Deletion Patterns Research Articles

Exon deletion pattern in duchene muscular dystrophy in north west of iran.

Duchene and Becker Muscular Dystrophy (DMD/ BMD) are x-linked disorders that both are the result of heterogeneous mutations in the dystrophin gene. The frequency and distribution of dystrophin gene deletions in DMD/ BMD patients show different patterns among different populations. This study investigates the deletion rate, type, and distribution of this gene in the Azeri Turk population of North West Iran. In this study, 110 patients with DMD/ BMD were studied for intragenic deletions in 24 exons and promoter regions of dystrophin genes by using multiplex PCR. Deletions were detected in 63 (57.3%) patients, and around 83% localized in the mid-distal hotspot of the gene (on exons 44-52), 21 cases (33.3 %) with single-exon deletions, and 42 cases (66.6%) with multi-exonic deletions. The most frequent deleted exons were exon 50 (15 %) and exon 49 (14%). No deletion was detected in exon 3. This study suggests that the frequency and pattern of dystrophin gene deletions in DMD/ BMD in the Azeri Turk population of North West Iran occur in the same pattern when compared with other ethnic groups.

D-loop somatic mutations and ∼5kb "common" deletion in mitochondrial DNA: important molecular markers to distinguish oral precancer and cancer.

Apart from genomic DNA, mutations at mitochondrial DNA (mtDNA) have been hypothesized to play vital roles in cancer development. In this study, ∼5kb deletion and D-loop mutations in mtDNA and alteration in mtDNA content were investigated in buccal smears from 104 healthy controls and 74 leukoplakia and 117 cancer tissue samples using Taqman-based quantitative assay and re-sequencing. The ∼5kb deletion in mtDNA was significantly less (9.8 and 10.5 folds, P < 0.0001) in cancer tissues compared to control and leukoplakia tissues, respectively. On the other hand, somatic mutations in D-loop, investigated in 54 controls, 50 leukoplakias and 56 cancer patients, were found to be significantly more in cancer tissues, but not in leukoplakia tissues, compared to control (Z-score = 5.4). MtDNA contents were observed to be significantly more in leukoplakia (2.1 folds, P = 0.004) and cancer (1.6 folds, P = 0.03) tissues compared to control tissues. So, D-loop somatic mutations and ∼5kb deletion patterns could be used as distinguishing markers between precancer and cancer tissues. This observation further suggests that somatic mutations in D-loop may facilitate carcinogenesis and cancer cells with less ∼5kb deletion, i.e., intact mtDNA, may become resistant to apoptosis.

Evolution of and evolutionary relationships between extant vaccinia virus strains.

Although vaccinia virus (VACV) was once used as a vaccine to eradicate smallpox on a worldwide scale, the biological origins of VACV are uncertain, as are the historical relationships between the different strains once used as smallpox vaccines. Here, we sequenced additional VACV strains that either represent relatively pristine examples of old vaccines (e.g., Dryvax, Lister, and Tashkent) or have been subjected to additional laboratory passage (e.g., IHD-W and WR). These genome sequences were compared with those previously reported for other VACVs as well as other orthopoxviruses. These extant VACVs do not always cluster in simple phylogenetic trees that are aligned with the known historical relationships between these strains. Rather, the pattern of deletions suggests that all existing strains likely come from a complex stock of viruses that has been passaged, distributed, and randomly sampled over time, thus obscuring simple historical or geographic links. We examined surviving nonclonal vaccine stocks, like Dryvax, which continue to harbor larger and now rare variants, including one that we have designated "clone DPP25." DPP25 encodes genes not found in most VACV strains, including an ankyrin-F-box protein, a homolog of the variola virus (Bangladesh) B18R gene which we show can be deleted without affecting virulence in mice. We propose a simple common mechanism by which recombination of a larger and hypothetical DPP25-like ancestral strain, combined with selection for retention of critically important genes near the terminal inverted repeat boundaries (vaccinia virus growth factor gene and an interferon alpha/beta receptor homolog), could produce all known VACV variants. Smallpox was eradicated by using a combination of intensive disease surveillance and vaccination using vaccinia virus (VACV). Interestingly, little is known about the historical relationships between different strains of VACV and how these viruses may have evolved from a common ancestral strain. To understand these relationships, additional strains were sequenced and compared to existing strains of VACV as well as other orthopoxviruses by using whole-genome sequence alignments. Extant strains of VACV did not always cluster in simple phylogenetic trees based on known historical relationships between these strains. Based on these findings, it is possible that all existing strains of VACV are derived from a single complex stock of viruses that has been passaged, distributed, and sampled over time.

