Comparison of GenFlex Tag array and Pyrosequencing in SNP genotyping

DNA methylation drives a new path in gastric cancer early detection: Current impact and prospects

Gastric cancer (GC) is one of the most common and deadly cancers worldwide. Early detection offers the best chance for curative treatment and reducing its mortality. However, the optimal population-based early screening for GC remains unmet. Aberrant DNA methylation occurs in the early stage of GC, exhibiting cancer-specific genetic and epigenetic changes, and can be detected in the media such as blood, gastric juice, and feces, constituting a valuable biomarker for cancer early detection. Furthermore, DNA methylation is a stable epigenetic alteration, and many innovative methods have been developed to quantify it rapidly and accurately. Nonetheless, large-scale clinical validation of DNA methylation serving as tumor biomarkers is still lacking, precluding their implementation in clinical practice. In conclusion, after a critical analysis of the recent existing literature, we summarized the evolving roles of DNA methylation during GC occurrence, expounded the newly discovered noninvasive DNA methylation biomarkers for early detection of GC, and discussed its challenges and prospects in clinical applications.

Detection of EGFR and KRAS Mutation by Pyrosequencing Analysis in Cytologic Samples of Non-Small Cell Lung Cancer

EGFR and KRAS mutations are two of the most common mutations that are present in lung cancer. Screening and detecting these mutations are of issue these days, and many different methods and tissue samples are currently used to effectively detect these two mutations. In this study, we aimed to evaluate the testing for EGFR and KRAS mutations by pyrosequencing method, and compared the yield of cytology versus histology specimens in a consecutive series of patients with lung cancer. We retrospectively reviewed EGFR and KRAS mutation results of 399 (patients with EGFR mutation test) and 323 patients (patients with KRAS mutation test) diagnosed with lung cancer in Konkuk University Medical Center from 2008 to 2014. Among them, 60 patients had received both EGFR and KRAS mutation studies. We compared the detection rate of EGFR and KRAS tests in cytology, biopsy, and resection specimens. EGFR and KRAS mutations were detected in 29.8% and 8.7% of total patients, and the positive mutation results of EGFR and KRAS were mutually exclusive. The detection rate of EGFR mutation in cytology was higher than non-cytology (biopsy or resection) materials (cytology: 48.5%, non-cytology: 26.1%), and the detection rate of KRAS mutation in cytology specimens was comparable to non-cytology specimens (cytology: 8.3%, non-cytology: 8.7%). We suggest that cytology specimens are good alternatives that can readily substitute tissue samples for testing both EGFR and KRAS mutations. Moreover, pyrosequencing method is highly sensitive in detecting EGFR and KRAS mutations in lung cancer patients.

KRAS mutations: analytical considerations

Colorectal cancer (CRC) is the third most common cancer and the second most common cause of cancer death globally. Significant improvements in survival have been made in patients with metastasis by new therapies. For example, Cetuximab and Panitumumab are monoclonal antibodies that inhibit the epidermal growth receptor (EGFR). KRAS mutations in codon 12 and 13 are the recognized biomarkers that are analyzed in clinics before the administration of anti-EGFR therapy. Genetic analyses have revealed that mutations in KRAS predict a lack of response to Panitumumab and Cetuximab in patients with metastatic CRC (mCRC). Notably, it is estimated that 35-45% of CRC patients harbor KRAS mutations. Therefore, KRAS mutation testing should be performed in all individuals with the advanced CRC in order to identify the patients who will not respond to the monoclonal EGFR antibody inhibitors. New techniques for KRAS testing have arisen rapidly, and each technique has advantages and disadvantages. Herein, we review the latest published literature specific to KRAS mutation testing techniques. Since reliability and feasibility are important issues in clinical analyses. Therefore, this review also summarizes the effectiveness and limitations of numerous KRAS mutation testing techniques.

