Single-nucleotide polymorphism analysis by pyrosequencing

Understanding the role of DNA methylation in colorectal cancer: Mechanisms, detection, and clinical significance

Colorectal cancer (CRC) is one of the deadliest malignancies worldwide, ranking third in incidence and second in mortality. Remarkably, early stage localized CRC has a 5-year survival rate of over 90%; in stark contrast, the corresponding 5-year survival rate for metastatic CRC (mCRC) is only 14%. Compounding this problem is the staggering lack of effective therapeutic strategies. Beyond genetic mutations, which have been identified as critical instigators of CRC initiation and progression, the importance of epigenetic modifications, particularly DNA methylation (DNAm), cannot be underestimated, given that DNAm can be used for diagnosis, treatment monitoring and prognostic evaluation. This review addresses the intricate mechanisms governing aberrant DNAm in CRC and its profound impact on critical oncogenic pathways. In addition, a comprehensive review of the various techniques used to detect DNAm alterations in CRC is provided, along with an exploration of the clinical utility of cancer-specific DNAm alterations.

PCR in Forensic Science: A Critical Review

The polymerase chain reaction (PCR) has played a fundamental role in our understanding of the world, and has applications across a broad range of disciplines. The introduction of PCR into forensic science marked the beginning of a new era of DNA profiling. This era has pushed PCR to its limits and allowed genetic data to be generated from trace DNA. Trace samples contain very small amounts of degraded DNA associated with inhibitory compounds and ions. Despite significant development in the PCR process since it was first introduced, the challenges of profiling inhibited and degraded samples remain. This review examines the evolution of the PCR from its inception in the 1980s, through to its current application in forensic science. The driving factors behind PCR evolution for DNA profiling are discussed along with a critical comparison of cycling conditions used in commercial PCR kits. Newer PCR methods that are currently used in forensic practice and beyond are examined, and possible future directions of PCR for DNA profiling are evaluated.

CRISPR/Cas-Based Diagnostics in Agricultural Applications

Pests and disease-causing pathogens frequently impede agricultural production. An early and efficient diagnostic tool is crucial for effective disease management. Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated protein (Cas) have recently been harnessed to develop diagnostic tools. The CRISPR/Cas system, composed of the Cas endonuclease and guide RNA, enables precise identification and cleavage of the target nucleic acids. The inherent sensitivity, high specificity, and rapid assay time of the CRISPR/Cas system make it an effective alternative for diagnosing plant pathogens and identifying genetically modified crops. Furthermore, its potential for multiplexing and suitability for point-of-care testing at the field level provide advantages over traditional diagnostic systems such as RT-PCR, LAMP, and NGS. In this review, we discuss the recent developments in CRISPR/Cas based diagnostics and their implications in various agricultural applications. We have also emphasized the major challenges with possible solutions and provided insights into future perspectives and potential applications of the CRISPR/Cas system in agriculture.

Combination of GWAS and FST-based approaches identified loci associated with economic traits in sugarcane

Sugarcane is a globally important plant for both sugar and biofuel production. Although conventional breeding has played an important role in increasing the productivity of sugarcane, it takes a long time to achieve breeding goals such as high yield and resistant to diseases. Molecular breeding, including marker-assisted breeding and genomic selection, can accelerate genetic improvement by selecting elites at the seedling stage with DNA markers. However, only a few DNA markers associated with important traits were identified in sugarcane. The purpose of this study was to identify DNA markers associated with sugar content, stalk diameter, and sugarcane top borer resistance. The sugarcane samples with trait records were genotyped using the restriction site-associated DNA sequencing (RADseq) technology. Using F_ST analysis and genome-wide association study (GWAS), a total of 9, 23 and 9 DNA variants (single nucleotide polymorphisms (SNPs)/insertions and deletions (indels)) were associated with sugar content, stalk diameter, and sugarcane top borer resistance, respectively. The identified genetic variants were on different chromosomes, suggesting that these traits are complex and determined by multiple genetic factors. These DNA markers identified by both approaches have the potential to be used in selecting elite clones at the seeding stage in our sugarcane breeding program to accelerate genetic improvement. Certainly, it is essential to verify the reliability of the identified DNA markers associated with traits before they are used in molecular breeding in other populations.

Association of single nucleotide polymorphism variations in CRYAA and CRYAB genes with congenital cataract in Pakistani population

Background

The purpose of present study was to analyze the association of single nucleotide polymorphism (SNPs) variant in CRYAA and CRYAB genes with Congenital Cataract.

Method

Total 196 blood samples of children were collected, out of which 102 samples were congenital cataract (case group) and 94 samples were normal individuals (control group). Genomic DNA was extracted by using optimized inorganic method. Tetra primers for SNPs were designed and TETRA-ARMs assay was performed on both groups. Genotypic, allelic frequency and haplotype analyses were obtained by using SNPstats software.

Results

The coordination of genotypic and allelic frequencies of CRYAA and CRYAB genes variants and the association between case and control groups showed increased risk of congenital cataract in children who contained rs13053109 G > C variant of CRYAA in all models (all P > 0.05). This depicts the evident difference between the frequencies of case and control groups. The haplotype analysis of SNPs rs3761382, rs7278468 and rs13051039 of CRYAA gene showed weak linkage disequilibrium between the 3 SNPs (r2 < 0.8). The haplotype CTC indicated the high risk of congenital cataract in infants based of its p value (OR = 1.60 95% CI = 0.11-22.64, P > 0.05).

Conclusion

The variation in CRYAA gene can be the risk factor for congenital cataract in infants.

Challenges at the APOE locus: a robust quality control approach for accurate APOE genotyping

BACKGROUND

Genetic variants within the APOE locus may modulate Alzheimer's disease (AD) risk independently or in conjunction with APOE*2/3/4 genotypes. Identifying such variants and mechanisms would importantly advance our understanding of APOE pathophysiology and provide critical guidance for AD therapies aimed at APOE. The APOE locus however remains relatively poorly understood in AD, owing to multiple challenges that include its complex linkage structure and uncertainty in APOE*2/3/4 genotype quality. Here, we present a novel APOE*2/3/4 filtering approach and showcase its relevance on AD risk association analyses for the rs439401 variant, which is located 1801 base pairs downstream of APOE and has been associated with a potential regulatory effect on APOE.

METHODS

We used thirty-two AD-related cohorts, with genetic data from various high-density single-nucleotide polymorphism microarrays, whole-genome sequencing, and whole-exome sequencing. Study participants were filtered to be ages 60 and older, non-Hispanic, of European ancestry, and diagnosed as cognitively normal or AD (n = 65,701). Primary analyses investigated AD risk in APOE*4/4 carriers. Additional supporting analyses were performed in APOE*3/4 and 3/3 strata. Outcomes were compared under two different APOE*2/3/4 filtering approaches.

