Haplotype estimation using sequencing reads.
paper
Cited
Public
Unavailable
- Authors
- Delaneau, Olivier; Howie, Bryan; Cox, Anthony J; Zagury, Jean-François; Marchini, Jonathan
- Year
- 2013
- Journal
- American journal of human genetics
- PMID
- 24094745
- DOI
- 10.1016/j.ajhg.2013.09.002
- PMCID
- PMC3791270
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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| Long-read sequencing in deciphering human genetics to a greater depth. | Midha MK et al. | — | 2019 | → |
| Multiple Deeply Divergent Denisovan Ancestries in Papuans. | Jacobs GS et al. | — | 2019 | → |
| Off the street phasing (OTSP): no hassle haplotype phasing for molecular PGD applications. | Zeevi DA et al. | — | 2019 | → |
| Parallel Molecular Evolution in Pathways, Genes, and Sites in High-Elevation Hummingbirds Revealed by Comparative Transcriptomics. | Lim MCW et al. | — | 2019 | → |
| Psychosocial moderation of polygenic risk for cannabis involvement: the role of trauma exposure and frequency of religious service attendance. | Meyers JL et al. | — | 2019 | → |
| Revisit Population-based and Family-based Genotype Imputation. | Liu CT et al. | — | 2019 | → |
| Risk of spontaneous preterm birth and fetal growth associates with fetal SLIT2. | Tiensuu H et al. | — | 2019 | → |
| Susceptibility Loci for Tanning Ability in the Japanese Population Identified by a Genome-Wide Association Study from the Tohoku Medical Megabank Project Cohort Study. | Shido K et al. | — | 2019 | → |
| Tacrolimus troughs and genetic determinants of metabolism in kidney transplant recipients: A comparison of four ancestry groups. | Mohamed ME et al. | — | 2019 | → |
| Towards population genomics in non-model species with large genomes: a case study of the marine zooplankton <i>Calanus finmarchicus</i>. | Choquet M et al. | — | 2019 | → |
| Very low-depth whole-genome sequencing in complex trait association studies. | Gilly A et al. | — | 2019 | → |
| Whole-exome sequencing in multiplex preeclampsia families identifies novel candidate susceptibility genes. | Melton PE et al. | — | 2019 | → |
| A Genome-wide Study of Common and Rare Genetic Variants Associated with Circulating Thrombin Activatable Fibrinolysis Inhibitor. | Stanne TM et al. | — | 2018 | → |
| Association of BRCA2 K3326* With Small Cell Lung Cancer and Squamous Cell Cancer of the Skin. | Rafnar T et al. | — | 2018 | → |
| Comparative analysis of de novo assemblers for variation discovery in personal genomes. | Tian S et al. | — | 2018 | → |
| Contrasting Patterns of Genomic Diversity Reveal Accelerated Genetic Drift but Reduced Directional Selection on X-Chromosome in Wild and Domestic Sheep Species. | Chen ZH et al. | — | 2018 | → |
| Detecting Somatic Mutations in Normal Cells. | Dou Y et al. | — | 2018 | → |
| Experimental evidence for rapid genomic adaptation to a new niche in an adaptive radiation. | Marques DA et al. | — | 2018 | → |
| Genetic Regulation of PCSK9 (Proprotein Convertase Subtilisin/Kexin Type 9) Plasma Levels and Its Impact on Atherosclerotic Vascular Disease Phenotypes. | Pott J et al. | — | 2018 | → |
| Genome-wide analysis of genetic determinants of circulating factor VII-activating protease (FSAP) activity. | Olsson M et al. | — | 2018 | → |
| Genome-wide association study: Exploring the genetic basis for responsiveness to ketogenic dietary therapies for drug-resistant epilepsy. | Schoeler NE et al. | — | 2018 | → |
| Genome-wide association study identifies the common variants in CYP3A4 and CYP3A5 responsible for variation in tacrolimus trough concentration in Caucasian kidney transplant recipients. | Oetting WS et al. | — | 2018 | → |
| Genome-wide association study of a nicotine metabolism biomarker in African American smokers: impact of chromosome 19 genetic influences. | Chenoweth MJ et al. | — | 2018 | → |
