Single nucleotide polymorphism libraries: why and how are we building them?

Association between urokinase-plasminogen activator gene T4065C polymorphism and risk of mitral valve prolapse

BACKGROUND

Abnormalities of collagen and elastic fibers were found in floppy mitral valves (FMV). Urokinase-plasminogen activator (PLAU) was suggested to be involved in the pathogenesis of elastin and collagen degradation in arterial aneurysm. The role of PLAU genetic variant in mitral valve prolapse (MVP) has not been studied. We, therefore, performed a case-controlled study investigating the possible relation between the PLAU gene polymorphisms and risk of MVP in Taiwan Chinese.

METHODS

We studied 100 patients with MVP diagnosed by echocardiography and 106 age- and sex-matched normal control subjects. The T4065C and T3995C polymorphisms of the PLAU gene were identified by polymerase chain reaction (PCR)-based restriction analysis.

RESULTS

There was a significant difference in either the genotype distribution or allelic frequencies between MVP cases and controls for PLAU gene T4065C polymorphism (P = 0.0001 and 0.0002, respectively). An odds ratio for risk of MVP associated with PLAU T4065C TC genotype was 6.03 (95% confidence interval 2.11-14.83). An odds ratio for risk of MVP associated with PLAU T4065C T allele was 4.99 (95% confidence interval 1.93-12.91). There was no significant difference in either the genotype distribution or allelic frequencies between MVP cases and controls for PLAU T3995C polymorphism. Further categorization of the MVP patients into mild and severe subgroups revealed no statistical difference between these two subgroups for PLAU T4065C and T3995C polymorphisms.

CONCLUSIONS

This study shows that patients with MVP have a higher frequency of PLAU T4065C TC genotype and T allele that supports a role of the PLAU T4065C polymorphism in determining the risk of MVP among the Chinese population in Taiwan.

Genome-wide discovery of loci influencing chemotherapy cytotoxicity

Little is known about the heritability of chemotherapy activity or the identity of genes that may enable the individualization of cancer chemotherapy. Although numerous genes are likely to influence chemotherapy response, current candidate gene-based pharmacogenetics approaches require a priori knowledge and the selection of a small number of candidate genes for hypothesis testing. In this study, an ex vivo familial genetics strategy using lymphoblastoid cells derived from Centre d'Etude du Polymorphisme Humain reference pedigrees was used to discover genetic determinants of chemotherapy cytotoxicity. Cytotoxicity to the mechanistically distinct chemotherapy agents 5-fluorouracil and docetaxel were shown to be heritable traits, with heritability values ranging from 0.26 to 0.65 for 5-fluorouracil and 0.21 to 0.70 for docetaxel, varying with dose. Genome-wide linkage analysis was also used to map a quantitative trait locus influencing the cellular effects of 5-fluorouracil to chromosome 9q13-q22 [logarithm of odds (LOD) = 3.44], and two quantitative trait loci influencing the cellular effects of docetaxel to chromosomes 5q11-21 (LOD = 2.21) and 9q13-q22 (LOD = 2.73). Finally, 5-fluorouracil and docetaxel were shown to cause apoptotic cell death involving caspase-3 cleavage in Centre d'Etude du Polymorphisme Humain lymphoblastoid cells. This study identifies genomic regions likely to harbor genes important for chemotherapy cytotoxicity using genome-wide linkage analysis in human pedigrees and provides a widely applicable strategy for pharmacogenomic discovery without the requirement for a priori candidate gene selection.

Association between COL3A1 collagen gene exon 31 polymorphism and risk of floppy mitral valve/mitral valve prolapse

BACKGROUND

Collagen structure is a key element in mitral valves. Collagen defects were proposed as the primary events causing floppy mitral valves (FMV). The role of collagen genetic variant in floppy mitral valve/mitral valve prolapse (FMV/MVP) has not been well studied. The purpose of this study is to investigate the possible relationship between the collagen gene polymorphisms and risk of FMV/MVP among the Chinese population in Taiwan.

METHODS

We studied 100 patients with FMV/MVP diagnosed by echocardiography and 243 age- and sex-matched normal control subjects. The polymorphisms of exon 31 and exon 52 of the collagen type III-alpha1 gene (COL3A1) were identified by polymerase chain reaction (PCR)-based restriction analysis.

