Insertion-deletion Polymorphism Research Articles

Ассоциация полиморфизмов I/D и T-786С генов ACE и NOS3 с особенностями течения ишемической болезни сердца на фоне сахарного диабета 2-го типа

to study relationship of ACE insertion-deletion (I/D) polymorphism and NOS3 T-786C polymorphism with characteristics of the course of ischemic heart disease (IHD) at the background of diabetes mellitus. Were examined 114 patients with IHD, 29.8% of patients had type 2 diabetes mellitus. ACE and NOS3 polymorphisms were determined by allele-specific polymerase chain reaction with primers by "Lytech". Patients with combined pathology belonged to older age group, had increased frequency of obesity and predominance of functional class II chronic heart failure. In this group we detected association of D allele of the ACE gene with higher frequency of dyslipidemia and obesity. Among patients with IHD without diabetes we observed associations of ACE I/D and NOS3 T-786C polymorphisms (close and moderate, respectively) with severity of effort angina. We also found that frequency of dyslipidemia among carriers of II and TT genotypes was lower than among carriers of other genotypes. Presence of type 2 diabetes as background pathology leads to a change of character of association of ACE I/D and NOS3 T-786C polymorphisms with clinical characteristics of patients with IHD.

Digital PCR Panel for Sensitive Hematopoietic Chimerism Quantification after Allogeneic Stem Cell Transplantation.

Accurate and sensitive determination of hematopoietic chimerism is a crucial diagnostic measure after allogeneic stem cell transplantation to monitor engraftment and potentially residual disease. Short tandem repeat (STR) amplification, the current “gold standard” for chimerism assessment facilitates reliable accuracy, but is hampered by its limited sensitivity (≥1%). Digital PCR (dPCR) has been shown to combine exact quantification and high reproducibility over a very wide measurement range with excellent sensitivity (routinely ≤0.1%) and thus represents a promising alternative to STR analysis. We here aimed at developing a whole panel of digital-PCR based assays for routine diagnostic. To this end, we tested suitability of 52 deletion/insertion polymorphisms (DIPs) for duplex analysis in combination with either a reference gene or a Y-chromosome specific PCR. Twenty-nine DIPs with high power of discrimination and good performance were identified, optimized and technically validated. We tested the newly established assays on retrospective patient samples that were in parallel also measured by STR amplification and found excellent correlation. Finally, a screening plate for initial genotyping with DIP-specific duplex dPCR assays was designed for convenient assay selection. In conclusion, we have established a comprehensive dPCR system for precise and high-sensitivity measurement of hematopoietic chimerism, which should be highly useful for clinical routine diagnostics.

Thirty autosomal insertion-deletion polymorphisms analyzed using the Investigator® DIPplex Kit in populations from Iraq, Lithuania, Slovenia, and Turkey

Thirty autosomal insertion-deletion (InDel) polymorphisms were analyzed in four populations from Iraq, Lithuania, Slovenia, and Turkey using the commercial kit Investigator® DIPplex. Genotyping issues were encountered for five of the 30 InDels. They were most probably caused by polymorphisms located in the primer binding sites. Population and forensic parameters were calculated. No significant deviations from Hardy-Weinberg equilibrium or significant linkage disequilibrium were detected. The observed heterozygosities ranged from 33% to 61% depending on the marker and the population. The combined probability of exclusion for the 30 markers was 99.7% in all four populations and the matching probabilities were 1 in 3–4×1012 individuals. The multidimensional scaling plot drawn from FST distances showed a good concordance between the relative position of the 15 populations included in the plot and their geographic locations.

Genetic architecture and pleiotropy shape costs of Rps2-mediated resistance in Arabidopsis thaliana.

