Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel.
paper
Cited
Public
- Authors
- Delaneau, Olivier; Marchini, Jonathan; 1000 Genomes Project Consortium; 1000 Genomes Project Consortium
- Year
- 2014
- Journal
- Nature communications
- PMID
- 25653097
- DOI
- 10.1038/ncomms4934
- PMCID
- PMC4338501
A major use of the 1000 Genomes Project (1000 GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000 GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants.
Methods comparison of genotype discordance and imputation accuracy using the CG1 dataPanel (a) shows the discordance at chr20 CG1 SNP genotypes of Beagle (green), Thunder (orange) and SHAPEIT2 without using a scaffold (light blue), using a 1M SNPs haplotype scaffold (medium blue) and using a 2.5M SNPs haplotype scaffold (dark blue). ALT stands for the discordance at genotypes involving at least one non-reference allele, and ALL for the overall discordance. Panel (b) shows the performance of the previous call sets when used as a reference panel to impute 4 CG1 European genotyped on Illumina 1M SNP array. The x-axis shows the non-reference allele frequency of the SNP being imputed. The y-axis shows imputation accuracy measure by aggregate R2.
Methods comparison of genotype discordance and imputation accuracy using the CG2 dataPanel (a) shows the whole genome genotype discordance of Beagle (green), Thunder (orange) and SHAPEIT2 using a 2.5M SNPs haplotype scaffold (dark blue) at CG2 SNPs. Panel (b) shows the performance of the 3 call sets to impute SNPs on chromosome 10 in 10 CG2 European samples typed on Illumina 1M and Omni2.5M chips. The x-axis shows the non-reference allele frequency of the SNP being imputed. The y-axis shows imputation accuracy measure by aggregate R2. Panels (c) and (d) show similar results than panels (a) and (b), respectively for short bi-allelic indels instead of SNPs.
Imputation accuracy at SNPs and Indels using the CG2 dataThe imputation performance at SNPs and indels are shown with the orange and green lines, respectively. Performance at all indels, isolated indels and non-isolated indels are shown using plain, dashed and dotted lines. An indel is isolated when no other indels is in the 50bp flanking regions. The x-axis shows the non-reference allele frequency of the SNP being imputed. The y-axis shows imputation accuracy measure by aggregate R2.
| # | Section | Preview |
|---|---|---|
| 40 | Methods — Complete Genomics (CG) validation data | SNPs and 27,511 Indels from set C. We defined as isolated, an indel with no other indel in the 50bp… |
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| A gene co-expression network-based analysis of multiple brain tissues reveals novel genes and molecular pathways underlying major depression. | Gerring ZF et al. | — | 2019 | → |
| An ABC Method for Whole-Genome Sequence Data: Inferring Paleolithic and Neolithic Human Expansions. | Jay F et al. | — | 2019 | → |
| A New Fast Phasing Method Based On Haplotype Subtraction. | Mocci E et al. | — | 2019 | → |
| Associations of Mitochondrial and Nuclear Mitochondrial Variants and Genes with Seven Metabolic Traits. | Kraja AT et al. | — | 2019 | → |
| A statistical method for joint estimation of cis-eQTLs and parent-of-origin effects under family trio design. | Zhabotynsky V et al. | — | 2019 | → |
| CSHAP: efficient haplotype frequency estimation based on sparse representation. | Zhou Y et al. | — | 2019 | → |
| Evaluating the quality of the 1000 genomes project data. | Belsare S et al. | — | 2019 | → |
| Evidence of Austronesian Genetic Lineages in East Africa and South Arabia: Complex Dispersal from Madagascar and Southeast Asia. | Brucato N et al. | — | 2019 | → |
| Exploring rare and low-frequency variants in the Saguenay-Lac-Saint-Jean population identified genes associated with asthma and allergy traits. | Morin A et al. | — | 2019 | → |
| Genetic Diversity of Persian Arabian Horses and Their Relationship to Other Native Iranian Horse Breeds. | Sadeghi R et al. | — | 2019 | → |
| Genetic influences on delayed reward discounting: A genome-wide prioritized subset approach. | MacKillop J et al. | — | 2019 | → |
| Genome-wide associated study identifies NAC42-activated nitrate transporter conferring high nitrogen use efficiency in rice. | Tang W et al. | — | 2019 | → |
