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publications [2017/08/22 13:04]
cassa
publications [2021/08/15 22:33]
cassa
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 ===== Selected Recent Publications ===== ===== Selected Recent Publications =====
  
-   +  - A framework for integrated clinical risk assessment using population sequencing data. Fife JD, Tran T, Bernatchez JR, Shepard 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 medRxiv. doi: https://doi.org/10.1101/2021.08.12.21261563 
-   +  - 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 
-   +  - Variants in STXBP3 Are Associated With Very Early Onset Inflammatory Bowel Disease, Bilateral Sensorineural Hearing Loss and Immune Dysregulation. Ouahed J, Kelsen JR, Spessott WA, Kooshesh K, Sanmillan ML, Dawany N, Sullivan KE, Hamilton K, Slowik V, Nejentsev S, Neves JF, Flores H, Chung WK, Wilson A, Yeboa KA, Wou K, Jain P, Field M, Tollefson S, Dent MH, Li D, Naito T, McGovern DPB, Kwong AC, Taliaferro F, Ordovas-Montanes J, Horwitz 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 M, Maas RL, Behrens EM, Giraudo CG, Snapper SB. J Crohns Colitis. 2021 Apr 23:jjab077. doi: 10.1093/ecco-jcc/jjab077. PMID: 33891011 
-  - **Cassa CA**, Jordan DM, Adzhubei I, Sunyaev SR. A literature review at genome scale: improving clinical variant assessment. Under Review +  - Louie W, Shen MW, Tahiry Z, Zhang S, Worstell D, **Cassa CA**, Sherwood RI, Gifford DK. Machine 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**, 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 +  - 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**, 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 +  - 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  
-  - 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 +  - 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  
-  - **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 +  - 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 
-  - 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 +  - 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.  
-  - 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 +  - 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. PMID: 31406347 https://www.nature.com/articles/s41588-019-0475-y 
-  - 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+  - 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 
 +  - **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. //Genet. Med.// 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