RESULTS

There was a significant difference in either the genotype distribution (P<0.0001) or allelic frequencies (P<0.0001) between FMV/MVP cases and controls for COL3A1 exon 31 polymorphism. An odds ratio for risk of FMV/MVP associated with COL3A1 exon 31 GG genotype was 7.42 (95% confidence interval 4.40-12.52). An odds ratio for risk of FMV/MVP associated with COL3A1 exon 31 G allele was 2.28 (95% confidence interval 1.57-3.29). There was no significant difference in the distribution of COL3A1 exon 52 genotypes (P=0.31) and allelic frequencies (P=0.32) between FMV/MVP cases and controls. Further categorization of the FMV/MVP patients into mild and severe subgroups revealed no statistical difference from the controls for exon 31 or exon 52 polymorphism.

CONCLUSIONS

This study shows that patients with FMV/MVP have higher frequency of COL3A1 exon 31 GG genotype that supports a role of the COL3A1 exon 31 polymorphism in determining the risk of FMV/MVP among the Chinese population in Taiwan.

Evaluation of TNF-α and IL-1β polymorphisms in Taiwan Chinese patients with pterygium

PURPOSE

Pterygium, a complex disease, is associated with ultraviolet radiation, immunoinflammatory process, genetic factors, and virus infection. Ultraviolet radiation induces secretion of proinflammatory cytokines by the ocular surface epithelium, inflammatory cells in the tear fluid, or both. Among these cytokines, tumour necrosis factor (TNF)alpha and interleukin (IL)-1beta activate pterygium body fibroblasts, resulting in a phenotype capable of expressing various proteinases associated with extracellular matrix remodelling, angiogenesis, and fibroblast proliferation, which are important for pterygium formation and recurrence. The genetic factor was proposed to play a role in pterygium formation, but there were few studies to clarify this proposition. For investigating genetic factors, the association between pterygium and TNF-alpha and IL-1beta polymorphisms is evaluated in this study.

METHODS

A total of 128 pterygium patients and 103 volunteers without pterygium were enrolled in this study. Polymerase chain reaction-based analysis was used to resolve the TNF-alpha-308 promoter, IL-1beta-511 promoter, IL-1beta exon 5, and IL-1 receptor antagonist (IL-1 Ra) polymorphisms.

RESULTS

There were no significant differences in the frequency of genotypes and alleles of TNF-alpha-308 promoter, IL-1beta-511 promoter, IL-1beta exon 5, and IL-1 Ra polymorphisms between both groups.

CONCLUSIONS

The correlation between pterygium and TNF-alpha-308 promoter, IL-1beta-511 promoter, IL-1beta exon 5, and IL-1 Ra polymorphisms does not exist and those polymorphisms are not useful genetic markers for pterygium susceptibility. Further studies on other polymorphisms or haplotypes of TNF-alpha and IL-1beta are necessary.

Association of the nicotinic receptor beta 2 subunit and febrile seizures

The nicotinic acetylcholine receptors are members of a superfamily of ligand-gated ion channels that mediate fast signal transmission at synapses. Mutations in neuronal nicotinic acetylcholine receptor beta 2 subunit have been associated with autosomal dominant nocturnal frontal lobe epilepsies. A major challenge is to establish whether the monogenic epilepsy gene also contributes to the common epilepsies. Because febrile seizures represent the majority of childhood seizures, and a genetic predisposition, we investigated the possibility that the nicotinic acetylcholine receptor beta 2 subunit might be involved in the etiology of febrile seizures. Children were divided into two groups: those with febrile seizures (group 1; n = 104) and control patients (group 2; n = 83). Polymerase chain reaction was used to identify the G/C and T/C polymorphisms of the nicotinic acetylcholine receptor beta 2 subunit gene, which is mapped on chromosome 1. Genotypes and allelic frequencies for nicotinic acetylcholine receptor beta 2 subunit gene polymorphisms in both groups were compared. The results indicated that genotypes and allelic frequencies in both groups were not significantly different. These data suggest that nicotinic acetylcholine receptor beta 2 subunit polymorphisms are not a useful marker for prediction of the susceptibility to febrile seizures.

