暗能星系
    • 登录
    • 搜索

    HBV分析

    微生物组分析
    1
    52
    82
    正在加载更多帖子
    • 从旧到新
    • 从新到旧
    • 最多赞同
    回复
    • 在新帖中回复
    登录后回复
    此主题已被删除。只有拥有主题管理权限的用户可以查看。
    • A
      anneng 最后由 编辑

      https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC4448583/
      Hepatitis B Virus Genotypes and Variants
      HBV 基因型、血清型、亚型的地理分布
      ec2b53eb-132a-4380-a9c0-69a046258090-image.png

      1 条回复 最后回复 回复 引用 0
      • A
        anneng 最后由 编辑

        https://www.ablsa.com/laboratory-applications/deepchek-hbv-software-ce-ivd/
        0d63d973-527d-49ea-b98f-0b3bbe3f5c16-image.png
        28afe20c-103a-40a8-952f-b55b4d1ce005-image.png
        d47e8b6a-ce26-4e97-b34b-c4b764d3dc54-image.png

        1 条回复 最后回复 回复 引用 0
        • A
          anneng 最后由 编辑

          https://www.nature.com/articles/srep28274
          A fast and low-cost genotyping method for hepatitis B virus based on pattern recognition in point-of-care settings

          1 条回复 最后回复 回复 引用 0
          • A
            anneng 最后由 anneng 编辑

            https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC7564258/
            9e3c2efc-187d-41c6-80e7-0894c75be13a-image.png
            分型的方法：
            Sanger sequencing：
            Sanger sequencing is often restricted to analyzing the S gene and is inaccurate for detecting minority genetic variants
            reverse hybridization：
            reverse hybridization detects only known mutations

            这个文档提到的分型方法
            The analyzed data was deposited in the NCBI SRA database under the bioproject number PRJNA659786 and the accession numbers SRR12535947, SRR12535946, SRR12535938, SRR12535937 and SRR12535936. The read quality was accessed using FastQC and reads of <150 nt were excluded using Trimmomaticv0.36 [22]; the latter program was also used to filter the reads (Illuminaclip, Headcrop = 14, Leading = 3, Trailing = 3, Slidingwindow = 4:30, Minlen = 18).

            The high-quality reads (all samples with minimum Q-Score = 30) were mapped, independently, over all genomes of all eight HBV genotypes obtained from HBVdb [21] using Bowtie2 v2.3.2. [23] with stringent parameters (–very-sensitive, –no-discordant –N 0 –L 4, –gbar 10). The aligned read counting was performed using Bed tools multiBamCov v2.25.0 [24] (default) and was loaded into an in-house Python script for mean coverage plot and genotype determination; moreover, genomic coverage throughout the A, D, and G genomes was compared using Circos plot [25].

            1 条回复 最后回复 回复 引用 0
            • A
              anneng 最后由 编辑

              https://www.news-medical.net/health/Hepatitis-B-Structure-Capsid-Flexibility-and-Function.aspx
              表达的抗原
              2e17c577-2f17-4507-8619-e3cdd7f547af-image.png

              1 条回复 最后回复 回复 引用 0
              • A
                anneng 最后由 anneng 编辑

                https://www.ncbi.nlm.nih.gov/nuccore/AB981583.1
                参考基因组

                https://hbvdb.lyon.inserm.fr/HBVdb/
                HBV数据库 可以找到各种分型好的序列
                https://academic.oup.com/nar/article/41/D1/D566/1051781
                HBVdb: a knowledge database for Hepatitis B Virus

                dfbfa074-495d-4f7e-87c7-411930e98eba-image.png

                1 条回复 最后回复 回复 引用 0
                • A
                  anneng 最后由 编辑

                  https://pubmed.ncbi.nlm.nih.gov/25034481/
                  Genotypes and genetic variability of hepatitis B virus
                  Based on an intergroup divergence of greater than 7.5%
                  across the complete genome, HBV has been classified phylogenetically into 9 genotypes, A–I, with a putative 10th genotype ‘J’, isolated from a single individual.
                  基因组之间差异7.5%作为分类的边界值