RESULTS

Using more conventional APOE*2/3/4 filtering criteria (approach 1), we showed that, when in-phase with APOE*4, rs439401 was variably associated with protective effects on AD case-control status. However, when applying a novel filter that increases the certainty of the APOE*2/3/4 genotypes by applying more stringent criteria for concordance between the provided APOE genotype and imputed APOE genotype (approach 2), we observed that all significant effects were lost.

CONCLUSIONS

We showed that careful consideration of APOE genotype and appropriate sample filtering were crucial to robustly interrogate the role of the APOE locus on AD risk. Our study presents a novel APOE filtering approach and provides important guidelines for research into the APOE locus, as well as for elucidating genetic interaction effects with APOE*2/3/4.

Visualized Genotyping from "Sample to Results" Within 25 Minutes by Coupling Recombinase Polymerase Amplification (RPA) With Allele-Specific Invasive Reaction Assisted Gold Nanoparticle Probes Assembling

A simple and rapid genotyping method with less-instrumentation is essential for realizing point-of-care detection of personalized medicine-related gene biomarkers. Herein, we developed a rapid and visualized genotyping method by coupling recombinase polymerase amplification (RPA) with allele-specific invader reaction assisted gold nanoparticle probes assembling. In the method, the DNA targets were firstly amplified by using RPA, which is a rapid isothermal amplification technology. Then an allele-specific invasion reaction was performed to recognize the single nucleotide polymorphisms (SNPs) site in the amplicons, to produce signal molecules that caused discoloration of gold nanoparticle probes. As a result, genotyping was achieved by observing the color change of the reaction by using naked eye without the requirement for any expensive instrument. In order to achieve rapid genotyping detection, the genomic DNA from oral swab lysate samples were used for the RPA templates amplification. In this way, a visualized genotyping from "samples to results" within 25 min was realized. Two clopidogrel related SNPs CYP2C19*2 and CYP2C19*3 of 56 clinical samples were correctly genotyped by using this rapid visualized genotyping assay. In addition, the feasibility for this pathogen genotyping method was also verified by detecting plasmid DNA containing three SARS-COV-2 gene mutation sites, indicating that this method has the potential for clinical sample detection.

Genetic analysis with pyrosequencing using loop pipetting and a light dependent resistor

DNA sequencing is among the most important techniques in biology to decipher the key genetic players of health and disease. The existing laboratory instruments for DNA sequencing are well established and reliable. However, these instruments are still out of reach of most laboratories in the world due to very high equipment and running costs and require trained personnel to keep them running. These instruments are also large and bulky making them unsuitable for analysis in remote settings away from laboratories. Here we describe a proof-of-concept of a DNA sequencing device LoopSeeq using a simple approach to address the said problems without minimizing the quality of results. The device was designed to perform pyrosequencing by iterative addition of dNTPs by contact dispensing through a loop pipette (loopette) and detection of chemiluminiscence with the cheapest sensor in the market, a light dependent resistor (LDR). Two small geared motors drive the moving parts in a controlled and coordinated manner with the help of a motor driver circuit, an Arduino Nano microcontroller and two small neodymium magnets. The real-time light intensity data from the LDR were transferred to a laptop computer for further analysis. Pyrosequencing was optimized using 55 nt self-primed oligo. In order to demonstrate the DNA sequencing ability with real samples, molecular genetic analysis was performed for a previously identified novel mutation from our lab in exon4 of the OCA2 gene. LoopSeeq successfully identified the homozygous normal (c.408-409_AA), homozygous mutant (c.408-409_delAA) and heterozygous carrier (c.408-409_AA/delAA) alleles in three individuals of a family affected with oculocutaneous albinism (OCA). Further, this can be implemented for molecular diagnostic applications for bacterial, viral or other pathogen detection and genotyping among different subtypes following some reports described earlier. A few drawbacks in the current implementation including the evaporation of liquid reagents, possible loopette contamination, etc. associated with use for longer times are also described along with suggestions to rectify these problems in future designs. With the described capabilities, the LoopSeeq device can be implemented in routine labs as well as in several real-world situations where conventional DNA sequencing instruments are unfeasible, for example, diagnostic testing at remote settings or at the point-of-care.

Predicting treatment response to IL6R blockers in rheumatoid arthritis

Patients with severe, active RA who have not responded to conventional therapy may receive biological disease modifying anti-rheumatic drugs (bDMARDs). However, 40% of cases do not achieve complete disease control, resulting in a negative impact on patient quality of life and representing a waste of healthcare resources. Ongoing research seeks to establish biomarkers, which can be used to predict treatment response to biologics in RA to enable more targeted approaches to treatment. However, much of the work has focused on one class of biologic drug, the TNF inhibitors (TNFi). Here, we will review the current state of research to identify biomarkers predictive of response to the class of bDMARDs targeting the IL6R. While success has been limited thus far, serum drug and low ICAM1 levels have shown promise, with associations reported in independent studies. The challenges faced by researchers and lessons learned from studies of TNFi will be discussed.

Genetic heterogeneity of polydactyly in Maine Coon cats

OBJECTIVES

Polydactyly has been described in two breeds of domestic cats (Maine Coon and Pixie Bob) and in some outbred domestic cats (eg, Hemingway cats). In most cases, feline polydactyly is a non-syndromic preaxial polydactyly. Three variants located in a regulatory sequence involved in limb development, named ZRS (zone of polarising activity regulatory sequence), have been identified to be responsible for feline polydactyly. These variants have been found in outbred domestic cats in the UK (UK1 and UK2 variants) and in Hemingway cats in the USA (Hw variant). The aim of this study was to characterise the genetic features of polydactyly in Maine Coon cats.

METHODS

Genotyping assay was used to identify the variant(s) segregating in a cohort of 75 polydactyl and non-polydactyl Maine Coon cats from different breeding lines from Europe, Canada and the USA. The authors performed a segregation analysis to identify the inheritance pattern of polydactyly in this cohort and analysed the population structure.

RESULTS

The Hw allele was identified in a subset of polydactyl cats. Sequencing of two regulatory sequences involved in limb development did not reveal any other variant in polydactyl cats lacking the Hw allele. Additionally, genotype-phenotype and segregation analyses revealed the peculiar inheritance pattern of polydactyly in Maine Coon cats. The population structure analysis demonstrated a genetic distinction between Hw and Hw-free polydactyl cats.

CONCLUSIONS AND RELEVANCE

Polydactyly in Maine Coon cats is inherited as an autosomal dominant trait with incomplete penetrance and variable expressivity, and this trait is characterised by genetic heterogeneity in the Maine Coon breed. Maine Coon breeders should be aware of this situation and adapt their breeding practices accordingly.