The mounting evidence that R-genes incur large fitness costs raises a question: how can there be a 5-10% fitness reduction for all 149 R-genes in the Arabidopsis thaliana genome? The R-genes tested to date segregate for insertion-deletion (indel) polymorphisms where susceptible alleles are complete deletions. Since costs of resistance are measured as the differential fitness of isolines carrying resistant and susceptible alleles, indels reveal costs that may be masked when susceptible alleles are expressed. Rps2 segregates for two expressed clades of alleles, one resistant and one susceptible. Plants with resistant Rps2 are not less fit than those with a susceptible Rps2 allele in the absence of disease. Instead, all alleles provide a fitness benefit relative to an artificial deletion, due to the role of RPS2 as a negative regulator of defense. Our results highlight the interplay between genomic architecture and the magnitude of costs of resistance.

The source of SYBR green master mix determines outcome of nucleic acid amplification reactions.

BackgroundQuantitative (q) PCR by amplification of nucleic acid with a fluorescent dye is widely used. Selection of adequate PCR reagents and devices is relevant to achieve reliable and consistent data. Our main objective was to test the robustness of different commercial SYBR green PCR mixes with respect to specificity and sensitivity of the PCR assay, across various PCR machines (Light Cycler 96, ViiA7) and amplification protocols. Herein, we applied PCR protocols for determining mRNA transcript levels, DNA copy numbers, and DNA genotype.ResultsFirst, we set up 70 primer-based assays that targeted immune-related mRNA transcripts. Of the 70 assays 66 (94.3 %) resulted in a single melting curve peak, indicating specificity of the amplification, with PCR mixes from large vendors (Roche, ABI, Bio-Rad). But this was only seen when the PCR protocol that was indicated in the vendor’s guidelines for each particular mix was applied. When deviating from the prescribed protocol, suboptimal melting curves were most often seen when using Roche SYBR green. With respect to PCR yields, the use of ABI mix more often led to lower Cq values. Second, we set up 20 primer-selective PCR assays to target different insertion-deletion and single nucleotide polymorphism regions throughout the genome. The variation in delta Cq between positive and negative DNA samples among the PCR assays was the lowest when using ABI master mix. Finally, the quality of high resolution melting (HRM) assays for DNA genotyping was compared between four commercial HRM PCR mixes (Roche, Bioline, PCR Biosystems, ABI). Only Roche and ABI mixes produced optimal clusters of melting profiles that clearly distinguished genotype variants.ConclusionsThe current results show a preference for the use of ABI mix when it comes to obtaining higher sensitivity in cDNA analysis and a higher consistency among assays in distinguishing DNA genotypes among different individuals. For HRM assays, it is advisable to use master mix from a relatively large vendor.Electronic supplementary materialThe online version of this article (doi:10.1186/s13104-016-2093-4) contains supplementary material, which is available to authorized users.

The Angiotensin Converting Enzyme Insertion/Deletion Polymorphism Associates with Habitual Physical Activity among European-American Adults

PURPOSE: The angiotensin converting enzyme (ACE) insertion (I) deletion (D) polymorphism (ACE DIP) (rs4340) is a 287 base pair sequence within intron 16 of chromosome 17q23 that accounts for half of the variation in plasma ACE levels. Due to its influence on cardiovascular and renal function, the ACE DIP has been examined for its association with sport performance. The literature regarding associations with habitual physical activity is limited and inconsistent. We examined associations of the ACE DIP and physical activity among 461 European-American adults. METHODS: 203 men and 258 women with a body mass index (BMI) of 24.3±4.8 kg·m2 completed the Paffenbarger Physical Activity Questionnaire to determine weekly walking distance. ACE II (n=119), ID (n=213), and DD (n=129) genotypes were determined using TaqMan allele discrimination assays. Multivariate analysis of covariance (MANCOVA) determined logtransformed differences among ACE DIP genotypes and weekly walking distance with gender as a fixed factor and age and BMI as covariates. Because a significant ACE DIPxBMI interaction was found (p=0.03), we categorized the sample into normal weight (NW:BMI≤24.9 kg·m2) and overweight (OW:BMI>24.9 kg·m2). We repeated the MANCOVA with gender and BMI groups as fixed factors and age as a covariate. Bonferroni corrections were used to control for multiple comparison testing with alpha levels at p<.05. RESULTS: For NW (BMI=21.7±1.8 kg·m2), participants with the ACE II reported walking 1.4±1.0 mi/wk, ID 1.2±0.9 mi/wk, and DD 1.6±1.2 mi/wk, with ID walking less than II and DD (p<0.05). For OW (BMI=29.6±4.4 kg·m2), participants with the ACE II reported walking 1.5±1.1 mi/wk, ID 1.2±1.0 mi/wk, and DD 0.6±0.8 mi/wk, with DD walking less than II (p=0.02). For NW vs OW, weekly walking distance was 1.0±2.2 mi/wk less among OW with the ACE DD genotype than NW with this genotype (p=0.02); there were no other genotype-physical activity differences within or between NW and OW (p>0.05). CONCLUSIONS: BMI interacted with ACE DD to modulate habitual physical activity levels such that weekly walking distance was ~1.0 mi/wk greater among NW than OW with ACE DD. Our findings may provide insight into the discrepancies of this literature, and have public health significance equating to a body weight differential of ~1.4 lb/yr.