                  1 条回复 最后回复 回复 引用 0
                  • A
                    anneng 最后由 anneng 编辑

                    https://github.com/DrTrevorBell/CCT

                    http://hbv-glue.cvr.gla.ac.uk/#/home
                    GLUE
                    http://hbv-glue.cvr.gla.ac.uk/#/aboutGlueProject

                    https://github.com/LosicLab/ViralMine
                    A pipeline tool that mines unmapped RNA/DNA reads for viral sequences and predicts viral genotype (built for HBV)

                    https://www.ncbi.nlm.nih.gov/projects/genotyping/formpagex.cgi
                    b2c14f82-f146-4762-bd98-df3bb39e5f20-image.png
                    https://pubmed.ncbi.nlm.nih.gov/15215470/

                    https://github.com/tacatanach/Hepatitis_B_Virus_alignment
                    NCBI的分型曲线解释：
                    1.矩形是按照窗口作为宽度 每个窗口内步进的各个矩形堆叠展示
                    2.曲线Y是score值 X是每个窗口的起始点坐标
                    这些数据可以下载下来 用excel处理 如下：
                    bb80e687-e881-4e69-a854-64158d0c093a-image.png

                    1 条回复 最后回复 回复 引用 0
                    • A
                      anneng 最后由 anneng 编辑

                      https://www.frontiersin.org/articles/10.3389/fmicb.2020.616023/full
                      Comprehensive Analysis of Clinically Significant Hepatitis B Virus Mutations in Relation to Genotype, Subgenotype and Geographic Region
                      临床样本的突变分析
                      immune escape,
                      antiviral resistance
                      hepatocellular carcinoma (HCC)

                      该文章提到了一些突变的临床意义
                      https://www.sciencedirect.com/science/article/abs/pii/S001650850901556X

                      1 条回复 最后回复 回复 引用 0
                      • A
                        anneng 最后由 编辑

                        分型方法研究：
                        https://www.sciencedirect.com/science/article/pii/S1201971210024239

                        https://onlinelibrary.wiley.com/doi/abs/10.1002/rmv.400
                        Hepatitis B virus genotypes: comparison of genotyping methods
                        35b0b9d6-f965-41ee-8204-e75835e9c3e9-image.png

                        https://journals.asm.org/doi/pdf/10.1128/cmr.00009-07
                        Molecular Testing in the Diagnosis and Management of
                        Chronic Hepatitis B

                        https://bmcinfectdis.biomedcentral.com/articles/10.1186/s12879-020-05269-z
                        Distribution of hepatitis B virus genotypes in the general population of Myanmar via nationwide study

                        https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC4431363/
                        Sequence-based genotyping of hepatitis B virus in general population

                        1 条回复 最后回复 回复 引用 0
                        • A
                          anneng 最后由 编辑

                          Illumina and Nanopore methods for whole genome sequencing of hepatitis B virus (HBV)
                          https://www.nature.com/articles/s41598-019-43524-9#Sec11

                          1 条回复 最后回复 回复 引用 0
                          • A
                            anneng 最后由 编辑

                            https://bmcinfectdis.biomedcentral.com/track/pdf/10.1186/s12879-017-2697-x.pdf
                            Molecular characterization of hepatitis B
                            virus in Vietnam
                            The Illumina fastq sequence files were assembled
                            using Genious 8.0.5, software package (Biomatters
                            Ltd, AK, New Zeland) utilizing a reference-based
                            mapping tool after primer sequence clipping (i.e. the
                            consensus sequence was obtained by mapping individual reads of each sample to a reference sequence).
                            Finally, screening of minor (sub-consensus) variants
                            was performed using the SNP detection tool available
                            in Geneious. A minimum variant frequency of 5% and
                            500-fold coverage were chosen as cut-off values.

