ArticleGenome research2011
A comprehensively molecular haplotype-resolved genome of a European individual.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed.
- A library of avian proteins improves palaeoproteomic taxonomic identification and reveals widespread intraspecies variability.Nature communications · 2025Article
- Haplotyping-Assisted Diploid Assembly and Variant Detection with Linked Reads.Methods in molecular biology (Clifton, N.J.) · 2023Review
- A Simple Cost-Effective Method for Whole-Genome Sequencing, Haplotyping, and Assembly.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Phased Genome Assemblies.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Analysis of 1276 Haplotype-Resolved Genomes Allows Characterization of Cis- and Trans-Abundant Genes.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing.Nucleic acids research · 2022Article
- Cataloguing experimentally confirmed 80.7 kb-long ACKR1 haplotypes from the 1000 Genomes Project database.BMC bioinformatics · 2021Article
- Determination of complete chromosomal haplotypes by bulk DNA sequencing.Genome biology · 2021Article
- Oligogenic Inheritance Underlying Incomplete Penetrance ofFrontiers in genetics · 2021Article
- Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly.Genome research · 2019Article
- Significant abundance of cis configurations of coding variants in diploid human genomes.Nucleic acids research · 2019Article
- Comparison of phasing strategies for whole human genomes.PLoS genetics · 2018Article
- Better ILP models for haplotype assembly.BMC bioinformatics · 2018Article
- Article
- Recent Advances in Experimental Whole Genome Haplotyping Methods.International journal of molecular sciences · 2017Review
- HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies.Genome research · 2017Article
- A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree.Genome research · 2017Article
- Chromosome-Range Whole-Genome High-Throughput Experimental Haplotyping by Single-Chromosome Microdissection.Methods in molecular biology (Clifton, N.J.) · 2017Article
- Article
- An accurate clone-based haplotyping method by overlapping pool sequencing.Nucleic acids research · 2016Article
Corrections and comments
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Independent determination of both haplotype sequences of an individual genome is essential to relate genetic variation to genome function, phenotype, and disease. To address the importance of phase, we have generated the most complete haplotype-resolved genome to date, "Max Planck One" (MP1), by fosmid pool-based next generation sequencing. Virtually all SNPs (>99%) and 80,000 indels were phased into haploid sequences of up to 6.3 Mb (N50 ~1 Mb). The completeness of phasing allowed determination of the concrete molecular haplotype pairs for the vast majority of genes (81%) including potential regulatory sequences, of which >90% were found to be constituted by two different molecular forms. A subset of 159 genes with potentially severe mutations in either cis or trans configurations exemplified in particular the role of phase for gene function, disease, and clinical interpretation of personal genomes (e.g., BRCA1). Extended genomic regions harboring manifold combinations of physically and/or functionally related genes and regulatory elements were resolved into their underlying "haploid landscapes," which may define the functional genome. Moreover, the majority of genes and functional sequences were found to contain individual or rare SNPs, which cannot be phased from population data alone, emphasizing the importance of molecular phasing for characterizing a genome in its molecular individuality. Our work provides the foundation to understand that the distinction of molecular haplotypes is essential to resolve the (inherently individual) biology of genes, genomes, and disease, establishing a reference point for "phase-sensitive" personal genomics. MP1's annotated haploid genomes are available as a public resource.
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