ArticleBMC bioinformatics2014
Efficient haplotype block recognition of very long and dense genetic sequences.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 2 of them syntheses that pooled it.
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Who cites it
31 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure.Briefings in bioinformatics · 2022Pooled it
- JAM: A Scalable Bayesian Framework for Joint Analysis of Marginal SNP Effects.Genetic epidemiology · 2016Pooled it
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- SNPs with High Linkage Disequilibrium Increase the Explained Genetic Variance and the Reliability of Genomic Predictions.Animals : an open access journal from MDPI · 2026Article
- Genomic and molecular evidence that the LncRNA DSP-AS1 modulates desmoplakin expression.Human genetics · 2025Article
- Genome-specific association study (GSAS) for exploration of variability in hemp (Cannabis sativa).Scientific reports · 2025Article
- Genomic analysis of three medieval parchments from German monasteries.Scientific reports · 2025Article
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- Computing linkage disequilibrium aware genome embeddings using autoencoders.Bioinformatics (Oxford, England) · 2024Article
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- Genomic evidence of sex chromosome aneuploidy and infection-associated genotypes in the tsetse fly Glossina fuscipes, the major vector of African trypanosomiasis in Uganda.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2023Article
- SNP- and haplotype-based single-step genomic predictions for body weight, wool, and reproductive traits in North American Rambouillet sheep.Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie · 2023Article
- On the origin and structure of haplotype blocks.Molecular ecology · 2023Article
- Rare and population-specific functional variation across pig lines.Genetics, selection, evolution : GSE · 2022Article
- Initiation of genomics-assisted breeding in Virginia-type peanuts through the generation of aFrontiers in plant science · 2022Article
- Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations.PLoS computational biology · 2022Article
- Bayesian optimization of multivariate genomic prediction models based on secondary traits for improved accuracy gains and phenotyping costs.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Article
- RAINBOW: Haplotype-based genome-wide association study using a novel SNP-set method.PLoS computational biology · 2020Article
- gpart: human genome partitioning and visualization of high-density SNP data by identifying haplotype blocks.Bioinformatics (Oxford, England) · 2019Article
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Abstract
backgroundThe new sequencing technologies enable to scan very long and dense genetic sequences, obtaining datasets of genetic markers that are an order of magnitude larger than previously available. Such genetic sequences are characterized by common alleles interspersed with multiple rarer alleles. This situation has renewed the interest for the identification of haplotypes carrying the rare risk alleles. However, large scale explorations of the linkage-disequilibrium (LD) pattern to identify haplotype blocks are not easy to perform, because traditional algorithms have at least Θ(n2) time and memory complexity.
resultsWe derived three incremental optimizations of the widely used haplotype block recognition algorithm proposed by Gabriel et al. in 2002. Our most efficient solution, called MIG ++, has only Θ(n) memory complexity and, on a genome-wide scale, it omits >80% of the calculations, which makes it an order of magnitude faster than the original algorithm. Differently from the existing software, the MIG ++ analyzes the LD between SNPs at any distance, avoiding restrictions on the maximal block length. The haplotype block partition of the entire HapMap II CEPH dataset was obtained in 457 hours. By replacing the standard likelihood-based D' variance estimator with an approximated estimator, the runtime was further improved. While producing a coarser partition, the approximate method allowed to obtain the full-genome haplotype block partition of the entire 1000 Genomes Project CEPH dataset in 44 hours, with no restrictions on allele frequency or long-range correlations. These experiments showed that LD-based haplotype blocks can span more than one million base-pairs in both HapMap II and 1000 Genomes datasets. An application to the North American Rheumatoid Arthritis Consortium (NARAC) dataset shows how the MIG ++ can support genome-wide haplotype association studies.
conclusionsThe MIG ++ enables to perform LD-based haplotype block recognition on genetic sequences of any length and density. In the new generation sequencing era, this can help identify haplotypes that carry rare variants of interest. The low computational requirements open the possibility to include the haplotype block structure into genome-wide association scans, downstream analyses, and visual interfaces for online genome browsers.
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