Leukotriene-related gene polymorphisms in ASA-intolerant asthma: an association with a haplotype of 5-lipoxygenase

A recent study has demonstrated the possible involvement of a leukotriene C4 synthase (LTC4S) gene polymorphism in ASA-intolerant asthma (AIA) in a Polish population, whereas no significant association was noted in other populations. To investigate the role of genetic polymorphism in AIA development, we screened single nucleotide polymorphisms (SNPs) of the key enzymes involved in arachidonate metabolism, and the cysteinyl leukotriene receptor 1 (CYSLTR1) in a large Korean population with AIA: 93 AIA and 181 ASA-tolerant asthma (ATA) patients, and 123 normal controls. The single-base extension method was used to genotype SNPs in 5-lipoxygenase (ALOX5, -1708G-->A, 21C-->T, 270G-->A, 1728G-->A), ALOX5-activating protein (ALOX5AP, 218A-->G), prostaglandin-endoperoxide synthase 2 (PTGS2, COX2, -162C-->G, 10T-->G, R228H, V511A), LTC4S (-444A-->C), and CYSLTR1 (927T-->C). Haplotype analyses were undertaken for the SNPs in ALOX5. No significant differences in allele and genotype frequencies of single SNPs were observed between the patient groups ( P>0.05). However, the frequency of the ALOX5-ht1[G-C-G-A] haplotype in the AIA group was significantly higher than its frequency in the ATA group with a probability ( P) of 0.01, odds ratio (OR) of 5.0, and 95% confidence interval (95%CI) of 1.54-17.9, and in the normal controls ( P=0.03, OR=4.5, 95%CI=1.1-18.4), by using a dominant model. These results suggest a lack of association between the ALOX5AP, PTGS2, LTC4S, and CYSLTR1 gene polymorphisms and the AIA phenotype in the Korean population. However, the possible involvement of ALOX5-ht1[G-C-G-A] in AIA development is suggested.

Association of E-cadherin gene 3'-UTR C/T polymorphism with calcium oxalate stone disease

INTRODUCTION

Urinary stone disease is one of the most commonly seen urological diseases in Taiwan. Single nucleotide polymorphisms (SNPs) are commonly used for the investigation of genetic markers for stone disease. E-cadherin (CDH-1) is one of the cellular junction proteins related to the integrity of epithelial cells. Our aim was to investigate a polymorphism of the CDH-1 gene 3'-UTR as a possible genetic marker in the search for the genetic causes.

MATERIALS AND METHODS

148 patients with calcium oxalate stone were compared with 103 healthy controls for the frequency of CDH-1 3'-UTR polymorphisms. The polymorphism was detected by polymerase chain reaction-based restriction analysis (PML I endonuclease).

RESULTS AND CONCLUSIONS

The results revealed significant differences between normal individuals and calcium stone disease patients (p = 0.0013). The distribution of genotype TT homozygote was higher in stone patients (51.5%) than in the control group (43.4%). The odds ratio for T allele compared to C allele was 2.0. We have concluded that polymorphisms of CDH-1 3'-UTR is a valid genetic marker for calcium stone disease.

Association of the neuronal nicotinic acetylcholine receptor subunit alpha4 polymorphisms with febrile convulsions

PURPOSE

The alpha4-subunit gene of the neuronal nicotinic acetylcholine receptor (CHRNA4) has been identified as the first gene underlying an idiopathic partial epilepsy syndrome in human autosomal-dominant nocturnal frontal lobe epilepsy. Studies provided evidence that the protein coded by CHRNA4 is one of the most abundant subunits of the neuronal nicotinic acetylcholine receptors in mammalian brains, and mutations of CHRNA4 seem to cause neuronal excitation. The CHRNA4 gene may have a role in the development of febrile convulsions (FCs), the majority of childhood seizures. This study assessed the distribution of genotypes of CHRNA4 in patients with FCs.

METHODS

A total of 102 children with FCs and 80 normal control subjects were included in the study. Polymerase chain reaction was used to identify the C/T polymorphism of the CHRNA4 gene. Genotypes and allelic frequencies for the CHRNA4 gene polymorphisms in both groups were compared.

RESULTS

The number of individuals with heterozygous CHRNA4 (Ser543Ser)-C/T genotype was significantly greater (60.8% vs. 32.5%; p = 0.001), and the CHRNA4 (Ser543Ser)-T allele frequency was significantly higher (p = 0.001), in patients with FCs compared with healthy controls. The odds ratio for developing FCs in individuals with the CHRNA4 (Ser543Ser)-CT genotype was 3.77 compared with individuals with two copies of the CHRNA4 (Ser543Ser)-C allele.

CONCLUSIONS

This study demonstrated an association between the CHRNA4 gene and FCs. Individuals with the T allele had a higher incidence of FCs. These data suggest that the CHRNA4 gene or a closely linked gene might be one of the susceptibility factors for FCs.

