Three novel avastroviruses identified in dead wild crows

P099 : A SINGLE CENTER COMPARISON OF HIGH-RESOLUTION HLA TYPING BY NEXT-GENERATION VERSUS SANGER SEQUENCING

BackgroundGermline DNA mutations that increase the susceptibility of a patient to certain cancers have been identified in various genes, and patients can be screened for mutations in these genes to assess their level of risk for developing cancer. Traditional methods using Sanger sequencing focus on small groups of genes and therefore are unable to screen for numerous genes from several patients simultaneously. The goal of the present study was to validate a 25-gene panel to assess genetic risk for cancer in 8 different tissues using next generation sequencing (NGS) techniques.MethodsTwenty-five genes associated with hereditary cancer syndromes were selected for development of a panel to screen for risk of these cancers using NGS. In an initial technical assessment, NGS results for BRCA1 and BRCA2 were compared with Sanger sequencing in 1864 anonymized DNA samples from patients who had undergone previous clinical testing. Next, the entire gene panel was validated using parallel NGS and Sanger sequencing in 100 anonymized DNA samples. Large rearrangement analysis was validated using NGS, microarray comparative genomic hybridization (CGH), and multiplex ligation-dependent probe amplification analyses (MLPA).ResultsNGS identified 15,877 sequence variants, while Sanger sequencing identified 15,878 in the BRCA1 and BRCA2 comparison study of the same regions. Based on these results, the NGS process was refined prior to the validation of the full gene panel. In the validation study, NGS and Sanger sequencing were 100% concordant for the 3,923 collective variants across all genes for an analytical sensitivity of the NGS assay of >99.92% (lower limit of 95% confidence interval). NGS, microarray CGH and MLPA correctly identified all expected positive and negative large rearrangement results for the 25-gene panel.ConclusionThis study provides a thorough validation of the 25-gene NGS panel and indicates that this analysis tool can be used to collect clinically significant information related to risk of developing hereditary cancers.

Genetic landscape for majority and minority HIV-1 drug resistance mutations in antiretroviral therapy naive patients in Accra, Ghana

To evaluate the diagnostic accuracy of droplet digital polymerase chain reaction (ddPCR) for detecting polymerase epsilon (POLE) mutations in endometrial cancer (EC), comparing it with traditional Sanger sequencing and next-generation sequencing (NGS). Tumor DNA from 132 patients with EC was analyzed initially using both ddPCR and Sanger sequencing. Discordant cases (n=20) underwent further analysis using NGS as the reference standard. This study compared the sensitivity, specificity, and overall concordance of ddPCR against Sanger sequencing results, validated by NGS. Among the 20 discrepant samples, ddPCR detected POLE mutations in 15 cases (75%). All ddPCR results matched exactly with NGS findings, including the detection of 11 low-frequency mutations missed by Sanger sequencing. ddPCR also corrected 2 false-positive results initially identified by Sanger sequencing. No false negatives were detected by ddPCR. ddPCR demonstrated superior sensitivity and specificity in detecting POLE mutations compared to Sanger sequencing and showed perfect agreement with NGS. With its rapid turnaround, simplicity, and cost-effectiveness, ddPCR is highly suitable for routine clinical use, potentially enhancing patient management and outcomes in EC.