Whole genome nucleosome sequencing identifies novel types of forensic markers in degraded DNA samples

In the case of mass disasters, missing persons and forensic caseworks, highly degraded biological samples are often encountered. It can be a challenge to analyze and interpret the DNA profiles from these samples. Here we provide a new strategy to solve the problem by taking advantage of the intrinsic structural properties of DNA. We have assessed the in vivo positions of more than 35 million putative nucleosome cores in human leukocytes using high-throughput whole genome sequencing, and identified 2,462 single nucleotide variations (SNVs), 128 insertion-deletion polymorphisms (indels). After comparing the sequence reads with 44 STR loci commonly used in forensics, five STRs (TH01, TPOX, D18S51, DYS391, and D10S1248)were matched. We compared these “nucleosome protected STRs” (NPSTRs) with five other non-NPSTRs using mini-STR primer design, real-time PCR, and capillary gel electrophoresis on artificially degraded DNA. Moreover, genotyping performance of the five NPSTRs and five non-NPSTRs was also tested with real casework samples. All results show that loci located in nucleosomes are more likely to be successfully genotyped in degraded samples. In conclusion, after further strict validation, these markers could be incorporated into future forensic and paleontology identification kits, resulting in higher discriminatory power for certain degraded sample types.

Evaluating a subset of ancestry informative SNPs for discriminating among Southwest Asian and circum-Mediterranean populations

Many different published sets of single nucleotide polymorphisms (SNPs) and/or insertion-deletion polymorphisms (InDels) can serve as ancestry informative markers (AIMs) to distinguish among continental regions of the world. For a focus on Southwest Asian ancestry we chose to start with the Kidd Lab panel of 55 ancestry-informative SNPs (AISNPs) because it already provided good global reference data (FROG-kb: frog.med.yale.edu) in a set of 73 population samples distinguishing at least 8 biogeographic clusters of populations. This panel serves as a good first tier ancestry panel. We are now interested in identifying region-specific second tier panels for more refined distinction among populations within each of the global regions. We have begun studying the global region centered on Southwest Asia and the region encompassing the Mediterranean Sea. We have incorporated 10 populations from North Africa, Turkey and Iran and included 31 of the original 73 populations and eleven 1000 Genomes Phase3 populations for a total of 3129 individuals from 52 populations, all typed for the 55 AISNPs. We have then identified the subset of the 55 AISNPs that are most informative for this region of the world using Heatmap, Fst, and Informativeness analyses to eliminate those SNPs essentially redundant or providing no information among populations in this region, reducing the number of SNPs to 32. STRUCTURE and PCA analyses show the remaining 32 SNPs identify the North African cluster and appropriately include the Turkish and Iranian samples with the Southwest Asian cluster. These markers provide the basis for building an improved, optimized panel of AISNPs that provides additional information on differences among populations in this part of the world. The data have also allowed an examination of the accuracy of the ancestry inference based on 32 SNPs for the newly studied populations from this region. The likelihood ratio approach to ancestry inference embodied in FROG-kb provides highly significant population assignments within one order of magnitude for each individual in the Turkish, Iranian, and Tunisian populations.

