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Title:           Comprehensive identification of somatic nucleotide variants in human brain tissue
Subject:         Genome Biology, 2021, doi:10.1186/s13059-021-02285-3
Keywords:        
Author:          Yifan Wang
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     Item: 
      Title: Abstract
      Destination: sectionAbs1
      Children: 
       Item: 
        Title: Background
        Destination: sectionASec1
       Item: 
        Title: Results
        Destination: sectionASec2
       Item: 
        Title: Conclusions
        Destination: sectionASec3
     Item: 
      Title: Introduction
      Destination: sectionSec1
     Item: 
      Title: Results
      Destination: sectionSec2
      Children: 
       Item: 
        Title: The detection of simulated somatic SNVs in DNA mixing experiments
        Destination: sectionSec3
       Item: 
        Title: The generation of a somatic SNV call set from a neurotypical brain sample
        Destination: sectionSec4
       Item: 
        Title: Sources of false-positive SNV calls and filtering strategies
        Destination: sectionSec5
        Children: 
         Item: 
          Title: Germline SNPs
          Destination: sectionSec6
         Item: 
          Title: Sequencing and/or mapping artifacts
          Destination: sectionSec7
         Item: 
          Title: Genomic context
          Destination: sectionSec8
         Item: 
          Title: Unrelated samples and replicate samples
          Destination: sectionSec9
       Item: 
        Title: Best practices for calling mosaic SNVs
        Destination: sectionSec10
       Item: 
        Title: Using somatic SNVs to recreate cell lineage trees
        Destination: sectionSec11
     Item: 
      Title: Discussion
      Destination: sectionSec12
     Item: 
      Title: Methods
      Destination: sectionSec13
      Children: 
       Item: 
        Title: Data generation
        Destination: sectionSec14
        Children: 
         Item: 
          Title: Mixing experiment (Mount Sinai School of Medicine, contributed by Attila G. Jones)
          Destination: sectionSec15
         Item: 
          Title: Sample processing (Lieber Institute for Brain Development, contributed by Daniel Weinberger)
          Destination: sectionSec16
         Item: 
          Title: Whole-exome sequencing replicate 1 (University of Michigan, contributed by Sarah Emery and Yifan Wang)
          Destination: sectionSec17
         Item: 
          Title: Whole-exome sequencing replicate 2 (University of California San Diego, contributed by Laurel Ball)
          Destination: sectionSec18
         Item: 
          Title: Whole-genome sequencing replicate 3 (Yale University and Institut de Biologia Evolutiva, contributed by Irene Lobon)
          Destination: sectionSec19
         Item: 
          Title: Whole-genome sequencing replicate 4 (Lieber Institute for Brain Development, contributed by Rujuta Narurkar and Joo Heon Shin)
          Destination: sectionSec20
         Item: 
          Title: Whole-genome sequencing replicate 5 (Harvard University, contributed by Javier Ganz)
          Destination: sectionSec21
         Item: 
          Title: Whole-genome sequencing replicate 6 (Yale University, contributed by Liana Fasching)
          Destination: sectionSec22
         Item: 
          Title: Whole genome sequencing of single cells (Yale University and Stanford University, contributed by Liana Fasching, Livia Tomasini, and Bo Zhou)
          Destination: sectionSec23
         Item: 
          Title: Chromium linked read sequencing (University of Michigan, contributed by Sarah Emery and Yifan Wang)
          Destination: sectionSec24
         Item: 
          Title: Data uniform processing at Amazon Web Services (Mayo Clinic, contributed by Taejeong Bae)
          Destination: sectionSec25
       Item: 
        Title: Calling variants in the reference brain
        Destination: sectionSec26
        Children: 
         Item: 
          Title: Method 1 (University of California in San Diego, contributed by Xiaoxu Yang)
          Destination: sectionSec27
         Item: 
          Title: Method 2 (Yale University and Institut de Biologia Evolutiva, contributed by Irene Lobon)
          Destination: sectionSec28
         Item: 