| Genome-wide association study of response to methotrexate in early rheumatoid arthritis patients. | Taylor JC et al. | — | 2018 | → |
| HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long reads. | Beretta S et al. | — | 2018 | → |
| Identification of 55,000 Replicated DNA Methylation QTL. | McRae AF et al. | — | 2018 | → |
| Identification of Genes Associated With Hirschsprung Disease, Based on Whole-Genome Sequence Analysis, and Potential Effects on Enteric Nervous System Development. | Tang CS et al. | — | 2018 | → |
| Imputation-Based Whole-Genome Sequence Association Study Reveals Constant and Novel Loci for Hematological Traits in a Large-Scale Swine F<sub>2</sub> Resource Population. | Yan G et al. | — | 2018 | → |
| IMPUTOR: Phylogenetically Aware Software for Imputation of Errors in Next-Generation Sequencing. | Jobin M et al. | — | 2018 | → |
| Insights into Platypus Population Structure and History from Whole-Genome Sequencing. | Martin HC et al. | — | 2018 | → |
| Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk. | Castel SE et al. | — | 2018 | → |
| Origin and age of the causative mutations in KLC2, IMPA1, MED25 and WNT7A unravelled through Brazilian admixed populations. | de Farias AA et al. | — | 2018 | → |
| Pipeline design to identify key features and classify the chemotherapy response on lung cancer patients using large-scale genetic data. | Valdés MG et al. | — | 2018 | → |
| Profile of common prostate cancer risk variants in an unscreened Romanian population. | Iordache PD et al. | — | 2018 | → |
| Revealing the complex genetic architecture of obsessive-compulsive disorder using meta-analysis. | International Obsessive Compulsive Disorder Foundation Genetics Collaborative (IOCDF-GC) and OCD Collaborative Genetics Association Studies (OCGAS) | — | 2018 | → |
| Sequence Analysis of Drug Target Genes with Suicidal Behavior in Bipolar Disorder Patients. | Zai CC et al. | — | 2018 | → |
| Six NSCL/P Loci Show Associations With Normal-Range Craniofacial Variation. | Indencleef K et al. | — | 2018 | → |
| SNPs Associated With Testosterone Levels Influence Human Facial Morphology. | Roosenboom J et al. | — | 2018 | → |
| Strategies for phasing and imputation in a population isolate. | Herzig AF et al. | — | 2018 | → |
| Systematic Mendelian randomization framework elucidates hundreds of CpG sites which may mediate the influence of genetic variants on disease. | Richardson TG et al. | — | 2018 | → |
| The genomic footprint of climate adaptation in Chironomus riparius. | Waldvogel AM et al. | — | 2018 | → |
| The genomic impact of historical hybridization with massive mitochondrial DNA introgression. | Seixas FA et al. | — | 2018 | → |
| The human leukemia virus HTLV-1 alters the structure and transcription of host chromatin in cis. | Melamed A et al. | — | 2018 | → |
| The multiple myeloma risk allele at 5q15 lowers ELL2 expression and increases ribosomal gene expression. | Ali M et al. | — | 2018 | → |
| Transethnic and race-stratified genome-wide association study of fibroid characteristics in African American and European American women. | Bray MJ et al. | — | 2018 | → |
| Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow. | Malinsky M et al. | — | 2018 | → |
| 11,670 whole-genome sequences representative of the Han Chinese population from the CONVERGE project. | Cai N et al. | — | 2017 | → |
| A Genome-wide Association Study of Dupuytren Disease Reveals 17 Additional Variants Implicated in Fibrosis. | Ng M et al. | — | 2017 | → |
| A genome-wide association study yields five novel thyroid cancer risk loci. | Gudmundsson J et al. | — | 2017 | → |
| Ancient hybridization and strong adaptation to viruses across African vervet monkey populations. | Svardal H et al. | — | 2017 | → |
