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publications [2018/11/07 20:09]
cassa
publications [2022/05/19 14:35] (current)
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 ===== Selected Recent Publications ===== ===== Selected Recent Publications =====
  
-  - Shen MWArbab MHsu JYWorstell D, Culbertson SJ, Krabbe O, **Cassa CA**, Liu DRGifford DKSherwood RIPredictable and precise template-free CRISPR editing of pathogenic variantsNature 2018   +  - Resolving Discordant Variant Classifications using Clinical Guideline Evidence. Bhat VAdzhubei IAFife JDLebo M, **Cassa CA**. Preprint on medRxiv. doi: https://doi.org/10.1101/2022.05.16.22275073 
-  - **Cassa CA**, Weghorn DBalick DJJordan DMNusinow DSamocha KE, O'Donnell-Luria A, MacArthur DGDaly MJBeier DRSunyaevSR. Response to comment on “Estimating the selective effects of heterozygous protein-truncating variants from human exome data”Cassa et al. Nat Genet. 2018  +  - A framework for integrated clinical risk assessment using population sequencing data. Fife JDTran TBernatchez JRShepard KE, Koch C, Patel AP, Fahed AC, Krishnamurthy S, Regeneron Genetics Center, DiscovEHR Collaboration, Wang W, Buchanan AH, Carey DJ, Metpally R, Khera AV, Lebo M, **Cassa CA**Preprint on medRxivdoi: https://doi.org/10.1101/2021.08.12.21261563 
-  Weghorn D, Balick DJ, **Cassa CA**, Kosmicki JDaly MJBeier DRSunyaev SR Applicability of the mutation-selection balance model to population genetics of heterozygous protein-truncating variants in humansbioRxiv Pre-printhttps://www.biorxiv.org/content/early/2018/10/03/433961 +  - The missing link between genetic association and regulatory function. Connally N, Nazeen S, Lee D, Shi H, Stamatoyannopoulos J, Chun S. Cotsapas C, **Cassa C**, Sunyaev S. Preprint on medRxiv. doi: https://doi.org/10.1101/2021.06.08.21258515 
-  - Kousi M, Soylemez O, Ozanturk A, Akle S, Jungreis I, Muller J, **Cassa  CA**, Brand H, Rosenfeld JA, Wolf MY, Sadeghpour A, McFadden K,  Lewis RA, Talkowski ME, Dollfus H, Kellis M, Davis EE, Sunyaev SR, Katsanis N. Evidence for secondary-variant genetic burden and non-random distribution across biological modules in a recessive ciliopathy. bioRxiv Pre-print: https://www.biorxiv.org/content/early/2018/07/05/362707 +  - Variants in STXBP3 Are Associated With Very Early Onset Inflammatory Bowel DiseaseBilateral Sensorineural Hearing Loss and Immune Dysregulation. Ouahed JKelsen JRSpessott WAKooshesh K, Sanmillan ML, Dawany N, Sullivan KE, Hamilton K, Slowik V, Nejentsev S, Neves JF, Flores H, Chung WK, Wilson A, Yeboa KAWou KJain PField MTollefson S, Dent MH, Li D, Naito T, McGovern DPB, Kwong AC, Taliaferro F, Ordovas-Montanes JHorwitz B, Kotlarz D, Klein C, Evans J, Dorsey J, Warner N, Elkadri A, Muise AM, Goldsmith J, Thompson B, Engelhardt KR, Cant AJ, Hambleton S, Barclay A, Toth-Petroczy A, Vuzman D, Carmichael N, Bodea C, **Cassa CA**, Devoto MMaas RLBehrens EM, Giraudo CGSnapper SBJ Crohns Colitis2021 Apr 23:jjab077. doi10.1093/ecco-jcc/jjab077PMID: 33891011 
