for GATA1 in endothelial cell biology and angiogenesis.
Preview · Article · Jun 2009 · Journal of Biological Chemistry
[Show abstract][Hide abstract] ABSTRACT: To identify the gene causing a severe form of progressive autosomal recessive cone-rod dystrophy presenting as Stargardt disease and to characterize clinical features in a large American family.
We characterized an American family who had an unusual retinal dystrophy with clinical features of Stargardt disease and severe progressive cone-rod dystrophy. Family members underwent complete ocular examinations with evaluation of visual acuity, visual fields, fundus examination, fluorescein angiography, and electroretinography. Genome-wide linkage analysis of the family was performed using 408 microsatellite markers spanning the entire human genome. Direct DNA sequence analysis was used for mutational analysis of the ABCA4 gene in all exons and exon-intron boundary regions and for testing cosegregation of the mutations with the disease in the family. DNA sequence analysis was used to determine the presence of the mutations in 200 unrelated controls.
The proband presented with a clinical phenotype that was initially compatible with Stargardt disease, only to progress to a severe cone-rod dystrophy over the course of a few years. The disease-causing gene in the family was linked to the ABCA4 locus on chromosomal 1p22. One novel mutation, c.655A>T, was identified in exon 6 and another novel splicing mutation, c.5312+3A>T, was identified in intron 37 of ABCA4. The mutations were not present in 200 controls. The two affected sisters in this pedigree were compound heterozygotes for the mutations. Unaffected family members either did not carry either or had only one of the two mutations.
We have identified two novel ABCA4 mutations, c.655A>T and c.5312+3A>T. When present as a compound heterozygous state, the mutations cause a phenotype of retinal dystrophy that initially manifests as Stargardt disease and slowly progresses to a severe cone-rod dystrophy. These results expand the wide range of clinical manifestations of ABCA4 mutations.
[Show abstract][Hide abstract] ABSTRACT: A three-generation Chinese family with Hailey-Hailey disease (HHD) was identified and characterized. The proband developed HHD with severe recurrent blisters and crusted erosions involving the body folds. Skin biopsy studies showed epidermal hyperkeratosis and defects in cell-to-cell adhesion. Three other members in the family were also affected with HHD and had the same clinical manifestations. The purpose of this study was to identify the pathogenic gene or mutation in the family.
All exons and exon-intron boundaries of ATP2C1 were polymerase chain reaction (PCR) amplified and sequenced with DNA samples from the proband. Restriction fragment length polymorphism (RFLP) analysis for the intron 23-exon 24 boundary of ATP2C1 was performed in all family members and in 100 normal control subjects.
A novel 2-bp deletion (c.2251delGT) was detected in exon 24 of the ATP2C1 gene. The mutation was present in the three other affected family members and in two asymptomatic young carriers, but not in the other normal family members or the 100 normal controls. The mutation resulted in a frameshift change and led to the formation of a premature termination codon (PTC) four amino acid residues downstream from the sixth transmembrane domain.
Our results indicate that the novel c.2251delGT (p.V751fs) mutation in the ATP2C1 gene is responsible for HHD in this Chinese family. This study expands the spectrum of ATP2C1 mutations associated with HHD.
No preview · Article · Feb 2009 · International journal of dermatology
[Show abstract][Hide abstract] ABSTRACT: Single nucleotide polymorphisms (SNPs) are common DNA sequence variations that occur at single bases within the genome. SNPs have been instrumental in elucidating the genetic basis of common, complex diseases using genome-wide association studies, candidate gene case-control association studies, and genome-wide linkage analyses. A key to these studies is genotyping of SNPs. Various methods for SNP genotyping have been developed. For a particular genotyping project, the choice of method is dependent on the number of SNPs (n) and the number of DNA samples (m) to be genotyped. For a genome-wide or large-scale project with very high n and small m, the Affymetrix SNP GeneChip and Illumina GoldenGate BeadChips assays are the ideal methods. For a project involving a small number of SNPs (small n) and a large population (high m), the TaqMan assay is the preferred technology as it has high throughput and is highly accurate, precise, time-efficient, and cost-effective. Here, we describe the detailed procedures for TaqMan SNP genotyping assay, including preparation of high-quality DNA samples, the operating protocol, clarification of technical issues, and discussion of several cautionary notes.
No preview · Article · Jan 2009 · Methods in molecular biology (Clifton, N.J.)