The TaqMan method for SNP genotyping

Interleukin-7 Risk Allele, Lymphocyte Counts, and Autoantibodies for Prediction of Risk of Immune-Related Adverse Events in Patients Receiving Atezolizumab plus Bevacizumab Therapy for Unresectable Hepatocellular Carcinoma

INTRODUCTION

Atezolizumab plus bevacizumab (AB) therapy was the effective immune checkpoint inhibitor (ICI) for unresectable hepatocellular carcinoma (u-HCC). However, immune-related adverse events (irAEs) are common in patients receiving ICI therapies. Our research aimed to explore the risk factors for irAE development, with attention to interleukin-7 (IL-7) risk alleles, lymphocyte counts, and autoantibodies.

METHODS

Seventy-six patients receiving AB therapy for u-HCC were recruited. Single nucleotide polymorphism genotyping was done for the analysis of rs16906115 polymorphism near IL-7-expressing genes using 20 μL of stored buffy coat at baseline. The association between IL-7 risk alleles, lymphocyte counts, autoantibodies, and irAE development was investigated.

RESULTS

irAEs were found in 14 (18%) patients. The incidence of irAEs did not differ significantly between the groups showing IL-7 AG/AA and the GG group (p = 0.72). The incidence in the group with a lymphocyte count of 1,130/µL or more at baseline was higher than in that with a value below 1,130/µL (p = 0.0093). The group showing IL-7 AG/AA or lymphocyte count >1,130/μL had a higher irAE prevalence rate than the others (p = 0.019). IL-7 AG/AA or lymphocyte count >1,130/μL and positivity for autoantibodies at baseline were the prognostic factors for irAE development. irAE incidence could be stratified using a combination of IL-7 AG/AA or lymphocyte counts ≥1,130/µL and positive autoantibodies (p = 0.016).

CONCLUSION

Patients with IL-7 risk alleles, high lymphocyte counts, and autoantibodies at baseline may require careful monitoring for irAE development.

Epistasis Between HLA-DRB1*16:02:01 and SLC16A11 T-C-G-T-T Reduces Odds for Type 2 Diabetes in Southwest American Indians

We sought to identify genetic/immunologic contributors of type 2 diabetes (T2D) in an indigenous American community by genotyping all study participants for both high-resolution HLA-DRB1 alleles and SLC16A11 to test their risk and/or protection for T2D. These genes were selected based on independent reports that HLA-DRB1*16:02:01 is protective for T2D and that SLC16A11 associates with T2D in individuals with BMI <35 kg/m2. Here, we test the interaction of the two loci with a more complete data set and perform a BMI sensitivity test. We defined the risk protection haplotype of SLC16A11, T-C-G-T-T, as allele 2 of a diallelic genetic model with three genotypes, SLC16A11*11, *12, and *22, where allele 1 is the wild type. Both earlier findings were confirmed. Together in the same logistic model with BMI ≥35 kg/m2, DRB1*16:02:01 remains protective (odds ratio [OR] 0.73), while SLC16A11 switches from risk to protection (OR 0.57 [*22] and 0.78 [*12]); an added interaction term was statistically significant (OR 0.49 [*12]). Bootstrapped (b = 10,000) statistical power of interaction, 0.4801, yielded a mean OR of 0.43. Sensitivity analysis demonstrated that the interaction is significant in the BMI range of 30-41 kg/m2. To investigate the epistasis, we used the primary function of the HLA-DRB1 molecule, peptide binding and presentation, to search the entire array of 15-mer peptides for both the wild-type and ancient human SLC16A11 molecules for a pattern of strong binding that was associated with risk and protection for T2D. Applying computer binding algorithms suggested that the core peptide at SLC16A11 D127G, FSAFASGLL, might be key for moderating risk for T2D with potential implications for type 1 diabetes.

ARTICLE HIGHLIGHTS

Techniques, procedures, and applications in host genetic analysis

This chapter overviews genetic techniques' fundamentals and methodological features, including different approaches, analyses, and applications that have contributed to advancing health and disease. The aim is to describe laboratory methodologies and analyses employed to understand the genetic landscape of different biological contexts, from conventional techniques to cutting-edge technologies. Besides describing detailed aspects of the polymerase chain reaction (PCR) and derived types as one of the principles for many novel techniques, we also discuss microarray analysis, next-generation sequencing, and genome editing technologies such as transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems. These techniques study several phenotypes, ranging from autoimmune disorders to viral diseases. The significance of integrating diverse genetic methodologies and tools to understand host genetics comprehensively and addressing the ethical, legal, and social implications (ELSI) associated with using genetic information is highlighted. Overall, the methods, procedures, and applications in host genetic analysis provided in this chapter furnish researchers and practitioners with a roadmap for navigating the dynamic landscape of host-genome interactions.

Pharmacogenetics of Biochemically Verified Abstinence in an Opioid Agonist Therapy Randomized Clinical Trial of Methadone and Buprenorphine/Naloxone

Methadone and buprenorphine/naloxone are opioid agonist therapies for opioid use disorder treatment. Genetic factors contribute to individual differences in opioid response; however, little is known regarding genetic associations with clinical outcomes in people receiving opioid agonist therapies. Participants diagnosed with opioid use disorder, principally consisting of prescription opioids (licit or illicit), were randomized to methadone or buprenorphine/naloxone for 24 weeks of daily treatment (NCT03033732). Urine was collected at 12 biweekly study visits and analyzed for non-treatment opioids. Variants in genes involved in methadone metabolism (CYP2B6, CYP2C19, and CYP3A4), buprenorphine metabolism (CYP3A4 and UGT2B7), and μ-opioid receptor function (OPRM1) were genotyped and analyzed for their association with the number of non-treatment opioid-free urine screens. Primary analyses focused on the last 12 weeks (6 study visits, post-titration) of treatment among those reporting White ethnicity. Additional sensitivity and exploratory analyses were performed. Among methadone-treated participants (n = 52), the OPRM1 rs1799971 AA genotype (vs. G-genotypes, i.e., having one or two G alleles) was associated with greater opioid-free urine screens (incidence rate ratio = 5.24, 95% confidence interval (CI) = 2.43-11.26, P = 0.000023); longitudinal analyses showed a significant genotype-by-time interaction over the full 24 weeks (12 study visits, β = -0.28, 95% CI = -0.45 to -0.11, P = 0.0015). Exploratory analyses suggest an OPRM1 rs1799971 genotype effect on retention. No evidence of association was found between other genetic variants, including in metabolic variants, and non-treatment opioid-free urine screens in the methadone or buprenorphine/naloxone arms. Those with the OPRM1 rs1799971 G-genotypes may have a poorer response to methadone maintenance treatment, an effect that persisted through 24 weeks of treatment.

Low-dose daily folic acid (400 μg) supplementation does not affect regulation of folate transporters found present throughout the terminal ileum and colon of humans: a randomized clinical trial

BACKGROUND

Folic acid supplementation during the periconceptional period reduces the risk of neural tube defects in infants, but concern over chronic folic acid exposure remains. An improved understanding of folate absorption may clarify potential risks. Folate transporters have been characterized in the small intestine, but less so in the colon of healthy, free-living humans. The impact of folic acid fortification or supplementation on regulation of these transporters along the intestinal tract is unknown.

OBJECTIVE

The objective was to characterize expression of folate transporters/receptor (FT/R) and folate hydrolase, glutamate carboxypeptidase II (GCPII), from the terminal ileum and throughout the colon of adults and assess the impact of supplemental folic acid.

METHODS

In this 16-wk open-labeled randomized clinical trial, adults consumed a low folic acid-containing diet, a folate-free multivitamin, and either a 400 μg folic acid supplement or no folic acid supplement. Dietary intakes and blood were assessed at baseline, 8 wk, and 16 wk (time of colonoscopy). Messenger RNA (mRNA) expression and protein expression of FT/R and GCPII were assessed in the terminal ileum, cecum, and ascending and descending colon.