A DNA-Based Intelligent Expert System for Personalised Skin-Health Recommendations

Intensive attention on personalised skin-health solutions is on account of incomparable love of skin and an urgent need for effective treatment. In the meanwhile, people have great expectations on how to utilise genetic knowledge of our body to provide a precise solution for different individuals, such as daily use of skin-health products, since the rapid development of genetic test services and skin-health science. However, the complexity of multi-modal data, the establishment of correlations between consumer genetic data and product ingredients are the main obstacles encountered today. Determining to settle such obstacles, a personalised recommendation expert system for selecting optimised skin-health product within the category based upon genetic phenotypes for each consumer was introduced in this article. Random Forests were implemented to achieve automatic product categorisation, the performance discussed and compared with SVM and Logistic Regression. Lastly, categorised skin-health product suggestion was made with an optimised recommendation model based on associated genetic phenotype information. Potential changes (up to 71.0% more phenotypic relevant ingredients) from experiments using real product data were demonstrated and compared with imitated cases of real-life human selections.

Selection favors loss of floral pigmentation in a highly selfing morning glory

A common evolutionary trend in highly selfing plants is the evolution of the “selfing syndrome”, in which traits associated with pollinator attraction are lost or greatly reduced. Limited information is available on whether these trait reductions are favored by natural selection or result from reduced purifying selection coupled with genetic drift. This study attempted to distinguish between these two possibilities for the evolutionary loss of floral pigmentation in the highly selfing species Ipomoea lacunosa. This study also tested the hypothesis that loss of floral pigmentation is caused by downregulation or loss of function in a tissue-specific anthocyanin transcription factor, as has been found in other plants. F2 individuals of a cross between white and pigmented individuals revealed segregation at two epistatically acting loci: one affecting pigmentation in both corolla throat and limbs (Anl1) and one affecting limb pigmentation (Anl2). Individuals that are homozygous for the “white” allele at Anl1 have white throats and limbs regardless of genotype at Anl2. In individuals with pigmented throats, homozygosity of the “white” allele at Anl2 produces white limbs. Flower color variation at Anl1 cosegregates with an R2R3-Myb anthocyanin transcription factor, which is down-regulated in white-flowers but not in pigmented flowers. Differential expression of the two alleles of this gene indicates that down regulation is caused by a cis-regulatory change. Finally, allele-frequency differences at Anl1 were substantially and significantly greater than differences in allele frequencies at four microsatellite loci. These results are consistent with the hypotheses that the identified R2R3-Myb gene corresponds to Anl1 and that evolutionary loss of pigmentation in I. lacunosa was caused by selection. They are also consistent with previous studies demonstrating that loss of floral pigmentation is usually caused by down-regulation or functional inactivation of an R2R3-Myb gene.

Single Locked Nucleic Acid-enhanced nanopore genetic discrimination of pathogenic serotypes and cancer driver mutations

Rapid and accurate detection of single-nucleotide polymorphism (SNP) in pathogenic mutants is crucial for broad fields from food safety monitoring to disease diagnostics and prognosis. Here, we developed a nanopore single-molecule sensor, coupled with the locked nucleic acid (LNA) technique, to accurately discriminate SNPs for detection of Shiga toxin producing Escherichia coli (STEC) O157:H7 pathogen serotype, and cancer-derived driver mutations EGFR L858R and KRAS G12D. This sensitive method, with a simplified, low cost, easy-to-operate LNA design, can be applied in food science and medical detection that need rapid and accurate determination of genetic variations.

Advances in Molecular Testing Techniques in Cytologic Specimens

There has been a paradigm shift in the practice of cytopathology with the advent of highly sensitive molecular tests using small amounts of tissue that can provide diagnostic, prognostic, and predictive information for clinical management. The cytopathologist plays a key role in providing a timely and accurate diagnosis as well as ensuring appropriate processing and handling of the specimen and judicious triaging of the tissue for molecular testing that guide therapeutic decisions. As the era of "precision medicine" continues to evolve and expand, cytopathology remains a dynamic field with advances in the practice of molecular cytopathology providing new paradigms in clinical care.

Prevalence of common hereditary risk factors for thrombophilia in Somalia and identification of a novel Gln544Arg mutation in coagulation factor V

Thrombophilia, commonly manifested as venous thromboembolism (VTE), is a worldwide concern but little is known on its genetic epidemiology in many parts of the globe particularly in the developing countries. Here we employed TaqMan genotyping and pyrosequencing to evaluate the prevalence of known common nucleotide polymorphisms associated with thrombophilia in a Somali population in the Puntland region of Somalia. We also employed next generation sequencing (NGS) to investigate other genetic variants in a Somali patient with deep venous thrombosis (DVT). As expected, we found no existence of factor V Leiden (rs6025) and prothrombin G20210A (rs1799963) in the Somali population. The G allele of ABO [261G/delG] polymorphism (rs8176719) was found at a frequency of 29%, similar to that observed in other African populations. We found the lowest so far reported frequency of MTHFR C677T (rs1801133) polymorphism in the Somali population (T allele frequency 1.5%). A novel and deleterious single nucleotide variation in exon 11 of coagulation factor V (c.1631A>G) causing Gln544Arg exchange in factor V was identified in a 29 years old Somali female with DVT. The same patient was heterozygous to VKORC1 Asp36Tyr polymorphism (rs61742245) that predisposes to warfarin resistance. In conclusion, this study shows that common hereditary factors for thromboembolism found in Caucasians are either less frequent or absent in the Somali population-similar to the situation in other Africans. NGS is possibly a better choice to detect genetic risk variants for thrombosis in this ethnic group.

Single Locked Nucleic Acid-Enhanced Nanopore Genetic Discrimination of Pathogenic Serotypes and Cancer Driver Mutations

Accurate and rapid detection of single-nucleotide polymorphism (SNP) in pathogenic mutants is crucial for many fields such as food safety regulation and disease diagnostics. Current detection methods involve laborious sample preparations and expensive characterizations. Here, we investigated a single locked nucleic acid (LNA) approach, facilitated by a nanopore single-molecule sensor, to accurately determine SNPs for detection of Shiga toxin producing Escherichia coli (STEC) serotype O157:H7, and cancer-derived EGFR L858R and KRAS G12D driver mutations. Current LNA applications that require incorporation and optimization of multiple LNA nucleotides. But we found that in the nanopore system, a single LNA introduced in the probe is sufficient to enhance the SNP discrimination capability by over 10-fold, allowing accurate detection of the pathogenic mutant DNA mixed in a large amount of the wild-type DNA. Importantly, the molecular mechanistic study suggests that such a significant improvement is due to the effect of the single-LNA that both stabilizes the fully matched base-pair and destabilizes the mismatched base-pair. This sensitive method, with a simplified, low cost, easy-to-operate LNA design, could be generalized for various applications that need rapid and accurate identification of single-nucleotide variations.

Comparison of single nucleotide polymorphisms in the 3' untranslated region of HLA-G in placentas between spontaneous preterm birth and preeclampsia

OBJECTIVE

To compare single nucleotide polymorphisms (SNPs) in the 3'-untranslated region (3'UTR) of human leukocyte antigen (HLA)-G in placentas between spontaneous preterm birth and preeclampsia pregnancies.