Association analysis of gamma 2 subunit of gamma- aminobutyric acid type A receptor polymorphisms with febrile seizures

An alternation of gamma-aminobutyric acid (GABA)-ergic neurotransmission has been implicated as an etiologic factor in epileptogenesis. Missense mutations in the GABRG2 gene, which encodes the gamma2 subunit of central nervous GABAA receptors, have recently been described in one family with childhood absence epilepsy and febrile seizures (FSs). FSs represent the majority of childhood seizures and have a genetic predisposition. It is not known, however, whether polymorphisms in those genes involved in familial epilepsies also contribute to the pathogenesis of FSs. By performing an association study, we used single-nucleotide polymorphisms to investigate the distribution of genotypes of GABRG2 in patients with FSs. A total of 104 children with FSs and 83 normal control subjects were included in the study. PCR was used to identify the C/T and A/G polymorphisms of the GABRG2 gene on chromosome 5q33. Genotypes and allelic frequencies for the GABRG2 gene polymorphisms in both groups were compared. The GABRG2 (nucleotide position 3145 in intron G-->A) gene in both groups was not significantly different. In contrast, the number of individuals with the GABRG2 (SNP211037)-C/C genotype in patients with FSs was significantly greater compared with that in healthy control subjects (p = 0.017), and the GABRG2 (SNP211037)-C allele frequency in patients with FSs was significantly higher than that in healthy control subjects (p = 0.009). The odds ratio for developing FSs in individuals with the GABRG2 (SNP211037)-C/C genotype was 2.56 compared with individuals with the GABRG2 (SNP211037)-T/T genotype. These data suggest that the GABRG2 gene might be one of the susceptibility factors for FSs.

The lack of association between febrile convulsions and polymorphisms in SCN1A

Febrile convulsions (FCs) represent the majority of childhood seizures, and patients have a genetic predisposition to their development. The genetic susceptibility to FCs seems to involve multiple genes in most instances. Recent studies provided evidence that mutations in SCN1A represent the most frequent cause of generalized epilepsy with febrile seizures plus an autosomal-dominant epilepsy syndrome. SCN1A mutations alter channel inactivation, resulting in persistent inward sodium current. It is not known if polymorphisms in those genes involved in familial epilepsies also contribute to the pathogenesis of FCs. By performing an association study, we used single nucleotide polymorphisms to investigate the distribution of genotypes of SCN1A in patients with FCs. A total of 104 Taiwanese children with FCs and 83 normal control subjects were included in the study. Polymerase chain reaction was used to identify the A/G polymorphism of the SCN1A gene. The results showed that genotypes and allelic frequencies for the SCN1A gene polymorphisms in both groups were not significantly different. These data suggest that the SCN1A gene might not be one of the susceptibility factors for FCs. Pure FCs and febrile convulsions associated with idiopathic generalized epilepsy may not share a common genetic etiology.

Candidate gene case-control studies

Two main approaches to the identification of genes are involved in polygenic diseases. Use of family studies has generally been the preferred approach up until recently, but this is only feasible if the genetic component of the disease is relatively strong and DNA samples are available from other family members. Population case-control studies are useful both as an alternative and an adjunct to family studies. These can involve either whole genome scanning or candidate gene approaches. While whole genome scanning is likely to be widely used in the future once more information on genome-wide single nucleotide polymorphism distributions is available, at present, candidate gene studies are more feasible. When performing candidate gene case-control studies factors such as study design, methods for recruitment of case and controls, selection of candidate genes, functional significance of polymorphisms chosen for study and statistical analysis require close attention to ensure that only genuine associations are detected. Some examples of the successful use of candidate gene case-control studies are discussed and, to illustrate some potential problems in the design and interpretation of association studies, some specific examples of association studies on cancer are considered.

Genetic predictors of cardiovascular disease: the use of chip technology

Cardiovascular disease, a primary cause of mortality in the United States, has a complex pathologic process involving many genes. The high-throughput technology (microarray or "DNA chip") used to decipher the human genome is now being employed to identify key genes in its development. A study focusing on candidate genes associated with premature cardiovascular disease discovered that missense variations in the thrombospondin 1 and 4 genes were associated with premature coronary artery disease, while a mutation in the non-coding region of a thrombospondin 2 gene imparts protection from developing heart disease. Although the clinical implications of microarray technology are still under investigation, this research may lead to a diagnostic test to determine a patient's risk for developing heart disease.