BackgroundHIV-1 resistance testing is recommended in clinical management and next-generation sequencing (NGS) methods are now available in many virology laboratories. ObjectivesTo evaluate the diagnostic performance of Long-Read Single Molecule Real-time (SMRT) sequencing (Sequel, PacBio) for HIV-1 polymerase genotyping. Study design111 prospective clinical samples (83 plasma and 28 leukocyte-enriched blood fraction) were analyzed for routine HIV-1 resistance genotyping using Sanger sequencing, Vela NGS, and SMRT sequencing. We developed a SMRT sequencing protocol and a bio-informatics pipeline to infer antiretroviral resistance on both haplotype and variant calling approaches. ResultsThe polymerase was successfully sequenced by the three platforms in 98 % of plasma RNA samples for viral loads above 4 log copies/mL. The success rate decreased to 83 % using Sanger or Vela sequencing and to 67 % using SMRT sequencing for viral loads of 3 to 4 log copies/mL. Sensitivities of 50 %, 54 % and 61 % were obtained using SMRT, Vela, and Sanger sequencing, respectively, in cellular DNA from patients with prolonged undetectable plasma HIV-1 RNA. Ninety-eight percent of resistance-associated mutations (RAMs) identified with Sanger sequencing were detected using SMRT sequencing. Furthermore, 91 % of RAMs (> 5 % threshold) identified with Vela NGS were detected using SMRT sequencing. RAM quantification using Vela and SMRT sequencing was well correlated (Spearman correlation ρ = 0.82; P < 0.0001). ConclusionsSMRT sequencing of the full-length HIV-1 polymerase appeared performant for characterizing HIV-1 genotypic resistance on both RNA and DNA clinical samples. Long-read sequencing is a new tool for mutation haplotyping and resistance analysis.

Introduction: Phenylketonuria (PKU) is a rare autosomal-recessive disorder inherited in accordance with the law of segregation. Detection tools for people with PKU can include Sanger Sequencing (SS) and Next Generation Sequencing (NGS). Diet therapy, Large Neutral Amino Acids (LNAA), and Specific Nutrient Combination (SNC) can help alleviate people with PKU. In the future, genetic manipulation techniques can help to eliminate PKU. Objectives: In this review, the author describes the progress in a study that focused on detection tools such as SS and NGS, the phenylalanine hydroxylase (PAH) gene and mutations in the PAH gene, use of drugs for PKU, and genetic manipulation techniques such as Adeno-associated virus (AAV) vectors and clustered regularly interspaced short palindromic repeats (CRISPR) RNA-guided FokI nuclease system (FokI-dCas9 system). AAV is abbreviation of AAV. CRISPR system is abbreviation of clustered regularly interspaced short palindromic repeats. Methods: The author searched the PubMed Database at National Center for Biotechnology Information (NCBI) for articles on PKU disorder. These articles were published between 2014 and 2019. Articles were open access and in English. Searches were also done at Google and ScienceDirect. Results: PKU derives from mutations in the PAH gene. Features of PKU may include ataxia, intellectual ability, and seizures. MassARRAY method, minisequencing method, SS and NGS can detect PKU on humans. Diet therapy, BH4, LNAA, SNC, enzyme therapy can help patients with PKU. However, these drugs cannot treat PKU permanently. In the future, genetic manipulation techniques can be used. AAV vectors and FokI-dCas9 system can be useful to eliminate PKU disorder. Conclusion: Guthrie method, MassARRAY, minisequencing, SS and NGS are tools for detecting PKU. Treatments with such as diet therapy, LNAA, SNC, and enzyme therapy are useful for PKU disorder. AAV vectors and FokI-dCas9 system are methods that can be useful for eliminating PKU in the future.

Background and objective Development of the next generation sequencing (NGS) platform was driven by the completion of the Human Genome Project in 2003. With the availability of NGS, the time taken for sequencing of humongous genomic regions was greatly reduced and data generated per unit DNA was also significantly increased. Though the cost to use NGS in a clinically setting is far from ideal, economically speaking, there is a significant decrease in the average cost per sequenced base. To validate findings of NGS on mutation detected for FBN1, TGFBR2, RAF1, RTEL1, LMNA, MID2, KCNK9, DMD, SMARCA2 and IQSEC2 by using gold standard, Sanger Sequencing.