Whole genome characterization of hepatitis B virus quasispecies with massively parallel pyrosequencing

Viral quasispecies analysis is important for basic and clinical research. This study was designed to detect hepatitis B virus (HBV) genome-wide mutation profiling with detailed variant composition in individual patients, especially quasispecies evolution correlating with liver disease progression. We characterized viral populations by massively parallel pyrosequencing at whole HBV genome level in 17 patients with advanced liver disease (ALD) and 30 chronic carriers (CC). An average sequencing coverage of 2047× and 687× in ALD and CC groups, respectively, were achieved. Deep sequencing data resolved the landscapes of HBV substitutions and a more complicated quasispecies composition than previously observed. The values of substitution frequencies in quasispecies were clustered as either more than 80% or less than 20%, forming a unique U-shaped distribution pattern in both clinical groups. Furthermore, quantitative comparison of mutation frequencies of each site between two groups resulted in a spectrum of substitutions associated with liver disease progression, and among which, C2288A/T, C2304A, and A/G2525C/T were novel candidates. Moreover, distinct deletion patterns in preS, X, and C regions were shown between the two groups. In conclusion, pyrosequencing of the whole HBV genome revealed a panorama of viral quasispecies composition, characteristics of substitution distribution, and mutations correlating to severe liver disease.

Abstract 5168: Gastric adenocarcinomas show pervasive loss of heterozygosity and enrichment for “STOP” genes in regions of hemizygous deletion

Abstract Purpose: Gastric cancer, the second leading cause of cancer death worldwide, has been little studied compared with other cancers that impose similar burdens on public health. Our goal is to assess loss of heterozygosity (LOH) and hemizygous deletion across a large series of gastric adenocarcinomas using the most sensitive and comprehensive method currently available. Experimental design: We used high-density single-nucleotide-polymorphism microarrays that assay genotype and copy number at 906,600 sites and analyzed the results to determine patterns of LOH and hemizygous deletion in 77 gastric adenocarcinomas. We investigated whether “STOP” genes - genes that tend to impede proliferation - are associated with hemizygous deletion. We also analyzed the extent to which hemizygous deletion affected CYCLOPS (Copy number alterations Yielding Cancer Liabilities Owing to Partial losS) genes - genes that may be attractive targets for therapeutic inhibition when hemizygously deleted. Results: We found that LOH is pervasive: on average 27% of each tumor genome is subject to LOH, and &amp;gt; 98% of single nucleotide polymorphisms assayed were subject to LOH in at least 10% of tumors. Furthermore, 26% of LOH was due to hemizygous deletion, and STOP genes were significantly associated with regions of frequent hemizygous deletion; on average, 61 STOP genes were hemizygously deleted per tumor. Furthermore, on average, 4.65 CYCLOPS genes were hemizygously deleted per tumor, and 54.5% of the tumors had at least one CYCLOPS gene deleted. Conclusions: These findings suggest that hemizygous deletion of anti-proliferative STOP genes contributes substantially to gastric carcinogenesis. Furthermore, the presence of several hemizygously deleted CYLOPS genes in some tumors suggests potential therapeutic targets in these tumors. Citation Format: Ioana Cutcutache, Alice Yingting Wu, John R. McPherson, Zhengdeng Lei, Niantao Deng, Wai Keong Wong, Khee Chee Soo, Weng Hoong Chan, London Lucien Ooi, Roy E. Welsch, Patrick Tan, Steven G. Rozen. Gastric adenocarcinomas show pervasive loss of heterozygosity and enrichment for “STOP” genes in regions of hemizygous deletion. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5168. doi:10.1158/1538-7445.AM2014-5168

Microarray analysis of 50 patients reveals the critical chromosomal regions responsible for 1p36 deletion syndrome-related complications.