RESULTS

Among 24 randomly assigned subjects, no differences in dietary folate intake or blood folate were observed at baseline. Mean ± SD red blood cell folate at 16 wk was 1765 ± 426 and 911 ± 242 nmol/L in the 400 and 0 μg folic acid group, respectively (P < 0.0001). Reduced folate carrier, proton-coupled folate transporter, and folate-receptor alpha expression were detected in the terminal ileum and colon, as were efflux transporters of breast cancer resistance protein and multidrug resistance protein-3. Other than a higher mRNA expression of FR-alpha and GCPII in the 400 μg supplement group in the ascending colon, no treatment differences were observed (P < 0.02).

CONCLUSIONS

Folate transporters are present throughout the terminal ileum and colon; there is little evidence that a low dose of folic acid supplementation affects colonic absorption. This trial was registered at clinicaltrials.gov as NCT03421483.

Physical Exercise and Serum BDNF Levels: Accounting for the Val66Met Polymorphism in Older Adults

BACKGROUND

Brain-derived neurotrophic factor (BDNF) expression, which can be measured in blood serum, has been found to increase with aerobic exercise. The link between BDNF level, physical exercise, and genetic status (Val66Met polymorphism) has not been well researched in older adults.

OBJECTIVE

To investigate the possible link between BDNF expression, acute aerobic exercise, and the Val66Met polymorphism in older adults.

METHOD

Twenty-three healthy older adults participated in one session of acute aerobic exercise. Their serum BDNF levels were measured both at baseline and post exercise. Saliva samples were collected to identify each individual's genetic status.

RESULTS

At baseline, the individuals' mean serum BDNF level was 16.03 ng/mL (Val66Val = 15.89 ng/mL; Val66Met = 16.34 ng/mL); post exercise, the individuals' mean serum BDNF level was 16.81 ng/mL (Val66Val = 16.14 ng/mL; Val66Met = 18.34 ng/mL).

CONCLUSION

One session of acute aerobic exercise significantly increased the individuals' mean serum BDNF level. Males had higher BDNF levels than females. There was a significant interaction between gender and BDNF expression post exercise and a significant between-group effect of gender. The Val66Met carriers had a more positive response to the acute aerobic exercise compared with the Val66Val carriers, although without a significant difference between the two groups.

Development of TaqMan PCR assay for genotyping SNP rs211250281 of the bovine agpat6 gene

Milk fat percentage is an important production trait of dairy cattle and is one of the goals of breeding programs. Over 95% of the milk fat accounts for triacylglycerols. AGPAT6 (1-acylglycerol-3-phosphate O-acyltransferase 6) catalyzes an intermediary step of triglyceride synthesis in the mammary cells. Genome-wide association studies identified SNP rs211250281 (g27: 36520069 G/T) in the agpat6 gene associated with milk fat content and fat-to-protein ratio in dairy cattle. The article presents data on the development of TaqMan PCR assay for genotyping SNP rs211250281 of the bovine agpat6 gene. In this method, a primer pair, initiating amplification of 75-bp fragments of the agpat6 gene, and two allele-specific TaqMan probes are used. Identification of the G and T alleles is based on a comparison of the final fluorescence intensity of FAM and VIC dyes, respectively. The developed TaqMan PCR assay was validated by Sanger sequencing method. The results of both methods fully coincided, that confirmed high accuracy of the developed TaqMan PCR assay. This reliable, simple, rapid, and high-throughput method could be a suitable tool for studying the distribution of the SNP rs211250281 among different cattle breeds and its association with milk fat content.

GJB2 p.V37I Mutation Associated With Moderate Nonsyndromic Hearing Loss in an Adult Taiwanese Population

BACKGROUND

Gap junction protein beta 2 ( GJB2 ) p.V37I mutations are the most important hereditary cause of sensorineural hearing loss (SNHL) in Taiwan. Hearing outcomes are associated with hearing levels at baseline and the duration of follow-up. However, the audiological features of GJB2 p.V37I mutations in the adult population are unknown. The objectives of the present study were to investigate the audiological features, progression rate, and allele frequency of GJB2 p.V37I mutations among an adult Taiwanese population.

METHODS

Subjects of this case-control study were chosen from 13,580 participants of the Taiwan Precision Medicine Initiative. The genetic variations of GJB2 p.V37I were determined by polymerase chain reaction. We analyzed existing pure-tone threshold data from 38 individuals who were homozygous or compound heterozygotes for GJB2 p.V37I, 129 who were heterozygotes, and 602 individuals who were wild-type. Phenome-wide association studies (PheWAS) analysis was also performed to identify phenotypes associated with GJB2 p.V37I.

RESULTS

The minor allele frequency of GJB2 p.V37I was 0.92% in our study population. The mean hearing level of participants with a p.V37I mutation indicated moderate to severe hearing loss with 38.2% ± 22.3% binaural hearing impairment. GJB2 p.V37I was associated with an increased risk of hearing disability (odds ratio: 21.46, 95% confidence interval: 8.62 to 53.44, p < 0.001) in an autosomal recessive pattern. In addition, PheWAS discovered a significant association between GJB2 p.V37I and fracture of the humerus. GJB2 p.V37I is a pathogenic and prevalent variant of SNHL among the adult population.

CONCLUSIONS

The present study recommends patients with known GJB2 p.V37I mutations receive regular audiometric evaluation and genetic counseling. Early assistive listening device intervention is suggested to improve the quality of hearing.

Rapid and accurate genotyping of human SNP rs671 in aldehyde dehydrogenase 2 gene using one-step CRISPR/Cas12b assay without DNA amplification

BACKGROUND

The SNP rs671 of Human aldehyde dehydrogenase (ALDH) is G-A transition at 1510th nucleotides, which is an important clinical indicator of alcoholic liver disease, digestive tract cancer and some drug efficiency. The commonly used genotyping assay of this polymorphism is relatively time-consuming and costly.

FINDING

This study develops a rapid and accurate one-step CRISPR/Cas12b assay to distinguish the G1510A polymorphism of human ALDH2 free of DNA amplification. The method we established requires only one step of adding 1 μl genomic DNA sample to premixed system, and waiting for the acquisition of fluorescent signal, taking approximate 30 min.

CONCLUSIONS

This method provides a potential tool for more accurate and reliable nucleic acid detection with a single base difference and supports the relevant disease diagnosis and personalized medicine.

Development and authentication of Panax ginseng cv. Sunhong with high yield and multiple tolerance to heat damage, rusty roots and lodging

Ginseng (Panax ginseng) has been used as a valuable medicinal plant in Asia, and the demand for ginseng production for health functional food is increasing worldwide after the COVID-19 crisis. Although a number of cultivars have been developed to increase ginseng production, none of them were widely cultivated in Korea because they could not resist various environmental stresses while being grown in one place for at least 4 years. To address this, Sunhong was developed as a ginseng cultivar with high yield and multiple stress tolerance by pure line selection. Sunhong showed high yield and heat tolerance comparable to Yunpoong, a representative high-yielding cultivar, and exhibited 1.4 times lower prevalence of rusty roots than Yunpoong, suggesting that Sunhong can keep its high yield and quality during long-term cultivation. In addition, distinct color and lodging resistance were expected to increase the convenience of cultivation. To supply pure seeds to farmers, we also established a reliable high-throughput authentication system for Sunhong and seven ginseng cultivars through genotyping-by-sequencing (GBS) analysis. The GBS approach enabled to identify a sufficient number of informative SNPs in ginseng, a heterozygous and polyploid species. These results contribute to the improvement of yield, quality, and homogeneity, and therefore promote the ginseng industry.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13580-023-00526-x.