| Cis-SNPs Set Testing and PrediXcan Analysis for Gene Expression Data using Linear Mixed Models. | Zeng P et al. | — | 2017 | → |
| Clinical exome sequencing in early-onset generalized dystonia and large-scale resequencing follow-up. | Zech M et al. | — | 2017 | → |
| Convergent evolution of SWS2 opsin facilitates adaptive radiation of threespine stickleback into different light environments. | Marques DA et al. | — | 2017 | → |
| Evaluating the Neolithic Expansion at Both Shores of the Mediterranean Sea. | Pimenta J et al. | — | 2017 | → |
| Genetic diversity of the African malaria vector Anopheles gambiae. | Anopheles gambiae 1000 Genomes Consortium et al. | — | 2017 | → |
| Genome-wide Ancestry and Demographic History of African-Descendant Maroon Communities from French Guiana and Suriname. | Fortes-Lima C et al. | — | 2017 | → |
| Genome-wide association study of alcohol consumption and genetic overlap with other health-related traits in UK Biobank (N=112 117). | Clarke TK et al. | — | 2017 | → |
| Genome-wide meta-analysis identifies novel loci of plaque burden in carotid artery. | Pott J et al. | — | 2017 | → |
| Genome-Wide SNP Analysis Reveals Distinct Origins of Trypanosoma evansi and Trypanosoma equiperdum. | Cuypers B et al. | — | 2017 | → |
| Identification of sequence variants influencing immunoglobulin levels. | Jonsson S et al. | — | 2017 | → |
| Improved imputation accuracy of rare and low-frequency variants using population-specific high-coverage WGS-based imputation reference panel. | Mitt M et al. | — | 2017 | → |
| Influence of genetic ancestry and socioeconomic status on type 2 diabetes in the diverse Colombian populations of Chocó and Antioquia. | Chande AT et al. | — | 2017 | → |
| Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species. | Nater A et al. | — | 2017 | → |
| Neuregulin signaling pathway in smoking behavior. | Gupta R et al. | — | 2017 | → |
| sCNAphase: using haplotype resolved read depth to genotype somatic copy number alterations from low cellularity aneuploid tumors. | Chen W et al. | — | 2017 | → |
| Securing the use of existing sample collections for future human genetic research. | Kanoungi G et al. | — | 2017 | → |
| Sequence variant at 4q25 near PITX2 associates with appendicitis. | Kristjansson RP et al. | — | 2017 | → |
| The Recombination Landscape in Wild House Mice Inferred Using Population Genomic Data. | Booker TR et al. | — | 2017 | → |
| A thrifty variant in CREBRF strongly influences body mass index in Samoans. | Minster RL et al. | — | 2016 | → |
| Characterization of the genome and transcriptome of the blue tit Cyanistes caeruleus: polymorphisms, sex-biased expression and selection signals. | Mueller JC et al. | — | 2016 | → |
| Complex disease and phenotype mapping in the domestic dog. | Hayward JJ et al. | — | 2016 | → |
| Evaluating the performance of selection scans to detect selective sweeps in domestic dogs. | Schlamp F et al. | — | 2016 | → |
| Fast and accurate long-range phasing in a UK Biobank cohort. | Loh PR et al. | — | 2016 | → |
| Genetic Complexity of Crohn's Disease in Two Large Ashkenazi Jewish Families. | Levine AP et al. | — | 2016 | → |
| Genome-wide association study of colorectal cancer in Hispanics. | Schmit SL et al. | — | 2016 | → |
| Genome-wide studies of von Willebrand factor propeptide identify loci contributing to variation in propeptide levels and von Willebrand factor clearance. | Ozel AB et al. | — | 2016 | → |
| Genome-wide time-to-event analysis on smoking progression stages in a family-based study. | He L et al. | — | 2016 | → |
| High rates of phasing errors in highly polymorphic species with low levels of linkage disequilibrium. | Bukowicki M et al. | — | 2016 | → |
