Main description:

This volume details protocols for genetic, molecular, cytological, and bioinformatic methods for determining haplotypes. Haplotyping: Methods and Protocols guides readers through methods that directly type haploid cells, difficult-to-resolve gene families, high-resolution, short range haplotyping for targeted loci, and long-range haplotyping for whole chromosomes or genomes. Written in the highly 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 laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and practical Haplotyping: Methods and Protocols, aims to provide researchers with an overview of experimental methods for haplotyping.

Contents:

Part I: Haplotyping with Long Range PCR

1. Haplotyping of Heterozygous SNPs in Genomic DNA using Long Range PCR

Barbara Arbeithuber, Angelika Heissl, and Irene Tiemann-Boege

2. Quantification and Sequencing of Crossover Recombinant Molecules from Arabidopsis Pollen DNA

Kyuha Choi, Nataliya E. Yelina, Heidi Serra, and Ian R. Henderson

Part II: Selective Sequencing of Gene Families (including the MHC)

3. Pacbio for Haplotyping in Gene Families

Wei Zhang and Joachim Messing

4. High Molecular Weight DNA Enrichment with Peptide Nucleic Acid Probes

Nicholas M. Murphy, Colin W. Pouton, and Helen R. Irving

5. High-Throughput Sequencing of the Major Histocompatibility Complex following Targeted Sequence Capture

Johannes Proell, Carina Fischer, Gabriele Michelitsch, Martin Danzer, and Norbert Niklas

6. Pedigree-defined Haplotypes and their Applications to Genetic Studies

Chester A. Alper and Charles E. Larsen

Part III: Haploid-cell Typing

7. Haplotyping a Non-Meiotic Diploid Fungal Pathogen using Induced Aneuploidies and SNP/CGH Microarray Analysis

Judith Berman and Anja Forche

8. Whole-genome Haplotyping of Single Sperm of Daphnia Pulex (Crustacea, Anomopoda)

Sen Xu and Kim Young

Part IV: Haplotyping Single Chromosomes

9. Chromosome-range Whole-genome High-throughput Experimental Haplotyping by single-chromosome Microdissection

Li Ma, Wenzhi Li, and Qing Song

10. Phased Genome Sequencing through Chromosome Sorting

Xi Chen, Hong Yang, and Wing Hung Wong

Part V: Genome Wide Haplotyping

11. Long Fragment Read (LFR) Technology: Cost-effective, High-quality Genome-wide Molecular Haplotyping

Mark A. McElwain, Rebecca Yu Zhang, Radoje Drmanac, and Brock A. Peters

12. Contiguity-Preserving Transposition Sequencing (CPT-seq) for Genome-Wide Haplotyping, Assembly, and Single-Cell ATAC-seq

Lena Christiansen, Sasan Amini, Fan Zhang, Mostafa Ronaghi, Kevin L. Gunderson, and Frank J. Steemers

13. Fosmid Pool-Based Next Generation Sequencing to Haplotype-Resolve Whole Genomes

Eun-Kyung Suk, Sabrina Schulz, Birgit Mentrup, Thomas Huebsch, Jorge Duitama,

and Margret R. Hoehe

Part VI: High throughput Haplotyping of Rare Variants

14. Discovery of Rare-haplotype Variants by Typing Millions of Single-molecules with Bead Emulsion Haplotyping (BEH)

Elisabeth Palzenberger, Ronja Reinhardt, Leila Muresan, Barbara Palaoro, and Irene Tiemann-Boege

Part VII: Computational Algorithms for Haplotyping

15. Computational Haplotype Inference from Pooled Samples

Quan Long