A fully integrated nucleic acid analysis system for multiplex detection of genetic polymorphisms related to folic acid metabolism

A sufficient intake of folic acid is essential during pregnancy, but several genetic polymorphisms reduce its absorption, threaten the lives of pregnant women and cause congenital disabilities in newborns. Traditional laboratory detection of genetic variants related to folic acid metabolism is time-consuming and labor-intensive. Microfluidics-based molecular diagnosis integrates sample pre-processing and nucleic acid amplification on-chip to achieve rapid, sensitive, high-throughput, and automated detection. Here, we developed a fully integrated microfluidic system for the detection of genetic polymorphisms related to folic acid metabolism in a "sample in-answer out" style. The system consists of nucleic acid extraction and amplification modules. During nucleic acid extraction, blood cells are lysed, and DNA is captured and eluted through a silica-gel membrane. After that, multiple gene loci are detected using loop-mediated isothermal amplification (LAMP) and the color of the reaction chamber indicates whether genetic mutations are present. The experimental results demonstrate that the system can accurately detect gene polymorphisms associated with folic acid metabolism in blood samples with high sensitivity and no cross-contamination between chambers. The blood samples of five patients were tested for mutant alleles on this system, and the test results were consistent with qPCR and DNA sequencing observations. The operation is fully automated, and the detection is completed in approximately 70 minutes. The proposed system has great potential in prenatal diagnosis and other types of nucleic acid detection.

Association of primary knee osteoarthritis with DVWA SNP in a group of Egyptian population: a case–control study

Background

Osteoarthritis (OA) is a highly prevalent medical condition which represents a high impact on public health. In addition, the underlying etiology still has been unelucidated. Osteoarthritis is a multifactorial disease with a high genetic predisposition. Identification of genes associated with higher OA predisposition can assist in elucidating the underlying molecular mechanisms as well as detecting possible areas for gene-targeted OA therapies. Among these genetic targets, double Von Willebrand factor domain A (DVWA) has been shown to be related to β-tubulin protein interaction which is considered a protecting factor from OA development. Studies have shown a reduction in protein binding strength with single-nucleotide polymorphism (SNP) rs11718863 in the Von Willebrand factor domain A (VWA domain). Development of weakness between β-tubulin and the wild protein has been linked with increased risk of OA development. We aimed to investigate the association between primary knee OA susceptibility and severity with DVWA rs11718863 SNP among a subset of Egyptian population.

Results

There was no statistically significant difference in the incidence of AA, AT and TT genotypes frequencies between patient group and control group (P = 0.502). There was no statistically significant difference between different genotypes of DVWA rs11718863 SNP as regards the radiological assessment of different knee joint compartments using Kellgren Lawrence scale (P = 0.960 for medial tibiofemoral compartment), (P = 0.260 for lateral tibiofemoral compartment) and (P = 0.597 for patellofemoral compartment).

Conclusions

DVWA rs11718863 SNP was not demonstrated to influence OA susceptibility and severity among the studied Egyptian population subset. Larger sample size with inclusion of more genetic variants of DVWA SNP would be necessary to support the presence or absence of any relationship between DVWA SNP and OA.

Association between primary osteoarthritis and ADAMTS14 single nucleotide polymorphism in Egyptian population: a case-control study

Background

Primary osteoarthritis is considered one of the most common and the most studied musculoskeletal disorder. Nevertheless, the risk factors remain unclear. A disintegrin and metalloproteinase with thrombospondin motifs (ADAMTS) 14 (ADAMTS14) gene is involved in the cleavage of amino-terminal propeptides from type II procollagen, a necessary step in the formation of collagen fibers. The abnormal metabolism of collagen fibers type II leads to a decreased mechanical strength of joint cartilage which is one of the most important contributing factors to joint osteoarthritis. We aimed at investigating the association between primary osteoarthritis and ADAMTS14 gene rs4747096 single nucleotide polymorphism in a sample of Egyptian patients and analyzing the relationship between this genetic polymorphism with the severity of osteoarthritis. Sixty-five Egyptian patients who fulfilled the American College of Rheumatology criteria for primary knee osteoarthritis were compared with thirty-one apparently healthy subjects. Genotyping was performed by TaqMan single nucleotide polymorphism genotyping assay.

Results

There was a statistically significantly higher frequency of AA genotype among osteoarthritis patients compared to the control group (P = 0.004). The number of affected hand joints was significantly higher among patients with ADAMTS14 AA genotype in comparison to patients with ADAMTS14 AG genotype (P = 0.002). In addition, AA genotype was associated with statistically significantly higher Kellgren-Lawrence radiological grades in the knee and hand joints (proximal interphalangeal and thumb interphalangeal joints) (P = 0.037, 0.003, and 0.030 respectively).

Conclusion

The study showed an association between the AA genotype of ADAMTS14 gene rs4747096 single nucleotide polymorphism with knee and hand osteoarthritis and osteoarthritis severity in these joints. The AA genotype of ADAMTS14 gene rs4747096 single nucleotide polymorphism could be implicated in the increased incidence of primary osteoarthritis development and elevated disease severity among the Egyptian population.

CHRIST: CD44-Incorporated Hepatocellular Carcinoma Risk Index Scoring Tool—A Novel Prognostic Scoring System for Hepatocellular Carcinoma Development and Aggressiveness

CD44 has been demonstrated to play a pivotal role in regulating tumor cell progression, including hepatocellular carcinoma (HCC) development. Here, we aimed to establish a scoring system to evaluate the risk of developing HCC utilizing CD44-rs187115 SNP polymorphism. A prospective cohort of 120 individuals was enrolled in four groups: 19 non-metastatic HCC patients, 21 metastatic, 40 patients with hepatitis C-related cirrhosis, and 40 controls. Allelic discrimination of the CD44-rs187115 gene polymorphism was assessed using TaqMan genotyping assay. HCC patients with CT/CC genotypes were more likely to have aggressive malignancy compared to TT carriers. A significant correlation was noted between the existence of CT/CC genotypes and tumor size, multicentricity, infiltration, portal vein thrombosis, and metastasis. A CD44-incorporated Hepatocellular Carcinoma Risk Index Scoring Tool (CHRIST) was formulated utilizing clinical and genetic variables. A score > 3 for HCC development demonstrated 87.5% sensitivity, 72.5% specificity, and a 76% positive predictive value (PPV) and 85% negative predictive value (NPV). Furthermore, a score > 5 for HCC metastasis demonstrated 90.4% sensitivity, 68.4% specificity, a 76% PPV and 86% NPV. A similarly significant score was noted following a six-month re-evaluation. We conclude that CD44-rs187115 may serve as a reliable prognostic biomarker for HCC and that the CHRIST prognostic model is highly predictive of the development of HCC and metastatic HCC.

Multiplex SNP Genotyping Using SWITCH: Sequence-Specific Nanoparticle with Interpretative Toehold-Mediated Sequence Decoding in Hydrogel

Single nucleotide polymorphisms (SNPs) that can alter phenotypes of individuals play a pivotal role in disease development and, more importantly, responses to therapy. However, SNP genotyping has been challenging due to the similarity of SNP alleles and their low concentration in biological samples. Sequence-specific nanoparticle with interpretative toehold-mediated sequence decoding in hydrogel (SWITCH) for multiplex SNP genotyping is presented. The encoding with gold nanoparticle probes transduces each SNP target to ≈1000 invaders with prominently different sequences between wild and mutant types, featuring polymerase chain reaction (PCR)-free amplification. Subsequently, the toehold-mediated DNA replacement in hydrogel microparticles decodes the invaders via SNP-specific fluorescence signals. The 4-plex detection of the warfarin-associated SNP targets spiked in commercially validated human serum (S1-100ML, Merck) is successfully demonstrated with excellent specificity. This work is the first technology development presenting PCR-free, multiplex SNP genotyping with a single reporting fluorophore, to the best of knowledge.

Validation of a multi-gene qPCR-based pharmacogenomics panel across major ethnic groups in Singapore and Indonesia

Aim: The clinical utility of pharmacogenomics (PGx) has been gaining traction alongside growing evidence that adverse drug reactions (ADRs) have significant genetic associations. Nala PGx Core^® is a multi-gene qPCR-based panel of 20 allele variants, comprising 18 SNPs and two CYP2D6 copy number markers across four pharmacogenes - CYP2C9, CYP2C19, CYP2D6 and SLCO1B1. Methods: In this study, we validated the performance of Nala PGx Core^® against benchmark methods, on the Singaporean and Indonesian populations. Results & conclusion: Nala PGx Core^® demonstrated robust and accurate genotyping when compared with other established benchmarks. Furthermore, the panel successfully characterized alleles of clinical relevance, such as CYP2D6*10 and CYP2D6*36, across major ethnic groups present of Singapore and Indonesia, suggesting its potential for adoption in clinical workflows regionally.

