Detection of sharing by descent, long-range phasing and haplotype imputation

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1. Copy number variants of schizophrenia susceptibility loci are associated with a spectrum of speech and developmental delays and behavior problems
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2. Comprehensive population-wide analysis of Lynch syndrome in Iceland reveals founder mutations in MSH6 and PMS2
   Sigurdís Haraldsdóttir, Þórunn Rafnar, Wendy L. Frankel, Sylvia Einarsdottir, Ásgeir Sigurðsson, Heather Hampel, Pétur Snæbjörnsson, Gísli Másson, Daniel Y. Weng, Reynir Arngrı́msson et al. · 2017 · Nature Communications
3. Detecting Rare Variant Associations by Identity-by-Descent Mapping in Case-Control Studies
   Sharon R. Browning, E. A. Thompson · 2012 · Genetics
4. Phasing of Many Thousands of Genotyped Samples
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5. Identification of sequence variants influencing immunoglobulin levels
   Stefan Jonsson, Garðar Sveinbjörnsson, Aitzkoa Lopez de Lapuente Portilla, Bhairavi Swaminathan, Rosina Plomp, Gillian Dekkers, Ram Ajore, Mina Ali, Arthur E. H. Bentlage, Evelina Elmér et al. · 2017 · Nature Genetics
6. A homozygous loss-of-function mutation leading to CYBC1 deficiency causes chronic granulomatous disease
   Gudny Anna Arnadottir, Gudmundur Logi Norddahl, Steinunn Guðmundsdóttir, Arna B. Agustsdottir, Snævar Sigurðsson, Brynjar Ö. Jensson, Kristbjörg Bjarnadóttir, Fannar Theódórs, Stefania Benónísdóttir, Erna V. Ivarsdottir et al. · 2018 · Nature Communications
7. Evolution and Population Genetics of Exotic and Re-Emerging Pathogens: Novel Tools and Approaches
   Niklaus J. Grünwald, Erica M. Goss · 2011 · Annual Review of Phytopathology
8. Variants associating with uterine leiomyoma highlight genetic background shared by various cancers and hormone-related traits
   T. Rafnar, Bjarni Gunnarsson, O. Stefansson, P. Sulem, A. Ingason, M. Frigge, L. Stefánsdóttir, J. K. Sigurdsson, V. Tragante, V. Steinthorsdottir et al. · 2018 · Nature Communications
9. Genetic effects on the timing of parturition and links to fetal birth weight
   Pol Solé-Navais, Christopher J. Flatley, Valgerður Steinthórsdóttir, Marc Vaudel, Julius Juodakis, Jing Chen, Triin Laisk, Abigail Leavitt LaBella, David Westergaard, Jonas Bačelis et al. · 2023 · Nature Genetics
10. Whole-genome sequencing identifies rare genotypes in COMP and CHADL associated with high risk of hip osteoarthritis
    Unnur Styrkársdóttir, Hannes Helgason, Ásgeir Sigurðsson, Gudmundur Logi Norddahl, Arna B. Agustsdottir, Louise N. Reynard, Amanda Villalvilla, Gisli Hreinn Halldorsson, Áslaug Jónasdóttir, Audur Magnusdottir et al. · 2017 · Nature Genetics
11. A rare functional cardioprotective APOC3 variant has risen in frequency in distinct population isolates
    Ioanna Tachmazidou, George V. Dedoussis, Lorraine Southam, Aliki‐Eleni Farmaki, Graham R. S. Ritchie, Dionysia K. Xifara, Angela Matchan, Konstantinos Hatzikotoulas, Nigel William Rayner, Yuan Chen et al. · 2013 · Nature Communications
12. Completely phased genome sequencing through chromosome sorting
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13. Accuracy of direct genomic values derived from imputed single nucleotide polymorphism genotypes in Jersey cattle
    KENT A. WEIGEL, G. de los Campos, Ana Ines Vazquez, Guilherme J. M. Rosa, Daniel Gianola B, Curtis P. Van Tassell · 2010 · Journal of Dairy Science
14. Using population isolates in genetic association studies
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15. Distinction between the effects of parental and fetal genomes on fetal growth
    Thorhildur Juliusdottir, Valgerður Steinthórsdóttir, Lilja Stefánsdóttir, Garðar Sveinbjörnsson, Erna V. Ivarsdottir, Rósa B. Þórólfsdóttir, Jon Karl Sigurdsson, Vinicius Tragante, Kristján Eldjárn Hjörleifsson, Anna Helgadóttir et al. · 2021 · Nature Genetics
16. The Architecture of Long-Range Haplotypes Shared within and across Populations
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17. Intellectual disability is associated with increased runs of homozygosity in simplex autism
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18. Genome-wide meta-analysis reveals common splice site acceptor variant in CHRNA4 associated with nicotine dependence
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19. Sequence variants in ARHGAP15, COLQ and FAM155A associate with diverticular disease and diverticulitis
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20. Common and rare variants associating with serum levels of creatine kinase and lactate dehydrogenase
    Ragnar P. Kristjansson, Ásmundur Oddsson, Hannes Helgason, Garðar Sveinbjörnsson, Gudny Anna Arnadottir, Brynjar Ö. Jensson, Áslaug Jónasdóttir, Aðalbjörg Jónasdóttir, G. Bragi Walters, Gerald Sulem et al. · 2016 · Nature Communications
21. Whole-genome haplotyping approaches and genomic medicine
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22. False discovery rate control in genome-wide association studies with population structure
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23. A rare missense mutation in MYH6 associates with non-syndromic coarctation of the aorta
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24. Efficient genome-wide genotyping strategies and data integration in crop plants