The polymorphisms of codon 727 and 52 of thyroid-stimulating hormone receptor gene are not associated with mitral valve prolapse syndrome in Taiwan Chinese

A germline mutation of the thyroid-stimulating hormone receptor (TSHR) gene has been reported to be associated with thyrotoxicosis and mitral valve prolapse syndrome (MVPS) in a Chinese family. The role of TSHR genetic variants in MVPS has not been well studied. This study investigated the possible relationship between the polymorphisms of codon 727 and 52 of the TSHR gene and MVPS among the Chinese population in Taiwan. We studied 100 patients with MVPS diagnosed by echocardiography and 100 ageand sex-matched normal control subjects. The polymorphisms of codon 727 and 52 of the TSHR gene were identified by polymerase chain reaction-based restriction analysis. There was no significant difference in either the genotype distribution or allelic frequencies between MVPS cases and controls for either TSHR gene D727E polymorphism ( = 0.51 and 0.45, respectively ) or P52T polymorphism (P = 0.60 and 0.31, respectively). The MVPS patients were divided into 2 subgroups: those with Graves' disease, and those without the thyroid disorder, and there were no statistical differences from the controls for both the TSHR gene D727E and P52T polymorphisms. Further categorization of the MVPS patients into mild and severe subgroups also revealed no statistical difference from controls for either the TSHR gene D727E or P52T polymorphisms. These findings suggest that the codon 727 and 52 polymorphisms of the TSHR gene are not the suitable genetic markers of MVPS in Taiwan Chinese.

The voltage-gated potassium channel KCNQ2 in Taiwanese children with febrile convulsions

Mutations in the voltage-gated potassium channel genes KCNQ2 and KCNQ3 have been found to cause benign familial neonatal convulsions. Recent studies provided evidence that KCNQ2 and KCNQ3 contribute to the M-current, which regulates the subthreshold electrical excitability in the CNS. Febrile convulsions represent the majority of childhood seizures, and show a strong family history, suggesting a genetic predisposition. By performing an association study, we investigated whether KCNQ2 gene polymorphisms can be used as markers of susceptibility to febrile convulsions. These data suggest that the KCNQ2 gene might not be a useful marker for prediction of the susceptibility of febrile convulsions.

Interleukin-4 intron 3 polymorphism is not related to susceptibility to febrile seizures

Interleukin-4 (IL-4) is a cytokine with anti-inflammatory properties. This study was undertaken to investigate whether IL-4 intron 3 gene polymorphism could be used as markers of susceptibility to febrile seizures and epilepsy of children. Children were divided into three groups: group 1, febrile seizures (n = 51); group 2, epilepsy (n = 43); and group 3, normal control group (n = 83). Polymorphisms for IL-4 intron 3 were detected by polymerase chain reaction. Genotypes and allelic frequencies for IL-4 intron 3 gene polymorphism in three groups were compared. We found that proportions of different IL-4 intron 3 polymorphisms in three groups were nonsignificantly different. Proportions of RP1 homozygote/heterozygote/RP2 homozygote for IL-4 intron 3 in three groups were as follows: group 1, 56.9/41.2/1.9%; group 2, 62.8/32.6/4.6%; and group 3, 62.7/33.7/3.6%. The proportion of RP1/RP2 for IL-4 intron 3 in three groups were as follows: group 1, 77.5/22.5%, group 2, 79.1/20.9%, and group 3, 79.5/20.5%. We concluded that the association of IL-4 polymorphisms with febrile seizures and epilepsy of children does not exist. IL-4 intron 3 polymorphism is not a useful marker for prediction of the susceptibility of febrile seizure and epilepsy of children.

How many SNPs does a genome-wide haplotype map require?

We derive and compare several estimates of the number of SNPs that would be required to form the basis of a complete haplotype survey of the human genome. Our estimates make use of reports published by Stephens et al. [1], Patil et al. [2] and Daly et al. [3]. The estimated number of SNPs required for a genome-wide haplotype survey ranges from 180K (based on a European sample of 16 chromosomes) to 600K (based on an ethnically diverse sample of 164 chromosomes). We discuss the implications of using cohorts of different size and ethnic composition and the usefulness of public SNP databases for this effort. Finally, we estimate the experimental effort and cost required to complete a genome-wide haplotype survey.

p21 gene codon 31 polymorphism is associated with bladder cancer

The function of p21 is related to cell apoptosis, progression and malignancies. It is thought that p21 is related to cancer formation but is not related to tumor grade. We aimed to investigative the polymorphism of p21 codon 31 as a candidate for the genetic marker of bladder cancer and its progression. The distribution was analyzed in 53 bladder cancer patients, 119 healthy controls in Taiwanese patients. Polymerase chain reaction based restriction analysis was used for the study of the association of p21 codon 31 polymorphism with bladder cancer. There was a significant difference in p21 codon 31 polymorphism between the control and the cancer patients (p < 0.01). The arginine form was prominent in the cancer patient (per copy of the A allele, odds ratio = 2.03, 95% confidence interval = 1.23-3.37). Furthermore, the distribution of this polymorphism was significantly different from non-invasive to invasive bladder cancer (p < 0.05). Serine heterozygote was more prominent in the invasive group with 25 to 1% respectively when compared with the non-invasive group. The polymorphism of p21 codon 31 is associated with bladder cancer. An individual possessing one allele of arginine form in p21 codon 31 has a higher risk of developing bladder cancer than the serine form. Although the mechanism is unclear, our results show p21 gene is associated with tumor grade.