                            1 条回复 最后回复 回复 引用 0
                            • A
                              anneng 最后由 编辑

                              https://sci-hub.st/10.1007/978-1-4939-6700-1_17
                              Deep Sequencing of the Hepatitis B Virus Genome: Analysis
                              of Multiple Samples by Implementation of the Illumina
                              Platform
                              A BLASTN comparison analysis is performed between clean
                              reads and the HBV genomic reference sequence, to eliminate
                              non-HBV sequences (anything with similarity<70%). After
                              this filtering step, the average coverage of HBV sequence site
                              should be above 2600× (Fig. 1).
                              6. Shan entropy and Relative entropy calculations are carried out.

                              1 条回复 最后回复 回复 引用 0
                              • A
                                anneng 最后由 编辑

                                Identification and Comparative Analysis of Hepatitis B Virus Genotype D/E Recombinants in Africa
                                https://stacks.cdc.gov/view/cdc/50437

                                1 条回复 最后回复 回复 引用 0
                                • A
                                  anneng 最后由 编辑

                                  https://sci-hub.st/10.1016/j.jviromet.2013.06.015
                                  08373011-71d4-4b31-9a33-846b89b5eebb-image.png

                                  1 条回复 最后回复 回复 引用 0
                                  • A
                                    anneng 最后由 编辑

                                    https://github.com/hr283

                                    1 条回复 最后回复 回复 引用 0
                                    • A
                                      anneng 最后由 编辑

                                      The Study of Hepatitis B Virus Using Bioinformatics
                                      https://www.intechopen.com/chapters/50624

                                      1 条回复 最后回复 回复 引用 0
                                      • A
                                        anneng 最后由 anneng 编辑

                                        https://hbv.geno2pheno.org/
                                        http://www.hiv-grade.de/hbv_grade/deployed/grade

                                        分型工具和耐药分型

                                        1 条回复 最后回复 回复 引用 0
                                        • A
                                          anneng 最后由 编辑

                                          https://www.niid.go.jp/niid/images/JJID/58/244.pdf
                                          Analysis of genomic-length HBV sequences to determine genotype and subgenotype reference sequences

                                          1 条回复 最后回复 回复 引用 0
                                          • A
                                            anneng 最后由 anneng 编辑

                                            https://www.sciencedirect.com/science/article/pii/S1567134821004846#bb0040
                                            Analysis of entire hepatitis B virus genomes reveals reversion of mutations to wild type in natural infection, a 15 year follow-up study

                                            2.6. NGS data preprocessing and sample genotyping
                                            Quality control and preprocessing of each sample's raw NGS short reads was performed by fastp v0.20.1 (Chen et al., 2018). The adapter sequences were removed and 15 bases of each read were trimmed from the 5’end. Any reads with an average quality score lower than 30, or length shorter than 50 nt, were filtered further. The remaining high quality reads from each sample were then mapped to a common reference sequence (accession no. X02763) using bowtie2 v2.3.4.1 (Langmead and Salzberg, 2012). After sorting and removing the duplications using Samtools v1.7 (Li et al., 2009), the consensus sequence was generated using CliqueSNV v1.5.3 (Knyazev et al., 2021). Consensus sequences of all samples were then multi-aligned with the reference sequences from HBVdb (Hayer et al., 2013) and three additional sequences, including FJ023664 of genotype I, AB486012 of genotype J, and AM117397 from Africa chimpanzees as the outgroup. A maximum-likelihood tree was then constructed using MEGA 7 (Kumar et al., 2016) and each sample was genotyped accordingly.

                                            这个文章里面做consensus序列的时候 用的是 cliqueSNV 该软件和samtools consensus 的对比需要研究下：
                                            48ce066a-c93b-45f1-8f55-f569eb742f4d-image.png

                                            2.7. Haplotype construction and diversity analysis
                                            分型完毕后 每个样本对应的参考序列就可以更具体 然后进行突变分析
                                            bowtie2's very-sensitive-local 比对
                                            Sambamba 去重
                                            CliqueSNV haplotype reconstruction
                                            haplotypes with a minimum abundance of 1%

                                            1 条回复 最后回复 回复 引用 0
                                            • First post
                                              Last post
                                            Powered by 暗能星系