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25. Rapid, Phase-free Detection of Long Identity-by-Descent Segments Enables Effective Relationship Classification
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26. The Use of Family Relationships and Linkage Disequilibrium to Impute Phase and Missing Genotypes in Up to Whole-Genome Sequence Density Genotypic Data
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27. Hunting human disease genes: lessons from the past, challenges for the future
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28. Coding variants in RPL3L and MYZAP increase risk of atrial fibrillation
    Rósa B. Þórólfsdóttir, Garðar Sveinbjörnsson, Patrick Sulem, Jonas Bille Nielsen, Stefan Jonsson, Gisli Hreinn Halldorsson, Páll Melsted, Erna V. Ivarsdottir, Olafur B. Davidsson, Ragnar P. Kristjansson et al. · 2018 · Communications Biology
29. Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle
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30. High-throughput inference of pairwise coalescence times identifies signals of selection and enriched disease heritability
    Pier Francesco Palamara, Jonathan Terhorst, Yun S. Song, Alkes L. Price · 2018 · Nature Genetics
31. Identity by descent estimation with dense genome-wide genotype data
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32. New basal cell carcinoma susceptibility loci
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33. Prediction of unobserved single nucleotide polymorphism genotypes of Jersey cattle using reference panels and population-based imputation algorithms
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34. Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates
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35. Rare SCARB1 mutations associate with high-density lipoprotein cholesterol but not with coronary artery disease
    Anna Helgadóttir, Patrick Sulem, Guðmundur Þorgeirsson, Sólveig Grétarsdóttir, Guðmar Þorleifsson, Brynjar Ö. Jensson, Gudny Anna Arnadottir, Ísleifur Ólafsson, Gudmundur Ingi Eyjolfsson, Ólöf Sigurðardóttir et al. · 2018 · European Heart Journal
36. Multi-trait genome-wide association study of opioid addiction: OPRM1 and beyond
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37. Infliximab-induced liver injury: Clinical phenotypes, autoimmunity and the role of corticosteroid treatment
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38. Genetic characterization of Greek population isolates reveals strong genetic drift at missense and trait-associated variants
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39. Imputation of Missing Genotypes From Sparse to High Density Using Long-Range Phasing
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40. Sequence variants in the PTCH1 gene associate with spine bone mineral density and osteoporotic fractures
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41. KmerStream: streaming algorithms for k -mer abundance estimation
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42. Genetic predisposition of the severity of joint destruction in rheumatoid arthritis: a population-based study
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43. Genome-wide associations for benign prostatic hyperplasia reveal a genetic correlation with serum levels of PSA
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44. Genetics and epidemiology of mutational barcode-defined clonal hematopoiesis
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45. Nationwide Study on Hypertrophic Cardiomyopathy in Iceland
    Berglind Aðalsteinsdóttir, Polakit Teekakirikul, Barry J. Maron, Michael A. Burke, Daniel Fannar Gudbjartsson, Hilma Hólm, Kāri Stefánsson, Steven R. DePalma, Erica Mazaika, Barbara A. McDonough et al. · 2014 · Circulation
46. Assigning breed origin to alleles in crossbred animals
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47. Haplotype Sharing Provides Insights into Fine-Scale Population History and Disease in Finland
    Alicia R. Martin, Konrad J. Karczewski, Sini Kerminen, Mitja Kurki, Antti‐Pekka Sarin, Mykyta Artomov, Johan Gunnar Eriksson, Tõnu Esko, Giulio Genovese, Aki Samuli Havulinna et al. · 2018 · The American Journal of Human Genetics
48. Recombination locations and rates in beef cattle assessed from parent-offspring pairs
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49. Sequence variants from whole genome sequencing a large group of Icelanders
    Daniel Fannar Gudbjartsson, Patrick Sulem, Hannes Helgason, Arnaldur Gylfason, Sigurjon Axel Gudjonsson, Florian Zink, Ásmundur Oddsson, Gisli Magnusson, Bjarni V. Halldórsson, Eirikur Hjartarson et al. · 2015 · Scientific Data
50. The study of interactions between genome and exposome in the development of systemic lupus erythematosus
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51. NARD: whole-genome reference panel of 1779 Northeast Asians improves imputation accuracy of rare and low-frequency variants
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52. A common variant at 8q24.21 is associated with renal cell cancer
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53. Rare variants with large effects provide functional insights into the pathology of migraine subtypes, with and without aura
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54. GIGI: An Approach to Effective Imputation of Dense Genotypes on Large Pedigrees
