{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"technology_type":["Illumina HiSeq 2000"],"study_type":["Other"],"full_dataset_link":["https://ega-archive.org/studies/EGAS00001000973"],"host":["EGA"],"description":["EGA study EGAS00001000973"],"dataset_title":["Dataset for Parkinson's disease target re-sequencing project"],"repository":["EGA"],"category":["restricted"],"pubmed_abstract":["Parkinson's disease (PD) can be divided into familial (Mendelian) and sporadic forms. A number of causal genes have been discovered for the Mendelian form, which constitutes 10-20% of the total cases. Genome-wide association studies have successfully uncovered a number of susceptibility loci for sporadic cases but those only explain a small fraction (6-7%) of PD heritability. It has been observed that some genes that confer susceptibility to PD through common risk variants also contain rare causing mutations for the Mendelian forms of the disease. These results suggest a possible functional link between Mendelian and sporadic PD and led us to investigate the role that rare and low-frequency variants could have on the sporadic form. Through a targeting approach, we have resequenced at 49× coverage the exons and regulatory regions of 38 genes (including Mendelian and susceptibility PD genes) in 249 sporadic PD patients and 145 unrelated controls of European origin. Unlike susceptibility genes, Mendelian genes show a clear general enrichment of rare functional variants in PD cases, observed directly as well as with Tajima's D statistic and several collapsing methods. Our findings suggest that rare variation on PD Mendelian genes may have a role in the sporadic forms of the disease."],"pubmed_title":["Mendelian genes for Parkinson's disease contribute to the sporadic forms of the disease."],"pubmed_authors":["Spataro Nino N, Calafell Francesc F, Cervera-Carles Laura L, Casals Ferran F, Pagonabarraga Javier J, Pascual-Sedano Berta B, Campolongo Antònia A, Kulisevsky Jaime J, Lleó Alberto A, Navarro Arcadi A, Clarimón Jordi J, Bosch Elena E"],"name_synonyms":["Parkinson's syndrome, Forms, Parkinsons, Parkinson's disease, other disease, Primary Parkinsonism, Materials, Parkinson's disease NOS, Lewy Body, PARKINSON DIS, disorders, Gene, Paralysis agitans, Primary, PARKINSON DIS IDIOPATHIC, Cistrons, IDIOPATHIC PARKINSON DIS, Idiopathic Parkinson Disease, LEWY BODY PARKINSON DIS, Idiopathic Parkinson's Disease, Paralysis Agitans, diseases, Parkinson's Disease, Lewy Body Parkinson Disease, Diseases, disease or disorder, Genetic Materials, condition, diseases and disorders, Genetic Material, human disease, Parkinsons disease, Parkinson disease, Genetic, Parkinson's disease (disorder), PARK, IDIOPATHIC PARKINSONS DIS, Idiopathic PD, Lewy Body Parkinson's Disease, Parkinsonian disorder, non-neoplastic, Parkinson's, disease, Idiopathic, Parkinson's disease NOS (disorder), paralysis agitans, Material, PARKINSONS DIS IDIOPATHIC, Parkinson Disease, Parkinsonism, PARKINSONS DIS, disorder, Cistron, Homo sapiens disease, medical condition., Parkinson syndrome, PD, associated, PARKINSONS DIS LEWY BODY"],"description_synonyms":["Parkinson's disease, High temperature requirement protein A2, Materials, Set1, Raw, mFLJ00387, Parkinson's disease NOS, ipd, IDIOPATHIC PARKINSON DIS, GCase, BC010250, Skd/Pap/Bli, Paralysis Agitans, A530073F09, PASK, DDPAC, Park, Antigen, Tnrc15, Snca, cd36l2, CG10971, UCH-L1, CG10855, Parkinsons disease, Parkinson disease, Parkinson's disease (disorder), dPink1, Dj1, HEL-S-67p, MCCA, HardwareType, 8430423A01Rik, SREBP1, LIMP-2, HLA DRB5 Chains, MGC138549, 110kDa, Trap240, AA589443, HLA-DRB5, AU042772, l(3)L7062, PHF-tau, DJ1, 6530420C11Rik, siren9, 3.1.13.