RESULTS

Placental samples matched for gestational age were obtained from 20 cases of spontaneous preterm births and 19 cases of preeclampsia. Genomic deoxyribonucleic acid was extracted from placenta tissue and the 3'UTR region of HLA-G was amplified via polymerase chain reaction. Nine SNPs were analyzed by direct Sanger sequencing. There was no significant difference in gestational age at delivery or birth weight between two groups. And there were no significant differences in the allele and phenotype frequencies between two groups.

Determination of mutated genes in the presence of wild-type DNA by using molecular beacons as probe

Low-abundance mutations in the presence of wild-type DNA can be determined using molecular beacon (MB) as probe. A MB is generally used as DNA probe because it can distinguish single-base mismatched target DNA from fully matched target DNA. However, the probe can not determine low-abundance mutations in the presence of wild-type DNA. In this study, this limitation is addressed by enhancing the stability of unpaired base-containing dsDNA with a hydrogen-bonding ligand, which was added after hybridization of the MB to the target DNA. The ligand formed hydrogen bonds with unpaired bases and stabilized the unpaired base-containing dsDNA if target DNA is mutated one. As a result, more MBs were opened by the mutant genes in the presence of the ligand and a further increase in the fluorescence intensity was obtained. By contrast, fluorescence intensity did not change if target DNA is wild-type one. Consequent increase in the fluorescence intensity of the MB was regarded as a signal derived from mutant genes. The proposed method was applied in synthetic template systems to determine point mutation in DNA obtained from PCR analysis. The method also allows rapid and simple discrimination of a signal if it is originated in the presence of mutant gene or alternatively by a lower concentration of wild gene.

Quantitative haplotyping of PCR products by nonsynchronous pyrosequencing with di-base addition

Molecular haplotyping is becoming increasingly important for studying the disease association of a specific allele because of its ability of providing more information than any single nucleotide polymorphism (SNP). Computational analysis and experimental techniques are usually performed for haplotypic determination. However, established methods are not suitable for analyzing haplotypes of massive natural DNA samples. Here we present a simple molecular approach to analyze haplotypes of conventional polymerase chain reaction (PCR) products quantitatively in a single sequencing run. In this approach, specific types and proportions of haplotypes in both individual and pooled samples could be determined by solving equations constructed from nonsynchronous pyrosequencing with di-base addition. Two SNPs (rs11176013 and rs11564148) in the gene for leucine-rich repeat kinase 2 (LRRK2) related to Parkinson's disease were selected as experimental sites. A series of DNA samples, including these two heterozygous loci, were investigated. This approach could accurately identify multiple DNA samples indicating that the approach is likely to be applied for haplotyping of unrestricted conventional PCR products from natural samples, and be especially applicable for analyzing short sequences in clinical diagnosis. Graphical Abstract One DNA sample consisting of 4 different DNA templates with different proportion are sequenced by nonsynchronous pyrosequencing with di-base addition. The number of incorporated nucleotides produced by a single sequencing reaction equals to the total of incorporated nucleotides. Four independent equations are constructed from the pyrograms of nonsynchronous pyrosequencing data. Molecular haplotypes of two adjacent SNPs can be quantitatively identified by solving these equations.

Nanoelectronic three-dimensional (3D) nanotip sensing array for real-time, sensitive, label-free sequence specific detection of nucleic acids

The improvements in our ability to sequence and genotype DNA have opened up numerous avenues in the understanding of human biology and medicine with various applications, especially in medical diagnostics. But the realization of a label free, real time, high-throughput and low cost biosensing platforms to detect molecular interactions with a high level of sensitivity has been yet stunted due to two factors: one, slow binding kinetics caused by the lack of probe molecules on the sensors and two, limited mass transport due to the planar structure (two-dimensional) of the current biosensors. Here we present a novel three-dimensional (3D), highly sensitive, real-time, inexpensive and label-free nanotip array as a rapid and direct platform to sequence-specific DNA screening. Our nanotip sensors are designed to have a nano sized thin film as their sensing area (~ 20 nm), sandwiched between two sensing electrodes. The tip is then conjugated to a DNA oligonucleotide complementary to the sequence of interest, which is electrochemically detected in real-time via impedance changes upon the formation of a double-stranded helix at the sensor interface. This 3D configuration is specifically designed to improve the biomolecular hit rate and the detection speed. We demonstrate that our nanotip array effectively detects oligonucleotides in a sequence-specific and highly sensitive manner, yielding concentration-dependent impedance change measurements with a target concentration as low as 10 pM and discrimination against even a single mismatch. Notably, our nanotip sensors achieve this accurate, sensitive detection without relying on signal indicators or enhancing molecules like fluorophores. It can also easily be scaled for highly multiplxed detection with up to 5000 sensors/square centimeter, and integrated into microfluidic devices. The versatile, rapid, and sensitive performance of the nanotip array makes it an excellent candidate for point-of-care diagnostics, and high-throughput DNA analysis applications.

Inflammatory markers and IL-6 polymorphism in peripheral arterial disease with and without diabetes mellitus

Peripheral arterial disease (PAD) is a manifestation of systemic atherosclerosis, recognized as an inflammatory disease of the vessel wall, probably accelerated by diabetes mellitus (DM). Elevated interleukin (IL)-6 levels have been associated with increased cardiovascular morbidity and a common polymorphism has been identified in the promoter region of the IL-6 gene. The aim of this prospective study was to investigate inflammatory mediators in PAD patients (±DM) and to investigate a possible relationship to the IL-6 gene polymorphism. Five groups of patients (DM, intermittent claudication ±DM, critical limb ischemia (CLI) ±DM) and a control group of 20 individuals each were included. Hemoglobin, high sensitive C-reactive protein (hsCRP), creatinine, blood lipids, white blood cells (WBC); CD11b/CD18; vascular cell adhesion molecule (sVCAM-1), intercellular adhesion molecule (sICAM-1), sE-selectin, sP-selectin; IL-6, IL-8, tumour necrosis factor (TNF)α, sTNFα-R1 and sTNFα-R2 were analysed. The IL-6 gene polymorphism was determined in all groups and also compared with 200 healthy controls from a larger study of blood donors. In a multiple regression analysis, adjusted for gender, smoking and age, the effect of CLI was significantly ( p < 0.05) associated with elevated levels of the WBC count, hsCRP, proinflammatory cytokines (IL-6, TNFα-R1-2) and endothelial (sICAM, sVCAM) and WBC (CD11b gran) markers. The effect of less advanced PAD (intermittent claudication) was related to an increased concentration of sVCAM-1 and the number of monocytes and granulocytes. DM or leg ulcers were not significantly related to any of the markers. No significant difference in frequency of the various IL-6 genotypes was found between the groups or when compared with the group of 200 blood donors ( p > 0.3). Activation of cytokines, endothelial cells and WBC was related to the Fontaine stage of PAD but not to the presence of DM or ulcers. No association was found between the polymorphism in the IL-6 promoter region and PAD.