Angiotensin II type 1 receptor gene adenine/cytosine1166 polymorphism is not associated with mitral valve prolapse syndrome in Taiwan Chinese

The adenine/cytosine1166 (A/C1166) polymorphism of the angiotensin-II type 1 receptor (AGTR1) gene is presumed to be associated with mitral valve prolapse syndrome (MVPS) in Caucasians. To investigate whether a similar association exists among the Chinese population in Taiwan, 100 patients with MVP diagnosed by echocardiography and 100 normal subjects were studied by polymerase chain reaction-based restriction analysis. The difference in genotype (chi2=0.24; p=0.89) and allelic (Yates' chi2=0.06; p=0.81) frequencies between the groups were not significant. Further categorization of the MVP patients into mild and severe subgroups also revealed no statistical difference from the controls. It was concluded that A/C1166 polymorphism of the AGTR1 gene is not a suitable genetic marker of MVPS in Taiwan Chinese.

Prognostic significance of the proline form of p53 codon 72 polymorphism in nasopharyngeal carcinoma

OBJECTIVES/ HYPOTHESIS

An important tumor suppressor gene, p53, plays a role in the regulation of cell progression and prevention of carcinogenesis. Mutated p53 is related to cell progression and malignancy. We aimed to evaluate the association between nasopharyngeal carcinoma and p53 polymorphism.

STUDY DESIGN

Case control study.

METHODS

All individuals were divided into two groups: nasopharyngeal carcinoma (n = 50) and non-nasopharyngeal carcinoma groups (n = 59). Their p53 codon 72 polymorphisms (arginine [Arg] homozygotes, heterozygotes, proline [Pro] homozygotes) were detected by polymerase chain reaction. Associations between nasopharyngeal carcinoma and p53 polymorphism were evaluated.

RESULTS

Distributions of various p53 polymorphisms significantly differed between the two groups. We noted a dominant presentation of Pro homozygotes in the nasopharyngeal carcinoma population over that in the non-nasopharyngeal carcinoma population. Proportions of Pro homozygotes and heterozygotes and Arg homozygotes were 32%, 28%, and 40% in the nasopharyngeal carcinoma population and were 13.5%, 44.1%, and 42.4% in the non-nasopharyngeal carcinoma population, respectively.

CONCLUSIONS

An association exists between nasopharyngeal carcinoma and p53 codon 72 polymorphism. The p53 Pro homozygotes are to a higher risk of development of nasopharyngeal carcinoma.

HyBeacon probes: a new tool for DNA sequence detection and allele discrimination

Technologies that permit rapid investigation of DNA sequences, such as those containing single nucleotide polymorphisms (SNPs), are of great consequence to many sectors that perform molecular diagnostic analyses. We have developed a novel fluorescent oligonucleotide probe technology, termed HyBeacons, which provides a new homogeneous method for fluorescence-based sequence detection, allele discrimination and DNA quantification. Hybridization of HyBeacons to complementary DNA target sequences results in a measurable elevation of probe fluorescence emission. HyBeacon probes may be incorporated into real-time polymerase chain reaction (PCR) assays to detect the presence and monitor the accumulation of specific DNA sequences. Furthermore, closely related sequences differing by as little as a single nucleotide may be discriminated by measuring the melting temperatures (T(m)) of various probe/target duplexes and exploiting the differences in T(m) that exist between different duplexes. We demonstrate here that HyBeacon probes are efficient tools for rapid sequence analysis and that a single probe may be employed to reliably identify homozygous and heterozygous samples. Additional benefits exhibited by the HyBeacon technology derive from their simple mode of action, ease of design, relatively inexpensive synthesis and potential for multiplex analysis.