Monosomy 1p36 syndrome is the most commonly observed subtelomeric deletion syndrome. Patients with this syndrome typically have common clinical features, such as intellectual disability, epilepsy, and characteristic craniofacial features. In cooperation with academic societies, we analyzed the genomic copy number aberrations using chromosomal microarray testing. Finally, the genotype-phenotype correlation among them was examined. We obtained clinical information of 86 patients who had been diagnosed with chromosomal deletions in the 1p36 region. Among them, blood samples were obtained from 50 patients (15 males and 35 females). The precise deletion regions were successfully genotyped. There were variable deletion patterns: pure terminal deletions in 38 patients (76%), including three cases of mosaicism; unbalanced translocations in seven (14%); and interstitial deletions in five (10%). Craniofacial/skeletal features, neurodevelopmental impairments, and cardiac anomalies were commonly observed in patients, with correlation to deletion sizes. The genotype-phenotype correlation analysis narrowed the region responsible for distinctive craniofacial features and intellectual disability into 1.8-2.1 and 1.8-2.2 Mb region, respectively. Patients with deletions larger than 6.2 Mb showed no ambulation, indicating that severe neurodevelopmental prognosis may be modified by haploinsufficiencies of KCNAB2 and CHD5, located at 6.2 Mb away from the telomere. Although the genotype-phenotype correlation for the cardiac abnormalities is unclear, PRDM16, PRKCZ, and RERE may be related to this complication. Our study also revealed that female patients who acquired ambulatory ability were likely to be at risk for obesity.

Mapping genetically controlled neural circuits of social behavior and visuo-motor integration by a preliminary examination of atypical deletions with Williams syndrome.

In this study of eight rare atypical deletion cases with Williams-Beuren syndrome (WS; also known as 7q11.23 deletion syndrome) consisting of three different patterns of deletions, compared to typical WS and typically developing (TD) individuals, we show preliminary evidence of dissociable genetic contributions to brain structure and human cognition. Univariate and multivariate pattern classification results of morphometric brain patterns complemented by behavior implicate a possible role for the chromosomal region that includes: 1) GTF2I/GTF2IRD1 in visuo-spatial/motor integration, intraparietal as well as overall gray matter structures, 2) the region spanning ABHD11 through RFC2 including LIMK1, in social cognition, in particular approachability, as well as orbitofrontal, amygdala and fusiform anatomy, and 3) the regions including STX1A, and/or CYLN2 in overall white matter structure. This knowledge contributes to our understanding of the role of genetics on human brain structure, cognition and pathophysiology of altered cognition in WS. The current study builds on ongoing research designed to characterize the impact of multiple genes, gene-gene interactions and changes in gene expression on the human brain.

Escape from Telomere-Driven Crisis Is DNA Ligase III Dependent

Short dysfunctional telomeres are capable of fusion, generating dicentric chromosomes and initiating breakage-fusion-bridge cycles. Cells that escape the ensuing cellular crisis exhibit large-scale genomic rearrangements that drive clonal evolution and malignant progression. We demonstrate that there is an absolute requirement for fully functional DNA ligase III (LIG3), but not ligase IV (LIG4), to facilitate the escape from a telomere-driven crisis. LIG3- and LIG4-dependent alternative (A) and classical (C) nonhomologous end-joining (NHEJ) pathways were capable of mediating the fusion of short dysfunctional telomeres, both displaying characteristic patterns of microhomology and deletion. Cells that failed to escape crisis exhibited increased proportions of C-NHEJ-mediated interchromosomal fusions, whereas those that escaped displayed increased proportions of intrachromosomal fusions. We propose that the balance between inter- and intrachromosomal telomere fusions dictates the ability of human cells to escape crisis and is influenced by the relative activities of A- and C-NHEJ at short dysfunctional telomeres.

Genome sequencing of Mycobacterium abscessus isolates from patients in the united states and comparisons to globally diverse clinical strains.