Genome-Wide Association of the Laboratory-Based Nicotine Metabolite Ratio in Three Ancestries.

Introduction:Metabolic enzyme variation and other patient and environmental characteristics influence smoking behaviors, treatment success, and risk of related disease. Population-specific variation in metabolic genes contributes to challenges in developing and optimizing pharmacogenetic interventions. We applied a custom genome-wide genotyping array for addiction research (Smokescreen), to three laboratory-based studies of nicotine metabolism with oral or venous administration of labeled nicotine and cotinine, to model nicotine metabolism in multiple populations. The trans-3′-hydroxycotinine/cotinine ratio, the nicotine metabolite ratio (NMR), was the nicotine metabolism measure analyzed.Methods:Three hundred twelve individuals of self-identified European, African, and Asian American ancestry were genotyped and included in ancestry-specific genome-wide association scans (GWAS) and a meta-GWAS analysis of the NMR. We modeled natural-log transformed NMR with covariates: principal components of genetic ancestry, age, sex, body mass index, and smoking status.Results:African and Asian American NMRs were statistically significantly (P values ≤ 5E-5) lower than European American NMRs. Meta-GWAS analysis identified 36 genome-wide significant variants over a 43 kilobase pair region at CYP2A6 with minimum P = 2.46E-18 at rs12459249, proximal to CYP2A6. Additional minima were located in intron 4 (rs56113850, P = 6.61E-18) and in the CYP2A6-CYP2A7 intergenic region (rs34226463, P = 1.45E-12). Most (34/36) genome-wide significant variants suggested reduced CYP2A6 activity; functional mechanisms were identified and tested in knowledge-bases. Conditional analysis resulted in intergenic variants of possible interest (P values < 5E-5).Conclusions:This meta-GWAS of the NMR identifies CYP2A6 variants, replicates the top-ranked single nucleotide polymorphism from a recent Finnish meta-GWAS of the NMR, identifies functional mechanisms, and provides pan-continental population biomarkers for nicotine metabolism.Implications:This multiple ancestry meta-GWAS of the laboratory study-based NMR provides novel evidence and replication for genome-wide association of CYP2A6 single nucleotide and insertion–deletion polymorphisms. We identify three regions of genome-wide significance: proximal, intronic, and distal to CYP2A6. We replicate the top-ranking single nucleotide polymorphism from a recent GWAS of the NMR in Finnish smokers, identify a functional mechanism for this intronic variant from in silico analyses of RNA-seq data that is consistent with CYP2A6 expression measured in postmortem lung and liver, and provide additional support for the intergenic region between CYP2A6 and CYP2A7.

MP32-10 NONINVASIVE RENAL TRANSPLANT GRAFT MONITORING IN A SINGLE INSTITUTION USING CELL-FREE DONOR NUCLEIC ACID IN RECIPIENT PLASMA VIA INSERTION-DELETION ALLELE POLYMORPHISM

