Everything about Haplotype

🧭 Start here: a 6-step reading path

1. Read the overview: HaplotypeA 5-minute orientation
2. Skim a recent paper: Haplotype-resolved assembly of diploid genomes without parental dataInfluential work since 2022
3. Pick up a classic book: New mathematical methods in human gene mappingThe most-reprinted book on the subject
4. Read the landmark paper: Haploview: analysis and visualization of LD and haplotype mapsCited 12,488 times
5. Go sideways: Unique-event polymorphismA closely related topic
6. Go sideways: List of genetic genealogy topicsA closely related topic

🏆 Landmark papers (most cited)

• Haploview: analysis and visualization of LD and haplotype maps

  J. C. Barrett, B. Fry, J. Maller · 2004 · Bioinformatics · 12,488 citations

• popart : full‐feature software for haplotype network construction

  Jessica W. Leigh, David Bryant · 2015 · Methods in Ecology and Evolution · 6,408 citations

• A New Statistical Method for Haplotype Reconstruction from Population Data

  Matthew Stephens, Nicholas J. Smith, Peter Donnelly · 2001 · The American Journal of Human Genetics · 6,355 citations

• Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

  Haoyu Cheng, Gregory T. Concepcion, Xiaowen Feng · 2021 · Nature Methods · 6,277 citations

• The Structure of Haplotype Blocks in the Human Genome

  Stacey B. Gabriel, Stephen F. Schaffner, Huy Nguyen · 2002 · Science · 4,815 citations

• A haplotype map of the human genome

  The International HapMap Consortium · 2005 · Nature · 4,800 citations

• A second generation human haplotype map of over 3.1 million SNPs

  The International HapMap Consortium · 2007 · Nature · 3,895 citations

• Rapid and Accurate Haplotype Phasing and Missing-Data Inference for Whole-Genome Association Studies By Use of Localized Haplotype Clustering

  Sharon R. Browning, Brian L. Browning · 2007 · The American Journal of Human Genetics · 3,101 citations

🆕 Influential since 2022

• Haplotype-resolved assembly of diploid genomes without parental data

  Haoyu Cheng, Erich D. Jarvis, Olivier Fedrigo · 2022 · Nature Biotechnology · 1,133 citations

• Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar

  Hequan Sun, Wen-Biao Jiao, Kristin Krause · 2022 · Nature Genetics · 222 citations

• Chromosome-level scaffolding of haplotype-resolved assemblies using Hi-C data without reference genomes

  Xiaofei Zeng, Zili Yi, Xingtan Zhang · 2024 · Nature Plants · 192 citations

• Haplotype-aware analysis of somatic copy number variations from single-cell transcriptomes

  Teng Gao, Ruslan Soldatov, Hirak Sarkar · 2022 · Nature Biotechnology · 190 citations

• Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation

  Mikhail Kolmogorov, Kimberley J. Billingsley, Mira Mastoras · 2023 · Nature Methods · 145 citations

📚 Books worth reading

• 📕New mathematical methods in human gene mappingJoseph Douglas Terwilliger · 1993
• 📕Influence of recombination on the diversification of the murine I regionRoy William Tarnuzzer · 1988

Ranked by number of editions on Open Library, a rough measure of how lasting a book is.

🔗 Related topics

• Unique-event polymorphism In genetic genealogy, a unique-event polymorphism (UEP) is a genetic marker that corresponds to a mutation that is likely to occur so infrequently that…
• List of genetic genealogy topics This is a list of genetic genealogy topics. Genetic genealogy Genealogical DNA test Human mitochondrial DNA haplogroups Human Y-chromosome DNA haplogroups…
• Linkage disequilibrium Linkage disequilibrium, often abbreviated to LD, is a term in population genetics referring to the association of genes, usually linked genes, in a population…
• Tag SNP A tag SNP is a representative single nucleotide polymorphism (SNP) in a region of the genome with high linkage disequilibrium that represents a group of…
• International HapMap Project The International HapMap Project is an organization that aimed to develop a haplotype map (HapMap) of the human genome, to describe the common patterns…
• Microfluidic whole genome haplotyping Microfluidic whole genome haplotyping is a technique for the physical separation of individual chromosomes from a metaphase cell followed by direct resolution…
• Mayan genetics The relationship of the Mayas to other indigenous peoples of the Americas has been assessed using traditional genetic markers. Mayas inhabited several…
• Genetic association Genetic association is when one or more genotypes within a population co-occur with a phenotypic trait more often than would be expected by chance occurrence…