KRAS and BRAF mutations in 203 esophageal squamous cell carcinomas: pyrosequencing technology and literature review

BACKGROUND

Epidermal growth factor receptor (EGFR) signaling is one of the most promising targets for molecular-targeted therapies in esophageal squamous cell carcinoma (ESCC). Thus, the molecular diagnosis of KRAS and BRAF mutations is clinically important in therapeutic decision making. However, the frequency of KRAS and BRAF mutations in ESCCs remains inconclusive because of the limited sample sizes of previous studies (all N ≤ 80). Pyrosequencing is a nonelectrophoretic nucleotide extension sequencing technology that can be used for mutation testing.

METHODS

The frequency of KRAS and BRAF mutations was examined using a nonbiased database of 203 resected ESCCs and a high-throughput pyrosequencing assay.

RESULTS

The validity of the KRAS pyrosequencing method was initially demonstrated by detection of all 4 types of KRAS mutations [c.35G>T (codon 12 GGT>GTT), c.35G>A (codon 12 GGT>GAT), c.34G>T (codon 12 GGT>TGT), c.38G>A mutation (codon 13 GGC>GAC)], which had been previously diagnosed using Scorpion-ARMS technology, in 9 colon cancer tissues (9 of 9; 100 %). Similar results were demonstrated for BRAF mutational status in 3 colon cancer cell lines (HCT116, Colo201, and HT29), which were validated by Sanger dideoxy sequencing. Subsequently, the KRAS mutation was found to be extremely rare (1 of 203; 0.5 %), and the BRAF mutation was absent (0 of 203; 0 %), in the dataset of 203 ESCCs.

CONCLUSIONS

These results suggest that KRAS and BRAF mutations play a limited role in the development of ESCC and that mutation analysis is not useful as a screening test for sensitivity to anti-EGFR therapy in ESCC.

Association of mitochondrial genetic variation with carotid atherosclerosis

In human pathology, several diseases are associated with somatic mutations in the mitochondrial genome (mtDNA). Even though mitochondrial dysfunction leads to increased oxidative stress, the role of mitochondrial mutations in atherosclerosis has not received much attention so far. In this study we analyzed the association of mitochondrial genetic variation with the severity of carotid atherosclerosis, as assessed by carotid intima-media thickness (cIMT) and the presence of coronary heart disease (CHD) in 190 subjects from Moscow, Russia, a population with high CHD occurrence. cIMT was measured by high-resolution B-mode ultrasonography and mtDNA heteroplasmies by a pyrosequencing-based method. We found that heteroplasmies for several mutations in the mtDNA in leukocytes, including C3256T, T3336C, G12315A, G13513A, G14459A, G14846A, and G15059A mutations, were significantly (p<0.001) associated with both the severity of carotid atherosclerosis and the presence of CHD. These findings indicate that somatic mitochondrial mutations have a role in the development of atherosclerosis.

Changes of mitochondria in atherosclerosis: possible determinant in the pathogenesis of the disease

Electron-microscopic analysis of atherosclerotic lesions demonstrated a high variability in the ultrastructural appearance of mitochondria in human aortic atherosclerotic lesions compared with the appearance of mitochondria in the normal parts of the aortic intima. This prompted us to suggest that the structural variations in the appearance of mitochondria might reflect the existence of somatic mutations in the human mitochondrial genome which could be a determinant of atherosclerosis. To test this hypothesis, we have compared the levels of heteroplasmy for several mitochondrial mutations previously proposed to be associated with different types of atherosclerotic lesions. The homogenates of unaffected aortic intimae and lipofibrous plaques of 12 male aortas were compared to reveal the average level of heteroplasmy for A1555G, C3256T, T3336T, G12315A, G14459A, and G15059A mutations of human mitochondrial genome. It has been shown at least four mutations of mitochondrial genome, namely, A1555G in MT-RNR1 gene, C3256T in MT-TL1 gene, G12315A in MT-TL2 gene, and G15059A in MT-CYB gene have significantly higher prevalence and mean value in lipofibrous plaques as compared to non-atherosclerotic intima, and therefore are associated with atherosclerosis. Somatic mutations in the human mitochondrial genome might play a role in the development of atherosclerosis. The mitochondrial mutations observed in our study should encourage further exploration of the concept that mitochondrial DNA heteroplasmy might be used as a biomarker of atherogenesis.