Validation of Single Nucleotide Variant Assays for Human Leukocyte Antigen Haplotypes HLA-B*15:02 and HLA-A*31:01 Across Diverse Ancestral Backgrounds

The human leukocyte antigen haplotypes HLA-B*15:02 and HLA-A*31:01 have been linked to life-threatening adverse drug reactions to the anticonvulsants carbamazepine and oxcarbazepine. Identification of these haplotypes via pharmacogenetic techniques facilitates implementation of precision medicine to prevent such reactions. Using reference samples from diverse ancestral origins, we investigated the test analytical validity (i.e., ability to detect whether or not the haplotypes were present or absent) of TaqMan assays for single nucleotide variants previously identified as potentially being able to "tag" these haplotypes. A TaqMan custom assay for rs10484555 and an inventoried assay for rs17179220 and were able to identify with 100% sensitivity and 100% specificity HLA-B*15:02 and HLA-A*31:01 respectively. A custom assay for rs144012689 that takes into account a neighboring single nucleotide variant with manual calling was also able to identify HLA-B*15:02 with 100% sensitivity and 100% specificity. A custom assay for rs106235 identified HLA-A*31:01 with 100% sensitivity and 95% specificity. The slight reduction in specificity for the latter was owing to another haplotype (HLA-A*33:03) also being detected. While any positive call using the rs106235 assay could therefore be further investigated, as the presence of the HLA-A*31:01 haplotype confers adverse drug reaction risk, the absence of false negatives (indexed by sensitivity) is more important than false positives. In summary, we present validated TaqMan assay methodology for efficient detection of HLA haplotypes HLA-B*15:02 and HLA-A*31:01. Our data are relevant for other genotyping technologies that identify, or have the potential to identify, these haplotypes using single nucleotide variants.

Molecular sexing of degraded DNA from elephants and mammoths: a genotyping assay relevant both to conservation biology and to paleogenetics

It is important to determine the sex of elephants from their samples-faeces from the field or seized ivory-for forensic reasons or to understand population demography and genetic structure. Molecular sexing methods developed in the last two decades have often shown limited efficiency, particularly in terms of sensitivity and specificity, due to the degradation of DNA in these samples. These limitations have also prevented their use with ancient DNA samples of elephants or mammoths. Here we propose a novel TaqMan-MGB qPCR assay to address these difficulties. We designed it specifically to allow the characterization of the genetic sex for highly degraded samples of all elephantine taxa (elephants and mammoths). In vitro experiments demonstrated a high level of sensitivity and low contamination risks. We applied this assay in two actual case studies where it consistently recovered the right genotype for specimens of known sex a priori. In the context of a modern conservation survey of African elephants, it allowed determining the sex for over 99% of fecal samples. In a paleogenetic analysis of woolly mammoths, it produced a robust hypothesis of the sex for over 65% of the specimens out of three PCR replicates. This simple, rapid, and cost-effective procedure makes it readily applicable to large sample sizes.

Genomic Characterization of Antimicrobial Resistance in Food Chain and Livestock-Associated Salmonella Species

The rising trend of antimicrobial resistance (AMR) by foodborne bacteria is a public health concern as these pathogens are easily transmitted to humans through the food chain. Non-typhoid Salmonella spp. is one of the leading foodborne pathogens which infect humans worldwide and is associated with food and livestock. Due to the lack of discovery of new antibiotics and the pressure exerted by antimicrobial resistance in the pharmaceutical industry, this review aimed to address the issue of antibiotic use in livestock which leads to AMR in Salmonella. Much attention was given to resistance to carbapenems and colistin which are the last-line antibiotics used in cases of multi drug resistant bacterial infections. In the present review, we highlighted data published on antimicrobial resistant Salmonella species and serovars associated with livestock and food chain animals. The importance of genomic characterization of carbapenem and colistin resistant Salmonella in determining the relationship between human clinical isolates and food animal isolates was also discussed in this review. Plasmids, transposons, and insertion sequence elements mediate dissemination of not only AMR genes but also genes for resistance to heavy metals and disinfectants, thus limiting the therapeutic options for treatment and control of Salmonella. Genes for resistance to colistin (mcr-1 to mcr-9) and carbapenem (blaVIM-1, blaDNM-1, and blaNDM-5) have been detected from poultry, pig, and human Salmonella isolates, indicating food animal-associated AMR which is a threat to human public health. Genotyping, plasmid characterization, and phylogenetic analysis is important in understanding the epidemiology of livestock-related Salmonella so that measures of preventing foodborne threats to humans can be improved.

Identification of Echinococcus granulosus Genotypes G1 and G3 by SNPs Genotyping Assays

Echinococcus granulosus sensu lato (s.l.) is the causative agent of cystic echinococcosis in animals and humans. Different E. granulosuss.l. genotypes exhibit great diversity in their life cycle, host selectivity and pathogenicity. For this reason, the study of genetic variation within Echinococcus species is of importance for their epidemiological implication. We employed two SNP genotyping technologies to distinguish G1 and G3 E. granulosus sensu stricto (s.s.). genotypes. The genotypes of DNA samples (n = 28) extracted from hydatid cysts of different animal species were identified by amplification and sequencing of a fragment of the mitochondrial nad5 gene. Two SYBR green and three TaqMan real time PCR assays were developed for targeting of three nad5 informative positions (SNP758, 1123, and 1380) known to be able to discriminate G1 from G3. Genotyping by SYBR Green PCR based on cycle threshold (Ct) with melting temperature (Tm) analysis and performed on SNP1123 and SNP1380 failed to identify one DNA sample. TaqMan assays for SNP758, 1123 and 1380 effectively confirmed genotype identification obtained by Sanger sequencing. Our results demonstrated that the combination of the three Taqman assays developed in this study represents a valuable and cost effective tool alternative to DNA sequencing for E. granulosus s.s. genotyping.

A breeding strategy to identify modifiers of high genetic risk for methamphetamine intake

Trace amine-associated receptor 1 (Taar1) impacts methamphetamine (MA) intake. A mutant allele (Taar1^m1J ) derived from the DBA/2J mouse strain codes for a non-functional receptor, and Taar1^m1J/m1J mice consume more MA than mice possessing the reference Taar1⁺ allele. To study the impact of this mutation in a genetically diverse population, heterogeneous stock-collaborative cross (HS-CC) mice, the product of an eight-way cross of standard and wild-derived strains, were tested for MA intake. HS-CC had low MA intake, so an HS-CC by DBA/2J strain F2 intercross was created to transfer the mutant allele onto the diverse background, and used for selective breeding. To study residual variation in MA intake existing in Taar1^m1J/m1J mice, selective breeding for higher (MAH) vs lower (MAL) MA intake was initiated from Taar1^m1J/m1J F2 individuals; a control line of Taar1^+/+ individuals (MAC) was retained. The lines were also examined for MA-induced locomotor and thermal responses, and fluid and tastant consumption. Taar1^m1J/m1J F2 mice consumed significantly more MA than Taar1^+/+ F2 mice. Response to selection was significant by generation 2 and there were corresponding differences in fluid consumed. Fluid consumption was not different in non-MA drinking studies. Taar1^m1J/m1J genotype (MAL or MAH vs MAC mice) was associated with heighted MA locomotor and reduced hypothermic responses. MAL mice exhibited greater sensitization than MAH mice, but the selected lines did not consistently differ for thermal or tastant phenotypes. Residual variation among high-risk Taar1^m1J/m1J mice appears to involve mechanisms associated with neuroadaptation to MA, but not sensitivity to hypothermic effects of MA.