Nontuberculous mycobacterial infections caused by Mycobacterium abscessus are responsible for a range of disease manifestations from pulmonary to skin infections and are notoriously difficult to treat, due to innate resistance to many antibiotics. Previous population studies of clinical M. abscessus isolates utilized multilocus sequence typing or pulsed-field gel electrophoresis, but high-resolution examinations of genetic diversity at the whole-genome level have not been well characterized, particularly among clinical isolates derived in the United States. We performed whole-genome sequencing of 11 clinical M. abscessus isolates derived from eight U.S. patients with pulmonary nontuberculous mycobacterial infections, compared them to 30 globally diverse clinical isolates, and investigated intrapatient genomic diversity and evolution. Phylogenomic analyses revealed a cluster of closely related U.S. and Western European M. abscessus subsp. abscessus isolates that are genetically distinct from other European isolates and all Asian isolates. Large-scale variation analyses suggested genome content differences of 0.3 to 8.3%, relative to the reference strain ATCC 19977(T). Longitudinally sampled isolates showed very few single-nucleotide polymorphisms and correlated genomic deletion patterns, suggesting homogeneous infection populations. Our study explores the genomic diversity of clinical M. abscessus strains from multiple continents and provides insight into the genome plasticity of an opportunistic pathogen.

Characterization of the emerging clinically-relevant multidrug-resistant Salmonella enterica serotype 4,[5],12:i:- (monophasic variant of S. Typhimurium) clones.

To better understand the recent success/emergence of Salmonella enterica serotype 4,[5],12:i:- we characterized the population diversity, fljAB deletion patterns, antibiotic resistance features and associated genetic elements of a comprehensive collection obtained in the last decade from Portugal (2002-2010). One hundred thirty-one isolates from human clinical specimens, food, environment and piggeries, verified by PCR as S. 4,[5],12:i:-, were studied for clonality (Pulsed-Field Gel Electrophoresis and Multilocus Sequence Typing), antibiotic resistance by phenotypic (disk diffusion and/or agar dilution) and genotypic (PCR/Restriction Fragment Length Polymorphism and sequencing, genomic location) methods and fljAB-deletions (PCR). Plasmid analysis included determination of size, content and characterization of the incompatibility group (PCR-Based Replicon Typing and I-CeuI/S1-hybridization). Results showed three multidrug-resistant (MDR) clones circulating and causing infections, associated with particular phenotypic and genotypic features. Most of the isolates belonged to the widespread European (ASSuT phenotype, RR1-RR2 resistance regions, ST34) and Spanish (carrying a sul3-type III integron within IncA/C plasmids, ST19) clones circulating in Europe. A third clone, here designated Southern European clone (carrying a sul3-type I integron within IncR plasmids, ST19), presents a fljAB region different from the previous clones and similar to the US strains, despite differences in the MDR mobile genetic platforms. The success of S. 4,[5],12:i:- might be related to the selective advantage offered by MDR profiles associated with stable genetic elements, also carrying virulence features, along with well adapted clones to the animal food production and causing human infections.

Molecular characterization of Thai Salmonella enterica serotype typhimurium and serotype 4,5,12:i:- reveals distinct genetic deletion patterns.

In order to better understand the relationship between Salmonella serotypes Typhimurium and its monophasic variant 4,5,12:i:- found in Thailand, a total of 138 isolates from various sources were characterized using different molecular subtyping methods (i.e., pulsed-field gel electrophoresis [PFGE] and polymerase chain reaction [PCR]) and antibiotic resistance (AbR) patterns. PFGE revealed 52 distinct band patterns among these isolates, 3 of which were shared between the two serotypes. PCR characterization of genomic deletion patterns reveals that Thai S. 4,5,12:i:- isolates contain a distinct deletion pattern in the fljAB region, which can be used as a specific genetic marker for primary identification of S. 4,5,12:i:- sources. AbR study shows that, among 50 representative serotype-confirmed strains, 48.28% (14/29) of Salmonella Typhimurium and 90.48% (19/21) of 4,5,12:i:- isolates are multidrug-resistant Salmonella as they are resistant to at least 3 antimicrobial categories. The AmpST pattern for resistance to ampicillin, streptomycin, and tetracycline was found in high proportions of Salmonella Typhimurium (10 of 29) and S. 4,5,12:i:- (15 of 21) isolates.

Genomic characterization of Salmonella Cerro ST367, an emerging Salmonella subtype in cattle in the United States.