Effect of low-frequency KRAS mutations on the response to anti-EGFR therapy in metastatic colorectal cancer

BACKGROUND

Only patients with wild-type (WT) KRAS tumors benefit from anti-epidermal growth factor receptor (EGFR) monoclonal antibodies (Mabs) in metastatic colorectal cancer (mCRC). Pyrosequencing is now widely used for the determination of KRAS mutation burden and a conservative cut-off point of 10% has been defined. Up until now, the impact of low-frequency KRAS mutations (<10%) on the response to anti-EGFR Mabs has yet to be evaluated.

PATIENTS AND METHODS

Tumors from patients receiving anti-EGFR Mabs based on a WT genotype for KRAS, as determined using direct sequencing, have been retrospectively analyzed by pyrosequencing. Patients were categorized as WT (no KRAS mutation) or low-frequency mutation when KRAS mutation was <10% (KRAS low MT).

RESULTS

A total of 168 patients treated by anti-EGFR Mabs for mCRC were analyzed. According to pyrosequencing, 138 tumors remained KRAS WT, while 30 tumors were KRAS low MT. In the KRAS low MT and KRAS WT groups, the response rates were 6.7% and 37.0%, respectively, while stabilization amounted to 23.3% versus 32.6% and progression to 70% versus 29% (P < 0.01). Progression-free survival (PFS) was 2.7 ± 0.5 months for KRAS low MT and was 6.0 ± 0.3 months for KRAS WT (P < 0.01).

CONCLUSIONS

These results appear to validate consideration of low-frequency KRAS mutation tumors as positive, and justify a large-scale prospective study.

Mutation C3256T of mitochondrial genome in white blood cells: novel genetic marker of atherosclerosis and coronary heart disease

This study was undertaken to examine the association between the level of heteroplasmy for the mutation C3256T in human white blood cells and the extent of carotid atherosclerosis, as well as the presence of coronary heart disease (CHD), the major clinical manifestation of atherosclerosis. Totally, 191 participants (84 men, 107 women) aged 65.0 years (SD 9.4) were recruited in the study; 45 (24%) of them had CHD. High-resolution B-mode ultrasonography of carotids was used to estimate the extent of carotid atherosclerosis by measuring of the carotid intima-media thickness (cIMT). DNA samples were obtained from whole venous blood, and then PCR and pyrosequencing were carried out. On the basis of pyrosequencing data, the levels of C3256T heteroplasmy in DNA samples were calculated. The presence of the mutant allele was detected in all study participants; the level of C3256T heteroplasmy in white blood cells ranged from 5% to 74%. The highly significant relationship between C3256T heteroplasmy level and predisposition to atherosclerosis was revealed. In individuals with low predisposition to atherosclerosis the mean level of C3256T heteroplasmy was 16.8%, as compared to 23.8% in moderately predisposed subjects, and further to 25.2% and 28.3% in significantly and highly predisposed subjects, respectively. The level of C3256T heteroplasmy of mitochondrial genome in human white blood cells is a biomarker of mitochondrial dysfunction and risk factor for atherosclerosis; therefore, it can be used as an informative marker of genetic susceptibility to atherosclerosis, coronary heart disease and myocardial infarction.

Mitochondrial mutations are associated with atherosclerotic lesions in the human aorta

