ArticleAmerican journal of human genetics2013
Haplotype estimation using sequencing reads.
Article in American journal of human genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 261 papers, 6 of them syntheses that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
261 citing papers in PubMed, 6 syntheses or guidelines pooled it.
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- Sex-specific analysis in Behçet's disease reveals higher genetic risk in male patients.Journal of autoimmunity · 2022Pooled it
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- Discovery of common and rare genetic risk variants for colorectal cancer.Nature genetics · 2019Pooled it
- Revealing the complex genetic architecture of obsessive-compulsive disorder using meta-analysis.Molecular psychiatry · 2018Pooled it
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- Genetic determinants of fatigue up to 2 years after radiotherapy in prostate cancer patients.Nature communications · 2026Article
- Genome-Wide Analysis Successfully Resolves Population Structure Shaped by Recent Divergence in the Endangered Bagrid CatfishEcology and evolution · 2026Article
- A two-phase clustering procedure based on allele specific expression.BMC bioinformatics · 2026Article
- A novel simulation tool for low-coverage whole-genome sequencing using multivariate Gaussian mixture models.BMC bioinformatics · 2026Article
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- Trans-ancestry genome-wide analyses of bipolar disorder in East Asian and European populations improve genetic discovery.Nature neuroscience · 2026Article
- The hybridization analysis of pedigree: whole-genome re-sequencing reveals genomics characterization and genetic basis of growth trait of Qinchuan black pigs.BMC genomics · 2026Article
- Shared and Unique Patterns of Genomic Differentiation and Introgression Between Japanese Stickleback Species Across Three Sympatric Sites.Molecular ecology · 2026Article
- MAGIC populations: a next-generation framework for dissecting complex quantitative traits and accelerating molecular breeding in crops.Frontiers in plant science · 2026Review
- Continent-wide view of genomic diversity and divergence in the wolves of Asia.Communications biology · 2025Article
- Transcriptome-wide association study revealed novel causal genes of renal-biopsy proven diabetic nephropathy.Genome medicine · 2025Article
- Real-world evaluation of gnomAD variant co-occurrence information for haplotype phasing in autosomal recessive disorders.Human genomics · 2025Article
201 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
High-throughput sequencing technologies produce short sequence reads that can contain phase information if they span two or more heterozygote genotypes. This information is not routinely used by current methods that infer haplotypes from genotype data. We have extended the SHAPEIT2 method to use phase-informative sequencing reads to improve phasing accuracy. Our model incorporates the read information in a probabilistic model through base quality scores within each read. The method is primarily designed for high-coverage sequence data or data sets that already have genotypes called. One important application is phasing of single samples sequenced at high coverage for use in medical sequencing and studies of rare diseases. Our method can also use existing panels of reference haplotypes. We tested the method by using a mother-father-child trio sequenced at high-coverage by Illumina together with the low-coverage sequence data from the 1000 Genomes Project (1000GP). We found that use of phase-informative reads increases the mean distance between switch errors by 22% from 274.4 kb to 328.6 kb. We also used male chromosome X haplotypes from the 1000GP samples to simulate sequencing reads with varying insert size, read length, and base error rate. When using short 100 bp paired-end reads, we found that using mixtures of insert sizes produced the best results. When using longer reads with high error rates (5-20 kb read with 4%-15% error per base), phasing performance was substantially improved.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.