Putting the search for genes in perspective

The sequencing of the human genome has been heralded by both the mass media and scientists as a breakthrough that will allow the detection of individuals at increased risk for common diseases and the tailoring of drugs to an individual's genetic profile in order to prevent disease. Sequencing is likely to benefit those at risk of developing rare diseases in which inherited mutations in a single gene play a major causal role. In the vast majority of people with common diseases, however, genotypes at many different loci, as well as environmental exposures, must be simultaneously present before disease appears. Elucidating the genes involved will prove elusive. In addition to the large number, different combinations account for a particular disease. Most of the genotypes that contribute to the constellation of necessary genes are uncommon and will be difficult to find. Common genotypes may confer susceptibility but will be weak predictors of disease. Because of the difficulty of discovering genes for common diseases, designing therapies will also prove difficult. More attention to environmental risk factors for particular diseases will have greater yield than a genetic search, but this too will be difficult because of environmental-genetic and other interactions. The search for risk factors for particular diseases neglects the political and social milieu in which individuals swim or sink and in which all diseases occur.

Implications of the Human Genome Project for obstetrics and gynecology

The initial sequencing of the human genome should be regarded as a milestone in a road that stretches years into the future; the full ramifications of the Human Genome Project are still only being theorized. Researchers will benefit from the catalog of human genes in studies of the genetics of disease susceptibility and the cell biology of gene interactions. Clinicians will increasingly offer genetic or biochemical testing to identify those at highest risk for a number of diseases. Drug discovery will eventually follow newly possible studies of gene expression and protein function. However the Human Genome Project eventually shapes medicine, it is certain that physicians, particularly obstetricians and gynecologists, will need to be well versed in the scientific and ethical issues involved, inasmuch as we will likely be at the center of the most heated debates.

p21 gene codon 31 arginine/serine polymorphism: non-association with endometriosis

p21, an important regulator of the cell cycle, acts as a mediator of the growth-suppressing and -promoting functions of p53. We aimed to investigate the association between codon 31 polymorphisms of p21 gene and endometriosis. Women were divided into two groups: endometriosis (n = 102) and nonendometriosis (n = 119). The gene polymorphism for p21 codon 31 involved a base change from AGC to AGA and amino acid changes from serine (Ser) to arginine (Arg). Polymorphisms (Ser homozygotes, heterozygotes, Arg homozygotes) between both groups were detected and compared. Associations between the endometriosis and polymorphisms were evaluated. The results revealed that the distributions of different p21 polymorphisms in both groups were nonsignificantly different. The proportions of Ser homozygote/heterozygote/Arg homozygote in endometriosis and nonendometriois populations were 26.5/48.0/25.5% and 17.6/50.4/31.9%, respectively. We concluded the noncorrelation between the endometriosis and the p21 codon 31 polymorphism. p21 gene codon 31 arginine/serine polymorphism is not a useful marker for prediction of endometriosis susceptibility.

Pharmacogenomics: unlocking the human genome for better drug therapy

There is great heterogeneity in the way humans respond to medications, often requiring empirical strategies to find the appropriate drug therapy for each patient (the "art" of medicine). Over the past 50 years, there has been great progress in understanding the molecular basis of drug action and in elucidating genetic determinants of disease pathogenesis and drug response. Pharmacogenomics is the burgeoning field of investigation that aims to further elucidate the inherited nature of interindividual differences in drug disposition and effects, with the ultimate goal of providing a stronger scientific basis for selecting the optimal drug therapy and dosages for each patient. These genetic insights should also lead to mechanism-based approaches to the discovery and development of new medications. This review highlights the current status of work in this field and addresses strategies that hold promise for future advances in pharmacogenomics.

Perspectives on the use of electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry for short tandem repeat genotyping in the post-genome era

The recent completion of the first rough draft of the human genome has provided fundamental information regarding our genetic make-up; however, the post-genome era will certainly require a host of new technologies to address complex biological questions. In particular, a rapid and accurate approach to characterize genetic markers, including short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) is demanded. STRs are the most informative of the two polymorphisms owing to their remarkable variability and even dispersity throughout eukaryotic genomes. Mass spectrometry is rapidly becoming a significant method in DNA analysis and has high probability of revolutionizing the way in which scientists probe the human genome. It is our responsibility as biomolecular mass spectrometrists to understand the issues in genetic analysis and the capabilities of mass spectrometry so that we may fulfill our role in developing a rapid, reliable technology to answer specific biological questions. This perspective is intended to familiarize the mass spectrometry community with modern genomics and to report on the current state of mass spectrometry, specifically electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry, for characterization of STRs.