-, SMCR, MLGP85, Parkinson syndrome, AW557854, 4921513O20Rik, transcription from bacterial-type RNA polymerase promoter, Pap, Parkinson's syndrome, RGD1307829, HEL-S-85p, Parkinsons, Rnl5, G protein beta1/gamma2 subunit-interacting factor 1, DJ-1, PRSS25, RIBA, PARKINSON DIS, MED13, PARKINSON DIS IDIOPATHIC, pap, RIPK7, Med13, Idiopathic Parkinson's Disease, 2700010L10Rik, RAB7L1, 2900016I08Rik, AI551861, Mcca, sytXI, CG4523, dPINK1, bHLHd1, FBX7, PD1, DmelCG5483, CD36L2, STX1B2, STX1B1, Gt1, 1810045E08Rik, ISPD3024, DOM3Z, AI481710, instrument, mem3, TRAP240, C78391, C88048, FTDP-17, PDJ, whole genome, LIMPII, TAU_HUMAN, GC, Stx2, human, CG1107, RGD1564327, mNSC1, AW556857, Material, eIF4GI, Skd, PARKINSONS DIS IDIOPATHIC, MAPTL, Rin, RIN, DOM3L, HEL-117, cI-46, Srebf1, PARK1, UME2, DmelCG9936, Cd36l2, dLRRK, Ly65, PARK8, paired helical filament-tau, PARK9, PARK6, PARK4, PARK5, PARK2, UNQ1725/PRO9925, 3.6.1.-, 2610016F01Rik, PKPS, Dgkd, 2310058B18Rik, Human, Serine protease 25, GENEX3414, HSA9947, Set1A, RYE3, SMS, mKIAA0642, MEM3, Mem3, Man, GYF2, Genomes., ROCO2, AW227544, KMT2F, NACP, Nucks, dTrap240, PINK, DmelCG10855, DmelCG10971, ARC250, EIF4GI, EIF-4G1, CD157, bli, CG5625, Dchil, Parkinson's, Gm927, Idiopathic, bls, l(3)rK760, A230052G17Rik, Parkinsonism, KC1epsilon, AURA17, AW260462, 9330185J12Rik, SP22, SPG67, HLA-DRB, Thrap1, Bp3, Primary Parkinsonism, D630008H06, LRRK2, FLJ31424, Serine proteinase OMI, RGD1311800, Paralysis agitans, Primary, NG6, mnd2, Idiopathic Parkinson Disease, LEWY BODY PARKINSON DIS, neuron cytoplasmic protein 9.5, dmMED13, Pap/Trap, Parkinson's Disease, CG9936, NUCKS, AI851970, mKIAA0655, Col4a-1, HIP12, PGP 9.5, LD28662, DCHT, microtubule-associated protein tau, Hip1R, 2410015K21Rik, dTRAP240, EIF4F, FBX07, EIF4G, primary structure of sequence macromolecule, Lewy Body Parkinson's Disease, dMED13, DAGK7, Dvps35, DmelCG5625, UCHL-1, DAGK4, PINK1, 1190006F07Rik, PD, SYT12, AW259676, Dagk4, DmelCG4523, Bru, Srebp1, D630001M17Rik, GBA1, lrrk, instrument configuration, GLUC, HSPC221, C85118, LRRK, FBXO7, AW822034, OMI, Omi, Syn1b, CLN12, Skd/Med13, Uch-L1, 1110012E06Rik, DXO, CT17358, 3.4.21.108, DAGK, Svc, mKIAA0339, SCA1, TNRC15, Man (Taxonomy), R75106, omi, HLA-DRB5 Antigen, SR-BII, NUT8, R75593, D5Ertd593e, pap/dTRAP240, BRPK, ADD-1, ubiquitin thioesterase L1, LPRS2, SPH203, NMB, CG5483, DmelCG1107, BP-3, Shaking palsy, MRT42, PPP1R103, dvps35, BST1, Bst1, AI117679, associated, BEST:GH23468, AA410023, HLA DRB5 Antigen, AI413597, GRD9, HIP3, NDGOA, RAB7L, Bsta1, LimpII, 5430404N14Rik, D530019K15Rik, Mtapt, Modern, UCHL1, htrA2, HGFIN, CATX-8, PGP95, 9330188B09Rik, CAP1, Omi stress-regulated endoprotease, Syn, Lewy Body Parkinson Disease, GAK, Genetic Materials, hip1, MSTD, D030023K18, VPT7, Stx1b2, MAPT, region, Genetic Material, PRKN, Prss25, DRIP250, MCCalpha, gad, BC006835, DC-HIL, Nsccn1, HtrA2/Omi, PNPLA9, GCB, paralysis agitans, bacterial transcription, RAB11C, SRB9, alphaSYN, microarray, Cistron, anon-WO0118547.393, Stx1bl, 1110067M05Rik, 114|A10, PARKINSONS DIS LEWY BODY, AI852361, human being, DARDARIN, AI647796, Lewy Body, A830080H02Rik, AI447669, Gene, DmHtrA2, iPla2, FBX, AW045860, hardware, pink1, Prkn, RF005, Homo sapiens, Del(8)44H, PERQ3, PERQ2, KRPPD, SREBP-1, Genetic, domi, CG8464, DNAJC26, RAI1, Rai1, EPM4, 3632445O20Rik, IDIOPATHIC PARKINSONS DIS, CK1epsilon, Idiopathic PD, SPAK, AW457082, rai1, PER17, AI426939, Dom-3 homolog Z, ILWEQ, AV012978, dOmi, Roc2, ROC2, SREBP-1c, SREBP-1a, Parkinson Disease, PARKINSONS DIS, site, PGP9.5, HtrA2, MTBT1, MTBT2, AMRF, AI647518, P220, HLGP85, 1500004A13Rik, Tau, TAU, D130045N16Rik, PPND, neurofibrillary tangle protein, SREBP1c, Cistrons, LGP85, vps35, tau, AU042072, PARK17, PARK18, PARK15, sequence, PARK13, PARK11, THRAP1, HLA DRB5, CKIe, MCC-B, DNAJ26, betaGC, DVps35, ADD1, E030015G23Rik, DmelCG8464, AR-JP, Parkinsonian disorder, Srb9/AMIB/PAP/TRAP240, auxilin, Parkinson's disease NOS (disorder), Modern Man, dAux, AW561911, A730055F12Rik, Scad78"],"pubmed_title_synonyms":["Parkinson's syndrome, Forms, Parkinson's disease, Parkinsons, other disease, Primary Parkinsonism, human disease, Materials, Genetic, Parkinson disease, Parkinson's disease (disorder), Parkinson's disease