Bioinformatics Approach in Plant Genomic Research

The advance in genomics technology leads to the dramatic change in plant biology research. Plant biologists now easily access to enormous genomic data to deeply study plant high-density genetic variation at molecular level. Therefore, fully understanding and well manipulating bioinformatics tools to manage and analyze these data are essential in current plant genome research. Many plant genome databases have been established and continued expanding recently. Meanwhile, analytical methods based on bioinformatics are also well developed in many aspects of plant genomic research including comparative genomic analysis, phylogenomics and evolutionary analysis, and genome-wide association study. However, constantly upgrading in computational infrastructures, such as high capacity data storage and high performing analysis software, is the real challenge for plant genome research. This review paper focuses on challenges and opportunities which knowledge and skills in bioinformatics can bring to plant scientists in present plant genomics era as well as future aspects in critical need for effective tools to facilitate the translation of knowledge from new sequencing data to enhancement of plant productivity.

Molecular Approaches to Genetically Improve the Accumulation of Health-Promoting Secondary Metabolites in Staple Crops-A Case Study: The Lipoxygenase-B1 Genes and Regulation of the Carotenoid Content in Pasta Products

Secondary metabolites, also known as phytochemicals, represent a large subset of plant molecules that include compounds with health-promoting effects. Indeed, a number of epidemiological studies have shown that, when taken regularly and in adequate amounts, these molecules can have long-term beneficial effects on human health, through reduction of the incidence of degenerative diseases, such as cardiovascular diseases, obesity, diabetes, and cancer. As the dietary intake of these phytochemicals is often inadequate, various strategies are in use to improve their content in staple crops, and the end-products thereof. One of the most effective strategies is crop improvement through genetic approaches, as this is the only way to generate new cultivars in which the high accumulation of a given phytochemical is stably fixed. Efforts to genetically improve quality traits are rapidly evolving, from classical breeding to molecular-assisted approaches; these require sound understanding of the molecular bases underlying the traits, to identify the genes/alleles that control them. This can be achieved through global analysis of the metabolic pathway responsible for phytochemical accumulation, to identify the link between phytochemical content and the activities of key enzymes that regulate the metabolic pathway, and between the key enzymes and their encoding genes/alleles. Once these have been identified, they can be used as markers for selection of new improved genotypes through biotechnological approaches. This review provides an overview of the major health-promoting properties shown to be associated with the dietary intake of phytochemicals, and describes how molecular approaches provide means for improving the health quality of edible crops. Finally, a case study is illustrated, of the identification in durum wheat of the Lipoxygenase-B1 genes that control the final carotenoid content in semolina-based foods, such as pasta products.

The A, C, G, and T of Genome Assembly

Genome assembly in its two decades of history has produced significant research, in terms of both biotechnology and computational biology. This contribution delineates sequencing platforms and their characteristics, examines key steps involved in filtering and processing raw data, explains assembly frameworks, and discusses quality statistics for the assessment of the assembled sequence. Furthermore, the paper explores recent Ubuntu-based software environments oriented towards genome assembly as well as some avenues for future research.

Pyrosequencing with di-base addition for single nucleotide polymorphism genotyping

We develop color code-based pyrosequencing with di-base addition for analysis of single nucleotide polymorphisms (SNPs). When a di-base is added into the polymerization, one or several two-color code(s) containing the type and the number of incorporated nucleotides will be produced. The code information obtained in a single run is useful to genotype SNPs as each allelic variant will give a specific pattern compared to the two other variants. Special care has to be taken while designing the di-base dispensation order. Here, we present a detailed protocol for establishing sequence-specific di-base addition to avoid nonsynchronous extension at the SNP sites. By using this technology, as few as 50 copies of DNA templates were accurately sequenced. Higher signals were produced and thus a relatively lower sample amount was required. Furthermore, the read length of per flow was increased, making simultaneous identification of multiple SNPs in a single sequencing run possible. Validation of the method was performed by using templates with two SNPs covering 37 bp and with three SNPs covering 58 bp as well as 82 bp. These SNPs were successfully genotyped by using only a sequencing primer in a single PCR/sequencing run. Our results demonstrated that this technology could be potentially developed into a powerful methodology to accurately determine SNPs so as to diagnose clinical settings.

Development of new SNP derived cleaved amplified polymorphic sequence marker set and its successful utilization in the genetic analysis of seed color variation in barley

The aim of the present study was to develop a new cost effective PCR based CAPS marker set using advantages of high-throughput SNP genotyping. Initially, SNP survey was made using 20 diverse barley genotypes via 9k iSelect array genotyping that resulted in 6334 polymorphic SNP markers. Principle component analysis using this marker data showed fine differentiation of barley diverse gene pool. Till this end, we developed 200 SNP derived CAPS markers distributed across the genome covering around 991cM with an average marker density of 5.09cM. Further, we genotyped 68 CAPS markers in an F2 population (Cheri×ICB181160) segregating for seed color variation in barley. Genetic mapping of seed color revealed putative linkage of single nuclear gene on chromosome 1H. These findings showed the proof of concept for the development and utility of a newer cost effective genomic tool kit to analyze broader genetic resources of barley worldwide.

Efficient SNP Discovery by Combining Microarray and Lab-on-a-Chip Data for Animal Breeding and Selection

The genetic markers associated with economic traits have been widely explored for animal breeding. Among these markers, single-nucleotide polymorphism (SNPs) are gradually becoming a prevalent and effective evaluation tool. Since SNPs only focus on the genetic sequences of interest, it thereby reduces the evaluation time and cost. Compared to traditional approaches, SNP genotyping techniques incorporate informative genetic background, improve the breeding prediction accuracy and acquiesce breeding quality on the farm. This article therefore reviews the typical procedures of animal breeding using SNPs and the current status of related techniques. The associated SNP information and genotyping techniques, including microarray and Lab-on-a-Chip based platforms, along with their potential are highlighted. Examples in pig and poultry with different SNP loci linked to high economic trait values are given. The recommendations for utilizing SNP genotyping in nimal breeding are summarized.

