Allele Length Research Articles

Microsatellite Instability (MSI) In High Risk Myelodysplastic Syndrome (MDS) and Acute Myeloid Leukaemia (AML) Cells Promotes Frameshift Mutations In DNA Repair Genes: Indications for PARP Inhibitor Therapy.

AbstractAbstract 1194Despite major advances in the biology and pathogenesis of myelodysplastic syndrome (MDS) and acute myeloid leukaemia (AML) identification of the most effective and safest form of treatment continue to present a formidable challenge particularly in older patients. Older patients (>70 years) that constitute the majority of MDS/AML patients are often resistant to chemotherapy, achieve short lived remission and are not candidates for stem cell transplantation. Therefore the emphasis is to prolong survival or improve the quality of life. Currently, a number of therapeutic strategies are being evaluated and these include treatment with DNA methyltransferase or histone deacetylase inhibitors. Seminal work in breast cancer have shown that inhibitors of poly ADP ribose polymerase (PARP) activity can selectively target tumour cells through exploitation of inherent DNA repair defects. MDS/AML are characterized by genomic instability (GI) and single nucleotide polymorphism arrays (SNPA) karyotyping show that loss of heterozygosity (LOH) and uniparental disomy (UPD) are common in MDS/AML and it has been suggested that the underlying cause of this GI is a defect in double strand DNA repair. We have demonstrated that non homologous end joining, a major pathway for the repair of double strand DNA breaks is overactive and associated with extensive joining errors in primary AML cells. Hence, potentially MDS/AML patients are candidates for PI therapy. We have also shown more recently, that 15% of MDS/AML primary patient cells and cell lines are sensitive to PARP inhibitors (PI) through exploitation of homologous recombination DNA repair defects. To further elucidate the mechanisms that underlie PI sensitivity in MDS/AML we tested for microsatellite instability (MSI) in MDS/AML cell lines and high risk MDS patients and the presence of frameshift mutations in specific DNA repair genes that confer PI sensitivity. MSI is a change in length of a microsatellite allele caused by insertion or deletion of nucleotides that are misincorporated during DNA replication and not removed by the mismatch repair pathway. Using fluorescent PCR analysis, PI sensitive cell lines, P39, KG-1 and Molm-13 showed MSI-high (instability at ≥ 2 loci) at 5 mononucleotide microsatellites, in contrast to 12 PI insensitive cell lines that showed no MSI at these loci. We also show using fluorescent PCR and DNA sequencing that these MSI positive cell lines demonstrate MSI (monoallelic 1–2 base pair [bp] deletion) in the coding region microsatellites of DNA repair genes, Ataxia telancgiectasia mutated gene (ATM), CTiP, and MRE11. Monoallelic 1–2 bp base pair deletions at these loci produced frameshift mutations that induced aberrant gene splicing transcripts in ATM and MRE11 and a markedly truncated CTiP gene transcript. No MSI was detected in DNA repair genes CHK1, RAD50, PTEN, BLM and ATR in these cell lines and no mutations were observed at any DNA repair gene microsatellite in the 13 PI insensitive cell lines. We then determined MSI in high risk MDS patients with or without monosomy 7 (-7/del7q). 13 of 63 (21%) high risk MDS patients showed MSI (9 MSI-low and 4 MSI-high). Of the 13 MSI positive patients, 7 (4 MSI-high, 3 MSI-low) had monosomy 7 and other complex chromosomal abnormalities (Group 1, 54%), 2 (MSI-low) patients had isolated monosomy 7 (Group 2, 15%) whilst 4 patients (MSI-low) had normal cytogenetics (Group 3, 30%). Constitutional DNA from these patients did not show MSI at these loci. Significantly, however, Group 3 with MSI and normal cytogenetics all had widespread UPD and cryptic chromosome changes determined by SNPA. Strikingly, thus all 13 patients with MSI possessed chromosomal abnormalities, both gross and cryptic. Furthermore, 12 patients (19%) found to be cytogenetically normal and lacking UPD and genomic aberrations by SNPA did not show MSI. We have also identified that 3 patients with MSI-high (Group 1) and 1 patient with MSI-low (Group 3) had a monoallelic 1 bp deletion in the CTiP exon coding microsatellite. 1 bp deletion within the coding exon of CTiP resulted in an abbreviated CTiP gene transcript. In conclusion, we have made the important correlation between MSI and subsequent frameshift mutations in specific DNA repair genes with the gross and cryptic chromosomal changes observed in MDS/AML. Identification of a cohort of MDS/AML patients with MSI would herald a significant advancement for the selection of candidates for PI therapy. Disclosures:No relevant conflicts of interest to declare.