Somatic mutations of the human mitochondrial genome can be a possible determinant of atherosclerosis. To test this possibility, forty mitochondrial mutations were analyzed in the present study in order to see which of these mutations might be associated with atherosclerosis. Ten mitochondrial mutations belonging to mitochondrial genes MT-RNR1 (rRNA 12S); MT-TL1 (tRNA-Leu, recognizes UUR); MT-TL2 (tRNA-Leu, recognizes CUN); MT-ND1, MT-ND2, MT-ND5, and MT-ND6 (subunits 1, 2, 5, and 6, respectively, of NADH dehydrogenase); and MT-CYB (cytochrome b) were potentially associated with atherosclerosis. From 29% (2 of 7 aortic samples) upto 86% (6 of 7 aortic samples) of aortic samples had a significant difference between atherosclerotic plaques and unaffected tissue, with the respect to the level of heteroplasmy for each mutation. Further, the homogenates of affected and normal intimae of 22 aortas were compared to reveal the average level of heteroplasmy for the above-mentioned 10 mutations. For five mutations, the mean level of heteroplasmy was significantly different in atherosclerotic intimal homogenates in comparison with the unaffected tissue. These mutations were A1555G, C3256T, T3336C, G13513A, and G15059A. Thus, it was demonstrated that at least five mitochondrial mutations occurring in MT-RNR1, MT-TL1, MT-ND2, MT-ND5, and MT-CYB genes are associated with atherosclerosis.

A rapid and reliable test for BRCA1 and BRCA2 founder mutation analysis in paraffin tissue using pyrosequencing

The founder mutations in BRCA (BRCA1*185delAG, BRCA1*5382insC, and BRCA2*6174delT) account for 95% of the detectable BRCA mutations in breast and ovarian cancer families of Ashkenazi Jewish ancestry. Optimal clinical management of individuals from these high-risk families relies on the identification of BRCA founder mutations in the laboratory. We have therefore developed a rapid and reliable approach using pyrosequencing, which allows for the detection of these frequent frameshift mutations on different types of specimens. We were able to correctly identify all mutants in a blinded analysis of 177 DNA samples, including 120 DNA samples extracted from paraffin tissues, 30 samples derived from blood specimens, and 27 samples derived from saliva. The mutation detection rate of pyrosequencing was 100% for all of the DNA samples tested with neither false-positive nor false-negative results. The assay also demonstrated both high accuracy and high precision for the detection of these common mutations in paraffin tissues. Furthermore, saliva collection is a noninvasive alternative for DNA isolation in both clinical and research settings. We show that pyrosequencing is a rapid and reliable method that serves as an excellent platform for BRCA founder mutation analysis, especially when only paraffin-embedded tissues are available.

Studies of the human aortic intima by a direct quantitative assay of mutant alleles in the mitochondrial genome

A mutant allele quantitative assay was developed to study somatic mitochondrial mutations associated with human diseases. This assay may be used in the clinical diagnostics for diseases associated with somatic mutations. To detect somatic mutations associated with atherosclerotic lesions of the aortal intima, we analyzed 40 mitochondrial mutations previously identified in several pathological conditions. 10 mutations associated with lipofibrosis plaques were found in mitochondrial genes that encode rRNA 12S, tRNA-Leu (UUR recognition codon), tRNA-Leu (CUN recognition codon), subunits of 1, 2, 5, and 6 NADH-dehydrogenase, and cytochrome B.

High-throughput homogeneous mass cleave assay technology for the diagnosis of autosomal recessive Parkinson's disease

To date, 11 gene loci that contribute to familial Parkinson's disease (PD) are known. Of these, mutations in six genes have been identified, allowing genetic testing and more accurate phenotypic characterization of genetically defined disease subtypes. In particular, mutations in Parkin, DJ-1, and Pink1 genes are associated with autosomal recessive PD and may also play a major role in early onset PD (EOPD). However, genetic testing for sequence alterations in these genes remains laborious. Therefore, our aim was to develop a flexible, rapid, high-throughput screening procedure using matrix-assisted laser desorption ionization/time of flight technology and homogeneous mass cleave assays. Using this novel approach, we screened all 27 coding exons of the Parkin, DJ-1, and Pink1 genes in 31 patients with EOPD, a total of 367,195 nucleotides. Four positive controls with known autosomal recessive PD mutations that had previously been screened by denaturing high performance liquid chromatography in combination with sequencing were also tested. All known alterations were detected by matrix-assisted laser desorption ionization/time of flight mass spectrometer, as well as additional polymorphisms in formerly unscreened regions. Overall, two previously described mutations in three patients with EOPD, 27 known polymorphisms with 386 occurrences, and eight unknown variants with 21 occurrences were detected. In total, we identified 410 sequence alterations in 31 patients with EOPD. In conclusion, this is the first study using matrix-assisted laser desorption ionization/time of flight mass spectrometry and homogeneous mass cleave assay for high-throughput mutation screening.