-  - Haghighi A, Krier JB, Toth-Petroczy A, **Cassa CA**, Frank NY, Carmichael N, Fieg E, Bjonnes A, Mohanty A, Briere LC, Lincoln S, Lucia S, Gupta VA, Söylemez O, Sutti S, Kooshesh K, Qiu H, Fay CJ, Perroni V, Valerius J, Hanna M, Frank A, Ouahed J, Snapper SB, Pantazi A, Chopra SS, Leshchiner I, Stitziel NO, Feldweg A, Mannstadt M, Loscalzo J, Sweetser DA, Liao E, Stoler JM, Nowak CB, Sanchez-Lara PA, Klein OD, Perry H, Patsopoulos NA, Raychaudhuri S, Goessling W, Green RC, Seidman CE, MacRae CA, Sunyaev SR, Maas RL, Vuzman D; Undiagnosed Diseases Network, Brigham and Women’s Hospital FaceBase Project, Brigham Genomic Medicine (BGM). An integrated clinical program and crowdsourcing strategy for genomic sequencing and Mendelian disease gene discovery. NPJ Genom Med. 2018 Aug 13;3:21. doi: 10.1038/s41525-018-0060-9. +  - Louie W, Shen MW, Tahiry Z, Zhang S, Worstell D, **Cassa CA**, Sherwood RI, Gifford DKMachine learning based CRISPR gRNA design for therapeutic exon skipping. PLoS Comput Biol. 2021 Jan 8;17(1):e1008605. doi: 10.1371/journal.pcbi.1008605. eCollection 2021 Jan. PMID: 33417623  
-  - **Cassa CA**, Jordan DM, Adzhubei I, Sunyaev SR. A literature review at genome scale: improving clinical variant assessment. Genet Med. 2018 Feb 1. doi: 10.1038/gim.2017.230. PMID: 29388949 PDF: http://rdcu.be/F3q3 +  - Kousi M, Soylemez O, Ozanturk A, Mourtzi N, Akle S, Jungreis I, Jungreis I, Muller J, **Cassa  CA**, Brand H, Mokry JA, Wolf MY, Sadeghpour A, McFadden K,  Lewis RA, Talkowski ME, Dollfus H, Kellis M, Davis EE, Sunyaev SR, Katsanis N. Evidence for secondary-variant genetic burden and non-random distribution across biological modules in a recessive ciliopathy. //Nat. Gen.// 2020 Oct 12. PMID: 33046855 DOI: 10.1038/s41588-020-0707-1 
-  - **Cassa CA**, Weghorn D, Balick DJ, Jordan DM, Nusinow D, Samocha KE, O'Donnell-Luria A, MacArthur DG, Daly MJ, Beier DR, Sunyaev, SR. Estimating the Selective Effects of Heterozygous Protein Truncating Variants from Human Exome Data. Nat Genet. 2017 May;49(5):806-810. doi: 10.1038/ng.3831. PMID: 28369035 PMC: https://www.ncbi.nlm.nih.gov/pubmed/28369035 +  - Akinci E, Cha M, Lin L, Yeo G, Hamilton MC, Donahue CJ, Bermudez-Cabrera HC, Zanetti LC, Chen M, Barkal SA, Khowpinitchai B, Chu N, Velimirovic M, Jodhani R, Fife JD, Sovrovic M, Cole PA, Davey RA, **Cassa CA**, Sherwood RI. Elucidation of remdesivir cytotoxicity pathways through genome-wide CRISPR-Cas9 screening and transcriptomics. //bioRxiv// 2020 Aug 28:2020.08.27.270819. doi: 10.1101/2020.08.27.270819. (Preprint.) PMID: 32869031  