You have accessJournal of UrologyTransplantation & Vascular Surgery: Renal Transplantation & Vascular Surgery II1 Apr 2016MP32-10 NONINVASIVE RENAL TRANSPLANT GRAFT MONITORING IN A SINGLE INSTITUTION USING CELL-FREE DONOR NUCLEIC ACID IN RECIPIENT PLASMA VIA INSERTION-DELETION ALLELE POLYMORPHISM Yen Seow Benjamin Goh, Sze Yee Sherry Ho, Yi Quan Tan, Lata Raman, Vathsala Anantharaman, Ting Hui Angeline Goh, Siew Chuan Evelyn Koay, and Ho Yee Tiong Yen Seow Benjamin GohYen Seow Benjamin Goh More articles by this author , Sze Yee Sherry HoSze Yee Sherry Ho More articles by this author , Yi Quan TanYi Quan Tan More articles by this author , Lata RamanLata Raman More articles by this author , Vathsala AnantharamanVathsala Anantharaman More articles by this author , Ting Hui Angeline GohTing Hui Angeline Goh More articles by this author , Siew Chuan Evelyn KoaySiew Chuan Evelyn Koay More articles by this author , and Ho Yee TiongHo Yee Tiong More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2016.02.1305AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookTwitterLinked InEmail INTRODUCTION AND OBJECTIVES Renal transplantation is the optimal and most cost-effective treatment of end-stage renal failure. 64% of renal allograft failure is biopsy-proven to result from rejection leading to catastrophic recipient morbidity and loss of precious donor kidneys. There is an unmet clinical need in early detection of donor organ tissue damage before irreversible, non-specific renal function deterioration (by means of serum creatinine) and use of invasive allograft biopsy. Cell-free donor DNA(cfdDNA) had been explored in cancer detection, prenatal diagnostics and solid organ transplants worldwide, albeit limited to sex-mismatched donor-recipients. Gender-independent insertion-deletion (INDELs) polymorphic sequences were applied for noninvasive prenatal testing at the hospital Molecular Diagnostic Centre (MDC) with high sensitivity. The 8 identified INDELs were analysed in our donor recipient pairs Aim - Detect cfdDNA in recipient plasma using real-time polymerase chain reaction (qPCR) - Monitor the trend, peak and troughs of cfdDNA METHODS 10 Han Chinese donor-recipient pairs undergoing living related renal transplant were prospectively recruited and consented from National University Centre for Organ Transplant. Immunosuppression regimen is per protocol, managed by renal physicians Donor blood sampling performed once prior to transplant. Recipient blood sampling performed daily while inpatient and processed in MDC as per protocol Institution review board approved study RESULTS 1 or more informative INDELs detected in 9 of 10 recipients post transplant. Where the informative INDEL was multiplexed with an INDEL present in both donor and recipient DNA, percentages of the former can be calculated The cfdDNA levels rose sharply to peak at post operative Day 1-2 and decreased to a trough by Day 3-6(refer to chart) CONCLUSIONS INDEL polymorphism is a plausible mechanism to detect cfdDNA in recipient plasma post renal transplant cfdDNA has been shown to spike with insults to donor graft. Current results have achieved a proof of concept and demonstrate ability of the this novel technique to potentially monitor graft health Future directions include correlation of cfDNA with long term graft outcome and peak level with various graft insults © 2016FiguresReferencesRelatedDetails Volume 195Issue 4SApril 2016Page: e431-e432 Advertisement Copyright & Permissions© 2016MetricsAuthor Information Yen Seow Benjamin Goh More articles by this author Sze Yee Sherry Ho More articles by this author Yi Quan Tan More articles by this author Lata Raman More articles by this author Vathsala Anantharaman More articles by this author Ting Hui Angeline Goh More articles by this author Siew Chuan Evelyn Koay More articles by this author Ho Yee Tiong More articles by this author Expand All Advertisement Advertisement PDF downloadLoading ...

Analysis of 30 Biallelic INDEL Markers Using the Investigator DIPplex(®) Kit.

Insertion/deletion polymorphisms (INDELs) are a relatively new class of a DNA marker to be used in forensic casework; used most commonly as a supplementary method to STR-based typing. INDELs, like SNPs, are particularly useful for the analysis of highly degraded DNA as the amplicon sizes are typically below 160 bp; they can also be valuable as an additional tool to help resolve kinship cases, with the advantage over STRs that they do not have high mutation rates. INDELs have an advantage over SNPs in that they are length polymorphisms and so can be analyzed by simply measuring the length of the allele(s). The Qiagen Investigator(®) DIPplex Kit is currently only one of two commercially available kits for the amplification of INDEL polymorphisms; it amplifies 30 biallelic INDEL loci and the amelogenin locus. The primers used are fluorescence labeled with 6-FAM, BTG, BTY, and BTR. This technique is robust, relatively simple, and the results are analyzed using the same capillary electrophoresis equipment and software as used for STR typing.