Differential genetic risk for methamphetamine intake confers differential sensitivity to the temperature-altering effects of other addictive drugs

Mice selectively bred for high methamphetamine (MA) drinking (MAHDR), compared with mice bred for low MA drinking (MALDR), exhibit greater sensitivity to MA reward and insensitivity to aversive and hypothermic effects of MA. Previous work identified the trace amine-associated receptor 1 gene (Taar1) as a quantitative trait gene for MA intake that also impacts thermal response to MA. All MAHDR mice are homozygous for the mutant Taar1 m1J allele, whereas all MALDR mice possess at least one copy of the reference Taar1 + allele. To determine if their differential sensitivity to MA-induced hypothermia extends to drugs of similar and different classes, we examined sensitivity to the hypothermic effect of the stimulant cocaine, the amphetamine-like substance 3,4-methylenedioxymethamphetamine (MDMA), and the opioid morphine in these lines. The lines did not differ in thermal response to cocaine, only MALDR mice exhibited a hypothermic response to MDMA, and MAHDR mice were more sensitive to the hypothermic effect of morphine than MALDR mice. We speculated that the μ-opioid receptor gene (Oprm1) impacts morphine response, and genotyped the mice tested for morphine-induced hypothermia. We report genetic linkage between Taar1 and Oprm1; MAHDR mice more often inherit the Oprm1 D2 allele and MALDR mice more often inherit the Oprm1 B6 allele. Data from a family of recombinant inbred mouse strains support the influence of Oprm1 genotype, but not Taar1 genotype, on thermal response to morphine. These results nominate Oprm1 as a genetic risk factor for morphine-induced hypothermia, and provide additional evidence for a connection between drug preference and drug thermal response.

Genotyping on blood and buccal cells using loop-mediated isothermal amplification in healthy humans

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Genetic variations contribute to phenotypic individual vulnerabilities to sleep debt.

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LAMP-MC is a recently developed method to characterize Single Nucleotide Polymorphism.

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Detection is performed directly from whole blood or buccal cells.

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LAMP-MC method produced specific melting curves for 5 sleep debt-related SNPs.

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High concordance of results was observed between LAMP-MC and Taqman referent method.

Genetic variations contribute to phenotypic individual vulnerabilities to sleep debt, particularly for five single nucleotide polymorphisms (SNPs). Loop-mediated isothermal amplification and melting curve analysis (LAMP-MC) is a recently developed method to characterize SNPs. The aim of present study was to evaluate the LAMP-MC method on blood and buccal cells for detection of five SNPs of interest in healthy humans.

We first analyzed signals obtained from LAMP-MC method on 42 samples. Then we compared the results with those of referent TaqMan method.

The LAMP-MC method produced specific melting curves for the five SNPs. A high concordance of genotyping results was observed between the two methods for rs5751876_ADORA2A, rs1800629_TNF-α, rs73598374_ADA and rs228697_PER3 in blood and saliva (Cohen’s kappa coefficient >0.80). A good agreement ( = 0.61) was observed for rs4680_COMT in blood only.

LAMP-MC is a simple and reliable method to study genetic influences on health, sleep debt-related performance impairments and countermeasures.

Towards low cost, multiplex clinical genotyping: 4-fluorescent Kompetitive Allele-Specific PCR and its application on pharmacogenetics

Single-nucleotide polymorphisms (SNPs) is associated with efficacy of specific drugs. Although there are several methods for SNP genotyping in clinical settings, alternative methods with lower cost, higher throughout and less complexity are still needed. In this study, we modified Kompetitive Allele Specific PCR to enable multiplex SNP genotyping by introducing additional fluorescent cassettes that specifically help to differentiate more amplification signals in a single reaction. This new format of assay achieved a limit of detection down to 310 copies/ reactions for simultaneous detection of 2 SNPs with only standard end-point PCR workflow for synthetic controls, and genotyped 117 clinical samples with results that were in 100% agreement with hospital reports. This study presented a simplified, cost-effective high-throughput SNP genotyping alternative for pharmacogenetic variants, and enabled easier access to pharmaceutical guidance when needed.

Analysis of Anti-RNA Polymerase III Antibody-positive Systemic Sclerosis and Altered GPATCH2L and CTNND2 Expression in Scleroderma Renal Crisis

OBJECTIVE

Scleroderma renal crisis (SRC) is a life-threatening complication of systemic sclerosis (SSc) strongly associated with anti-RNA polymerase III antibody (ARA) autoantibodies. We investigated genetic susceptibility and altered protein expression in renal biopsy specimens in ARA-positive patients with SRC.

METHODS

ARA-positive patients (n = 99) with at least 5 years' follow-up (49% with a history of SRC) were selected from a well characterized SSc cohort (n = 2254). Cases were genotyped using the Illumina Human Omni-express chip. Based on initial regression analysis, 9 single-nucleotide polymorphisms (SNP) were chosen for validation in a separate cohort of 256 ARA-positive patients (40 with SRC). Immunostaining of tissue sections from SRC or control kidney was used to quantify expression of candidate proteins based upon genetic analysis of the discovery cohort.

RESULTS

Analysis of 641,489 SNP suggested association of POU2F1 (rs2093658; P = 1.98 × 10^-5), CTNND2 (rs1859082; P = 5.58 × 10^-5), HECW2 (rs16849716; P = 1.2 × 10^-4), and GPATCH2L (rs935332; P = 4.92 × 10^-5) with SRC. Further, the validation cohort showed an association between rs935332 within the GPATCH2L region, with SRC (P = 0.025). Immunostaining of renal biopsy sections showed increased tubular expression of GPATCH2L (P = 0.026) and glomerular expression of CTNND2 (P = 0.026) in SRC samples (n = 8) compared with normal human kidney controls (n = 8), despite absence of any genetic replication for the associated SNP.

CONCLUSION

Increased expression of 2 candidate proteins, GPATCH2L and CTNND2, in SRC compared with control kidney suggests a potential role in pathogenesis of SRC. For GPATCH2L, this may reflect genetic susceptibility in ARA-positive patients with SSc based upon 2 independent cohorts.

Typing and determination of SNP functional gene based on highly selective and signal-amplified fluorescence double-probe with the help of ExoIII nuclease and magnetic bead

We have developed a fluorescence double-probe detection system with signal amplification for simple typing and determination of single nucleotide polymorphism (SNP) functional gene based on non-sequence dependence of ExoIII nuclease on dsDNA and rapid separation of magnetic bead. Matched detected gene can cyclically release abundant fluorescence-labeled ssDNA from the probe and the corresponding measured fluorescence signal is amplified up to 6063 times. In this case, the probe cannot release the measured fluorescence signal for the point mutation gene and then the corresponding measured signal is inhibited. According to signal amplification and inhabitation of the probe, we proposed both an accurate genotyping approach with strong specificity and a sensitive determination approach with high selectivity for SNP functional gene. For qualitative genotyping, there are obvious genotype-based differences of measured fluorescence phenotypes among three kinds of the samples of the investigated SNP. The quantitative determinations of its wild-type gene and mutant gene have all a good linearity in the range from 0.5 to 500 pmol/L with the correlation coefficients R² of 0.9940 and 0.9911, and a high sensitivity with the detection limits of 0.11 and 0.20 pmol/L, respectively. Compared to the usual single-probe detection system, the developed double-probe system can achieve not only accurate genotyping but also the sensitive gene determination. Meanwhile, it is also a simple and reliable method for both quantitative and qualitative analysis of functional gene.

A derived Polymorphic Amplified Cleaved Sequence assay for detecting the Δ210 PPX2L codon deletion conferring target-site resistance to protoporphyrinogen oxidase-inhibiting herbicides

BACKGROUND

Resistance to protoporphyrinogen oxidase (PPO)-inhibiting herbicides in Amaranthus rudis from corn/soybean production systems in the USA appears to be mainly due to a codon deletion at position 210 of the target PPX2L gene. In this study, we have developed a simple and cost-effective derived Polymorphic Amplified Cleaved Sequenced (dPACS) marker for detecting this resistance-causing deletion in A. rudis and other relevant weed species.