| Genome-wide association study of breakfast skipping links clock regulation with food timing. | Dashti HS et al. | — | 2019 | → |
| Genome-wide meta-analysis of macronutrient intake of 91,114 European ancestry participants from the cohorts for heart and aging research in genomic epidemiology consortium. | Merino J et al. | — | 2019 | → |
| Genome-wide scan identified genetic variants associated with skin aging in a Chinese female population. | Liu Y et al. | — | 2019 | → |
| Heritability of skewed X-inactivation in female twins is tissue-specific and associated with age. | Zito A et al. | — | 2019 | → |
| Identification of Main Genetic Causes Responsible for Non-Syndromic Hearing Loss in a Peruvian Population. | Figueroa-Ildefonso E et al. | — | 2019 | → |
| Identification of somatic mutations in single cell DNA-seq using a spatial model of allelic imbalance. | Luquette LJ et al. | — | 2019 | → |
| Identity-by-Descent Analysis Reveals Susceptibility Loci for Severe Acne in Chinese Han Cohort. | Yang X et al. | — | 2019 | → |
| INDEX-db: The Indian Exome Reference Database (Phase I). | Ahmed P H et al. | — | 2019 | → |
| Joint imputation of whole-genome sequence variants and large chromosomal deletions in cattle. | Mesbah-Uddin M et al. | — | 2019 | → |
| Linked-read analysis identifies mutations in single-cell DNA-sequencing data. | Bohrson CL et al. | — | 2019 | → |
| Local ancestry at APOE modifies Alzheimer's disease risk in Caribbean Hispanics. | Blue EE et al. | — | 2019 | → |
| Polygenic risk associated with post-traumatic stress disorder onset and severity. | Misganaw B et al. | — | 2019 | → |
| Population-specific long-range linkage disequilibrium in the human genome and its influence on identifying common disease variants. | Park L | — | 2019 | → |
| Rare variant phasing using paired tumor:normal sequence data. | Buckley AR et al. | — | 2019 | → |
| The <i>MS4A</i> gene cluster is a key modulator of soluble TREM2 and Alzheimer's disease risk. | Deming Y et al. | — | 2019 | → |
| Uromodulin in a Pathway Between Decreased Renal Urate Excretion and Albuminuria. | Krajcoviechova A et al. | — | 2019 | → |
| Variant calling on the GRCh38 assembly with the data from phase three of the 1000 Genomes Project. | Lowy-Gallego E et al. | — | 2019 | → |
| A data-driven investigation of relationships between bipolar psychotic symptoms and schizophrenia genome-wide significant genetic loci. | Leonenko G et al. | — | 2018 | → |
| A molecule-based genetic association approach implicates a range of voltage-gated calcium channels associated with schizophrenia. | Li W et al. | — | 2018 | → |
| An adult-based insulin resistance genetic risk score associates with insulin resistance, metabolic traits and altered fat distribution in Danish children and adolescents who are overweight or obese. | Graae AS et al. | — | 2018 | → |
| Ancestral origin of ApoE ε4 Alzheimer disease risk in Puerto Rican and African American populations. | Rajabli F et al. | — | 2018 | → |
| Association of LPA Variants With Aortic Stenosis: A Large-Scale Study Using Diagnostic and Procedural Codes From Electronic Health Records. | Chen HY et al. | — | 2018 | → |
| Brain APOE expression quantitative trait loci-based association study identified one susceptibility locus for Alzheimer's disease by interacting with APOE ε4. | Zhang A et al. | — | 2018 | → |
| Disentangling the biological pathways involved in early features of Alzheimer's disease in the Rotterdam Study. | Ahmad S et al. | — | 2018 | → |
| Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks. | Pelikan RC et al. | — | 2018 | → |
| Evidence for genetic contribution to the increased risk of type 2 diabetes in schizophrenia. | Hackinger S et al. | — | 2018 | → |
| Evidence of positive selection towards Zebuine haplotypes in the BoLA region of Brangus cattle. | Goszczynski DE et al. | — | 2018 | → |
| Genetic Architecture of Adaptive Immune System Identifies Key Immune Regulators. | Lagou V et al. | — | 2018 | → |
| Genetic determinants and an epistasis of <i>LILRA3</i> and HLA-B*52 in Takayasu arteritis. | Terao C et al. | — | 2018 | → |
| Genetic risk of prostate cancer in Ugandan men. | Du Z et al. | — | 2018 | → |