Association Between Angiotensin Converting Enzyme Gene Insertion\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\Deletion Polymorphism and Coronary Heart Disease in Gaza Strip

The insertion deletion (ID) polymorphism in intron 16 of the ACE gene is a marker for a functional polymorphism, and it is also reported to influence levels of ACE in healthy subjects. ACE ID polymorphism is associated with an elevated risk of thrombosis and may be causally associated with coronary heart disease (CHD). To investigate the association between ACE gene polymorphism and CHD in the Gaza strip population, we conducted case-control study included 260 samples comprised 160 CHD patients and 100 control subjects. Questionnaire interview was applied. Blood samples were collected in EDTA tube for DNA extraction. Polymerase Chain Reaction (PCR) used to detect ACE ID polymorphism. There was significant association between CHD and age, physical activity, education level, occupation, and family history of CHD. No significant association was observed between CHD and gender and smoking. The genotype frequencies were: ID (36.9%, 42%), DD (53.8%, 54%) and II (9.4%, 4%) in case and control groups respectively. The ACE ID allele frequencies were: I (27%, 25%) and D (72.2%, 75%) in case and control group respectively. The D allele was the most frequent allele in both groups. No association between ACE ID polymorphism and gender. The DD genotype was the most frequent in both study groups. There was no statistically significant association between the ACE ID polymorphism and CHD in Gaza strip. The results showed that there was no significant association between the ACE ID gene polymorphism and CHD in Gaza strip.

The Role of Genetic Ancestry in Brazilian Patients With Primary Congenital Glaucoma.

The relationship between clinical data and genetic ancestry in Brazilian patients with primary congenital glaucoma (PCG) was studied. Thirty patients with PCG and 60 unrelated controls underwent a complete ophthalmological examination. The PCG inclusion criterion was prior surgery with a minimum follow-up of 6 months after the last surgical procedure. Clinical data were recorded and DNA from each individual was extracted and genotyped for a panel of 40 validated ancestry-informative insertion-deletion DNA polymorphisms (indels). Eighteen (60%) children had bilateral disease and 16 (53.3%) were male. The mean age at diagnosis was 6.3 months and surgical follow-up time varied from 8 to 85 months. For the PCG group, the proportion of Europeans, Africans, and Amerindians was 0.784±0.044 (mean±SEM), 0.149±0.035, and 0.067±0.023, respectively, whereas for the control group was 0.730±0.048, 0.132±0.034, and 0.138±0.032, respectively. An increased proportion of African indels was associated with worse surgical prognosis (P=0.036). There was also a statistically significant (P<0.05) positive correlation between axial length and African component (initial: R=0.625; final: R=0.567). An increased proportion of African indels was associated with worse prognosis for PCG in a mixed population. Genetic ancestry markers may be helpful in assessing risk factors for surgical outcomes in PCG. Further studies are needed to unveil the role of ancestry in heterogeneous populations such as Brazilians with PCG.

Characterization of equine CSN1S2 variants considering genetics, transcriptomics, and proteomics