Rates and patterns of microsatellite mutations in common carp (Cyprinus carpio L.).

During genotyping 150 microsatellites in a F1 family of common carp, six mutations were found at five microsatellite loci. The overall mutation rate of common carp microsatellites was 2.53 X 10(-4) per locus per generation. At five loci, mutations increased the length of alleles by at least one repeat unit, suggesting mutations at microsatellite loci in common carp do not follow strict stepwise mutation model. The data on mutation rates and patterns can facilitate population genetics studies, and provide useful parameters for estimating a long-term effective population size of common carp.

It Is Not Just About Testosterone: Physiological Mediators and Moderators of Testosterone’s Behavioral Effects

The inclusion of hormones in social and personality psychology research offers researchers a powerful methodological tool, although careful consideration must be paid to the complex and dynamic biological systems that connect hormones to behavior. Testosterone has been clearly established as a biological fuel for dominance, although behavioral findings have been inconsistent and weak. We suggest a number of physiological systems that affect the influence of testosterone on behavior. Vasopressin synthesis and the aromatization into estradiol both serve to facilitate testosterone’s effects. Testosterone’s behavioral responses to threats are suppressed by basal cortisol and moderated by allele length on the serotonin transporter gene. Variation in the expression of monoamine oxidase A regulates the levels of neurotransmitters responsible for impulse control, potentially suppressing testosterone’s influence over behavior. We argue that researchers must consider these dynamic relationships between hormones and other biological systems when engaging in future social endocrinology research.

Functional Variant in Complement C3 Gene Promoter and Genetic Susceptibility to Temporal Lobe Epilepsy and Febrile Seizures

BackgroundHuman mesial temporal lobe epilepsies (MTLE) represent the most frequent form of partial epilepsies and are frequently preceded by febrile seizures (FS) in infancy and early childhood. Genetic associations of several complement genes including its central component C3 with disorders of the central nervous system, and the existence of C3 dysregulation in the epilepsies and in the MTLE particularly, make it the C3 gene a good candidate for human MTLE.Methodology/Principal FindingsA case-control association study of the C3 gene was performed in a first series of 122 patients with MTLE and 196 controls. Four haplotypes (HAP1 to 4) comprising GF100472, a newly discovered dinucleotide repeat polymorphism [(CA)8 to (CA)15] in the C3 promoter region showed significant association after Bonferroni correction, in the subgroup of MTLE patients having a personal history of FS (MTLE-FS+). Replication analysis in independent patients and controls confirmed that the rare HAP4 haplotype comprising the minimal length allele of GF100472 [(CA)8], protected against MTLE-FS+. A fifth haplotype (HAP5) with medium-size (CA)11 allele of GF100472 displayed four times higher frequency in controls than in the first cohort of MTLE-FS+ and showed a protective effect against FS through a high statistical significance in an independent population of 97 pure FS. Consistently, (CA)11 allele by its own protected against pure FS in a second group of 148 FS patients. Reporter gene assays showed that GF100472 significantly influenced C3 promoter activity (the higher the number of repeats, the lower the transcriptional activity). Taken together, the consistent genetic data and the functional analysis presented here indicate that a newly-identified and functional polymorphism in the promoter of the complement C3 gene might participate in the genetic susceptibility to human MTLE with a history of FS, and to pure FS.Conclusions/SignificanceThe present study provides important data suggesting for the first time the involvement of the complement system in the genetic susceptibility to epileptic seizures and to epilepsy.