-  - **Cassa CA**, Akle S, Jordan DM, Rosenfeld JA. When “N of 2” is not enough: Integrating statistical and functional data in gene discovery. Cold Spring Harb Mol Case Stud. 2017 May;3(3):a001099. doi: 10.1101/mcs.a001099. PMID: 28487880 +  Fahed AC, Wang M, Homburger JR, Patel AP, Bick AG, Neben CL, Lai C, Brockman D, Philippakis A, Ellinor PT, **Cassa CA**, Lebo M, Ng K, Lander ES, Zhou AY, Kathiresan S, Khera AV. Polygenic background modifies penetrance of monogenic variants for tier 1 genomic conditions. //Nat. Commun.// 2020 Aug 20;11(1):3635. doi: 10.1038/s41467-020-17374-3. PMID: 32820175  
-  - Akle S, Chun S, Jordan DM, **Cassa CA**. Mitigating false-positive associations in rare disease gene discovery. Hum Mutat. 2015 Oct;36(10):998-1003. doi: 10.1002/humu.22847. PMID: 26378430 +  - Arbab M, Shen MW, Mok B, Wilson C, Matusek Z, **Cassa CA**, Lui DR. Determinants of Base Editing Outcomes from Target Library Analysis and Machine Learning. //Cell// 2020 https://doi.org/10.1016/j.cell.2020.05.037 
-  - **Cassa CA**, Smith SE, Docken W, Hoffman E, McLaughlin H, Chun S, Leshchiner I, Miraoui H, Raychaudhuri S, Frank NY, Wilson BJ, Sunyaev SR, Maas RL; Brigham Genomic Medicine, Vuzman D. An argument for early genomic sequencing in atypical cases: a WISP3 variant leads to diagnosis of progressive pseudorheumatoid arthropathy of childhood. Rheumatology (Oxford). 2015 Oct 22. pii: kev367. PMID: 26493744 +  - Patel AP, Wang M, Fahed AC, Mason-Suares H, Brockman D, Pelletier R, Amr S, Machini K, Hawley M, Witkowski L, Koch C, Philippakis A, **Cassa CA**, Ellinor PT, Kathiresan S, Ng K, Lebo M, Khera AV. Association of Rare Pathogenic DNA Variants for Familial Hypercholesterolemia, Hereditary Breast and Ovarian Cancer Syndrome, and Lynch Syndrome With Disease Risk in Adults According to Family History. //JAMA Netw Open// 2020 Apr 1;3(4):e203959. doi: 10.1001/jamanetworkopen.2020.3959.  
-  - Chopra SS, Leshchiner I, Duzkale H, McLaughlin H, Giovanni M, Zhang C, Stitziel N, Fingeroth J, Joyce RM, Lebo M, Rehm H, Vuzman D, Maas R, Sunyaev SR, Murray M, **Cassa CA**. Inherited CHST11/MIR3922 deletion is associated with a novel recessive syndrome presenting with skeletal malformation and malignant lymphoproliferative disease. Mol Genet Genomic Med. 2015 Sep;3(5):413-23. doi: 10.1002/mgg3.152. Epub 2015 May 10. PMID: 26436107 +  - Nissim S, Leshchiner I, Mancias JD, Greenblatt MB, Maertens O, **Cassa CA**, Rosenfeld JA, Cox AG, Hedgepeth J, Wucherpfennig JI, Kim AJ, Henderson JE, Gonyo P, Brandt A, Lorimer E, Unger B, Prokop JW, Heidel JR, Wang XX, Ukaegbu CI, Jennings BC, Paulo JA, Gableske S, Fierke CA, Getz G, Sunyaev SR, Wade Harper J, Cichowski K, Kimmelman AC, Houvras Y, Syngal S, Williams C, Goessling W. Mutations in RABL3 alter KRAS prenylation and are associated with hereditary pancreatic cancer. //Nat Genet.// 2019 Sep;51(9):1308-1314. PMID31406347 https://www.nature.com/articles/s41588-019-0475-y 