Currently, research interest is increasing in horse milk composition and its effect on human health. Despite previously published studies describing the presence of intra- and interbreed variability of equine milk components, no investigations have focused on the genetic background of this variation. Among horse caseins and the genes encoding them, least is known about the structure and expression of the α-S2 casein gene, CSN1S2. Herein, based on direct sequencing of the equine CSN1S2 coding sequence, we describe the presence of 51-bp insertion-deletion (in/del) polymorphism, which significantly changes the protein sequence (lack or presence of 17-amino acid serine-rich peptide). Bioinformatic analysis revealed that the observed in/del polymorphism spanned exactly 2 exons; therefore, we hypothesized that we were observing different CSN1S2 splicing isoforms. However, further investigation indicated that the detected sequence variation was caused by a large (1.3-kb) deletion in the genomic DNA. We found that the polymorphic forms (A, longer; B, shorter; KP658381 and KP658382 GenBank records, respectively) were unevenly distributed among different horse breeds (the highest frequency of variant B was observed in coldblood horses and Haflingers). We propose that the analyzed polymorphism is associated with CSN1S2 expression level (the highest expression was recorded for individuals carrying the BB genotype), which was much more pronounced for milk CSN1S2 protein content than for relative transcript abundance (measured in milk somatic cells). Our results provide insight into the equine CSN1S2 structure and lay a foundation for further functional analyses regarding, for example, allergenicity or physiochemical properties of the observed CSN1S2 variants.

Role of ACE and PAI-1 Polymorphisms in the Development and Progression of Diabetic Retinopathy.

In the present study we determined the association of angiotensin converting enzyme (ACE) and plasminogen activator inhibitor-1 (PAI-1) gene polymorphisms with diabetic retinopathy (DR) and its sub-clinical classes in Pakistani type 2 diabetic patients. A total of 353 diabetic subjects including 160 DR and 193 diabetic non retinopathy (DNR) as well as 198 healthy controls were genotyped by allele specific polymerase chain reaction (PCR) for ACE Insertion/Deletion (ID) polymorphism, rs4646994 in intron 16 and PAI-1 4G/5G (deletion/insertion) polymorphism, rs1799768 in promoter region of the gene. To statistically assess the genotype-phenotype association, multivariate logistic regression analysis was applied to the genotype data of DR, DNR and control individuals as well as the subtypes of DR. The ACE genotype ID was found to be significantly associated with DR (p = 0.009, odds ratio (OR) 1.870 [95% confidence interval (CI) = 1.04–3.36]) and its sub-clinical class non-proliferative DR (NPDR) (p = 0.006, OR 2.250 [95% CI = 1.098–4.620]), while PAI polymorphism did not show any association with DR in the current cohort. In conclusion in Pakistani population the ACE ID polymorphism was observed to be significantly associated with DR and NPDR, but not with the severe form of the disease i.e. proliferative DR (PDR).

Analysis of catechol-O-methyltransferase gene mutation and identification of new pathogenic gene for paroxysmal kinesigenic dyskinesia

We aimed to analyze the mutation site and frequency of catechol-O-methyltransferase (COMT) gene, to explore the relationship between COMT genotype and phenotype, and to find new pathogenic genes for paroxysmal kinesigenic dyskinesia (PKD). PKD patients who were treated from December 2011 to January 2014 were selected and subjected to genetic testing in the exon region of COMT. Two patients and one intrafamilial healthy control were subjected to exome sequencing using whole exome capture in combination with high-throughput sequencing to find candidate pathogenic gene sites. The results were verified by Sanger sequencing. A total of 11 familial PKD patients from 4 families and 9 sporadic patients without family history were included. Pathogenic c.634dupC(p.P220fsX7) mutation of COMT gene was found in 7 familial PKD patients and3 sporadic patients. Mutated COMT gene carriers suffered from PKD earlier (average age of onset: 11.61 ± 2.33 vs 16.21 ± 2.58, P = 0.001) with symmetric symptoms in most cases, while the mutation-negative group only showed unilateral symptoms (P = 0.001). The mutation-positive group also had more daily attacks (P = 0.038). Carbamazepine worked for all mutation-positive patients (10/10, 100%), but only for a part of mutation-negative patients (3/10, 30.0%). About 90000 single nucleotide polymorphisms and 2000 insertion-deletion polymorphisms were detected in each of the three samples. c.737C → T(p.T246 M) mutation of POC1B gene was a new pathogenic site for a selected family. COMT gene mutation, which was the pathogenesis of most familial PKD patients and a part of sporadic patients, predicted the response to carbamazepine. POC1B may be a novel pathogenic gene for PKD.