GSTM1/T1 Genotypes and Benzo(A)Pyrene Hemoglobin Adducts in Maternal and Fetal Blood

Both genetic and environmental factors are involved in the development of cancer. The capacity to metabolize certain drugs and carcinogens is known to be variable in humans and appears to be of critical importance in determining the risk an individual has of developing cancer when exposed to carcinogens. For many phase I and phase II enzyme systems involved in foreign compound metabolism it is now understood that germ-line genetic variation within the genes encoding these enzymes leads to altered phenotypic expression impacting the metabolic capacity of the individual. This genetic variation is referred to as genetic polymorphism and the study of the association between genetic polymorphism and the resulting phenotypic changes in drug or foreign compound metaboism is referred to as pharmacogenetics. This variation in metabolic capacity is linked to environment–gene interactions on carcinogenesis and has been well demonstrated by enzymes that are involved in the metabolism of carcinogens including several human cytochrome P450 enzymes as well as certain glutathione S-transferases and N-acetyltransferases. The genetic lesion may involve a single but critical base pair change or complete gene deletion. Screening assays based on PCR amplification coupled to restriction fragment length polymorphism (RFLP) analysis or allele specific PCR have been developed to correlate genetic polymorphism with phenotypic expression and susceptibility to genotoxicity or carcinogenesis. The phase II enzymes, including GSTs, N-acetyltransferases, as well as epoxide hydrolase, are all involved in the detoxification of activated metabolites of carcinogens, including those carcinogens found in tobacco smoke. The substrates of GSTs include benzo(a)pyrene as well as other carcinogens. In the present study, we investigated the relationship between polymorphism of glutathione S-transferase in maternal and fetal cord blood samples obtained at delivery and correlated genotype with presence of hemoglobin adducts to the tobacco carcinogen benzo(a)pyrene.

I09 Brain glucose hypometabolism in a subject carrying an unstable allele of intermediate CAG33 repeat length in the Huntington's disease gene

BackgroundIt is a general belief that below 36 CAG triplet number, Huntington's disease (HD) does not manifest although unstable transmission of paternal alleles with intermediate length (27–35 CAG repeats) may...

Xyloglucan endotransglycosylase/hydrolase genes in cotton and their role in fiber elongation

Plant cell wall extensibility is mediated, in part, by xyloglucan endotransglycosylases/hydrolases (XTH) that are able to cleave and reattach xyloglucan polymers that make up the hemicelluloses matrix of type I cell walls. In Arabidopsis and other plants, XTHs are encoded by relatively large gene families that are regulated in specific spatial and temporal patterns. In silico screening of a cotton expressed sequence tag (EST) database identified 23 sequences with close sequence similarity to Arabidopsis XTH coding sequences. Analysis of full-length cotton cDNAs derived from these ESTs allow for the identification of three distinct GhXTH cDNAs (denoted GhXTH1, GhXTH2 and GhXTH3) based primarily on their 3' untranslated sequences. The three GhXTH genes were expressed differently with GhXTH1 predominantly expressed in elongating cotton fibers. The function of GhXTH1 in mediating cotton fiber elongation was analyzed in transgenic cotton plants that express a transgene consisting of the GhXTH1 coding sequence under transcriptional control of the CaMV 35S promoter. Plants that over-expressed GhXTH1 had increased XTH activity and produced mature cotton fibers that were between 15 and 20% longer than wild-type cotton plants under both greenhouse and field growth conditions. Segregation analysis showed that the 35S::GhXTH1 transgene acts as a dominant fiber length allele in transgenic cotton. These results confirm that GhXTH1 is the predominant XTH in elongating fibers and its expression limits cotton fiber elongation.