Next-generation sequencing (NGS) for HIV drug resistance (DR) testing has an increasing number of applications for the detection of low-abundance drug-resistant variants (LA-DRVs) in regard to its features as a quasi-species. However, there is less information on its detection performance in DR detection with NGS. To determine the feasibility of using NGS technology in LA-DRV detection for HIV-1 pretreatment drug resistance, 80 HIV-infected individuals who had never undergone antiretroviral therapy were subjected to both NGS and Sanger sequencing (SS) in HIV-1 drug resistance testing. The results reported in this study show that NGS exhibits higher sensitivity for drug resistance identification than SS at a 5% detection threshold. NGS showed a better consistency compared with that of SS for both protease inhibitors (PIs) and integrase inhibitors (INSTIs), with a figure amounting to more than 90%, but worse consistency in nucleotide reverse transcriptase inhibitors (NRTIs), with a consistency ranging from only 61.25% to 87.50%. The consistency of non-nucleotide reverse transcriptase inhibitors (NNRTIs) between NGS and SS was around 85%. NGS showed the highest sensitivity of 87.0% at a 5% threshold. The application of NGS technology in HIV-1 genotype resistance detection in different populations infected with HIV requires further documentation and validation.

The therapeutic choice for patients with lung adenocarcinoma depends on the presence of EGF receptor (EGFR) mutations. In many cases, only cytologic samples are available for molecular diagnosis. Bronchoalveolar lavage (BAL) and pleural fluid, which represent a considerable proportion of cytologic specimens, cannot always be used for molecular testing because of low rate of tumor cells. We tested the feasibility of EGFR mutation analysis on BAL and pleural fluid samples by next-generation sequencing (NGS), an innovative and extremely sensitive platform. The study was devised to extend the EGFR test to those patients who could not get it due to the paucity of biologic material. A series of 830 lung cytology specimens was used to select 48 samples (BAL and pleural fluid) from patients with EGFR mutations in resected tumors. These samples included 36 cases with 0.3% to 9% of neoplastic cells (series A) and 12 cases without evidence of tumor (series B). All samples were analyzed by Sanger sequencing and NGS on 454 Roche platform. A mean of 21,130 ± 2,370 sequences per sample were obtained by NGS. In series A, EGFR mutations were detected in 16% of cases by Sanger sequencing and in 81% of cases by NGS. Seventy-seven percent of cases found to be negative by Sanger sequencing showed mutations by NGS. In series B, all samples were negative for EGFR mutation by Sanger sequencing whereas 42% of them were positive by NGS. The very sensitive EGFR-NGS assay may open up to the possibility of specific treatments for patients otherwise doomed to re-biopsies or nontargeted therapies.

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; The therapeutic choice for patients with lung adenocarcinoma depends on the presence of EGF receptor (&lt;i&gt;EGFR&lt;/i&gt;) mutations. In many cases, only cytologic samples are available for molecular diagnosis. Bronchoalveolar lavage (BAL) and pleural fluid, which represent a considerable proportion of cytologic specimens, cannot always be used for molecular testing because of low rate of tumor cells.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We tested the feasibility of &lt;i&gt;EGFR&lt;/i&gt; mutation analysis on BAL and pleural fluid samples by next-generation sequencing (NGS), an innovative and extremely sensitive platform. The study was devised to extend the &lt;i&gt;EGFR&lt;/i&gt; test to those patients who could not get it due to the paucity of biologic material. A series of 830 lung cytology specimens was used to select 48 samples (BAL and pleural fluid) from patients with &lt;i&gt;EGFR&lt;/i&gt; mutations in resected tumors. These samples included 36 cases with 0.3% to 9% of neoplastic cells (series A) and 12 cases without evidence of tumor (series B). All samples were analyzed by Sanger sequencing and NGS on 454 Roche platform. A mean of 21,130 ± 2,370 sequences per sample were obtained by NGS.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; In series A, &lt;i&gt;EGFR&lt;/i&gt; mutations were detected in 16% of cases by Sanger sequencing and in 81% of cases by NGS. Seventy-seven percent of cases found to be negative by Sanger sequencing showed mutations by NGS. In series B, all samples were negative for &lt;i&gt;EGFR&lt;/i&gt; mutation by Sanger sequencing whereas 42% of them were positive by NGS.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; The very sensitive &lt;i&gt;EGFR&lt;/i&gt;-NGS assay may open up to the possibility of specific treatments for patients otherwise doomed to re-biopsies or nontargeted therapies. &lt;i&gt;Clin Cancer Res; 19(3); 691–8. ©2012 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;