Development of INDEL Markers for Genetic Mapping Based on Whole Genome Resequencing in Soybean

Soybean [Glycine max (L.) Merrill] is an important crop worldwide. In this study, a Chinese local soybean cultivar, Hedou 12, was resequenced by next generation sequencing technology to develop INsertion/DELetion (INDEL) markers for genetic mapping. 49,276 INDEL polymorphisms and 242,059 single nucleotide polymorphisms were detected between Hedou 12 and the Williams 82 reference sequence. Of these, 243 candidate INDEL markers ranging from 5–50 bp in length were chosen for validation, and 165 (68%) of them revealed polymorphisms between Hedou 12 and Williams 82. The validated INDEL markers were also tested in 12 other soybean cultivars. The number of polymorphisms in the pairwise comparisons of 14 soybean cultivars varied from 27 to 165. To test the utility of these INDEL markers, they were used to perform genetic mapping of a crinkly leaf mutant, and the CRINKLY LEAF locus was successfully mapped to a 360 kb region on chromosome 7. This research shows that high-throughput sequencing technologies can facilitate the development of genome-wide molecular markers for genetic mapping in soybean.

Genetic diversity of 38 insertion–deletion polymorphisms in Jewish populations

Population genetic data of 38 non-coding biallelic autosomal indels are reported for 466 individuals, representing six populations with Jewish ancestry (Ashkenazim, Mizrahim, Sephardim, North African, Chuetas and Bragança crypto-Jews). Intra-population diversity and forensic parameters values showed that this set of indels was highly informative for forensic applications in the Jewish populations studied. Genetic distance analysis demonstrated that this set of markers efficiently separates populations from different continents, but does not seem effective for molecular anthropology studies in Mediterranean region. Finally, it is important to highlight that although the genetic distances between Jewish populations were small, significant differences were observed for Chuetas and Bragança Jews, and therefore, specific databases must be used for these populations.

DiSNPindel: improved intra-individual SNP and InDel detection in direct amplicon sequencing of a diploid.

BackgroundAmplicon re-sequencing based on the automated Sanger method remains popular for detection of single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (InDels) for a spectrum of genetics applications. However, existing software tools for detecting intra-individual SNPs and InDels in direct amplicon sequencing of diploid samples are insufficient in analyzing single traces and their accuracy is still limited.ResultsWe developed a novel computation tool, named DiSNPindel, to improve the detection of intra-individual SNPs and InDels in direct amplicon sequencing of a diploid. Neither reference sequence nor additional sample was required. Using two real datasets, we demonstrated the usefulness of DiSNPindel in its ability to improve largely the true SNP and InDel discovery rates and reduce largely the missed and false positive rates as compared with existing detection methods.ConclusionsThe software DiSNPindel presented here provides an efficient tool for intra-individual SNP and InDel detection in diploid amplicon sequencing. It will also be useful for identification of DNA variations in expressed sequence tag (EST) re-sequencing.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0790-y) contains supplementary material, which is available to authorized users.

Analysis of 30 insertion-deletion polymorphisms in the Japanese population using the Investigator DIPplex® kit.

Allele frequencies and forensic parameters for 30 insertion-deletion polymorphisms (INDELs) were investigated in a sample of 251 unrelated Japanese individuals using the Investigator DIPplex® kit (QIAGEN). The frequency distributions showed no deviations from Hardy-Weinberg equilibrium expectations. The combined powers of discrimination and match probability for the 30 INDELs were 0.9999999998 and 2.67×10(-11), respectively. To assess the effectiveness of the kit in typing degraded DNA, an ancient bone sample of a Jomon skeleton was analyzed; most of 30 INDELs and amelogenin were typed successfully. We concluded that the kit offers considerable potential for personal identification from degraded DNA samples due to the small amplicon length and high degree of polymorphisms.