Efficacy of metformin therapy in adolescent girls with androgen excess: relation to sex hormone–binding globulin and androgen receptor polymorphisms

We studied the effects of the SHBG (TAAAA)(n) and androgen receptor gene [AR] (CAG)(n) allele length on endocrine-metabolic features and body composition (by dual-energy X-ray absorptiometry) before and after 1 year on metformin (850 mg/d) in 70 girls with polycystic ovary syndrome after precocious pubarche; allele lengths were assessed by polymerase chain reaction in both patients and in population control subjects (n = 107). Longer SHBG (TAAAA)(n) alleles (>8 repeats) were associated with more improvement of the lipid profile after 1 year on metformin, whereas longer AR (CAG)(n) alleles were related to more normalization of the androgen and lipid levels after therapy; longer alleles in both genes had an additive effect on the beneficial changes of SHBG, T, and lipids after metformin.

Androgen receptor status predicts response to chemotherapy, not risk of breast cancer in Indian women

BackgroundConsiderably little is known about the biological role and clinical significance of androgen receptor expression in breast cancer. The objectives of this study were to characterize AR-CAG repeat genotypes in a cohort of women with breast cancer and to determine the influence of AR on response to neoadjuvant chemotherapy and clinical outcome.Materials and methodsGenotyping of the AR CAG repeat region was done on 70 patients and 80 healthy aged- matched female controls. To assess response to NACT, tissue samples from 30 LABC cases were evaluated quantitatively by real time for AR mRNA expression. The clinical response was correlated with both the pre and post chemotherapy AR expression. The CAG alleles did not show differences between cases and controls when the mean of short, long and average length of both CAG alleles was considered. However, analysis when done defining short allele as CAGn < 20 (AR1) and the long as CAGn ≥ 20 (AR2), risk was found associated with AR2 allele with marginal significance (P = 0.09). Stratification by age of onset, FH, stage, grade ER and AR status failed to reveal any association with breast cancer risk. Genotype carriers with ≥20 CAGn showed decrease of AR mRNA expression although significance could not be established (P = 0.47). Tumours in responders had the higher AR mRNA expression levels in pre neo-adjuvant chemotherapy condition (p < 0.02) which got reduced after neoadjuvant chemotherapy and the difference was found to be significant (P = 0.014).ConclusionsAlthough, expansion of the CAGn in the AR gene doesn't show any major effect on breast cancer risk, patients with positive AR expression, pre neoadjuvant chemotherapy, were found to be good responders and a decrease in mRNA level of AR gene related to the chemotherapy-induced apoptosis could serve as an important independent predictor of response to NACT.

Low variability and absence of phenotypic correlates of Clock gene variation in a great tit Parus major population

Studies of a range of taxa, including birds, have revealed latitudinal clines in allele length at the conserved Clock locus, a gene with known influences on behaviour and physiology. Such clines might reflect adaptation to seasonal variation, a suggestion supported by a recent within‐population analysis of blue tits Cyanistes caeruleus, which found associations between Clock genotype and timing of breeding in females. To test the generality of this pattern, we sequenced the polymorphic poly‐Q locus of the Clock gene in 521 female great tits Parus major, which were selected based on possession of extreme breeding phenotypes. In total, we identified five alleles with one allele accounting for 96% of allelic diversity in the sample set. Overall variability at the poly‐Q locus was very low, and the spatial distribution of Clock alleles across Wytham was highly homogenous. Our data further provide no evidence for a connection between Clock genotype and reproductive timing phenotype in female great tits; further, we found no effect of Clock genotype on reproductive success. Hence, these results are in contrast to the pattern found for the sympatric blue tit population inhabiting the same woodlands, suggesting that phenotypic effects of Clock are not general in passerine birds.