          Title: Method 3 (Harvard University, contributed by Alon Galor and Max Sherman)
          Destination: sectionSec29
         Item: 
          Title: Method 4 (Kennedy Krieger Institute, contributed by Jeremy Thorpe)
          Destination: sectionSec30
         Item: 
          Title: Method 5 (Mayo Clinic, contributed by Taejeong Bae)
          Destination: sectionSec31
         Item: 
          Title: Method 6 (University of Michigan, contributed by Yifan Wang)
          Destination: sectionSec32
       Item: 
        Title: Validation with targeted PCR amplicon-based sequencing approaches
        Destination: sectionSec33
        Children: 
         Item: 
          Title: Amplicon 1 (Yale University, contributed by Liana Fasching and Simone Tomasi)
          Destination: sectionSec34
         Item: 
          Title: Amplicon 2 (University of Michigan, contributed by Sarah Emery and Yifan Wang)
          Destination: sectionSec35
         Item: 
          Title: Amplicon 3 (Mount Sinai School of Medicine, contributed by Chaggai Rosenbluh)
          Destination: sectionSec36
         Item: 
          Title: Amplicon 4 (Harvard University, contributed by Javier Ganz)
          Destination: sectionSec37
         Item: 
          Title: Amplicon 5 (Kennedy Krieger Institute, contributed by Jeremy Thorpe)
          Destination: sectionSec38
         Item: 
          Title: Amplicon sequencing data analysis pipeline (University of Michigan, contributed by Yifan Wang)
          Destination: sectionSec39
         Item: 
          Title: Variant validation using single cells (Harvard University, contributed by Alon Galor and Max Sherman)
          Destination: sectionSec40
         Item: 
          Title: Variant validation using 10X linked read data (University of Michigan, contributed by Yifan Wang and Jeffrey Kidd)
          Destination: sectionSec41
         Item: 
          Title: Variant validation using ddPCR (Stanford University, contributed by Reenal Pattni)
          Destination: sectionSec42
         Item: 
          Title: Validation result consolidation (University of Michigan and Mayo Clinic, contributed by Yifan Wang and Alexej Abyzov)
          Destination: sectionSec43
         Item: 
          Title: Panel of normal (PON) mask using 1000 genomes 2504 whole-genome sequencing libraries (University of Michigan, contributed by Yifan Wang and Jeffrey Kidd)
          Destination: sectionSec44
         Item: 
          Title: Classifying false-positive calls (Harvard University, contributed by Max Sherman)
          Destination: sectionSec45
         Item: 
          Title: Naive Bayes classifier combining validation approaches (Harvard University, contributed by Max Sherman)
          Destination: sectionSec46
         Item: 
          Title: Implementation of the best practices workflow (Mayo Clinic, contributed by Taejeong Bae)
          Destination: sectionSec47
         Item: 
          Title: Cell lineage tree reconstruction (Mayo Clinic, contributed by Taejeong Bae)
          Destination: sectionSec48
         Item: 
          Title: Predicting early cell lineages from bulk DNA (Mayo Clinic, contributed by Taejeong Bae)
          Destination: sectionSec49
     Item: 
      Title: Supplementary Information
      Destination: sectionSec50
     Item: 
      Title: Acknowledgements
      Destination: section1
     Item: 
      Title: Review history
      Destination: sectionFPar1
     Item: 
      Title: Peer review information
      Destination: sectionFPar2
     Item: 
      Title: Authors’ contributions
      Destination: section2
     Item: 
      Title: Funding
      Destination: section3
     Item: 
      Title: Availability of data and materials
      Destination: section4
     Item: 
      Title: Ethics approval and consent to participate
      Destination: sectionFPar3
     Item: 
      Title: Competing interests
      Destination: sectionFPar4
     Item: 
      Title: Author details
      Destination: section5
     Item: 
      Title: References
      Destination: sectionBib1
     Item: 
      Title: Publisher’s Note
      Destination: ArtNote1
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    Author: Yifan Wang
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    Keywords: 
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   Type: CRC32
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