Common polymorphisms of the PAI1 gene do not play a major role in the development of diabetic nephropathy in Type 1 diabetes

AIM

Plasminogen activator inhibitor 1 (PAI1) plays a key role in the regulation of extracellular matrix (ECM) degradation. ThePAI1 gene is therefore an excellent candidate gene for diabetic nephropathy. The aim of this study was to employ gene resequencing to identify common DNA polymorphisms in thePAI1gene, and subsequently assess haplotype tagged single nucleotide polymorphisms(htSNPs) using a case control design. METHODS All nine exons, exon-intron boundaries, introns 1, 4 and 7 and approximately 3 kb upstream and 5 kb downstream of thePAI1 gene were screened for DNA polymorphisms in 15 case and 15 control subjects using WAVE denaturing high-performance liquid chromatography technology and confirmed by DNA sequencing. Polymorphisms were genotyped in 86 healthy individuals using direct sequencing and haplotype tagged single nucleotide polymorphisms (htSNPs) identified. Genotyping of the htSNPs was performed in 583 Type 1 diabetic patients (222 with nephropathy, 361 without nephropathy)using Pyrosequencing.

RESULTS

Twenty-one polymorphisms with a minor allele frequency (MAF)>1%were identified; 14 had a MAF> or =10%. Five htSNPs [c.-1968_69insG, c.43 G-->A (Ala15Thr), c.1092-105 A-->G, c.*1737 G-->A, c.*3711 C-->T] were identified. Haplotype frequencies were similar in case and control groups (likelihood ratio chi2 test,P=0.66).

CONCLUSION

It is unlikely that common polymorphisms of thePAI1 gene strongly influence susceptibility to diabetic nephropathy in the White Type 1 diabetic population.

TAMGeS: a Three-array Method for Genotyping of SNPs by a dual-colour approach

Background

Many of the most effective high-throughput protocols for SNP genotyping employ microarrays. Genotypes are assessed by comparing the signal intensities that derive from the hybridization of different allele-specific probes labelled either by using four fluorescent dyes, one for each base, or by using only two dyes and investigating the polymorphic alleles two by two on separate arrays. The employment of only two dyes makes it possible to use a dual-laser scanner, which has the advantage of being present in every microarray laboratory. However, this protocol may present some drawbacks. To infer all the six possible genotypes it is necessary to compare signals from two arrays, but this comparison not always is successful. A number of systematic errors in the experimental protocol, in fact, may differently affect signal intensities on separate arrays. Here we present TAMGeS (Three-Array Method for Genotyping of SNPs), an exhaustive method for SNP genotyping through SBE (Single Base Extension) and dual-colour microarrays, which makes the comparison of signals on distinct arrays reliable by using a third array and a data handling method for signal normalization based on bilinear regression theory.

Results

We tested the effectiveness of the proposed method by evaluating the results obtained from the direct comparison of the two arrays or by applying TAMGeS, both on experimental and synthetic data. With synthetic data, TAMGeS reduced the frequency of errors by an order of magnitude, when the incidence of systematic errors was not negligible. With the experimental data, produced by genotyping 25 SNPs in 437 subjects, TAMGeS reduced the percentage of missing genotypes from 54% (Two-Array Method) to 14.5%. Allelic and genotypic call rates were 99.3% and 99.5%, respectively. The normalization procedure takes into account also systematic errors, which can be generated by a time-delayed assay, thus making the protocol more flexible.

Conclusion

TAMGeS represents an innovative method, which proved to be very effective in producing reliable SNP genotyping data by dual-colour microarrays. The requirement of a third array is well balanced by the strong enhancement in data quality and by the greater flexibility of the experimental protocol.