-  - Balick DJ, Do R, **Cassa CA**, Reich D, Sunyaev SR. Dominance of Deleterious Alleles Controls the Response to a Population Bottleneck. PLoS Genet. 2015 Aug 28;11(8):e1005436. doi: 10.1371/journal.pgen.1005436. eCollection 2015 Aug. PMID: 26317225 +  - Weghorn D, Balick DJ, **Cassa C**, Kosmicki JA, Daly MJ, Beier DR, Sunyaev SR. Applicability of the Mutation-Selection Balance Model to Population Genetics of Heterozygous Protein-Truncating Variants in Humans. //Mol Biol Evol.// 2019 Aug 1;36(8):1701-1710. doi: 10.1093/molbev/msz092. PMID: 31004148 
-  - Jordan DM, Frangakis SG, Golzio C, **Cassa CA**, Kurtzberg J; Task Force for Neonatal Genomics, Davis EE, Sunyaev SR, Katsanis N. Identification of cis-suppression of human disease mutations by comparative genomics. Nature. 2015 Aug 13;524(7564):225-9. doi: 10.1038/nature14497. Epub 2015 Jun 29. PMID: 26123021+  - **Cassa CA**, Weghorn D, Balick DJ, Jordan DM, Nusinow D, Samocha KE, O'Donnell-Luria A, MacArthur DG, Daly MJ, Beier DR, Sunyaev SR. Reply to 'Selective effects of heterozygous protein-truncating variants'. Nat Genet. 2019 Jan; 51(1):3-4. PMID: 30478437. 
 +  - Kumar Mohanty A, Vuzman D, Francioli L, **Cassa C**, Toth-Petroczy A, Sunyaev S. novoCaller: A Bayesian network approach for de novo variant calling from pedigree and population sequence data. //Bioinformatics.// 2018 Aug 30. PMID: 30169785. 
 +  - Shen MW, Arbab M, Hsu JY, Worstell D, Culbertson SJ, Krabbe O, **Cassa CA**, Liu DR, Gifford DK, Sherwood RI. Predictable and precise template-free CRISPR editing of pathogenic variants. //Nature// 2018. https://www.nature.com/articles/s41586-018-0686-x 
 +  - **Cassa CA**, Weghorn D, Balick DJ, Jordan DM, Nusinow D, Samocha KE, O'Donnell-Luria A, MacArthur DG, Daly MJ, Beier DR, Sunyaev, SR. Response to comment on “Estimating the selective effects of heterozygous protein-truncating variants from human exome data”, Cassa et al. //Nat Genet.// 2018  
 +  - Haghighi A, Krier JB, Toth-Petroczy A, **Cassa CA**, Frank NY, Carmichael N, Fieg E, Bjonnes A, Mohanty A, Briere LC, Lincoln S, Lucia S, Gupta VA, Söylemez O, Sutti S, Kooshesh K, Qiu H, Fay CJ, Perroni V, Valerius J, Hanna M, Frank A, Ouahed J, Snapper SB, Pantazi A, Chopra SS, Leshchiner I, Stitziel NO, Feldweg A, Mannstadt M, Loscalzo J, Sweetser DA, Liao E, Stoler JM, Nowak CB, Sanchez-Lara PA, Klein OD, Perry H, Patsopoulos NA, Raychaudhuri S, Goessling W, Green RC, Seidman CE, MacRae CA, Sunyaev SR, Maas RL, Vuzman D; Undiagnosed Diseases Network, Brigham and Women’s Hospital FaceBase Project, Brigham Genomic Medicine (BGM). An integrated clinical program and crowdsourcing strategy for genomic sequencing and Mendelian disease gene discovery. //NPJ Genom Med.// 2018 Aug 13;3:21. doi: 10.1038/s41525-018-0060-9. 