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55. Genotype imputation via matrix completion
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56. Rare mutations associating with serum creatinine and chronic kidney disease
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57. Utilizing Graph Theory to Select the Largest Set of Unrelated Individuals for Genetic Analysis
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58. Next-generation association studies for complex traits
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59. Association of Genetically Predicted Lipid Levels With the Extent of Coronary Atherosclerosis in Icelandic Adults
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60. An ensemble-based approach to imputation of moderate-density genotypes for genomic selection with application to Angus cattle
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61. A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis
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62. Rare SLC13A1 variants associate with intervertebral disc disorder highlighting role of sulfate in disc pathology
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63. Epigenetic and genetic components of height regulation
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64. Heterozygote carriers for CNVs inPARK2are at increased risk of Parkinson's disease
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65. The genetic architecture of age-related hearing impairment revealed by genome-wide association analysis
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66. Genetic links between ovarian ageing, cancer risk and de novo mutation rates
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67. Genome-wide association study yields variants at 20p12.2 that associate with urinary bladder cancer
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68. Germline sequence variants in TGM3 and RGS22 confer risk of basal cell carcinoma
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69. Genotype Imputation in Genome‐Wide Association Studies
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70. Rare and Common Variants Conferring Risk of Tooth Agenesis
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71. Ensuring privacy and security of genomic data and functionalities
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72. Imputation accuracy to whole-genome sequence in Nellore cattle
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73. Rapid detection of identity-by-descent tracts for mega-scale datasets
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74. Improved risk prediction for Crohn's disease with a multi-locus approach.
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75. Common variants upstream of KDR encoding VEGFR2 and in TTC39B associate with endometriosis
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76. Estimating Recombination Rates from Genetic Variation in Humans
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77. Complete human recombination maps
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78. Genotype calling and phasing using next-generation sequencing reads and a haplotype scaffold
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79. Genotype Imputation in Genome‐Wide Association Studies
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80. The Frequency of Sex: Population Genomics Reveals Differences in Recombination and Population Structure of the Aflatoxin-Producing Fungus Aspergillus flavus
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81. A genome-wide meta-analysis uncovers six sequence variants conferring risk of vertigo
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82. Population structure and genome-wide patterns of variation in Ireland and Britain
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83. Reducing Pervasive False-Positive Identical-by-Descent Segments Detected by Large-Scale Pedigree Analysis
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84. Two Rare Mutations in theCOL1A2Gene Associate With Low Bone Mineral Density and Fractures in Iceland
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85. Predicted loss and gain of function mutations in ACO1 are associated with erythropoiesis
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86. A genome-wide meta-analysis identifies 50 genetic loci associated with carpal tunnel syndrome
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87. Genotype Imputation Methods and Their Effects on Genomic Predictions in Cattle
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88. Sequence Variants in TAAR5 and Other Loci Affect Human Odor Perception and Naming
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89. How Real-World Data Can Facilitate the Development of Precision Medicine Treatment in Psychiatry
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90. General lessons from large‐scale studies to identify human cancer predisposition genes
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91. Sequence variants associating with urinary biomarkers
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92. The Variance of Identity-by-Descent Sharing in the Wright–Fisher Model
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93. Determination of complete chromosomal haplotypes by bulk DNA sequencing
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