RESULTS

Ninety-six plants from 16 diverse fomesafen-sensitive and resistant A. rudis populations from Illinois and Iowa were used to establish the dPACS procedure. The assay requires forced mismatches in both the forward and reverse PCR primers and uses the restriction enzyme XcmI for the positive identification of wild type glycine residue at PPX2L codon position 210. The data from the dPACS method, using either leaf tissues or seeds as starting material, were completely correlated with direct Sanger sequencing results for samples that gave readable nucleotide peaks around codon 210 of PPX2L. Furthermore, the assay was directly transferable to all four other Amaranthus species tested, and to Ambrosia artemisiifolia using species-specific primers.

CONCLUSION

The proposed assay will allow the rapid detection of the Δ210 codon deletion in the PPX2L gene and the timely development of management strategies for tackling growing resistance to PPO-inhibiting herbicides in A. rudis and other broadleaf weed species. © 2019 Society of Chemical Industry.

The genetic side of type 2 diabetes - A review

AIM

Type 2 diabetes (T2DM) is a complex disease. Interactions between genetic susceptible variants and environmental cues results in the development of this heterogenous disease. Having an understanding of the genetics of T2DM may lead to a better perspective and management of the pathogenesis contributing to T2DM.

MATERIALS AND METHODS

Published primary and secondary sources were reviewed covering the keywords "genetics + type 2 diabetes" using PubMed and Google Scholar as the main databases. Full articles were considered when the title and the abstract was found to be sufficiently related to the review's aim.

RESULTS

Various genetic aspects of T2DM were summarised including a general understanding of the heritability and heterogeneity of T2DM. Furthermore, an explanation of the different genetic modalities that can be used to identify T2DM susceptible genes was provided.

CONCLUSION

In this day and era, researchers and healthcare professionals working in the field of metabolic disorders should have an understanding of T2DM genetics. The future lies in preventive and management action plans targeting the combination of genetics and environmental risk factors for a better health outcome.

Tumor Necrosis Factor Alpha-308G/A Polymorphism and the Risk of Multiple Myeloma: A Meta-Analysis of Pooled Data from Twelve Case-Control Studies

Objective:

Tumor necrosis factor alpha (TNF-α) is an important cytokine involved in inflammation, immune response, and other biological processes. The association between polymorphism -308G/A in its promoter and the risk of multiple myeloma (MM) is not clear. Thus, we conducted a meta-analysis to clarify this question.

Materials and Methods:

Twelve eligible studies, which included 2204 MM cases and 3478 controls, were enrolled in our meta-analysis by searching the PubMed, China National Knowledge Infrastructure, Scopus, Web of Science, and Google Scholar databases up to December 2018. The effect of polymorphism -308G/A on MM risk was evaluated by calculating the pooled odds ratio (OR) and the 95% confidence interval (CI). Furthermore, the Q-test and I2 statistical analyses were used to estimate the degree of heterogeneity. Sensitivity analysis was conducted to test the robustness of the meta-analysis results. Publication bias was assessed by Egger’s test and visual inspection of a funnel plot.

Results:

In the dominant model, -308G/A polymorphism was associated with reduced MM risk (OR=0.80, 95% CI: 0.65-0.97), and it also demonstrated a significant protective effect with a pooled OR of 0.82 (95% CI: 0.68-0.99) in the Caucasian subgroup. Because of the limited number of individual studies with AA genotype carriers, only eight studies were included in the recessive model, and no significant difference was observed. Moreover, the meta-analysis of the allele frequency demonstrated that the A allele has a protective effect against MM risk with a pooled OR of 0.83 (95% CI: 0.69-0.99). Sensitivity analysis suggested that the synthesized effect size was not influenced by any individual study. Moreover, the Egger’s test statistical analysis suggested that publication bias was not obvious in the present analysis.

Conclusion:

Overall, the -308G/A polymorphism was associated with reduced MM risk in the dominant model and allele frequency. Further investigation is needed to gain better insight.

Physical exercise augmented cognitive behaviour therapy for older adults with generalised anxiety disorder (PEXACOG): study protocol for a randomized controlled trial

Background

Generalised anxiety disorder (GAD) is a frequent and severe anxiety disorder among older adults. GAD increases the risk of developing other disorders such as depression and coronary heart disease. Older adults with GAD exhibit a poorer response to cognitive behaviour therapy (CBT) compared to younger patients with GAD. The normal age-related cognitive decline can be a contributor to reduced treatment efficacy. One strategy for improving treatment efficacy is to combine CBT with adjunctive interventions targeted at improving cognitive functions. Physical exercise is a viable intervention in this regard. Increased levels of brain-derived neurotrophic factor may mediate improvement in cognitive function. The present study aims to investigate the proposed effects and mechanisms related to concomitant physical exercise.

Methods

The sample comprises 70 participants aged 60–75 years, who have GAD. Exclusion criteria comprise substance abuse and unstable medication; inability to participate in physical exercise; and conditions which precludes GAD as primary diagnosis. The interventions are individual treatment in the outpatient clinic at the local psychiatric hospital, with two experimental arms: (1) CBT + physical exercise and (2) CBT + telephone calls. The primary outcome measure is symptom reduction on the Penn State Worry Questionnaire. Other measures include questionnaires, clinical interviews, physiological, biological and neuropsychological tests. A subset of 40 participants will undergo magnetic resonance imaging (MRI). After inclusion, participants undergo baseline testing, and are subsequently randomized to a treatment condition. Participants attend five sessions of the add-on treatment in the pre-treatment phase, and move on to interim testing. After interim testing, participants attend 10 sessions of CBT in parallel with continued add-on treatment. Participants are tested post-intervention within 2 weeks of completing treatment, with follow-up testing 6 and 12 months later.

Discussion

This study aims to develop better treatment for GAD in older adults. Enhancing treatment response will be valuable from both individual and societal perspectives, especially taking the aging of the general population into account.

Trial registration

ClinicalTrials.gov, NCT02690441. Registered on 24 February 2016.

Electronic supplementary material

The online version of this article (10.1186/s13063-019-3268-9) contains supplementary material, which is available to authorized users.

Linkage Analysis of the Chromosome 5q31-33 Region Identifies JAKMIP2 as a Risk Factor for Graves' Disease in the Chinese Han Population

Background

This study aimed to investigate susceptibility to Graves’s disease and the association with the 5q32–33.1 region on chromosome 5 in a Chinese Han population.

Material/Methods

Eighty Chinese Han multiplex families included first-degree and second-degree relatives with Graves’ disease. Eight microsatellite markers on chromosome 5 at the 5q32–33.1 region underwent linkage analysis and the association between the regions D5S1480–D5S2014 were studied.

Results

The maximal heterogeneity logarithm of the odds (HLOD) score of D5S2090 was 4.29 (α=0.42) and of D5S2014 was 4.01 (α=0.34). A nonparametric linkage (NPL) score of 3.14 (P<0.001) was found for D5S2014. The D5S1480–D5S2014 region on chromosome 5 was associated with Graves’ disease, with eight haplotype domains. There were significant differences in the sixth and eighth haplotype domains between patients with Graves’ disease compared with normal individuals. Tagging single nucleotide polymorphisms (SNPs) of the sixth and eighth haplotype domains showed that individuals with SNP62 (rs12653715 G/C) who were GG homozygous had a significantly increased risk of Graves’ disease compared GC heterozygous or CC homozygous individuals. The transmission disequilibrium test (TDT) indicated that SNP62 (rs12653715) and SNP63 (rs12653081) loci in the Janus kinase and microtubule interacting protein 2 (JAKMIP2) gene showed dominant transmission from heterozygous parents to the affected offspring, and SNPs in the secretoglobin family 3A member 2 (SCGB3A2) gene showed no transmission disequilibrium. The haplotype JAKMIP2-1 was identified as being particularly significant.

Conclusions

JAKMIP2 gene polymorphism require further study as potential risk factors for Graves’ disease in the Chinese Han population.