 +  - **Cassa CA**, Jordan DM, Adzhubei I, Sunyaev SR. A literature review at genome scale: improving clinical variant assessment. //GenetMed.// 2018 Feb 1. doi: 10.1038/gim.2017.230. PMID: 29388949 PDF: http://rdcu.be/F3q3 
 +  - **Cassa CA**, Weghorn D, Balick DJ, Jordan DM, Nusinow D, Samocha KE, O'Donnell-Luria A, MacArthur DG, Daly MJ, Beier DR, Sunyaev, SR. Estimating the Selective Effects of Heterozygous Protein Truncating Variants from Human Exome Data. //Nat Genet.// 2017 May;49(5):806-810. doi: 10.1038/ng.3831. PMID: 28369035 PMC: https://www.ncbi.nlm.nih.gov/pubmed/28369035 
 +  - **Cassa CA**, Akle S, Jordan DM, Rosenfeld JA. When “N of 2” is not enough: Integrating statistical and functional data in gene discovery. C//old Spring Harb Mol Case Stud.// 2017 May;3(3):a001099. doi: 10.1101/mcs.a001099. PMID: 28487880 
 +  - Akle S, Chun S, Jordan DM, **Cassa CA**. Mitigating false-positive associations in rare disease gene discovery. //Hum Mutat.// 2015 Oct;36(10):998-1003. doi: 10.1002/humu.22847. PMID: 26378430 
 +  - **Cassa CA**, Smith SE, Docken W, Hoffman E, McLaughlin H, Chun S, Leshchiner I, Miraoui H, Raychaudhuri S, Frank NY, Wilson BJ, Sunyaev SR, Maas RL; Brigham Genomic Medicine, Vuzman D. An argument for early genomic sequencing in atypical cases: a WISP3 variant leads to diagnosis of progressive pseudorheumatoid arthropathy of childhood. //Rheumatology// (Oxford). 2015 Oct 22. pii: kev367. PMID: 26493744 
 +  - Chopra SS, Leshchiner I, Duzkale H, McLaughlin H, Giovanni M, Zhang C, Stitziel N, Fingeroth J, Joyce RM, Lebo M, Rehm H, Vuzman D, Maas R, Sunyaev SR, Murray M, **Cassa CA**. Inherited CHST11/MIR3922 deletion is associated with a novel recessive syndrome presenting with skeletal malformation and malignant lymphoproliferative disease. //Mol Genet Genomic Med.// 2015 Sep;3(5):413-23. PMID: 26436107 
 +  - Balick DJ, Do R, **Cassa CA**, Reich D, Sunyaev SR. Dominance of Deleterious Alleles Controls the Response to a Population Bottleneck. //PLoS Genet.// 2015 Aug 28;11(8):e1005436. PMID: 26317225 
 +  - Jordan DM, Frangakis SG, Golzio C, **Cassa CA**, Kurtzberg J; Task Force for Neonatal Genomics, Davis EE, Sunyaev SR, Katsanis N. Identification of cis-suppression of human disease mutations by comparative genomics. //Nature.// 2015 Aug 13;524(7564):225-9. doi: 10.1038/nature14497. Epub 2015 Jun 29. PMID: 26123021
   - Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, DeChene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie D Jr, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, **Cassa CA**, ... Kohane IS, Margulies DM. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.\\ Genome Biol. 15(3):R53 (2014) PubMed [[http://www.ncbi.nlm.nih.gov/pubmed/24667040|PMID:24667040]].   - Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, DeChene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie D Jr, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, **Cassa CA**, ... Kohane IS, Margulies DM. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.\\ Genome Biol. 15(3):R53 (2014) PubMed [[http://www.ncbi.nlm.nih.gov/pubmed/24667040|PMID:24667040]].
   - **Cassa CA**, Tong MY, Jordan DM. Large numbers of genetic variants considered to be pathogenic are common in asymptomatic individuals. Hum Mutat 34(9):1216-20 (2013). PubMed [[http://www.ncbi.nlm.nih.gov/pubmed/23818451|PMID:23818451   - **Cassa CA**, Tong MY, Jordan DM. Large numbers of genetic variants considered to be pathogenic are common in asymptomatic individuals. Hum Mutat 34(9):1216-20 (2013). PubMed [[http://www.ncbi.nlm.nih.gov/pubmed/23818451|PMID:23818451