updated GWAS catalog

README.md

@@ -22,7 +22,7 @@ Here is a guide to the lists we currently have in this repo:
 | [Homozygous LoF tolerant](lists/homozygous_lof_tolerant_twohit.tsv) | 330 | Genes with at least two different high-confidence LoF variants found in a homozygous state in at least one individual in ExAC. By Konrad Karczewski. | Just cite the ExAC paper [[Lek 2016]] |
 | [Essential in culture](lists/core_essentials_hart.tsv) | 283 | Genes deemed essential in multiple cultured cell lines based on shRNA screen data | [[Hart 2014]] |
 | [Essential in mice](lists/mgi_essential.tsv) | 2,454 | Genes where homozygous knockout in mice results in pre-, peri- or post-natal lethality. The mouse phenotypes were reported by Jackson Labs [[Blake 2011]], then essential gene list was extracted via manual review of phenotypes by [[Georgi 2013]], and the essential/non-essential flag was put into dbNSFP [[Liu 2013]]. We extracted the genes from dbNSFP. | [[Blake 2011], [Georgi 2013], and [Liu 2013]] |
-| [Genes nearest to GWAS peaks](lists/gwascatalog.tsv) | 3,762 | Closest gene 3' and 5' of GWAS hits in the NHGRI GWAS catalog as of Feb 9, 2015 | See instructions [here](http://www.genome.gov/gwastudies/). Cite [[Welter 2014]] and include a web reference to [genome.gov/gwastudies/](http://www.genome.gov/gwastudies/). |
+| [Genes nearest to GWAS peaks](lists/gwascatalog.tsv) | 6,336 | Closest gene to GWAS hits  with *P* < 5-e8 in the NHGRI GWAS catalog (MAPPED_GENE column) as of Sep 13, 2018 | [[MacArthur 2017]] |
 | [DNA Repair Genes, WoodRD](lists/DRG_WoodRD.tsv) | 178 | An updated inventory of human DNA repair genes. (Last modified on Tuesday 15th April 2014). For details see [src/DRG_WoodRD.R](src/DRG_WoodRD.R) | Cite [[Wood 2005]] and include a web reference to [this URL](http://sciencepark.mdanderson.org/labs/wood/dna_repair_genes.html). |
 | [DNA Repair Genes, KangJ](lists/DRG_KangJ.tsv) | 151 | Supplementary Table 1. 151 DNA repair genes. DNA repair genes from DNA repair pathways: ATM, BER, FA/HR, MMR, NHEJ, NER, TLS, XLR, RECQ, and other. | Cite [[Kang 2012]] |
 | [ClinGen haploinsufficient genes](lists/clingen_level3_genes_2018_09_13.tsv) | 294 | Genes with sufficient evidence for dosage pathogenicity (level 3) as determined by the ClinGen Dosage Sensitivity Map as of Sep 13, 2018 | Cite [[Rehm 2015]]. See also [ClinGen's TOU](https://www.clinicalgenome.org/about/terms-of-use/) |
@@ -93,6 +93,8 @@ We welcome pull requests for adding additional lists, provided they are licensed
 
 [Alexander 2017]: https://www.ncbi.nlm.nih.gov/pubmed/29055040 "Alexander SP, Christopoulos A, Davenport AP, Kelly E, Marrion NV, Peters JA, Faccenda E, Harding SD, Pawson AJ, Sharman JL, Southan C, Davies JA; CGTP Collaborators. THE CONCISE GUIDE TO PHARMACOLOGY 2017/18: G protein-coupled receptors. Br J Pharmacol. 2017 Dec;174 Suppl 1:S17-S129. doi: 10.1111/bph.13878. PubMed PMID: 29055040; PubMed Central PMCID: PMC5650667."
 
+[MacArthur 2017]: https://www.ncbi.nlm.nih.gov/pubmed/27899670/ "MacArthur J, Bowler E, Cerezo M, Gil L, Hall P, Hastings E, Junkins H, McMahon A, Milano A, Morales J, Pendlington ZM, Welter D, Burdett T, Hindorff L, Flicek P, Cunningham F, Parkinson H. The new NHGRI-EBI Catalog of published genome-wide  association studies (GWAS Catalog). Nucleic Acids Res. 2017 Jan 4;45(D1):D896-D901. doi: 10.1093/nar/gkw1133. Epub 2016 Nov 29. PubMed PMID: 27899670; PubMed Central PMCID: PMC5210590."
+
 [Harding 2018]: https://www.ncbi.nlm.nih.gov/pubmed/29149325 "Harding SD, Sharman JL, Faccenda E, Southan C, Pawson AJ, Ireland S, Gray AJG, Bruce L, Alexander SPH, Anderton S, Bryant C, Davenport AP, Doerig C, Fabbro D, Levi-Schaffer F, Spedding M, Davies JA; NC-IUPHAR. The IUPHAR/BPS Guide to PHARMACOLOGY in 2018: updates and expansion to encompass the new guide to IMMUNOPHARMACOLOGY. Nucleic Acids Res. 2018 Jan 4;46(D1):D1091-D1106. doi: 10.1093/nar/gkx1121. PubMed PMID: 29149325; PubMed Central PMCID: PMC5753190."
 
 [Wishart 2018]: https://www.ncbi.nlm.nih.gov/pubmed/29126136/ "Wishart DS, Feunang YD, Guo AC, Lo EJ, Marcu A, Grant JR, Sajed T, Johnson D,  Li C, Sayeeda Z, Assempour N, Iynkkaran I, Liu Y, Maciejewski A, Gale N, Wilson A, Chin L, Cummings R, Le D, Pon A, Knox C, Wilson M. DrugBank 5.0: a major update to the DrugBank database for 2018. Nucleic Acids Res. 2018 Jan 4;46(D1):D1074-D1082. doi: 10.1093/nar/gkx1037. PubMed PMID: 29126136; PubMed Central PMCID: PMC5753335."