G994T polymorphism in exon 9 of plasma platelet-activating factor acetylhydrolase gene and lung ultrasound score as prognostic markers in evaluating the outcome of acute respiratory distress syndrome

The present study aimed to discover potential biomarkers for predicting the prognosis of acute respiratory distress syndrome (ARDS) in conjunction with lung ultrasound (LUS). Blood samples from 112 ARDS patients were collected to compare their partial oxygen pressure (PaO₂)/fraction of inspired oxygen (FiO₂), positive end-expiratory pressure (PEEP), lactic acid, sequential organ failure assessment (SOFA) score, clinical pulmonary infection score (CPIS) and APACHE II score. Kaplan-Meier plots and the log-rank test were performed to analyse the association between the platelet-activating factor acetylhydrolase (PAFAH) G994T polymorphism and the outcome of ARDS regarding mortality. A negative correlation between the LUS score and PaO₂/FiO₂, PEEP and lactic acid, as well as with the SOFA, CPIS and APACHE II score was confirmed with correlation coefficients of -0.493, -0.548, -0.642, -0.598, -0.566 and -0.567, respectively (all P<0.05). The activity of PAFAH and high-density lipoprotein-PAFAH in the serum collected from subjects of the GG genotype was similar to that in subjects of the GT genotype, but the low-density lipoprotein-PAFAH activity in the serum collected from GG subjects was significantly higher than that in GT subjects. An evident reduction in the PEEP, level of lactic acid, as well as the SOFA, CPIS and APACHE II score was observed in GG subjects, accompanied by a significantly increased PaO₂/FiO₂. Kaplan-Meier analysis indicated that subjects with a high LUS score had a significantly higher survival rate than those with a low LUS score, and the mortality risk for GG subjects was significantly lower than that for GT subjects. Finally, among all groups (genotype and LUS groups), GG subjects with a high LUS score had the lowest mortality risk, whereas GT subjects with a low LUS score had the highest mortality risk. In addition, the survival rate of GT subjects with a high LUS score was higher than that of GG subjects with a low LUS score. In conclusion, the combination of the LUS score and the G994T polymorphism in exon 9 of the PAFAH gene may be used as a potential prognostic marker for ARDS.

Rare Variant Quantitation Using Droplet Digital PCR

Droplet digital PCR (ddPCR) allows precise quantitation of individual copies of DNA. Using allele-specific fluorescent oligonucleotide probes, ddPCR can enumerate both mutant and wild-type alleles enabling highly sensitive detection and quantitation of the variant allele frequency of mutated genes. In this protocol, we describe a method for using ddPCR to detect mutations in genomic DNA with a sensitivity of up to 1 in 50,000 DNA copies.

Development of High-Throughput SNP Genotyping Assays for Rapid Detection of Strawberry Colletotrichum Species and the G143A Mutation

Colletotrichum spp. cause major diseases of strawberry and disease management depends on the species present. However, species identification based on symptoms and spore morphology is difficult. Therefore, development of molecular techniques for trustworthy and high-throughput identification of Colletotrichum spp. is vital for the accurate diagnosis. A high-resolution melting (HRM) assay was developed for simultaneous identification and differentiation of Colletotrichum spp. from fungal colonies or from symptomatic strawberry tissue. HRM markers were designed based on the internal transcribed spacer region of Colletotrichum acutatum and C. gloeosporioides from strawberry, and accurately identified and differentiated the two species. In addition, for the rapid detection of a single-nucleotide polymorphism (SNP) in the cytochrome b (cytb) gene of C. acutatum and C. gloeosporioides associated with resistance to quinone-outside inhibitor fungicides, an endpoint SNP genotyping analysis was developed. The HRM and endpoint SNP genotyping assays are useful methods that can be implemented in plant diagnostic clinics for the rapid and accurate identification of Colletotrichum spp. and detection of the G143A mutation in the cytb gene of C. acutatum and C. gloeosporioides.

Methylation in 3' near region of GC gene and its association with the level of vitamin D binding protein and type 2 diabetes mellitus

As the major vitamin D binding protein (DBP), the group-specific component (GC) plays an important role in the bioactivity of vitamin D. Abnormal expression of GC gene may be associated with vitamin D related disease, type 2 diabetes mellitus (T2DM). DNA methylation is an important regulator of gene expression. It has been reported that methylation in 3' untranslated region played a role in regulation of protein expression via interaction with miRNA. This study hypothesized that DNA methylation of 3' near region of GC gene (3'GC) might be associated with T2DM. The methylation status of the 3'GC was assessed with high resolution melt method. Logistic regression was applied to assess the risk of T2DM at different levels of 3'GC methylation. The results showed that methylation level of the 3'GC was higher in T2DM patients than in non-T2DM individuals (P=.038). There was a significant association between 3'GC methylation level and T2DM (adjusted OR 1.282; 95% CI 1.062-1.548; P=.01). The association was independent upon serum glucose and insulin (adjusted OR 1.561; 95% CI 1.083-2.249; P=.017). Furthermore, there was a positive correlation between methylation level and the level of DBP in T2DM patients (r=0.126, P=.036). The association was also significant after adjusting the potential impact of rs705117 (P=.044). Besides, a positive correlation between methylation level and the level of fasting serum insulin was observed in non-T2DM (r=0.101, P<.001). These results suggest that methylation status of the 3'GC is most likely associated with DBP expression, insulin secretion, and T2DM.

A Spontaneous Mutation in Taar1 Impacts Methamphetamine-Related Traits Exclusively in DBA/2 Mice from a Single Vendor

Major gene effects on traits associated with substance use disorders are rare. Previous findings in methamphetamine drinking (MADR) lines of mice, bred for high or low voluntary MA intake, and in null mutants demonstrate a major impact of the trace amine-associated receptor 1 (Taar1) gene on a triad of MA-related traits: MA consumption, MA-induced conditioned taste aversion and MA-induced hypothermia. While inbred strains are fundamentally genetically stable, rare spontaneous mutations can become fixed and result in new or aberrant phenotypes. A single nucleotide polymorphism in Taar1 that encodes a missense proline to threonine mutation in the second transmembrane domain (Taar1^m1J) has been identified in the DBA/2J strain. MA is an agonist at this receptor, but the receptor produced by Taar1^m1J does not respond to MA or endogenous ligands. In the present study, we used progeny of the C57BL/6J × DBA/2J F2 cross, the MADR lines, C57BL/6J × DBA/2J recombinant inbred strains, and DBA/2 mice sourced from four vendors to further examine Taar1-MA phenotype relations and to define the chronology of the fixation of the Taar1^m1J mutation. Mice homozygous for Taar1^m1J were found at high frequency early in selection for high MA intake in multiple replicates of the high MADR line, whereas Taar1^m1J homozygotes were absent in the low MADR line. The homozygous Taar1^m1J genotype is causally linked to increased MA intake, reduced MA-induced conditioned taste aversion, and reduced MA-induced hypothermia across models. Genotype-phenotype correlations range from 0.68 to 0.96. This Taar1 polymorphism exists in DBA/2J mice sourced directly from The Jackson Laboratory, but not DBA/2 mice sourced from Charles River (DBA/2NCrl), Envigo (formerly Harlan Sprague Dawley; DBA/2NHsd) or Taconic (DBA/2NTac). By genotyping archived samples from The Jackson Laboratory, we have determined that this mutation arose in 2001–2003. Our data strengthen the conclusion that the mutant Taar1^m1J allele, which codes for a non-functional receptor protein, increases risk for multiple MA-related traits, including MA intake, in homozygous Taar1^m1J individuals.

NPR-C gene polymorphism is associated with increased susceptibility to coronary artery disease in Chinese Han population: a multicenter study

To find a new locus that confers significant susceptibility to CAD in Chinese Han population, a genome-wide association study in 200 “extreme individuals” from a Shandong cohort and a pathway-based candidate gene study from a Shanghai cohort (293 CAD/293 controls) were simultaneously performed. Amongst them, 13 SNPs associated with CAD were selected to conduct validation and replication studies in additional 3363 CAD patients and 3148 controls. A novel locus rs700926 in natriuretic peptide receptor C (NPR-C) was identified in Shandong and Hubei cohorts. Then rs700926 and other nine tag SNPs were genotyped in four geographically different populations (Shandong, Shaanxi, Hubei and Sichuan cohorts), and 6 SNPs (rs700926, rs1833529, rs2270915, rs17541471, rs3792758 and rs696831) showed stronger association with CAD, regardless of single or combined analysis. We further genotyped rs2270915 and 10 additional tag SNPs in a central China cohort and identified rs12697273 and rs10066436 as the loci associated with CAD. All these positive associations remained significant after adjustment for traditional risk factors of CAD. NPR-C gene SNPs significantly contribute to CAD susceptibility in the Chinese Han population.