High-throughput sequencing of 16S rDNA amplicons characterizes bacterial composition in bronchoalveolar lavage fluid in patients with ventilator-associated pneumonia

Ventilator-associated pneumonia (VAP) is a life-threatening disease that is associated with high rates of morbidity and likely mortality, placing a heavy burden on an individual and society. Currently available diagnostic and therapeutic approaches for VAP treatment are limited, and the prognosis of VAP is poor. The present study aimed to reveal and discriminate the identification of the full spectrum of the pathogens in patients with VAP using high-throughput sequencing approach and analyze the species richness and complexity via alpha and beta diversity analysis. The bronchoalveolar lavage fluid samples were collected from 27 patients with VAP in intensive care unit. The polymerase chain reaction products of the hypervariable regions of 16S rDNA gene in these 27 samples of VAP were sequenced using the 454 GS FLX system. A total of 103,856 pyrosequencing reads and 638 operational taxonomic units were obtained from these 27 samples. There were four dominant phyla, including Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. There were 90 different genera, of which 12 genera occurred in over ten different samples. The top five dominant genera were Streptococcus, Acinetobacter, Limnohabitans, Neisseria, and Corynebacterium, and the most widely distributed genera were Streptococcus, Limnohabitans, and Acinetobacter in these 27 samples. Of note, the mixed profile of causative pathogens was observed. Taken together, the results show that the high-throughput sequencing approach facilitates the characterization of the pathogens in bronchoalveolar lavage fluid samples and the determination of the profile for bacteria in the bronchoalveolar lavage fluid samples of the patients with VAP. This study can provide useful information of pathogens in VAP and assist clinicians to make rational and effective therapeutic decisions.

High-throughput sequencing of 16S rDNA amplicons characterizes bacterial composition in cerebrospinal fluid samples from patients with purulent meningitis

Purulent meningitis (PM) is a severe infectious disease that is associated with high rates of morbidity and mortality. It has been recognized that bacterial infection is a major contributing factor to the pathogenesis of PM. However, there is a lack of information on the bacterial composition in PM, due to the low positive rate of cerebrospinal fluid bacterial culture. Herein, we aimed to discriminate and identify the main pathogens and bacterial composition in cerebrospinal fluid sample from PM patients using high-throughput sequencing approach. The cerebrospinal fluid samples were collected from 26 PM patients, and were determined as culture-negative samples. The polymerase chain reaction products of the hypervariable regions of 16S rDNA gene in these 26 samples of PM were sequenced using the 454 GS FLX system. The results showed that there were 71,440 pyrosequencing reads, of which, the predominant phyla were Proteobacteria and Firmicutes; and the predominant genera were Streptococcus, Acinetobacter, Pseudomonas, and Neisseria. The bacterial species in the cerebrospinal fluid were complex, with 61.5% of the samples presenting with mixed pathogens. A significant number of bacteria belonging to a known pathogenic potential was observed. The number of operational taxonomic units for individual samples ranged from six to 75 and there was a comparable difference in the species diversity that was calculated through alpha and beta diversity analysis. Collectively, the data show that high-throughput sequencing approach facilitates the characterization of the pathogens in cerebrospinal fluid and determine the abundance and the composition of bacteria in the cerebrospinal fluid samples of the PM patients, which may provide a better understanding of pathogens in PM and assist clinicians to make rational and effective therapeutic decisions.

Software-Based Pyrogram® Evaluation

Pyrosequencing(®) is a widely used technology to detect gene mutations in a molecular research or diagnostics laboratory. Compared to Sanger sequencing, it is inherently more quantitative with a superior limit of detection, although it has a shorter read length and has difficulty with homopolymeric sequences.Results of Pyrosequencing experiments are typically presented as traces with sequential peaks, called Pyrograms(®). For the majority of clinical diagnostic cases, Pyrograms are straightforward to read. However, there are occasionally complex results that are uninterpretable or difficult to interpret. In this chapter, we demonstrate a computer software, named Pyromaker that has been developed to help with the analysis of Pyrograms. Pyromaker is a freely and publically available software program to assist in the recognition of patterns of mutations, interpretation of difficult or ambiguous testing results and design of an optimal strategy to detect potential mutations by generating simulated Pyrograms. In addition to help diagnostic activities, Pyromaker can also be used as a virtual and user-friendly educational tool to teach newcomers the fundamental mechanism of Pyrosequencing, and correct interpretation of actual Pyrosequencing data.

Presence and impact of allelic variations of two alternative s-kdr mutations, M918T and M918L, in the voltage-gated sodium channel of the green peach aphid Myzus persicae

BACKGROUND

Pyrethroids have been widely employed in order to control several agricultural pests, including Myzus persicae. Target-site resistance is the main mechanism that confers insensitivity to this class of compounds, and the most common amino acid substitutions are kdr (L1014F) and s-kdr (M918T), but recently another mutation in the s-kdr locus (M918L) has been described in French and Korean populations of M. persicae.

RESULTS

Molecular analysis of several Italian populations of M. persicae by pyrosequencing revealed the presence of the new s-kdr mutation (M918L) in different forms. It was found in two different nucleotide polymorphisms (a/t or a/c substitution), in heterozygous or homozygous status, and also in combination with the classic kdr and s-kdr. Bioassays on populations carrying the M918L mutation show that it strongly affects pyrethroid efficacy, particularly of type II pyrethroids such as lambda-cyhalothrin, while it has no effect against DDT.

CONCLUSION

This work provides more information about the new s-kdr M918L mutation in M. persicae, describing a more complicated situation arising from the possible combination with the classic L1014F and M918T. Our data open new questions concerning the origin of these new genotypes with different combinations of target-site mutations, and also their possible influence on control strategies.

Immune responses following meningococcal serogroups A, C, Y and W polysaccharide vaccination in C2-deficient persons: evidence for increased levels of serum bactericidal antibodies

Complement C2 deficiency (C2D) is associated with immunological diseases and increased susceptibility to invasive infections caused by encapsulated bacteria such as Neisseria menigitidis. In this study we evaluate the immunogenicity of vaccination against N. menigitidis in C2D. C2D patients (n=22) and controls (n=52) were given a tetravalent meningococcal polysaccharide vaccine. Serum bactericidal antibody (SBA) titres (serogroups A, C, Y and W) were analysed using a rabbit complement source. Levels of IgG, IgM, and IgA, factor B, and factor H, polymorphisms of MBL and Fc-gamma receptors were determined. The C2D patients responded with an increased SBA titre to all four serogroups (p<0.001). The response rates define as SBA titres ≥8 were found to be between 85.7% and 92.5%. The post-vaccination titres for serogroups C, Y and W were equal to healthy controls. C2D patients with a history of invasive infection had a lower post-vaccination SBA titres both compared to healthy C2D persons (p=0.03) and compared to controls (p<0.0001). We found that the G2M*n/G2M*n genotype were associated with a higher SBA titres after immunization (p=0.03). None of the other investigated immunological factors appear to be important in influencing the vaccine responses. Autoimmune diseases in C2D did not affect the vaccine response. In general, vaccination against meningococci gave rise to antibody responses in the C2D patients that equal healthy controls. The response rate was lower to serogroup A and among C2D patients with history of invasive infections. The presence of G2M*n/G2M*n genotype was associated with higher SBA titres after immunization.