BackgroundWithin the last decade, Salmonella enterica subsp. enterica serovar Cerro (S. Cerro) has become one of the most common serovars isolated from cattle and dairy farm environments in the northeastern US. The fact that this serovar is commonly isolated from subclinically infected cattle and is rarely associated with human disease, despite its frequent isolation from cattle, has led to the hypothesis that this emerging serovar may be characterized by reduced virulence. We applied comparative and population genomic approaches to (i) characterize the evolution of this recently emerged serovar and to (ii) gain a better understanding of genomic features that could explain some of the unique epidemiological features associated with this serovar.ResultsIn addition to generating a de novo draft genome for one Salmonella Cerro strain, we also generated whole genome sequence data for 26 additional S. Cerro isolates, including 16 from cattle operations in New York (NY) state, 2 from human clinical cases from NY in 2008, and 8 from diverse animal sources (7 from Washington state and 1 from Florida). All isolates sequenced in this study represent sequence type ST367. Population genomic analysis showed that isolates from the NY cattle operations form a well-supported clade within S. Cerro ST367 (designated here “NY bovine clade”), distinct from isolates from Washington state, Florida and the human clinical cases. A molecular clock analysis indicates that the most recent common ancestor of the NY bovine clade dates back to 1998, supporting the recent emergence of this clone.Comparative genomic analyses revealed several relevant genomic features of S. Cerro ST367, that may be responsible for reduced virulence of S. Cerro, including an insertion creating a premature stop codon in sopA. In addition, patterns of gene deletion in S. Cerro ST367 further support adaptation of this clone to a unique ecological or host related niche.ConclusionsOur results indicate that the increase in prevalence of S. Cerro ST367 is caused by a highly clonal subpopulation and that S. Cerro ST367 is characterized by unique genomic deletions that may indicate adaptation to specific ecological niches and possibly reduced virulence in some hosts.Electronic supplementary materialThe online version of this article (doi: 10.1186/1471-2164-15-427) contains supplementary material, which is available to authorized users.

Molecular characterization of atoxigenic Aspergillus flavus isolates collected in China

Aspergillus flavus strains were isolated from peanut fields of Liaoning, Shandong, Hubei and Guangdong Provinces in China, and identified through phenotypic and molecular approaches. Of the 323 A. flavus strains isolated, 76 strains did not produce aflatoxins detectable by UPLC. The incidence of atoxigenic A. flavus strains decreased with increase in temperature and increased with increase in latitude in different geographical locations. Amplification of all the aflatoxin genes in the aflatoxin gene cluster in the atoxigenic isolates showed that there were 25 deletion patterns (A-Y), with 22 deletion patterns identified for the first time. Most of the atoxigenic A. flavus isolates with gene deletions (97%) had deletions in at least one of the four genes (aflT, nor-1, aflR, and hypB), indicating that these four genes could be targeted for rapid identification of atoxigenic strains. The atoxigenic isolates with gene deletions, especially the isolates with large deletions, are potential candidates for aflatoxin control.

Association of hepatitis B virus pre-S deletions with the development of hepatocellular carcinoma in Qidong, China.

Background/AimTo investigate the roles of mutations in pre-S and S regions of hepatitis B virus (HBV) on the progression of hepatocellular carcinoma (HCC) in Qidong, China.MethodsWe conducted an age matched case-control study within a cohort of 2387 male HBV carriers who were recruited from August, 1996. The HBV DNA sequence in pre-S/S regions was successfully determined in 96 HCC cases and 97 control subjects. In addition, a consecutive series of samples from 11 HCC cases were employed to evaluate the pre-S deletion patterns before and after the occurrence of HCC.ResultsAfter adjustment for age, history of cigarette smoking and alcohol consumption, HBeAg positivity, pre-S deletions, pre-S2 start codon mutations, and T53C mutation were significantly associated with HCC, showing adjusted odds ratios (ORs) from 1.914 to 3.199. HCC patients also had a lower frequency of T31C mutation in pre-S2 gene, compared with control subjects (0.524; 95% CI 0.280-0.982). HBV pre-S deletions were clustered mainly in the 5′ end of pre-S2 region. Multivariate analysis showed that pre-S deletions and pre-S2 start codon mutations were independent risk factors for HCC. The OR (95% CI) were 2.434 (1.063–5.573) and 3.065 (1.099–8.547), respectively. The longitudinal observation indicated that the pre-S deletion mutations were not acquired at the beginning of HBV infection, but that the mutations occurred during the long course of liver disease.ConclusionPre-S deletions and pre-S2 start codon mutations were independently associated with the development of HCC. The results also provided direct evidence that pre-S deletion mutations were not acquired from the beginning of infection but arose de novo during the progression of liver disease.