Exercise Capacity and Idebenone Intervention in Children and Adolescents With Friedreich Ataxia

Drinkard BE, Keyser RE, Paul SM, Arena R, Plehn JF, Yanovski JA, Di Prospero NA. Exercise capacity and idebenone intervention in children and adolescents with Friedreich ataxia. Objective To determine the exercise capacity of children and adolescents with Friedreich's Ataxia (FA) and to evaluate the effects of 6 months of idebenone treatment on exercise capacity. Design Exploratory endpoint in a randomized double-blind, placebo-controlled, phase II clinical trial designed to investigate the effects of idebenone on a biomarker of oxidative stress. Setting Exercise physiology laboratory in a single clinical research center. Participants Ambulatory subjects (N=48; age range, 9–17y) with genetically confirmed FA. Intervention Idebenone administered orally 3 times a day for a total daily dose of approximately 5, 15, and 45mg/kg or matching placebo for 6 months. Main Outcome Measures Peak oxygen consumption per unit time (peak VO 2) and peak work rate (WR) were measured during incremental exercise testing at baseline and after treatment. Echocardiography and neurologic assessments were also completed before and after treatment. Results Baseline mean peak VO 2 ± SD was 746±246mL/min (16.2±5.8mL/kg/min), and WR was 40±23W for all subjects. Peak VO 2 and WR were correlated with short guanine-adenine-adenine allele length and neurologic function. Relative left ventricular wall thickness was increased but left ventricular ejection fraction was normal in most subjects; there was no relationship between any exercise and echocardiographic measures. There were no significant changes in mean peak VO 2 or WR after idebenone treatment at any dose level relative to placebo. Conclusions Exercise capacity in children and adolescents with FA was significantly impaired. The basis for the impairment appears to be multifactorial and correlated to the degree of neurologic impairment. Although idebenone has previously been shown potentially to improve features of FA, idebenone treatment did not increase exercise capacity relative to placebo.

Tumor necrosis factor–α polymorphisms and expression in Guillain–Barré syndrome

Tumor necrosis factor–α (TNF-α) polymorphisms with increased expression is associated with many autoimmune and inflammatory diseases. Possible role of TNF-α polymorphism in the pathogenesis of Guillain–Barré syndrome (GBS) largely remains unknown. We investigated polymorphisms in the promoter region of TNF-α gene and its expression in GBS patients and healthy controls. TNF-α (−308 G>A, −857 C>T, and −863 C>A) polymorphisms in 140 GBS patients and 206 healthy controls were studied using polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) and allele specific-PCR. TNF-α level in serum by ELISA was determined in 60 patients and an equal number of controls. Prevalence of TNF-α −308 G > A polymorphic A allele was associated with increased risk of GBS ( p < 0.001; OR = 2.58, 95% CI = 1.61–4.14). Heterozygous genotype (G/A) had an association with acute motor axonal neuropathy ( p < 0.001; OR = 4.23, 95% CI = 2.00–8.95) and variant genotype A/A with both axonal subtypes, acute motor axonal neuropathy ( p = 0.015, OR = 7.00, 95% CI = 1.46–33.57) and acute motor sensory axonal neuropathy ( p = 0.017; OR = 7.73, 95% CI = 1.44–41.37). Variant genotype T/T of TNF-α −857 C>T polymorphism was also significantly associated with acute motor axonal neuropathy ( p = 0.034; OR = 3.93, 95% CI = 1.11–13.91). Patients with A and T alleles had higher TNF-α level in serum. TNF-α −308 G > A and −857 C>T (only T/T) polymorphisms with increased TNF-α level may predict susceptibility to axonal subtypes of GBS.

