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Haplotyping

Methods and Protocols

  • Book
  • © 2023

Overview

Editors:
  1. Brock A. Peters

    1. Advanced Genomics Technology Laboratory, Complete Genomics/MGI, San Jose, USA

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    You can also search for this editor in PubMed   Google Scholar

  2. Radoje Drmanac

    1. Advanced Genomics Technology Laboratory, Complete Genomics/MGI, San Jose, USA

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2590)

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Interrogating the Human Diplome: Computational Methods, Emerging Applications, and Challenges

    • Agnes P. Chan, Yongwook Choi, Aditya Rangan, Guangfa Zhang, Avijit Podder, Michael Berens et al.
    Pages 1-30

  3. Targeted Locus Amplification and Haplotyping

    • Juliet W. Lefferts, Vera Boersma, Marne C. Hagemeijer, Karima Hajo, Jeffrey M. Beekman, Erik Splinter
    Pages 31-48Open Access

  4. Full-Length Transcript Phasing with Third-Generation Sequencing

    • Nenad Svrzikapa, Ramakrishna Boyanapalli
    Pages 49-57

  5. Large-Scale Complete Sequencing and Haplotyping of 1–10 kb DNA Molecules Using Short Massively Parallel Reads

    • Youtao Liu, Fei Fan, Radoje Drmanac, Brock A. Peters, Ou Wang
    Pages 59-70

  6. Accurate Sequencing and Haplotyping from 10 Cells Using Long Fragment Read (LFR) Technology

    • Mark A. McElwain, Brock A. Peters
    Pages 71-84

  7. Low-Cost Genome-Scale Phasing with Barcode-Linked Sequencing

    • David Redin
    Pages 85-99

  8. A Simple Cost-Effective Method for Whole-Genome Sequencing, Haplotyping, and Assembly

    • Ou Wang, Xiaofang Cheng, Radoje Drmanac, Brock A. Peters
    Pages 101-125

  9. Read-Based Phasing and Analysis of Phased Variants with WhatsHap

    • Marcel Martin, Peter Ebert, Tobias Marschall
    Pages 127-138Open Access

  10. HapCUT2: A Method for Phasing Genomes Using Experimental Sequence Data

    • Vikas Bansal
    Pages 139-147

  11. Determining Complete Chromosomal Haplotypes by mLinker

    • Sumit Sinha, Cheng-Zhong Zhang
    Pages 149-159

  12. Haplotyping-Assisted Diploid Assembly and Variant Detection with Linked Reads

    • Yunfei Hu, Chao Yang, Lu Zhang, Xin Zhou
    Pages 161-182

  13. Chromosome-Length Haplotypes with StrandPhaseR and Strand-seq

    • Vincent C. T. Hanlon, David Porubsky, Peter M. Lansdorp
    Pages 183-200

  14. Gamete Binning to Achieve Haplotype-Resolved Genome Assembly

    • Hequan Sun, José A. Campoy, Korbinian Schneeberger
    Pages 201-218

  15. Phasing DNA Methylation

    • Vahid Akbari, Steven J. M. Jones
    Pages 219-235

  16. Analysis of 1276 Haplotype-Resolved Genomes Allows Characterization of Cis- and Trans-Abundant Genes

    • Margret R. Hoehe, Ralf Herwig
    Pages 237-272

  17. Phased Genome Assemblies

    • Jorge Duitama
    Pages 273-286

  18. Haplotype-Assisted Noninvasive Prenatal Diagnosis of Genetic Diseases by Massively Parallel Sequencing of Maternal Plasma Cell-Free DNA

    • Jia Ju, Fengxia Su, Chao Chen, Jun Sun, Ya Gao
    Pages 287-294

  19. Back Matter

    Pages 295-298
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Keywords

About this book

This book aims to be an introduction to haplotype information for both the wet and dry labs. Chapters detail co-barcoding and linked-reads based methods, third generation sequencing based methods, Hi-C based methods, single-cell and Strand-seq, and methods for using haplotype data once obtained. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls.

 

Authoritative and cutting-edge, Haplotyping: Methods and Protocols aims to provide compréhensive and accessible methods to undergraduate, graduate, and established scientists.


Editors and Affiliations

  • Advanced Genomics Technology Laboratory, Complete Genomics/MGI, San Jose, USA

    Brock A. Peters, Radoje Drmanac

Bibliographic Information

  • Book Title: Haplotyping

  • Book Subtitle: Methods and Protocols

  • Editors: Brock A. Peters, Radoje Drmanac

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-2819-5

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2023

  • Hardcover ISBN: 978-1-0716-2818-8Published: 07 November 2022

  • Softcover ISBN: 978-1-0716-2821-8Published: 08 November 2023

  • eBook ISBN: 978-1-0716-2819-5Published: 06 November 2022

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 298

  • Number of Illustrations: 10 b/w illustrations, 40 illustrations in colour

  • Topics: Genetics and Genomics

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