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Haplotyping

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Cover of 'Haplotyping'

Table of Contents

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    Book Overview
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    Chapter 1 Haplotyping of Heterozygous SNPs in Genomic DNA Using Long-Range PCR.
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    Chapter 2 Quantification and Sequencing of Crossover Recombinant Molecules from Arabidopsis Pollen DNA.
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    Chapter 3 PacBio for Haplotyping in Gene Families
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    Chapter 4 High Molecular Weight DNA Enrichment with Peptide Nucleic Acid Probes
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    Chapter 5 High-Throughput Sequencing of the Major Histocompatibility Complex following Targeted Sequence Capture
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    Chapter 6 Pedigree-Defined Haplotypes and Their Applications to Genetic Studies
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    Chapter 7 Haplotyping a Non-meiotic Diploid Fungal Pathogen Using Induced Aneuploidies and SNP/CGH Microarray Analysis.
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    Chapter 8 Whole-Genome Haplotyping of Single Sperm of Daphnia pulex (Crustacea, Anomopoda).
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    Chapter 9 Chromosome-Range Whole-Genome High-Throughput Experimental Haplotyping by Single-Chromosome Microdissection
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    Chapter 10 Phased Genome Sequencing Through Chromosome Sorting
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    Chapter 11 Long Fragment Read (LFR) Technology: Cost-Effective, High-Quality Genome-Wide Molecular Haplotyping
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    Chapter 12 Contiguity-Preserving Transposition Sequencing (CPT-Seq) for Genome-Wide Haplotyping, Assembly, and Single-Cell ATAC-Seq
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    Chapter 13 A Fosmid Pool-Based Next Generation Sequencing Approach to Haplotype-Resolve Whole Genomes
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    Chapter 14 Discovery of Rare Haplotypes by Typing Millions of Single-Molecules with Bead Emulsion Haplotyping (BEH)
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    Chapter 15 Computational Haplotype Inference from Pooled Samples
Attention for Chapter 6: Pedigree-Defined Haplotypes and Their Applications to Genetic Studies
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Chapter title
Pedigree-Defined Haplotypes and Their Applications to Genetic Studies
Chapter number 6
Book title
Haplotyping
Published in
Methods in molecular biology, January 2017
DOI 10.1007/978-1-4939-6750-6_6
Pubmed ID
Book ISBNs
978-1-4939-6748-3, 978-1-4939-6750-6
Authors

Chester A. Alper M.D., Charles E. Larsen, Chester A. Alper

Editors

Irene Tiemann-Boege, Andrea Betancourt

Abstract

A haplotype is a string of nucleotides or alleles at nearby loci on one chromosome, usually inherited as a unit. Within the major histocompatibility complex (MHC) region on human chromosome 6p, independent population studies of multiple families have identified conserved extended haplotypes (CEHs) that segregate as long stretches (≥1 megabase) of essentially identical DNA sequence at relatively high (≥0.5 %) population frequency ("genetic fixity"). CEHs were first identified through segregation analysis in the early 1980s. In European Caucasian populations, the most frequent 30 CEHs account for at least one-third of all MHC haplotypes. These CEHs provide all of the known individual MHC susceptibility and protective genetic markers within those populations for several complex genetic diseases. Haplotypes are rigorously determined directly by sequencing single chromosomes or by Mendelian segregation analysis using families with informative genotypes. Four parental haplotypes are assigned unambiguously using genotypes from the two parents and from two of their haploidentical (to each other) children. However, the most common current technique to phase haplotypes is probabilistic statistical imputation, using unrelated subjects. Such probabilistic techniques have failed to detect CEHs and are thus of questionable value in identifying long-range haplotype structure and, consequently, genetic structure-function relationships. Finally, with haplotypes rigorously defined, association studies can determine frequencies of alleles among unrelated patient haplotypes vs. those among only unaffected family members (i.e., control alleles/haplotypes). Such studies reduce, as much as possible, the confounding effects of population stratification common to all genetic studies.

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Mendeley readers

The data shown below were compiled from readership statistics for 5 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 5 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 2 40%
Student > Bachelor 1 20%
Student > Doctoral Student 1 20%
Student > Master 1 20%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 3 60%
Agricultural and Biological Sciences 1 20%
Unknown 1 20%