An Inherited Variable Poly-T Repeat Genotype in TOMM40 in Alzheimer Disease

I coauthored a recently published research article describing a variable length, poly-T polymorphism in the TOMM40 gene, adjacent to apolipoprotein E (APOE) on chromosome 19, that accounts for the age at onset distribution for a complex disease, late-onset Alzheimer disease. These new data explain the mean age at disease onset for patients with the APOE4/4 genotype and differentiate 2 forms of TOMM40 poly-T polymorphisms linked to APOE, with each form associated with a different age at disease onset distribution. When linked to APOE3 (encoding the epsilon3 isoform of APOE), the longer TOMM40 poly-T repeats (19-39 nucleotides) at the rs10524523 (hereafter, 523) locus are associated with earlier age at onset and the shorter TOMM40 523 alleles (11-16 nucleotides) are associated with later age at onset. The data suggest that the poly-T alleles are codominant, with the age at onset phenotype determined by the 2 inherited 523 alleles, but with variable expressivity. Additional data will further refine the relationship between the length of the poly-T alleles and age at disease onset and determine if the relationship is linear.

Epidermal growth factor receptor ( EGFR) intron 1 polymorphism and clinical outcome in pancreatic adenocarcinoma

Background Epidermal growth factor receptor ( EGFR) intron 1 has a polymorphic region of CA repeats that is believed to be associated with increased EGFR expression, tumor aggressiveness, and worse survival in cancer patients. Methods A large population of pancreatic adenocarcinoma patients was investigated to evaluate this polymorphism as a potential prognostic marker of clinical outcome. Deoxyribonucleic acid obtained from 50 resected pancreatic adenocarcinomas and from 85 diagnostic endoscopic ultrasound-guided fine-needle aspiration procedures corresponding to patients with unresectable tumors was included. The correlation between CA repeat length and EGFR messenger ribonucleic acid levels was also examined. Results Analysis of the 135 patients revealed no correlation between EGFR intron 1 CA repeat length and tumor stage. There was no difference in overall patient survival when stratified by allele length. A correlation between EGFR intron 1 length and EGFR transcript and protein levels could not be established. Conclusions The length of the EGFR intron 1 CA repeats does not correlate with levels of EGFR expression and cannot be used as marker of clinical prognosis in pancreatic cancer patients.

Polymorphisms in genes of the steroid hormone biosynthesis and metabolism pathways and endometrial cancer risk

Objectives: The incidence of endometrial cancer has recently increased substantially and studies have shown that altered levels of exogenous and endogenous hormones are associated with individual variation in endometrial cancer risk. The environmental and reproductive risk factors that influence these hormones are well known, however, genetic variants involved in hormone biosynthesis and estrogen metabolism have not been well established in endometrial cancer. Methods: To determine whether polymorphisms in genes of the steroid hormone biosynthesis and metabolism pathways are associated with endometrial cancer risk, 28 polymorphisms in 18 genes were genotyped in 191 endometrial cancer cases and 291 healthy controls. Results: The GSTM1 deletion and the variant (GG) genotype of the CYP1B1 rs1800440 polymorphism were associated with a decreased risk of developing endometrial cancer. Furthermore, combinations of haplotypes in CYP1A1, CYP1B1 and GSTs were associated with a decreased risk. The analysis of the repeat polymorphisms revealed that women with the long repeat allele length of the ESR1 (GT)n repeat polymorphism were at an increased risk of developing endometrial cancer. Conversely, women with two long repeat length alleles of the (CAG)n repeat polymorphism in the AR correlated with a decrease in endometrial cancer risk compared to women with one or two alleles with the short repeat length. Conclusions: The findings are consistent with our hypothesis that variability in genes involved in steroidogenesis and estrogen metabolism may alter the risk of developing endometrial cancer, suggesting that they may be useful as biomarkers for genetic susceptibility to endometrial cancer.