Genomic Evolution of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Isolates Revealed by Deep Sequencing

Most studies on PRRSV evolution have been limited to a particular region of the viral genome. A thorough genome-wide understanding of the impact of different mechanisms on shaping PRRSV genetic diversity is still lacking. To this end, deep sequencing was used to obtain genomic sequences of a diverse set of 16 isolates from a region of Hong Kong with a complex PRRSV epidemiological record. Genome assemblies and phylogenetic typing indicated the co-circulation of strains of both genotypes (type 1and type 2) with varying Nsp2 deletion patterns and distinct evolutionary lineages (“High Fever”-like and local endemic type). Recombination analyses revealed genomic breakpoints in structural and non-structural regions of genomes of both genotypes with evidence of many recombination events originating from common ancestors. Additionally, the high fold of coverage per nucleotide allowed the characterization of minor variants arising from the quasispecies of each strain. Overall, 0.56–2.83% of sites were found to be polymorphic with respect to cognate consensus genomes. The distribution of minor variants across each genome was not uniform indicating the influence of selective forces. Proportion of variants capable of causing an amino acid change in their respective codons ranged between 25–67% with many predicted to be non-deleterious. Low frequency deletion variants were also detected providing one possible mechanism for their sudden emergence as cited in previous reports.

TMPRSS2:ETS fusions and clinicopathologic characteristics of prostate cancer patients from Eastern China.

TMPRSS2:ERG gene fusions in prostate cancer have a dominant prevalence of approximately 50.0%, but infomration is limited on differences among ethnic and geographical groups. Some studies focusing on Japanese and Korean patients reported a lower incidence. Investigations concerning Chinese revealed controversial results. We evaluated TMPRSS2:ERG, TMPRSS2:ETV1 and TMPRSS2:ETV4 fusions in more than 100 Eastern Chinese prostate cancer patients. Paraffin blocks of needle biopsy and radical prostatectomy were collected from 91 and 18 patients respectively. All patients' clinicopathologic factors were gathered. TMPRSS2:ERG, TMPRSS2:ETV1 and TMPRSS2:ETV4 fusions were tested by multi-probe fluorescence in situ hybridization (FISH) assay. TMPRSS2:ERG fusions was present in 14.3% biopsy specimens and 11.1% radical prostatectomy patients. Neither TMPRSS2:ETV1 nor TMPRSS2:ETV4 fusion was found in any case. Altogether, 13 (86.7%) TMPRSS2:ERG fusion positive cases possessed deletion pattern and 7 (46.6%) and insertion pattern. Some 5 cases had both deletion and insertion patterns. While 38.5% (5/13) patients with deletion pattern had distant metastasis, except for one metastatic case harboring both deletion and insertion, there were no patients with insertion pattern accompanied with metastasis. There were no differences between fusion positive and negative cases in the distribution of age, PSA, Gleason score and TNM stage. Eastern Chinese prostate cancer patients have a significantly low incidence of TMPRSS2:ERG fusion. They also lack TMPRSS2:ETV1 and TMPRSS2:ETV4 fusion. There are more deletion pattern than insertion pattern in TMPRSS2:ERG positive cases. Fusion positive and negative patients have no clinicopathologic factor differences.

Familial Cushing syndrome due to thymic carcinoids in a multiple endocrine neoplasia type 1 kindred

The objective of this study is to present a familial Cushing syndrome (CS) caused by multiple endocrine neoplasia type 1 (MEN-1)-associated thymic carcinoid. Immunohistochemistry, gene sequencing, loss of heterozygosity analysis, and Western blot were used to determine the expression of ACTH in MEN-1-related thymic tumors, MEN1 gene mutation, the pattern and extent of allelic deletion, and the expression of Menin in MEN-1-associated tumors, respectively. Tumor cells from thymus ectopic-secreted ACTH. A deletion involving the MEN1 gene locus was confirmed. The expression of Menin in MEN-1-associated tumors declined. To conclude, we presented an unusual kindred of MEN-1, which pointed out the significance of making screening of MEN-1 for both male and female patients with CS and thymic carcinoid.