Rationalisation of a mechanism for sensing single point variants in target DNA using anthracene-tagged base discriminating probes

The fluorescence sensing mechanism for identifying single base changes in target DNA strands has been established through detailed biophysical measurements.

Significant genetic association of a functional TFPI variant with circulating fibrinogen levels and coronary artery disease

The tissue factor pathway inhibitor (TFPI) gene encodes a protease inhibitor with a critical role in regulation of blood coagulation. Some genomic variants in TFPI were previously associated with plasma TFPI levels, however, it remains to be further determined whether TFPI variants are associated with other coagulation factors. In this study, we carried out a large population-based study with 2313 study subjects for blood coagulation data, including fibrinogen levels, prothrombin time (PT), activated partial thromboplastin time (APTT), and thrombin time (TT). We identified significant association of TFPI variant rs10931292 (a functional promoter variant with reduced transactivation) with increased plasma fibrinogen levels (P = 0.017 under a recessive model), but not with PT, APTT or TT (P > 0.05). Using a large case-control association study population with 4479 CAD patients and 3628 controls, we identified significant association between rs10931292 and CAD under a recessive model (OR 1.23, P = 0.005). For the first time, we show that a TFPI variant is significantly associated with fibrinogen levels and risk of CAD. Our finding contributes significantly to the elucidation of the genetic basis and biological pathways responsible for fibrinogen levels and development of CAD.

Identification of single nucleotide polymorphisms in carnosine-related genes and effects of genotypes on pork meat quality attributes

Carnosine has pH-buffering and antioxidant properties that may bring advantages in terms of meat quality attributes. This study aimed at identifying polymorphisms in carnosine-related genes (CARNS1, SLC6A6, SLC15A3, SLC15A4) that might associate with muscle carnosine content and meat quality traits in pigs (Duroc, Landrace, Yorkshire). Twenty seven SNPs were identified and association analyses performed for SLC15A3 c.*35C>T and c.*52C>T (3' UTR region), and SLC15A4 c.658A>G (Ile220Val) and c.818G>A (Ser273Asn) SNPs. Associations were observed for SNP c.658A>G with carnosine content, color b* and L*, drip and cooking losses, pH24h and glycolytic potential values (P≤0.05). The same associations were observed for SNP c.818G>A, but they were not significant after FDR correction. Results suggest that specific SLC15A4 gene variants might increase muscle carnosine content and improve meat quality. With a minor allele frequency of 0.17 for SNP c.658A>G in Yorkshire pigs, selection in favor of the c.658A allele may be considered as a mean to improve pork quality attributes.

Quantitative Disease Resistance: Dissection and Adoption in Maize

Maize is the world's most produced crop, providing food, feed, and biofuel. Maize production is constantly threatened by the presence of devastating pathogens worldwide. Characterization of the genetic components underlying disease resistance is a major research area in maize which is highly relevant for resistance breeding programs. Quantitative disease resistance (QDR) is the type of resistance most widely used by maize breeders. The past decade has witnessed significant progress in fine-mapping and cloning of genes controlling QDR. The molecular mechanisms underlying QDR remain poorly understood and exploited. In this review we discuss recent advances in maize QDR research and strategy for resistance breeding.

Nanofluidic Allele-Specific Digital PCR Method for Quantifying IDH1 and IDH2 Mutation Burden in Acute Myeloid Leukemia

Precise quantitation of allelic burden for a pathogenic mutation has diverse clinical and research applications but can be difficult to achieve with conventional qPCR-based techniques, especially at lower mutant allele frequencies. Digital PCR overcomes many of the limitations of qPCR and can be highly quantitative even for single-nucleotide variants, with distinct advantages over next-generation sequencing approaches. Here we describe a method combining the principles of TaqMan®-chemistry SNP genotyping with microfluidic digital PCR to generate a highly sensitive, quantitative allele-specific digital PCR assay for the six most common IDH1 and IDH2 mutations encountered in myeloid malignancy. The concept and approach could easily be applied to other suitable SNVs.

Galectin-3 and Its Genetic Variation rs4644 Modulate Enterovirus 71 Infection

Galectin-3, a chimeric type β-galactoside-binding protein, is known to modulate viral infection; however, its role in enterovirus 71 (EV71) infection has not been investigated. We generated galectin-3 null rhabdomyosarcoma (RD) cells and evaluated whether EV71 infection would be affected. In galectin-3 null cells, the released and intracellular EV71 viral loads were suppressed after 24 h of infection, and cell death rates were significantly lower, while cell proliferation remained unaltered. In addition, RD cells expressing a nonsynonymous genetic variant of galectin-3, rs4644 (LGALS3 +191C/A, P64H), produced lower virus titers than those with wild-type galectin-3 (C allele). To clarify whether the in vitro viral load reduction correlates with clinical severity, we enrolled children with laboratory-confirmed EV71 infection. Since hyperglycemia is an indicator of severe EV71 infection in children, 152 of 401 enrolled children had glucose examinations at admission, and 59 subjects had serum glucose levels ≥ 150 mg/dL. In comparison to the rs4644 AA genotype (2.2 ± 0.06 log10 mg/dL), serum glucose levels during EV71 infection were higher in patients with CC (2.4 ± 0.17 log10 mg/dL, p = 0.03) and CA (2.4 ± 0.15 log10 mg/dL, p = 0.02) genotypes, respectively. These findings suggest that the rs4644 AA genotype of galectin-3 might exert a protective effect. In summary, galectin-3 affects EV71 replication in our cellular model and its variant, rs4644, is associated with hyperglycemia in the clinical setting. The underlying mechanism and its potential therapeutic application warrant further investigation.

Genetic polymorphism in DNMTs and gastric cancer: A systematic review and meta-analysis

Highlights

Single nucleotide polymorphisms (SNPs) in DNA methyltransferases (DNMTs) modulate protein expression and affect DNA methylation.Aberrant DNA methylation, have been associated with gastric carcinogenesis.DNMT2 rs11254413 is associated with protection for GC development.DNMT3A rs7560488, DNMT3A rs36012910 and, specially, DNMT1 rs16999593 are associated with increased susceptibility for GC development.

Abstract

Epigenetics alterations, including aberrant DNA methylation, have been associated with gastric carcinogenesis. Single nucleotide polymorphisms (SNPs) in DNA methyltransferases (DNMTs) may influence protein expression and therefore affect DNA regulation and susceptibility for Gastric Cancer (GC).We have performed a systematic review and meta-analysis involving 11 studies and a total of 24 SNPs in DNMTs were analyzed. According to literature, only 4 SNPs, DNMT1 rs16999593, DNMT2 rs11254413 and DNMT3A rs7560488 and DNMT3A rs36012910, were associated with GC. DNMT1 rs16999593 and DNMT3A rs7560488C allele and DNMT3A rs36012910 G allele showed an increased risk for GC. On the other hand, DNMT2 rs11254413 G allele presented a protective effect for GC. Additionally, the meta-analysis evaluated the SNPs analyzed in more than one study (n = 6). Results revealed that only DNMT1 rs16999593 had a statistically significant association with GC development (OR = 1.31; 95% CI = 1.08-1.60; p = 0.006 for TC + CC genotypes).Our study suggests that DNMT2 rs11254413, DNMT3A rs7560488, DNMT3A rs36012910 and, specially, DNMT1 rs16999593 may have an association with GC development. Nevertheless, further studies are need using different populations to clarify this association with GC risk.