Endothelial Nitric Oxide Synthase Gene Polymorphisms (894G&gt; T and −786T&gt; C) and Risk of Coronary Artery Disease

Endothelial nitric oxide synthase gene polymorphisms, either independently or through gene environmental interactions, are associated with cardiovascular diseases in multiple ethnic populations. However, no information is available with regard to such associations in Saudi population despite a high incidence of cardiovascular abnormalities. Here we studied the associations of 894G&gt; T and −786T&gt; C polymorphisms of endothelial nitric oxide synthase gene with coronary artery disease in Saudi population. Variants 894G&gt; T and −786T&gt; C were studied in 142 coronary artery disease patients and 145 normal controls by PCR‐ restriction fragment length polymorphism analysis and allele specific PCR respectively. Carriers of GT and TT genotypes of 894G&gt; T polymorphism were significantly high (p&lt; 0.0001) in patients (47.2%, and 7%, respectively), than in controls (27.6% and 4.8%, respectively). Likewise, carriers for TC and CC genotypes of −786T&gt; C polymorphism were significantly high (p&lt; 0.001) in patients (50% and 32%, respectively) than in controls (34.5% and 22.5%, respectively). Genotype distributions of 894G&gt; T and −786T&gt; C polymorphisms in the disease and control populations matched with those found in Caucasian populations. This study, for the first time, suggests an independent association of 894G&gt; T and −786T&gt; C polymorphisms of endothelial nitric oxide synthase gene with coronary artery disease in Saudi population.

Qualitative assessment of FMR1 (CGG)n triplet repeat status in normal, intermediate, premutation, full mutation, and mosaic carriers in both sexes: Implications for fragile X syndrome carrier and newborn screening

PurposeFragile X syndrome is caused by expansion and subsequent methylation of a CGG trinucleotide repeat in the FMR1 5′-untranslated region. Southern blot analysis is typically required to determine expansion size for triplet repeat lengths >200. We describe a triplet-primed polymerase chain reaction-based method using automated capillary electrophoresis detection for qualitative assessment of expanded CGG repeats. MethodsThe assay uses triplet-primed polymerase chain reaction in combination with GC-melting reagents and substitution of 7-deaza-2-deoxyGTP for dGTP. Amplicons are resolved by capillary electrophoresis. ResultsA distinctive pattern of tapering or “stutter” polymerase chain reaction amplification was evident on capillary electrophoresis in male and female patients harboring all expanded allele lengths examined (up to 2000 CGG repeats) and could be used to differentiate normal, intermediate, premutation, and full mutation alleles. Full mutation alleles exhibited an additional late-migrating amplicon on capillary electrophoresis. Mixing experiments demonstrated sensitivity as low as 1% for detection of the full mutation allele. In a 1275-sample concordance study against our existing polymerase chain reaction platform (with Southern blot analysis for repeat lengths ≥55), the triplet-primed polymerase chain reaction method exhibited 100% concordance for normal, intermediate, expanded, and full mutation alleles. This method also detected the full mutation alleles in DNA isolated from blood spots. ConclusionThis assay provides an accurate assessment of FMR1 repeat status and holds promise for use in carrier and newborn screening. The method distinguishes normal homozygous females from full mutation carrying females. Although the method is not useful for accurate sizing, it supplements the classic polymerase chain reaction method and results in significant reduction in the number of Southern blot analyses required to be performed in the laboratory to accurately assess the FMR1 genotype in all individuals.

An Optimized Pentaplex PCR for Detecting DNA Mismatch Repair-Deficient Colorectal Cancers

