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://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
                                        • A
                                          anneng 最后由 编辑

                                          https://sci-hub.st/10.1053/j.gastro.2009.08.063

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

                                            https://jbiomedsci.biomedcentral.com/articles/10.1186/s12929-018-0442-4
                                            Applications of next-generation sequencing analysis for the detection of hepatocellular carcinoma-associated hepatitis B virus mutations
                                            这篇文章分析了HBV突变和肝癌的相关性
                                            1.对于组装 文章提到有参组装更好 相对de novo 组装而言 毕竟illumina的reads比较短

                                            2.文章里面提到了一个sample-specific 参考序列、同基因型的参考序列、其他不兼容参考序列对假阳性的影响。
                                            0b892b14-29b7-4e7f-8349-f0a7309cc54e-image.png
                                            这个文章很水 没有提到生信是怎么做的

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