Association of the vitamin D receptor gene start codon Fok I polymorphism with calcium oxalate stone disease

OBJECTIVE

To assess the use of Fok I polymorphism (the most frequent polymorphism, at the start codon of the vitamin D receptor gene, VDR) as a convenient genetic marker in identifying the cause of urolithiasis.

PATIENTS, SUBJECTS AND METHODS

A normal control group of 90 healthy subjects and 146 patients with calcium oxalate stones were examined. Using polymerase chain reaction (PCR)-based restriction analysis, the relationship between Fok I polymorphism and urolithiasis was evaluated. An unexcisable length of 265 bp was identified (allele CC) and two fragments (169 bp and 96 bp) identified as excisable lengths (allele TT).

RESULTS

There was a statistically significant difference between the groups (chi-square test, P < 0.05) for the genotype of the VDR Fok I start codon polymorphism. The odds ratio (95% confidence interval) for the C allele in those at risk of stone disease was 1.672 (1.149-2.432).

CONCLUSIONS

These results suggest that the VDR Fok I start codon polymorphism may be a good candidate for a genetic marker in calcium oxalate stone disease.

Regions of low single-nucleotide polymorphism incidence in human and orangutan xq: deserts and recent coalescences

While scanning for single-nucleotide polymorphisms (SNPs) in the human Xq25-q28 region of CEPH families, we found six long "deserts" of low SNP incidence representing 28% of the investigated genome. One was 1.66 Mb in length. To determine whether these SNP deserts were due to reduced input of mutations or to recent coalescent events such as bottlenecks or selective sweeps, comparative sequence was determined from a female orangutan. The mean divergence was 2.9% and was not reduced in deserts compared with nondesert regions. Thus, the best explanation for the SNP deserts is recent coalescent events in humans. These events are the cause of substantial variation in human noncoding SNP incidence. In addition, the mutational spectrum in humans and orangutans was estimated as 63% AG (and CT), 17% AC (and GT), 8% CG, 4% AT, and 8% insertion/deletions. The average lifetime of a SNP destined to become fixed for a new allele between these species was estimated as 284,000 years.

Use of single nucleotide polymorphisms (SNP) and real-time polymerase chain reaction for bone marrow engraftment analysis

Allogeneic bone marrow transplant engraftment assays use polymorphisms in the human genome to determine the relative percentages of donor and recipient cells present in the recipient. We describe a novel posttransplant assay approach using single nucleotide polymorphisms (SNPs), the most common type of polymorphism in humans. Using samples of defined genotype, we used real-time polymerase chain reaction (PCR) and allele-specific fluorescent TaqMan probes to assay a SNP of the cytochrome P450 CYP2C9 gene. Standard curves of chimeric mixes showed a linear relationship between the ratio of two alleles and the ratio of their respective fluorophore emission, except for mixes with a low percentage (< 5%) of the less common allele. We validated the SNP real-time PCR assay by comparing it to Southern hybridization analysis, analyzing DNA mixes in a blinded fashion with both methods. The correlation between the two methods was high. We have produced a statistical model that varies allele frequency to predict how many SNPs would be required to produce a functional SNP panel. Additional development will be necessary to produce such a panel of highly informative SNPs for clinical use. A real-time PCR SNP assay may ultimately provide more accurate quantification and shortened turnaround time compared to current post-engraftment assays.

Consulting the source code: prospects for gene-based medical diagnostics

Gene-based diagnostics has been slow to enter medical routine practice in a grand way, but it is now spurred on by three important developments: the total genetic informational content of humans and most of our pathogens is rapidly becoming available; a very large number of genetic factors of diagnostic value in disease are being identified; and such factors include the identity of genes frequently targeted by mutations in specific diseases, common DNA sequence variants associated with disease or responses to therapy, and copy number alterations at the level of DNA or RNA that are characteristic of specific diseases. Finally, improved methodology for genetic analysis now brings all of these genetic factors within reach in clinical practice. The increasing opportunities for genetic diagnostics may gradually influence views on health and normality, and on the genetic plasticity of human beings, provoking discussions about some of the central attributes of genetics.

The predictive power of haplotypes in clinical response

A variety of approaches have been proposed to find genetic markers that can be used in a clinical setting. Single nucleotide polymorphisms (SNPs) are the basis of the most commonly used approaches. Here we describe an approach using gene-based haplotypes, which are collections of SNPs located throughout the ftinctional regions of candidate genes, and organised as they occur separately on an individual's two chromosomes. The main point of this review is that the haplotype has greater power than any individual SNP to track an unobsenrved, but evolutionarily linked, variable site.