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publications [2020/09/09 14:46]
cassa
publications [2022/05/19 14:35]
cassa
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 ===== Selected Recent Publications ===== ===== Selected Recent Publications =====
  
 +  - Resolving Discordant Variant Classifications using Clinical Guideline Evidence. Bhat V, Adzhubei IA, Fife JD, Lebo M, **Cassa CA**. Preprint on medRxiv. doi: https://doi.org/10.1101/2022.05.16.22275073
 +  - 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
 +  - 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 
 +  - 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
   - 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    - 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 
-  - 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 +  - 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. //NatCommun.// 2020 Aug 20;11(1):3635. doi: 10.1038/s41467-020-17374-3. PMID: 32820175 
   - 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   - 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
   - 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.    - 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. 
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   - 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   - 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    - **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 
-  - 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 
   - 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.   - 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**, 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