resolved conflicts

README.md

@@ -7,7 +7,7 @@ Here is a guide to the lists we currently have in this repo:
 | List | Count | Description | Please cite |
 | ---- | ---- | ---- | ---- |
 | [Universe](lists/universe.tsv) | 18,991 | Approved symbols for 18,991 protein-coding genes according to HGNC as of Feb 9, 2015. For details see [src/create_universe.bash](src/create_universe.bash). This list is the "universe" of which all subsequent lists are subsets. | See [genenames.org/about/overview](http://www.genenames.org/about/overview). Users are asked to web reference "HUGO Gene Nomenclature Committee at the European Bioinformatics Institute" (http://www.genenames.org/) if possible. |
-| [FDA-approved drug targets](lists/fda_approved_drug_targets.tsv) | 286 | Genes whose protein products are known to be the mechanistic targets of FDA-approved drugs. For details on the exact criteria we used for inclusion in this list, see [src/drug_targets.py](src/drug_targets.py) | See [drugbank.ca/about](http://www.drugbank.ca/about). Please cite [[Law 2014], [Knox 2011], [Wishart 2008] and/or [Wishart 2006]]. | 
+| [FDA-approved drug targets](lists/fda_approved_drug_targets.tsv) | 286 | Genes whose protein products are known to be the mechanistic targets of FDA-approved drugs. For details on the exact criteria we used for inclusion in this list, see [src/drug_targets.py](src/drug_targets.py) | See [drugbank.ca/about](http://www.drugbank.ca/about). Please cite [[Law 2014], [Knox 2011], [Wishart 2008] and/or [Wishart 2006]]. |
 | [Drug targets by Nelson et al 2012](lists/drug_targets_nelson.tsv) | 201 | Drug targets according to Nelson et al 2012, with reference to Russ & Lampel 2005. | [[Nelson 2012], [Russ & Lampel 2005]] |
 | [Autosomal dominant genes by Blekhman et al 2008](lists/blekhman_ad.tsv) | 307 | OMIM disease genes deemed to follow autosomal dominant inheritance according to extensive manual curation by Molly Przeworski's group. | [[Blekhman 2008]] |
 | [Autosomal dominant genes by Berg et al 2013](lists/berg_ad.tsv) | 631 | OMIM disease genes (as of June 2011) deemed to follow autosomal dominant inheritance according Berg et al, 2013. | [[Berg 2013]] |
@@ -20,7 +20,7 @@ Here is a guide to the lists we currently have in this repo:
 | [All dominant genes](lists/all_ad.tsv) | 709 | Currently the union of the Berg and Blekhman dominant lists, may add more lists later. | [[Blekhman 2008], [Berg 2013]] |
 | [All recessive genes](lists/all_ar.tsv) | 1183 | Currently the union of the Berg and Blekhman recessive lists, may add more lists later. | [[Blekhman 2008], [Berg 2013]] |
 | [Essential in culture](lists/core_essentials_hart.tsv) | 285 | 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]] | 
+| [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/). |
 | [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]] |
@@ -30,6 +30,8 @@ Here is a guide to the lists we currently have in this repo:
 | [Kinases](lists/kinases.tsv) | 351 | From UniProt's [pkinfam list](http://www.uniprot.org/docs/pkinfam) | [According to UniProt](http://www.uniprot.org/docs/pkinfam) this list is based on 3 publications: [[Hunter 2000], [Manning 2002], [Miranda-Saavedra & Barton 2007]] |
 | [GPCRs](lists/gpcr.tsv) | 1705 | GPCR list from [guidetopharmacology.org](http://www.guidetopharmacology.org/GRAC/GPCRListForward?class=A) | Please read citing instructions [here](http://www.guidetopharmacology.org/citing.jsp) and at a minimum, cite [[Pawson 2014]]. |
 | [Natural product targets](lists/natural_product_targets.tsv) | 37 | List of hand-curated targets of natural products from supplement of [[Dancik 2010]] | [[Dancik 2010]] |
+| [BROCA - Cancer Risk Panel](lists/BROCA_Cancer_Risk_Panel.tsv) | 66 | BROCA is useful for the evaluation of patients with a suspected hereditary cancer predisposition, with a focus on syndromes that include breast or ovarian cancer as one of the cancer types. Depending on the causative gene involved, these cancers may co-occur with other cancer types (such as colorectal, endometrial, pancreatic, endocrine, or melanoma). | [University of Washington](http://depts.washington.edu/labweb/Divisions/MolDiag/MolDiagGen/index.htm) |
+| [ACMG V2.0](lists/ACMG_list_2_0.tsv) | 59 | The minimum list of genes to be reported as incidental or secondary findings as published by the American College of Medical Genetics and Genomics (ACMG) | [[Kalia 2017]] |
 | [GPI-anchored proteins](lists/gpi_anchored.tsv) | 135 | Gene symbols encoding proteins [annotated by UniProt](https://www.uniprot.org/uniprot/?query=keyword:%22GPI-anchor%20[KW-0336]%22&fil=organism%3A%22Homo+sapiens+%28Human%29+%5B9606%5D%22) as being GPI-anchored. | Cite the latest UniProt paper: [[UniProt Consortium 2017]] |
 