The History of Pyrosequencing(®)

One late afternoon in the beginning of January 1986, bicycling from the lab over the hill to the small village of Fulbourn, the idea for an alternative DNA sequencing technique came to my mind. The basic concept was to follow the activity of DNA polymerase during nucleotide incorporation into a DNA strand by analyzing the pyrophosphate released during the process. Today, the technique is used in multidisciplinary fields in academic, clinical, and industrial settings all over the word. This technique can be used for both single-base sequencing and whole-genome sequencing, depending on the format used.In this chapter, I give my personal account of the development of Pyrosequencing(®)-beginning on a winter day in 1986, when I first envisioned the method-until today, nearly 30 years later.

Allele Quantification Pyrosequencing® at Designated SNP Sites to Detect Allelic Expression Imbalance and Loss-of-Heterozygosity

Pyrosequencing(®) is able to quantitate the level of a nucleotide at a designated germ-line or somatic variant, including single nucleotide polymorphisms (SNPs). SNPs within a gene of interest may be used to distinguish between the two genetic alleles and study their behavior in heterozygous individuals. With regard to cancer etiology and development, identification of alleles and the detection of allelic imbalances, such as transcriptional loss from one allele or loss-of-heterozygosity (due to deletion of one allele), within a tumor are particularly useful. Lynch syndrome, the most common form of hereditary bowel and uterine cancer, is caused by heterozygous germ-line mutations within the DNA mismatch repair genes and tumors develop following inactivation of the remaining functional allele within somatic tissues, usually by acquired loss-of-heterozygosity. MLH1 is the most frequently mutated gene in Lynch syndrome; however, some cases whose tumors display immunohistochemical loss of the MLH1 protein have no apparent mutation within the coding region of MLH1. Allelic loss of expression or reduced function of MLH1 can also result in the propensity to develop Lynch syndrome associated cancers. In this chapter we describe allele quantification Pyrosequencing assays designed at a common benign SNP within the MLH1 coding region for application to either DNA or mRNA (cDNA) templates, which enabled us to detect pathological allelic imbalances in such cases with suspected Lynch syndrome. Our allele quantification Pyrosequencing assays at the MLH1 c.655A > G (rs1799977) exonic SNP were applied to clinical specimens and detected both constitutional allelic expression loss and tumor loss-of-heterozygosity in some cases, facilitating the identification of the mechanistic cause underlying their cancer development. We provide detailed protocols for implementing these Pyrosequencing assays and illustrative examples of their application in patients.

Genetic mapping of legume orthologs reveals high conservation of synteny between lentil species and the sequenced genomes of Medicago and chickpea

Lentil (Lens culinaris Medik.) is a global food crop with increasing importance for food security in south Asia and other regions. Lens ervoides, a wild relative of cultivated lentil, is an important source of agronomic trait variation. Lens is a member of the galegoid clade of the Papilionoideae family, which includes other important dietary legumes such as chickpea (Cicer arietinum) and pea (Pisum sativum), and the sequenced model legume Medicago truncatula. Understanding the genetic structure of Lens spp. in relation to more fully sequenced legumes would allow leveraging of genomic resources. A set of 1107 TOG-based amplicons were identified in L. ervoides and a subset thereof used to design SNP markers for mapping. A map of L. ervoides consisting of 377 SNP markers spread across seven linkage groups was developed using a GoldenGate genotyping array and single SNP marker assays. Comparison with maps of M. truncatula and L. culinaris documented considerable shared synteny and led to the identification of a few major translocations and a major inversion that distinguish Lens from M. truncatula, as well as a translocation that distinguishes L. culinaris from L. ervoides. The identification of chromosome-level differences among Lens spp. will aid in the understanding of introgression of genes from L. ervoides into cultivated L. culinaris, furthering genetic research and breeding applications in lentil.

Two recessive mutations in FGF5 are associated with the long-hair phenotype in donkeys

Background

Seven donkey breeds are recognized by the French studbook. Individuals from the Pyrenean, Provence, Berry Black, Normand, Cotentin and Bourbonnais breeds are characterized by a short coat, while those from the Poitou breed (Baudet du Poitou) are characterized by a long-hair phenotype. We hypothesized that loss-of-function mutations in the FGF5 (fibroblast growth factor 5) gene, which are associated with a long-hair phenotype in several mammalian species, may account for the special coat feature of Poitou donkeys. To the best of our knowledge, mutations in FGF5 have never been described in Equidae.

Methods

We sequenced the FGF5 gene from 35 long-haired Poitou donkeys, as well as from a panel of 67 short-haired donkeys from the six other French breeds and 131 short-haired ponies and horses.

Results

We identified a recessive c.433_434delAT frameshift deletion in FGF5, present in Poitou and three other donkey breeds and a recessive nonsense c.245G > A substitution, present in Poitou and four other donkey breeds. The frameshift deletion was associated with the long-hair phenotype in Poitou donkeys when present in two copies (n = 31) or combined with the nonsense mutation (n = 4). The frameshift deletion led to a stop codon at position 159 whereas the nonsense mutation led to a stop codon at position 82 in the FGF5 protein. In silico, the two truncated FGF5 proteins were predicted to lack the critical β strands involved in the interaction between FGF5 and its receptor, a mandatory step to inhibit hair growth.

Conclusions

Our results highlight the allelic heterogeneity of the long-hair phenotype in donkeys and enlarge the panel of recessive FGF5 loss-of-function alleles described in mammals. Thanks to the DNA test developed in this study, breeders of non-Poitou breeds will have the opportunity to identify long-hair carriers in their breeding stocks.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-014-0065-5) contains supplementary material, which is available to authorized users.

Gene expression and metabolic pathways related to cell growth and lipid synthesis in diatom Nitzschia ZJU2 after two rounds of mutagenesis by γ-rays

3939 genes including cell growth and lipid synthesis key enzymes were up-regulated in mutant Nitzschia ZJU2 after two mutations by γ-rays which exhibited rapid growth and higher lipid productivity.

Genetic Polymorphisms Associated with Endometriosis in Pakistani Women

Background

Endometriosis is a common disease that causes pain and infertility. The heritable predisposition toward endometriosis motivates an interest to identify the genes and genomic variants involved in the pathogenesis of endometriosis. Both genetic and environmental factors contribute to this disease. Here we investigated in Pakistani women the association of endometriosis and single nucleotide polymorphisms (SNP) in genes previously identified in the development of this disease.

Methods

DNA samples from 52 genetically unrelated endometriosis subjects with endometriosis and 52 randomly selected controls were analyzed by direct sequencing to determine polymorphisms in four genes. These included estrogen receptor alpha (ESR1) (rs2234693 C/T, rs9340799 G/A SNP), estrogen receptor beta (ESR2) (rs4986938 G/A SNP), progesterone receptor (PGR) (rs1042838 G/T, rs10895068 G/A SNPs) and interleukin 10 (IL10) (rs1800871 C/T, rs1800872 C/A and rs1800896 G/A SNPs).

Results

The allele A at −592, T at −819 and G at −1080 of IL10 and all of the SNPs studied at ESR2 and PGR show strong, statistically significant associations with the disease. However, the genetic variation at ESR1 was distributed similarly among cases and control groups.