NOS, Lewy Body, disorders, Gene, Paralysis agitans, Primary, Cistrons, Idiopathic PD, Idiopathic Parkinson Disease, Lewy Body Parkinson's Disease, Parkinsonian disorder, non-neoplastic, disease, Idiopathic Parkinson's Disease, Idiopathic, Parkinson's disease NOS (disorder), Paralysis Agitans, diseases, Material, paralysis agitans, Parkinson's Disease, Shaking palsy, Lewy Body Parkinson Disease, Diseases, Parkinson Disease, Parkinsonism, disease or disorder, Genetic Materials, condition, disorder, Cistron, diseases and disorders, Homo sapiens disease, medical condition., Parkinson syndrome, PD, Genetic Material"],"pubmed_abstract_synonyms":["Forms, Genome-Wide Association, Parkinson's disease, other disease, Materials, Procedures, Parkinson's disease NOS, Lewy Body, Genome Wide Association Analysis, Whole Genome Association Study, number, Gene, Mini Exon, clefted, Mutations, Relative, Techniques, GWA Studies, Caucasian, Paralysis Agitans, reduced, diseases, Roles, Method, Mini-Exon, Studies, symptoms, disease or disorder, Concepts, diseases and disorders, Low, tiny, Technique, GWA Study, human disease, me75, Occidental, Parkinson disease, Genetic, Parkinson's disease (disorder), occurrence, GWA, prevalence, hypoplasia, procedures, D17Mit170, Idiopathic PD, T1, Genome Wide Association Scan, Genome-Wide Association Studies, genetic, non-neoplastic, Study, Idiopathic, Methodological Studies, Shaking palsy, Clients, Role Concepts, Parkinson Disease, Parkinsonism, disorder, Homo sapiens disease, Parkinson syndrome, constitutitional genetic, incidence, Parkinson's syndrome, small, screening, Parkinsons, Primary Parkinsonism, findings, subdivided, cou, frequency, familial, disorders, white, Paralysis agitans, Primary, medical condition, Procedure, Tl3, Cistrons, Tl2, Genome-Wide, Client, results, Idiopathic Parkinson Disease, Concept, Idiopathic Parkinson's Disease, Lr, Role Concept, Genome Wide Association Study, Parkinson's Disease, Lewy Body Parkinson Disease, European, Relative Risks, Diseases, Role, Genetic Materials, condition, rare (European definition), Whole Genome Association Analysis, techniques, outbreaks, Genetic Material, Caucasoid, forked, Relative Risk, Caucasians, susceptibility, divided, Risk, underdeveloped, Mini-Exons, Risks, Exon, signs, common, Methodological, septate, surveillance, Methodological Study, morbidity, endemics, Genome Wide Association Studies, Lewy Body Parkinson's Disease, Parkinsonian disorder, disease, clear, hyaline, Parkinson's disease NOS (disorder), Patient, paralysis agitans, Material, Whites, cardinality, Bra, Association Studies, Cistron, epidemics, White, medical condition., PD, inherited genetic, Association Study, hereditary, methodology"],"additional_accession":[]},"is_claimable":false,"name":"High coverage target resequencing of coding and regulatory regions of 38 Parkinson disease genes associated either to the Mendelian or the sporadic forms of the disease","description":"Coding sequences and putative regulatory sequences (retrieved from Ensembl and including up to 2500 bp of promoter sequence upstream the transcription start site) were re-sequenced to a mean depth of 49X on 38 genes associated to Parkinson's disease (RAB25, NUCKS1, RAB7L1, GBA, SYT11, ACMSD, STK39, MCCC1, STBD1, GAK, DGKQ, BST1, SCARB2, HLA-DRB5, GPNMB, FGF20, ITGA8, HIP1R, STX1B, SETD1A, SREBF1, MED13, RAI1, MAPT, RIT2, GIGYF2, HTRA2, EIF4G1, SNCA, LRRK2, VPS35, PINK1, DJ1, ATP13A2, UCHL1, PARK2, FBXO7, and PLA2G6). Sequencing was performed on 249 Parkinson's idiopathic cases and 145 unrelated controls of Spanish origin. All sequencing data was generated with an Illumina Hiseq2000 instrument after enrichment with a custom NimbleGen array. Raw reads were mapped to human reference genome hg19/GRCh37 using BWA aligner.","dates":{"updated":"2017-07-26 15:39:25"},"accession":"EGAS00001000973","cross_references":{"TAXONOMY":["9606"],"pubmed":["25504046"],"EGA":["EGAD00001001029","EGAC00001000244"]}}