| Genetic Risk Score Is Associated with Vertical Cup-to-Disc Ratio and Improves Prediction of Primary Open-Angle Glaucoma in Latinos. | Nannini DR et al. | — | 2018 | → |
| Genetic variations in TAS2R3 and TAS2R4 bitterness receptors modify papillary carcinoma risk and thyroid function in Korean females. | Choi JH 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 Reveals Genetic Link between Diarrhea-Associated Entamoeba histolytica Infection and Inflammatory Bowel Disease. | Wojcik GL et al. | — | 2018 | → |
| Genome-wide variants of Eurasian facial shape differentiation and a prospective model of DNA based face prediction. | Qiao L et al. | — | 2018 | → |
| Genome-Wide Variation, Candidate Regions and Genes Associated With Fat Deposition and Tail Morphology in Ethiopian Indigenous Sheep. | Ahbara A et al. | — | 2018 | → |
| Genomic Analyses of Human European Diversity at the Southwestern Edge: Isolation, African Influence and Disease Associations in the Canary Islands. | Guillen-Guio B et al. | — | 2018 | → |
| Genomic coordinates and continental distribution of 120 blood group variants reported by the 1000 Genomes Project. | Montemayor-Garcia C et al. | — | 2018 | → |
| GWAS of lifetime cannabis use reveals new risk loci, genetic overlap with psychiatric traits, and a causal influence of schizophrenia. | Pasman JA et al. | — | 2018 | → |
| Identification of <i>ST3AGL4</i>, <i>MFHAS1, CSNK2A2</i> and <i>CD226</i> as loci associated with systemic lupus erythematosus (SLE) and evaluation of SLE genetics in drug repositioning. | Wang YF et al. | — | 2018 | → |
| Identification of nine new susceptibility loci for endometrial cancer. | O'Mara TA et al. | — | 2018 | → |
| Integration of human adipocyte chromosomal interactions with adipose gene expression prioritizes obesity-related genes from GWAS. | Pan DZ et al. | — | 2018 | → |
| Investigating the origins of eastern Polynesians using genome-wide data from the Leeward Society Isles. | Hudjashov G et al. | — | 2018 | → |
| Joint genome-wide association study of progressive supranuclear palsy identifies novel susceptibility loci and genetic correlation to neurodegenerative diseases. | Chen JA et al. | — | 2018 | → |
| Putative Loci Causing Early Embryonic Mortality in Duroc Swine. | Zhang C et al. | — | 2018 | → |
| Sparse Tensor Decomposition for Haplotype Assembly of Diploids and Polyploids. | Hashemi A et al. | — | 2018 | → |
| The Comoros Show the Earliest Austronesian Gene Flow into the Swahili Corridor. | Brucato N et al. | — | 2018 | → |
| The germline genetic component of drug sensitivity in cancer cell lines. | Menden MP et al. | — | 2018 | → |
| The TLR1 gene is associated with higher protection from leprosy in women. | Alvarenga Niitsuma EN et al. | — | 2018 | → |
| Thyrotropin receptor antibodies and a genetic hint in antithyroid drug-induced adverse drug reactions. | Chang LC et al. | — | 2018 | → |
| Trans-Ethnic Mapping of <i>BANK1</i> Identifies Two Independent SLE-Risk Linkage Groups Enriched for Co-Transcriptional Splicing Marks. | Martínez-Bueno M et al. | — | 2018 | → |
| Whole Exome Sequencing of Patients from Multicase Families with Systemic Lupus Erythematosus Identifies Multiple Rare Variants. | Delgado-Vega AM et al. | — | 2018 | → |
| A genome-wide association study of thyroid stimulating hormone and free thyroxine in Danish children and adolescents. | Nielsen TR et al. | — | 2017 | → |
| A Genome-Wide Association Study of Vertical Cup-Disc Ratio in a Latino Population. | Nannini DR et al. | — | 2017 | → |
| A Genome-Wide Association Study to Identify Single-Nucleotide Polymorphisms for Acute Kidney Injury. | Zhao B et al. | — | 2017 | → |
| An endophenotype approach to the genetics of alcohol dependence: a genome wide association study of fast beta EEG in families of African ancestry. | Meyers JL et al. | — | 2017 | → |
| A novel TCF7L2 type 2 diabetes SNP identified from fine mapping in African American women. | Haddad SA et al. | — | 2017 | → |
| Association between a common immunoglobulin heavy chain allele and rheumatic heart disease risk in Oceania. | Parks T et al. | — | 2017 | → |
| A strategy to improve phasing of whole-genome sequenced individuals through integration of familial information from dense genotype panels. | Faux P et al. | — | 2017 | → |
| Case-control association mapping by proxy using family history of disease. | Liu JZ et al. | — | 2017 | → |