Intramolecular controls for the generation of clinical-quality SNP genotypes and the assessment of normal heterozygote imbalance

We present an inventive method that generates intramolecular controls for SNP analysis, termed Mirror SNPs. Using the ovine diseases of callipyge and scrapie as examples, we describe the PCR-driven production of balanced heterozygote copies of the various SNPs implicated in these diseases. In the absence of a callipyge-positive control DNA, we generated a balanced heterozygote Mirror SNP that represents both the wild-type and mutant forms of the causal polymorphism. Simultaneous analysis of this artificial Mirror SNP and the Real (target) SNP was used to prove the absence of the mutant form of the nucleotide at the Real SNP position in tested samples. Scrapie susceptibility was assessed using a PCR-driven system which generated four separate Mirror SNPs, and these enabled the confirmation of an apparent departure from 'balanced' heterozygote appearance at Real SNPs tested. Mirror SNP technology is generic and will enable the accurate assessment of rare and medically important SNP variants, more accurate frequency determinations, and the potential assessment of SNPs in 'mixed template' samples common in forensic analyses.

Molecular Genetic Testing of Polymorphisms Associated With Venous Thrombosis

The growing knowledge of genetic polymorphisms predisposing to venous thrombosis has increased the demand for genetic testing of associated risk factors. This has prompted the need for simple, fast, reliable, and cost-effective genotyping methods for identification of those mutations. In the past decade, a large variety of DNA mutation analysis methods have been developed for detection of genetic variants associated with venous thrombosis, including PCR-based and PCR-independent technologies. Each of these technologies possesses unique advantages, but all have a common goal of simplifying and expediting mutation analysis. This review describes some of the commonly used technologies and commercially available platforms employed in clinical laboratories for genetic testing of thrombophilia. The choice of a technology for each individual laboratory would primarily depend on the specific requirements for the assay's accuracy, reliability, speed, throughput, and cost-effectiveness.

Sensitive sequencing method for KRAS mutation detection by Pyrosequencing

Both benign and malignant tumors represent heterogenous tissue containing tumor cells and non-neoplastic mesenchymal and inflammatory cells. To detect a minority of mutant KRAS alleles among abundant wild-type alleles, we developed a sensitive DNA sequencing assay using Pyrosequencing, ie, nucleotide extension sequencing with an allele quantification capability. We designed our Pyrosequencing assay for use with whole-genome-amplified DNA from paraffin-embedded tissue. Assessing various mixtures of DNA from mutant KRAS cell lines and DNA from a wild-type KRAS cell line, we found that mutation detection rates for Pyrosequencing were superior to dideoxy sequencing. In addition, Pyrosequencing proved superior to dideoxy sequencing in the detection of KRAS mutations from DNA mixtures of paraffin-embedded colon cancer and normal tissue as well as from paraffin-embedded pancreatic cancers. Quantification of mutant alleles by Pyrosequencing was precise and useful for assay validation, monitoring, and quality assurance. Our Pyrosequencing method is simple, robust, and sensitive, with a detection limit of approximately 5% mutant alleles. It is particularly useful for tumors containing abundant non-neoplastic cells. In addition, the applicability of this assay for DNA amplified by whole-genome amplification technique provides an expanded source of DNA for large-scale studies.

Genetic variation analyses by Pyrosequencing

Pyrosequencing is a real-time bioluminometric technique for determination of nucleic acid sequence. Here, we review recent advances and discuss new applications of this technique. Cost reduction efforts and future potentials of this technique for large-scale genotyping applications will also be discussed.

A universal method for automated gene mapping

A high-throughput method for genotyping by mapping InDels. This method has been used to create fragment-length polymorphism maps for Drosophila and C. elegans.

Small insertions or deletions (InDels) constitute a ubiquituous class of sequence polymorphisms found in eukaryotic genomes. Here, we present an automated high-throughput genotyping method that relies on the detection of fragment-length polymorphisms (FLPs) caused by InDels. The protocol utilizes standard sequencers and genotyping software. We have established genome-wide FLP maps for both Caenorhabditis elegans and Drosophila melanogaster that facilitate genetic mapping with a minimum of manual input and at comparatively low cost.