PurposeMicrosatellite instability (MSI) is used to screen colorectal cancers (CRC) for Lynch Syndrome, and to predict outcome and response to treatment. The current technique for measuring MSI requires DNA from normal and neoplastic tissues, and fails to identify tumors with specific DNA mismatch repair (MMR) defects. We tested a panel of five quasi-monomorphic mononucleotide repeat markers amplified in a single multiplex PCR reaction (pentaplex PCR) to detect MSI.Experimental DesignWe investigated a cohort of 213 CRC patients, comprised of 114 MMR-deficient and 99 MMR-proficient tumors. Immunohistochemical (IHC) analysis evaluated the expression of MLH1, MSH2, PMS2 and MSH6. MSI status was defined by differences in the quasi-monomorphic variation range (QMVR) from a pool of normal DNA samples, and measuring differences in allele lengths in tumor DNA.ResultsAmplification of 426 normal alleles allowed optimization of the QMVR at each marker, and eliminated the requirement for matched reference DNA to define MSI in each sample. Using ≥2/5 unstable markers as the criteria for MSI resulted in a sensitivity of 95.6% (95% CI = 90.1–98.1%) and a positive predictive value of 100% (95% CI = 96.6%–100%). Detection of MSH6-deficiency was limited using all techniques. Data analysis with a three-marker panel (BAT26, NR21 and NR27) was comparable in sensitivity (97.4%) and positive predictive value (96.5%) to the five marker panel. Both approaches were superior to the standard approach to measuring MSI.ConclusionsAn optimized pentaplex (or triplex) PCR offers a facile, robust, very inexpensive, highly sensitive, and specific assay for the identification of MSI in CRC.

Endothelial Nitric Oxide Synthase Gene Polymorphisms (894G > T and −786T > C) and Risk of Coronary Artery Disease in a Saudi Population

Endothelial nitric oxide synthase gene polymorphisms, either independently or through gene environmental interactions, are associated with cardiovascular diseases in multiple ethnic populations. However, no information is available with regard to such associations in a Saudi population despite a high incidence of cardiovascular abnormalities. We studied the associations of 894G>T and -786T>C polymorphisms of endothelial nitric oxide synthase gene with coronary artery disease in Saudi population. Variants 894G>T and -786T>C were studied in 142 coronary artery disease patients and 145 normal controls by PCR-restriction fragment length polymorphism analysis and allele specific PCR, respectively. Carriers of GT and TT genotypes of 894G>T polymorphism were significantly high (p <0.0001) in patients (47.2 and 7%, respectively) than in controls (27.6 and 4.8%, respectively). Likewise, carriers for TC and CC genotypes of -786T>C polymorphism were significantly high (p <0.001) in patients (50 and 32% respectively) than in controls (34.5 and 22.5% respectively). Both 894G>T [OR (95% CI); 4.39 (1.69-11.42)] and -786T>C [OR (95% CI); 2.74 (1.02-7.32]) variants were independently associated with the disease status. Genotype distributions of 894G>T and -786T>C polymorphisms in the diseased and control populations matched with those found in Caucasian populations. This study, for the first time, suggests an independent association of 894G>T and -786T>C polymorphisms of endothelial nitric oxide synthase gene with coronary artery disease in a Saudi population.

Worldwide diversity of the Y-chromosome tetra-local microsatellite DYS464

Of all DNA markers on the human Y-chromosome, the tetra-local Y-linked microsatellite DYS464 is the most polymorphic. We genotyped DYS464 in 677 male samples collected worldwide, maintained in the HGDP-CEPH Human Genome Diversity Cell Line Panel. Fourteen different alleles were found, with allele lengths varying from 9 to 23 repeats. One hundred and seventy-five different genotypes were detected, of which 90 appeared to be continent-specific. The region with the highest percentage of unique genotypes was Africa. Genotype diversity was 0.98 for Europe, 0.97 for Central and East Asia, 0.95 for Africa, 0.94 for Oceania, 0.92 for the Middle East, and 0.90 for the Americas. A hierarchical analysis of molecular variance showed low levels of worldwide genetic structure; 88.42% of the genetic variance was found within populations, 9.62% between populations within regions and 1.96% between regions. Since the four DYS464 repeats are identical, one cannot assign each peak in the electropherogram to a specific locus. Thus, the same genotype may correspond to several haplotypes, with different permutations of alleles. Consequently, genotypes are degenerate, which limits phylogeographical analyses. Yet, because of its high variability, DYS464 still constitutes an informative tool for population and evolutionary studies.