| Complex Patterns of Admixture across the Indonesian Archipelago. | Hudjashov G et al. | — | 2017 | → |
| Coronary collateralization shows sex and racial-ethnic differences in obstructive artery disease patients. | Liu Z et al. | — | 2017 | → |
| Decreased STARD10 Expression Is Associated with Defective Insulin Secretion in Humans and Mice. | Carrat GR et al. | — | 2017 | → |
| Discovery and fine-mapping of adiposity loci using high density imputation of genome-wide association studies in individuals of African ancestry: African Ancestry Anthropometry Genetics Consortium. | Ng MCY et al. | — | 2017 | → |
| Fine Mapping and Functional Analysis Reveal a Role of SLC22A1 in Acylcarnitine Transport. | Kim HI et al. | — | 2017 | → |
| G6PD deficiency alleles in a malaria-endemic region in the Western Brazilian Amazon. | Dombrowski JG et al. | — | 2017 | → |
| Genome-wide analyses identify common variants associated with macular telangiectasia type 2. | Scerri TS et al. | — | 2017 | → |
| Genome-wide analysis of clopidogrel active metabolite levels identifies novel variants that influence antiplatelet response. | Backman JD 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 identifies four novel loci associated with Alzheimer's endophenotypes and disease modifiers. | Deming Y et al. | — | 2017 | → |
| Genome-wide genetic analyses highlight mitogen-activated protein kinase (MAPK) signaling in the pathogenesis of endometriosis. | Uimari O et al. | — | 2017 | → |
| Genome-wide imaging association study implicates functional activity and glial homeostasis of the caudate in smoking addiction. | Qian DC et al. | — | 2017 | → |
| Genome-wide mapping of genetic determinants influencing DNA methylation and gene expression in human hippocampus. | Schulz H et al. | — | 2017 | → |
| Genomic admixture tracks pulses of economic activity over 2,000 years in the Indian Ocean trading network. | Brucato N et al. | — | 2017 | → |
| High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE. | Majoros WH et al. | — | 2017 | → |
| Identification of Four Novel Loci in Asthma in European American and African American Populations. | Almoguera B 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 | → |
| Joint genetic analysis using variant sets reveals polygenic gene-context interactions. | Casale FP et al. | — | 2017 | → |
| Leveraging cell type specific regulatory regions to detect SNPs associated with tissue factor pathway inhibitor plasma levels. | Dennis J et al. | — | 2017 | → |
| Omics Informatics: From Scattered Individual Software Tools to Integrated Workflow Management Systems. | Ma T et al. | — | 2017 | → |
| The last sea nomads of the Indonesian archipelago: genomic origins and dispersal. | Kusuma P et al. | — | 2017 | → |
| A Novel Pathway-Based Approach Improves Lung Cancer Risk Prediction Using Germline Genetic Variations. | Qian DC et al. | — | 2016 | → |
| Assessing the role of insulin-like growth factors and binding proteins in prostate cancer using Mendelian randomization: Genetic variants as instruments for circulating levels. | Bonilla C et al. | — | 2016 | → |
| A thrifty variant in CREBRF strongly influences body mass index in Samoans. | Minster RL et al. | — | 2016 | → |
| Candidate SNP Markers of Chronopathologies Are Predicted by a Significant Change in the Affinity of TATA-Binding Protein for Human Gene Promoters. | Ponomarenko P et al. | — | 2016 | → |
| Comparing performance of modern genotype imputation methods in different ethnicities. | Roshyara NR et al. | — | 2016 | → |
| Genetic variation in MHC proteins is associated with T cell receptor expression biases. | Sharon E et al. | — | 2016 | → |
| Genome-wide association analyses identify new risk variants and the genetic architecture of amyotrophic lateral sclerosis. | van Rheenen W et al. | — | 2016 | → |
| Genome-wide association studies in oesophageal adenocarcinoma and Barrett's oesophagus: a large-scale meta-analysis. | Gharahkhani P et al. | — | 2016 | → |
| Genome-wide association study identifies WNT7B as a novel locus for central corneal thickness in Latinos. | Gao X et al. | — | 2016 | → |
| Genome-Wide Association Study of Bone Mineral Density in Korean Men. | Bae YS et al. | — | 2016 | → |