 We welcome pull requests for adding additional lists, provided they are licensed for redistribution. If possible, please provide the source code used to extract the list from its original source, and an appropriate description for this readme.
@@ -78,4 +80,8 @@ We welcome pull requests for adding additional lists, provided they are licensed
 
 [Landrum 2014]: http://www.ncbi.nlm.nih.gov/pubmed/24234437 "Landrum MJ, Lee JM, Riley GR, Jang W, Rubinstein WS, Church DM, Maglott DR. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 2014 Jan;42(Database issue):D980-5. doi: 10.1093/nar/gkt1113. Epub 2013 Nov 14. PubMed PMID: 24234437; PubMed Central PMCID: PMC3965032."
 
+<<<<<<< HEAD
 [UniProt Consortium 2017]: https://www.ncbi.nlm.nih.gov/pubmed/27899622 "The UniProt Consortium. UniProt: the universal protein knowledgebase. Nucleic Acids Res. 2017 Jan 4;45(D1):D158-D169. doi: 10.1093/nar/gkw1099. Epub 2016 Nov 29. PubMed PMID: 27899622; PubMed Central PMCID: PMC5210571."
+=======
+[Kalia 2017]: https://www.ncbi.nlm.nih.gov/pubmed/27854360 "Kalia SS, Adelman K2, Bale SJ, Chung WK, Eng C, Evans JP, Herman GE, Hufnagel SB, Klein TE, Korf BR, McKelvey KD, Ormond KE, Richards CS, Vlangos CN, Watson M, Martin CL, Miller DT; Recommendations for reporting of secondary findings in clinical exome and genome sequencing, 2016 update (ACMG SF v2.0): a policy statement of the American College of Medical Genetics and Genomics. Genet Med. 2017 Feb;19(2):249-255. doi: 10.1038/gim.2016.190. Epub 2016 Nov 17."
+>>>>>>> 34b59cb702a0757ccbab2b2d320428755de6eb5e

lists/ACMG_2_0.tsv

@@ -0,0 +1,59 @@
+BRCA1
+BRCA2
+TP53
+STK11
+MLH1
+MSH2
+MSH6
+PMS2
+APC
+MUTYH
+BMPR1A
+SMAD4
+VHL
+MEN1
+RET
+PTEN
+RB1
+SDHD
+SDHAF2
+SDHC
+SDHB
+TSC1
+TSC2
+WT1
+NF2
+COL3A1
+FBN1
+TGFBR1
+TGFBR2
+SMAD3
+ACTA2
+MYH11
+MYBPC3
+MYH7
+TNNT2
+TNNI3
+TPM1
+MYL3
+ACTC1
+PRKAG2
+GLA
+MYL2
+LMNA
+RYR2
+PKP2
+DSP
+DSC2
+TMEM43
+DSG2
+KCNQ1
+KCNH2
+SCN5A
+LDLR
+APOB
+PCSK9
+ATP7B
+OTC
+RYR1
+CACNA1S

lists/BROCA_Cancer_Risk_Panel.tsv

@@ -0,0 +1,66 @@
+AKT1
+APC
+ATM
+ATR
+AXIN2
+BAP1
+BARD1
+BMPR1A
+BRCA1
+BRCA2
+BRIP1
+CDH1
+CDK4
+CDKN2A
+CHEK1
+CHEK2
+CTNNA1
+EPCAM
+FAM175A
+FANCM
+FH
+FLCN
+GALNT12
+GEN1
+GREM1
+HOXB13
+MEN1
+MET
+MITF
+MLH1
+MRE11A
+MSH2
+MSH6
+MUTYH
+NBN
+NF1
+NTHL1
+PALB2
+PALLD
+PDGFRA
+PIK3CA
+PMS2
+POLD1
+POLE
+POT1
+PRKAR1A
+PRSS1
+PTCH1
+PTEN
+RAD51B
+RAD51C
+RAD51D
+RB1
+RECQL
+RET
+RINT1
+RPS20
+SDHB
+SDHC
+SDHD
+SLX4
+SMAD4
+SMARCA4
+TP53
+VHL
+XRCC2