| Multimarker analysis suggests the involvement of BDNF signaling and microRNA biosynthesis in suicidal behavior. | Pulay AJ et al. | — | 2016 | → |
| Multiple Independent Retroelement Insertions in the Promoter of a Stress Response Gene Have Variable Molecular and Functional Effects in Drosophila. | Merenciano M et al. | — | 2016 | → |
| Phasing for medical sequencing using rare variants and large haplotype reference panels. | Sharp K et al. | — | 2016 | → |
| Population genomics of the filarial nematode parasite Wuchereria bancrofti from mosquitoes. | Small ST et al. | — | 2016 | → |
| Rare variant phasing and haplotypic expression from RNA sequencing with phASER. | Castel SE et al. | — | 2016 | → |
| Read-based phasing of related individuals. | Garg S et al. | — | 2016 | → |
| Reference-based phasing using the Haplotype Reference Consortium panel. | Loh PR et al. | — | 2016 | → |
| A candidate gene study of capecitabine-related toxicity in colorectal cancer identifies new toxicity variants at DPYD and a putative role for ENOSF1 rather than TYMS. | Rosmarin D et al. | — | 2015 | → |
| A Genome-Wide Association Study of a Biomarker of Nicotine Metabolism. | Loukola A et al. | — | 2015 | → |
| A haplotype-based framework for group-wise transmission/disequilibrium tests for rare variant association analysis. | Chen R et al. | — | 2015 | → |
| Ancestral alleles in the human genome based on population sequencing data. | Park L | — | 2015 | → |
| BrainSeq: Neurogenomics to Drive Novel Target Discovery for Neuropsychiatric Disorders. | BrainSeq: A Human Brain Genomics Consortium. Electronic address: drweinberger@libd.org et al. | — | 2015 | → |
| Combined Genetic and Genealogic Studies Uncover a Large BAP1 Cancer Syndrome Kindred Tracing Back Nine Generations to a Common Ancestor from the 1700s. | Carbone M et al. | — | 2015 | → |
| Detecting balancing selection in genomes: limits and prospects. | Fijarczyk A et al. | — | 2015 | → |
| Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus. | Bentham J et al. | — | 2015 | → |
| Genetics of Plasma Soluble Receptor for Advanced Glycation End-Products and Cardiovascular Outcomes in a Community-based Population: Results from the Atherosclerosis Risk in Communities Study. | Maruthur NM et al. | — | 2015 | → |
| Genome-wide association study of colorectal cancer identifies six new susceptibility loci. | Schumacher FR et al. | — | 2015 | → |
| Genome-wide association study of corticobasal degeneration identifies risk variants shared with progressive supranuclear palsy. | Kouri N et al. | — | 2015 | → |
| Haplotype-resolved genome sequencing: experimental methods and applications. | Snyder MW et al. | — | 2015 | → |
| Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort. | Vockley CM et al. | — | 2015 | → |
| On the design and analysis of next-generation sequencing genotyping for a cohort with haplotype-informative reads. | Zhi D et al. | — | 2015 | → |
| Stable recombination hotspots in birds. | Singhal S et al. | — | 2015 | → |
| WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads. | Patterson M et al. | — | 2015 | → |
| Incorporating functional annotation information in prioritizing disease associated SNPs from genome wide association studies. | Hou L et al. | — | 2014 | → |
| Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel. | Delaneau O et al. | — | 2014 | → |
| The power comparison of the haplotype-based collapsing tests and the variant-based collapsing tests for detecting rare variants in pedigrees. | Guo W et al. | — | 2014 | → |
| Using familial information for variant filtering in high-throughput sequencing studies. | Bahlo M et al. | — | 2014 | → |
| Whole-genome haplotyping approaches and genomic medicine. | Glusman G et al. | — | 2014 | → |
| Whole-genome haplotyping using long reads and statistical methods. | Kuleshov V et al. | — | 2014 | → |