Deleterious sequence variants play an important role in the initiation and progression of many different cancer types. The detection of germline variants by the gold standard Sanger sequencing has been well established, however, the detection of somatic mutations, especially in heterogeneous tumor samples where variants may be present at a lower level, has been more challenging. To facilitate analysis of somatic mutations in tumor samples, we have developed Sanger sequencing panels that cover the entire coding regions of specific genes implicated in tumorigenesis (e.g. TP53, KRAS and NRAS). We have also developed companion software, Minor Variant Finder (MVF), that facilitates detection of low levels of somatic mutations in Sanger sequencing studies. To demonstrate the workflow of these panels with MVF, we analyzed DNA from lung cancer FFPE samples. We initially determined variants of TP53 and KRAS in these samples using Ion Torrent™ Personal Genome Machine (PGM™) next generation sequencing (NGS). We confirmed the identity and variant allele frequency of these variants by Sanger sequencing coupled with MVF. Furthermore, we were able to confirm these results in 1 ng, 0.5 ng or 0.1 ng of DNA from these samples. Finally, we made serial dilutions of one of these samples to establish limit of detection (LOD). We show that this workflow can detect as little as 3% of a minor variant in an FFPE sample. Sanger sequencing is the gold standard for confirmation of minor variants detected by NGS. In this study, we show that Sanger sequencing of limited number of targets, in conjunction with the MVF software, can also be an ideal first line screening choice for tumor FFPE samples where limited amount of DNA is available. For Research Use only - Not for use in diagnostic procedures. Citation Format: Arpad Gerstner, Edgar Schreiber, Stephen Jackson, Kamini Varma. Low level somatic variant detection by Sanger sequencing of formalin-fixed paraffin-embedded (FFPE) samples. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3645.

Comparative study of TERT gene mutation analysis on voided liquid-based urine cytology and paraffin-embedded tumorous tissue.

Next Generation Exome Sequencing for Identification of the Gene Mutations Associated with Loss of Heterozygozity on Chromosome 7 In Myeloid Malignancies

To summarize the genetic characteristics of 671 Chinese pedigrees affected with Duchenne/Becker muscular dystrophy (DMD/BMD). Clinical data of the pedigrees were collected. Multiplex PCR, multiple ligation dependent probe amplification (MLPA), next generation sequencing (NGS), Sanger sequencing and long read sequencing were used to detect the variant of DMD gene in the probands and their mothers, and prenatal diagnosis was provided for high risk pregnant women. Among 178 pedigrees analyzed by multiplex PCR, 44 variants of the DMD gene were detected, with the genetic diagnosis attained in 110 pedigrees. Among 493 pedigrees analyzed by MLPA in combination with NGS or Sanger sequencing, 294 pathogenic/possible pathogenic variants were identified, among which 45 were unreported previously, and the genetic diagnosis attained in 484 pedigrees. Structural variants of the DMD gene were identified in two pedigrees by long-read sequencing. Among 444 probands, 341 have inherited the DMD gene variant from their mothers (76.8%). Among 390 women with a high-risk, 339 have opted to have natural pregnancy and 51 chose preimplantation genetic testing for monogenetic disease (PGT-M). The detection rate of neonatal patients and carriers following natural pregnancy was significantly higher than that for PGT-M. Combined application of MLPA, NGS, Sanger sequencing and long-read sequencing is an effective strategy to detect DMD/BMD. PGT-M can effectively reduce the risk of fetuses. Above finding has expanded the spectrum of DMD gene variants and provided a basis for reproductive intervention for pregnancies with a high risk for DMD/BMD.

The Use of NGS for Molecular Investigations in Leukemia Adds Important Biological, Clinical and Prognostic Information Due to Its Higher Sensitivity in Comparison to the Gold Standard Sanger Sequencing