{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["AB 3730xL Genetic Analyzer;CAPILLARY"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001003454"],"sample_count":["8"],"description":["EGA dataset EGAD00001003454"],"repository":["EGA"],"title":["GenomeDenmark Phase 2 - HLA validation sequencing data"],"pubmed_abstract":["Hundreds of thousands of human genomes are now being sequenced to characterize genetic variation and use this information to augment association mapping studies of complex disorders and other phenotypic traits. Genetic variation is identified mainly by mapping short reads to the reference genome or by performing local assembly. However, these approaches are biased against discovery of structural variants and variation in the more complex parts of the genome. Hence, large-scale de novo assembly is needed. Here we show that it is possible to construct excellent de novo assemblies from high-coverage sequencing with mate-pair libraries extending up to 20 kilobases. We report de novo assemblies of 150 individuals (50 trios) from the GenomeDenmark project. The quality of these assemblies is similar to those obtained using the more expensive long-read technology. We use the assemblies to identify a rich set of structural variants including many novel insertions and demonstrate how this variant catalogue enables further deciphering of known association mapping signals. We leverage the assemblies to provide 100 completely resolved major histocompatibility complex haplotypes and to resolve major parts of the Y chromosome. Our study provides a regional reference genome that we expect will improve the power of future association mapping studies and hence pave the way for precision medicine initiatives, which now are being launched in many countries including Denmark."],"pubmed_title":["Sequencing and de novo assembly of 150 genomes from Denmark as a population reference."],"pubmed_authors":["Maretty Lasse L, Jensen Jacob Malte JM, Petersen Bent B, Sibbesen Jonas Andreas JA, Liu Siyang S, Villesen Palle P, Skov Laurits L, Belling Kirstine K, Theil Have Christian C, Izarzugaza Jose M G JMG, Grosjean Marie M, Bork-Jensen Jette J, Grove Jakob J, Als Thomas D TD, Huang Shujia S, Chang Yuqi Y, Xu Ruiqi R, Ye Weijian W, Rao Junhua J, Guo Xiaosen X, Sun Jihua J, Cao Hongzhi H, Ye Chen C, van Beusekom Johan J, Espeseth Thomas T, Flindt Esben E, Friborg Rune M RM, Halager Anders E AE, Le Hellard Stephanie S, Hultman Christina M CM, Lescai Francesco F, Li Shengting S, Lund Ole O, Løngren Peter P, Mailund Thomas T, Matey-Hernandez Maria Luisa ML, Mors Ole O, Pedersen Christian N S CNS, Sicheritz-Pontén Thomas T, Sullivan Patrick P, Syed Ali A, Westergaard David D, Yadav Rachita R, Li Ning N, Xu Xun X, Hansen Torben T, Krogh Anders A, Bolund Lars L, Sørensen Thorkild I A TIA, Pedersen Oluf O, Gupta Ramneek R, Rasmussen Simon S, Besenbacher Søren S, Børglum Anders D AD, Wang Jun J, Eiberg Hans H, Kristiansen Karsten K, Brunak Søren S, Schierup Mikkel Heide MH"],"additional_accession":[]},"is_claimable":false,"name":"ena-DATASET-DTU-19-07-2017-17:57:54:089-201 - samples","description":"Validation of HLA variation of 8 individuals from the GenomeDenmark Phase 2 study. Validation is performed Sanger sequencing of selected amplicons (5-10 amplicons per sample).","dates":{"updated":"2017-07-26 15:39:30"},"accession":"EGAD00001003454","cross_references":{"TAXONOMY":["9606"],"pubmed":["28746312"],"EGA":["EGAC00001000562","EGAS00001002108"]}}