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.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
                                    • A
                                      anneng 最后由 anneng 编辑

                                      二代数据分析过程
                                      对比分型
                                      使用比对 直接将reads比对到参考基因组上 然后进行统计

                                      blast分型
                                      使用blast直接和hdvdb进行对比查询（ncbi自己的分型工具对查询序列进行了分段 类似kmer 我们一般拿到的reads双端文件 感觉和这种分段很类似 可以直接查询 也不用组装了）ncbi宣称好处是可以找出“重组”过的病毒类型 即一个病毒由多个病毒拼接而成 这种情况很难和混合样本（一个样本有多个分型的感染）区分开
                                      e76e0106-c88e-4c78-80c6-d707708cc59b-image.png
                                      直接使用reads 来分型 可以参考这个文章
                                      https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC4382110/
                                      进化树方式进行分型：
                                      1.fastp ：质控和预处理
                                      2.去接头（可选）
                                      3.过滤：碱基质量
                                      4.比对：bowtie2、bwa-mem 和通用株X02763
                                      5.排序、去重：Samtools
                                      6.生成一致性序列：CliqueSNV
                                      7.多序列比对：和hdvdb数据库进行多序列比对（blast方法不需要这个步骤 由于病毒的变化很多 很可能在多序列比对时无法有效对齐）
                                      8.构建进化树：MEGA 7 maximum-likelihood方法 该步骤就可以得到每个样本的分型

                                      构建单倍型 Haplotype construction
                                      1.比对：和该样本的对应分型参考序列进行比对
                                      bowtie2's very-sensitive-local
                                      2.去重：Sambamba
                                      3.构建单倍型：CliqueSNV

                                      diversity analysis
                                      香农商Shannon entropy (Sn)：
                                      S = −pilnpi, where pi is the frequency of each haplotype in the viral quasispecies population
                                      genetic diversity (D) ：MEGA X v10.1.8 genetic distance of the haplotypes
                                      病毒进化率 viral evolutionary rates：MEGA 7 HKY substitution model 、BEAST v2.6.3、Tracer

                                      统计分析
                                      SPSS

                                      突变分析
                                      Samtools mpileup：

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

                                        https://www.rivm.nl/mpf/typingtool/hev/introduction
                                        一个在线的hev的分型工具 有参考报告

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

                                          https://livedataoxford.shinyapps.io/1510659619-3Xkoe2NKkKJ7Drg/
                                          一个shinyapps 展示了非洲的HBV耐药性
                                          https://github.com/martinjhnhadley/hbv-alignment-viz

                                          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/11230757/
                                            Nomenclature for antiviral-resistant human hepatitis B virus mutations in the polymerase region
                                            HBV耐药性突变的命名规则 rtL180M

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