Genetic Diversity Analysis of Genotype 2 Porcine Reproductive and Respiratory Syndrome Viruses Emerging in Recent Years in China

Porcine reproductive and respiratory syndrome virus (PRRSV) is characterized by its extensive genetic diversity. Here we analyzed 101 sequences of NSP2 hypervariable region, 123 ORF3 sequences, and 118 ORF5 sequences from 128 PRRSV-positive clinical samples collected in different areas of China during 2008–early 2012. The results indicated that the amino acid identities of the three genes among these sequences were 87.6%–100%, 92.5%–100%, and 77%–100%, respectively. Meanwhile, 4 novel patterns of deletion and insertion in NSP2 region or GP5 were first found. The phylogenetic analysis on these 3 genes revealed that the Chinese PRRSV strains could be divided into three subgroups; majority of genes analyzed here were clustered in subgroup 3 with multiple branches; the strains with 30-aa deletion in NSP2-coding region were still the dominant virus in the field. Further phylogenetic analysis on four obtained complete genomic sequences showed that they were clustered into different branches with the Chinese corresponding representative strains. Our analyses suggest that the genetic diversity of genotype 2 PRRSV in the field displays a tendency of increasing in recent years in China, and the 30-aa deletion in NSP2-coding region should be no longer defined as the molecular marker of the Chinese HP-PRRSV.

Duchenne/Becker muscular dystrophy: A report on clinical, biochemical, and genetic study in Gujarat population, India.

Objective:In India, various groups have studied different regions to find out deletion pattern of dystrophin gene. We have investigated its deletion pattern among Duchenne/Becker muscular dystrophy (D/BMD) patients across Gujarat. Moreover, in this study we also correlate the same with reading frame rule. However, we too consider various clinicopathological features to establish as adjunct indices when deletion detection fails.Materials and Methods:In this pilot study, a total of 88 D/BMD patients consulting at our centers in Gujarat, India were included. All patients were reviewed on basis of their clinical characteristics, tested by three primer sets of 10-plex, 9-plex, and 7-plex polymerase chain reaction (PCR) for genetic analysis; whereas, biochemical indices were measured using automated biochemical analyzers.Results:The diagnosis of D/BMD was confirmed by multiplex-PCR (M-PCR) in D/BMD patients. A number of 65 (73.86%) out of 88 patients showed deletion in dystrophin gene. The exon 50 (58.46%) was the most frequent deletion found in our study. The mean age of onset of DMD and BMD was 4.09 ± 0.15 and 7.14 ± 0.55 years, respectively. In patients, mean creatine phosphokinase (CPK), lactate dehydrogenase (LDH), and myoglobin levels were elevated significantly (P < 0.05) in comparison to controls. Addition to CPK, LDH and myoglobin are good adjunct when deletion detection failed. These data are further in accordance with world literature when correlated with frame rule.Conclusion:The analysis has been carried out for the first time for a total of 88 D/BMD patients particularly from Gujarat, India. More research is essential to elucidate specific mutation pattern in association with management and therapies of proband.

Genetic variability of Aspergillus flavus isolates from a Mississippi corn field.

A nontoxigenic Aspergillus flavus strain, K49, is currently being tested as a biological control agent in corn fields in the Mississippi Delta. However, little is known about the overall genetic diversity of A. flavus from year to year in corn fields and specifically in Mississippi. Our objective was to assess the genetic variability of A. flavus isolates from different seasons, inoculum sources, and years, from a no-till corn field. Of the 175 A. flavus isolates examined, 74 and 97 had the typical norB-cypA type I (1.5 kb) and type II (1.0 kb) deletion patterns, respectively. Variability in the sequence of the omtA gene of the majority of the field isolates (n = 118) was compared to strain K49. High levels of haplotypic diversity (24 omtA haplotypes; Hd = 0.61 ± 0.04) were found. Among the 24 haplotypes, two were predominant, H1 (n = 71), which consists of mostly toxigenic isolates, and H49 (n = 18), which consists of mostly atoxigenic isolates including K49. Toxigenic isolates were prevalent (60%) in this natural population. Nonetheless, about 15% of the population likely shared the same ancestral origin with K49. This study provides valuable information on the diversity of A. flavus. This knowledge can be further used to develop additional biological control strains.