Conclusion

These findings suggest that the functional promoter polymorphism of the IL10 gene, identified by the “ATG” genotype, may contribute to the risk of endometriosis. Genetic variants of ESR2 and PGR gene may also be a risk factor as well as influence the fertility status of patients with endometriosis.

Validation of SNP allele frequencies determined by pooled next-generation sequencing in natural populations of a non-model plant species

Sequencing of pooled samples (Pool-Seq) using next-generation sequencing technologies has become increasingly popular, because it represents a rapid and cost-effective method to determine allele frequencies for single nucleotide polymorphisms (SNPs) in population pools. Validation of allele frequencies determined by Pool-Seq has been attempted using an individual genotyping approach, but these studies tend to use samples from existing model organism databases or DNA stores, and do not validate a realistic setup for sampling natural populations. Here we used pyrosequencing to validate allele frequencies determined by Pool-Seq in three natural populations of Arabidopsis halleri (Brassicaceae). The allele frequency estimates of the pooled population samples (consisting of 20 individual plant DNA samples) were determined after mapping Illumina reads to (i) the publicly available, high-quality reference genome of a closely related species (Arabidopsis thaliana) and (ii) our own de novo draft genome assembly of A. halleri. We then pyrosequenced nine selected SNPs using the same individuals from each population, resulting in a total of 540 samples. Our results show a highly significant and accurate relationship between pooled and individually determined allele frequencies, irrespective of the reference genome used. Allele frequencies differed on average by less than 4%. There was no tendency that either the Pool-Seq or the individual-based approach resulted in higher or lower estimates of allele frequencies. Moreover, the rather high coverage in the mapping to the two reference genomes, ranging from 55 to 284x, had no significant effect on the accuracy of the Pool-Seq. A resampling analysis showed that only very low coverage values (below 10-20x) would substantially reduce the precision of the method. We therefore conclude that a pooled re-sequencing approach is well suited for analyses of genetic variation in natural populations.

Pyrosequencing: powerful and quantitative sequencing technology

Pyrosequencing is a sequencing-by-synthesis method for DNA analysis that has emerged as a platform not only for de novo sequencing applications, but also for quantitative analysis of genomic methylation, single-nucleotide polymorphisms, and allele quantification. In this unit, we describe a complete workflow from sample to result that is suitable for each of these applications. As cytosine conversion is a key element of successful methylation analysis using pyrosequencing, a support protocol for bisulfite treatment is also included.

Sex-specific effects of cis-regulatory variants in Drosophila melanogaster

Sexual dimorphism at the level of gene expression is common and well documented, but much less is known about how different cis-regulatory alleles interact with the different trans-regulatory environments present in males and females. Here we show that sex-specific effects of cis-regulatory variants are common in Drosophila.

Fundamentals of pyrosequencing

CONTEXT

DNA sequencing is critical to identifying many human genetic disorders caused by DNA mutations, including cancer. Pyrosequencing is less complex, involves fewer steps, and has a superior limit of detection compared with Sanger sequencing. The fundamental basis of pyrosequencing is that pyrophosphate is released when a deoxyribonucleotide triphosphate is added to the end of a nascent strand of DNA. Because deoxyribonucleotide triphosphates are sequentially added to the reaction and because the pyrophosphate concentration is continuously monitored, the DNA sequence can be determined.

OBJECTIVE

To demonstrate the fundamental principles of pyrosequencing.

DATA SOURCES

Salient features of pyrosequencing are demonstrated using the free software program Pyromaker ( http://pyromaker.pathology.jhmi.edu ), through which users can input DNA sequences and other pyrosequencing parameters to generate the expected pyrosequencing results.

CONCLUSIONS

We demonstrate how mutant and wild-type DNA sequences result in different pyrograms. Using pyrograms of established mutations in tumors, we explain how to analyze the pyrogram peaks generated by different dispensation sequences. Further, we demonstrate some limitations of pyrosequencing, including how some complex mutations can be indistinguishable from single base mutations. Pyrosequencing is the basis of the Roche 454 next-generation sequencer and many of the same principles also apply to the Ion Torrent hydrogen ion-based next-generation sequencers.

Alternative reliable method for cytochrome P450 2D6 poor metabolizers genotyping

High-resolution melting curve analysis (HRM) of polymerase chain reaction (PCR) amplicons has been described as a fast, cheap, and reliable closed-tube method of genotyping with no need for labeled primers or labeled probes. We adapted this melting analysis assay for the detection of the most common nonfunctional alleles of cytochrome P-450 (CYP) 2D6 in the Caucasian population that affect the metabolism of many commonly used drugs. We used this method to genotype 91 patients under paroxetine therapy. The presence and the constitution of the most common single-nucleotide polymorphisms (1846G>A, 2988G>A, 100C>T, 2549delA, 2615_2617delAAG, and 1707delT) in poor and intermediate metabolizers from the Caucasian population were detected in short amplicons (≤148 bp). After fluorescence normalization, the wild-type, homozygous, and heterozygous samples were easily distinguishable from each other by their specific melting curve shape. A total of 92.6% of the 1846G>A heterozygotes, 96% of the 100C>T heterozygotes, and 100% of the 2988G>A, 2549delA, 2615_2617delAAG, and 1707delT heterozygotes have been correctly distinguished from the wild types. One hundred percent of all the homozygotes in this group of patients have been detected without any error. HRM of short amplicons is a simple tool for effective, rapid, and reliable CYP2D6 genotyping that does not require real-time PCR, labeled probes, processing or any separations after PCR. The reaction is performed in a closed-tube system and is highly specific and sensitive. We proved that this technique is highly reliable for use in routine diagnostics.

The prevalence of loss of imprinting of H19 and IGF2 at birth

Imprinted genes are monoallelically expressed according to the parent of origin and are critical for proper placental and embryonic development. Disruption of methylation patterns at imprinted loci resulting in loss of imprinting (LOI) may lead to serious imprinting disorders (e.g., Beckwith-Wiedemann syndrome) and is described in some cancers (e.g., Wilms' tumor). As most research has focused on children with cancer or other abnormal phenotypes, the imprinting status in healthy infants at birth has not been characterized. We examined the prevalence of H19 and IGF2 LOI at birth by allele-specific expression assays analysis on 114 human individuals. Overall expression and methylation analyses were performed on a subset of samples. We found that LOI of H19 was observed for 4% of individuals in cord blood and 3.3% in placenta, and for IGF2 of 22% of individuals in the cord blood and 0% in placenta. Interestingly, LOI status did not correspond to aberrant methylation levels of the imprinted DMRs or with changes in overall gene expression for the majority of individuals. Our observations suggest that LOI is present in phenotypically healthy infants. Determining a "normal" human epigenotype range is important for discovering factors required to maintain a healthy pregnancy and embryonic development.