| Genomic analysis of Andamanese provides insights into ancient human migration into Asia and adaptation. | Mondal M et al. | — | 2016 | → |
| HLA-B*38:02:01 predicts carbimazole/methimazole-induced agranulocytosis. | Cheung CL et al. | — | 2016 | → |
| Increasing The Genetic Admixture of Available Lines of Human Pluripotent Stem Cells. | Tofoli FA et al. | — | 2016 | → |
| Meta-Analysis of Genome-Wide Association Studies and Network Analysis-Based Integration with Gene Expression Data Identify New Suggestive Loci and Unravel a Wnt-Centric Network Associated with Dupuytren's Disease. | Becker K et al. | — | 2016 | → |
| Polymorphisms in HLA Class II Genes Are Associated With Susceptibility to Staphylococcus aureus Infection in a White Population. | DeLorenze GN et al. | — | 2016 | → |
| Prenatal Air Pollution Exposures, DNA Methyl Transferase Genotypes, and Associations with Newborn LINE1 and Alu Methylation and Childhood Blood Pressure and Carotid Intima-Media Thickness in the Children's Health Study. | Breton CV et al. | — | 2016 | → |
| Rapid genotype refinement for whole-genome sequencing data using multi-variate normal distributions. | Arthur R et al. | — | 2016 | → |
| Read-based phasing of related individuals. | Garg S et al. | — | 2016 | → |
| Single nucleotide polymorphisms in an intergenic chromosome 2q region associated with tissue factor pathway inhibitor plasma levels and venous thromboembolism. | Dennis J et al. | — | 2016 | → |
| Small Traditional Human Communities Sustain Genomic Diversity over Microgeographic Scales despite Linguistic Isolation. | Cox MP et al. | — | 2016 | → |
| Software Application Profile: RVPedigree: a suite of family-based rare variant association tests for normally and non-normally distributed quantitative traits. | Oualkacha K et al. | — | 2016 | → |
| Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection. | Crellen T et al. | — | 2016 | → |
| Whole-genome sequencing in French Canadians from Quebec. | Low-Kam C et al. | — | 2016 | → |
| A global reference for human genetic variation. | 1000 Genomes Project Consortium et al. | — | 2015 | → |
| Association of SLC2A9 genotype with phenotypic variability of serum urate in pre-menopausal women. | Topless RK et al. | — | 2015 | → |
| Common variants in LEPR, IL6, AMD1, and NAMPT do not associate with risk of juvenile and childhood obesity in Danes: a case-control study. | Hollensted M et al. | — | 2015 | → |
| DISTMIX: direct imputation of summary statistics for unmeasured SNPs from mixed ethnicity cohorts. | Lee D et al. | — | 2015 | → |
| Exact Inference for Hardy-Weinberg Proportions with Missing Genotypes: Single and Multiple Imputation. | Graffelman J et al. | — | 2015 | → |
| Fast imputation using medium or low-coverage sequence data. | VanRaden PM et al. | — | 2015 | → |
| Genome-wide association study identifies TF as a significant modifier gene of iron metabolism in HFE hemochromatosis. | de Tayrac M et al. | — | 2015 | → |
| Genomic approaches for understanding the genetics of complex disease. | Lowe WL et al. | — | 2015 | → |
| GWA meta-analysis of personality in Korean cohorts. | Kim BH et al. | — | 2015 | → |
| hapbin: An Efficient Program for Performing Haplotype-Based Scans for Positive Selection in Large Genomic Datasets. | Maclean CA et al. | — | 2015 | → |
| Identification of shared and unique susceptibility pathways among cancers of the lung, breast, and prostate from genome-wide association studies and tissue-specific protein interactions. | Qian DC et al. | — | 2015 | → |
| Scanning and Filling: Ultra-Dense SNP Genotyping Combining Genotyping-By-Sequencing, SNP Array and Whole-Genome Resequencing Data. | Torkamaneh D et al. | — | 2015 | → |
| The role of common genetic variation in educational attainment and income: evidence from the National Child Development Study. | Davies NM et al. | — | 2015 | → |
| Uncovering the genetic history of the present-day Greenlandic population. | Moltke I et al. | — | 2015 | → |
| Accuracy of imputation to infer unobserved APOE epsilon alleles in genome-wide genotyping data. | Radmanesh F et al. | — | 2014 | → |
| Hormone metabolism pathway genes and mammographic density change after quitting estrogen and progestin combined hormone therapy in the California Teachers Study. | Lee E et al. | — | 2014 | → |