Biostat 581. Statistical Genetics Seminar. http://courses.washington.edu/b581/

Winter 2019 Topic: Predicting Variant Consequences

Instructor: Liz Blue, em27@uw.edu

Note on attendance for registered students: Please let Liz know if you will be missing one of the meetings due to illness or other excusable absence.

Schedule:

January 15. Nishizaki SS, Boyle AP. (2017) Mining the Unknown: Assigning Function to Noncoding Single Nucleotide Polymorphisms. Trends in Genetics 33(1):34-45. https://www.ncbi.nlm.nih.gov/pubmed/27939749

Presenters: Alan Ming and Tony Yang (Liz Blue)

January 22. Kirchner M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. (2014) A general framework for estimating the relative pathogenicity of human genetic variants. Nature Genetics 46(3):310-5. https://www.ncbi.nlm.nih.gov/pubmed/24487276

and updated version: Rentzsch P, Witten D, Cooper GM, Shendure J, Kircher M. (in press) CADD: predicting the deleteriousness of variants throughout the human genome. Nucleic Acids Research. https://www.ncbi.nlm.nih.gov/pubmed/30371827

Presenters: Amarise Little and Zhenman Yuan (Saonli Basu)

January 29. Ioannidis NM et al. (2016) REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants. American Journal of Human Genetics 99(4):877-885. https://www.ncbi.nlm.nih.gov/pubmed/27666373

Presenters: Anya Mikhaylova and Charles Wolock (Ellen Wijsman)

February 5. Alirezaie N, Kernohan KD, Hartley T, Majewski J, Hocking TD. (2018) ClinPred: Prediction Tool to Identify Disease-Relevant Nonsynonymous Single-Nucleotide Variants. American Journal of Human Genetics 103(4):474-483. https://www.ncbi.nlm.nih.gov/pubmed/30220433

Presenters: Yu-Ting Lin and Lluvia Xia (Liz Blue)

February 12. Siveley RM, Sheehan JH, Kropski JA, Cogan J, Blackwell TS, Phillips JA, Bush WS, Meiler J, Capra JA. (2018) Three-dimensional spatial analysis of missense variants in RTEL1 identifies pathogenic variants in patients with Familial Interstitial Pneumonia. BMC Bioinformatics 19(1):18. https://www.ncbi.nlm.nih.gov/pubmed/29361909

Presenters: Maria Valdez and Joe Zhou (Liz Blue)

February 19. Huang YF, Gulko B, Siepel A. (2017) Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data. Nature Genetics 49(4): 618-624. https://www.ncbi.nlm.nih.gov/pubmed/28288115

Presenters: Esther Gu and Edward Zhao (Elizabeth Thompson)

February 26. Wang J, Dayem Ullah AZ, Chelala C. (2018) IW-Scoring: an Integrative Weighted Scoring framework for annotating and prioritizing genetic variations in the noncoding genome. Nucleic Acids Research 46(8):e47. https://www.ncbi.nlm.nih.gov/pubmed/29390075

Presenters: Kelsey Grinde and Pearl Liu (Liz Blue)

March 5. Backenroth D, He Z, Kiryluk K, Boeva V, Pethukova L, Khurana E, Christiano A, Buxbaum JD, Ionita-Laza I. (2018) FUN-LDA: A Latent Dirichlet Allocation Model for Predicting Tissue-Specific Functional Effects of Noncoding Variation: Methods and Applications. American Journal of Human Genetics 102(5):920-942. https://www.ncbi.nlm.nih.gov/pubmed/29727691

Presenters: Hongjie Chen and Xiaowen Tian (Liz Blue)

March 12. Zhou J, Theesfeld CL, Yao K, Chen KM, Wong AK, Troyanskaya OG. (2018) Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk. Nature Genetics 50(8):1171-1179. https://www.ncbi.nlm.nih.gov/pubmed/30013180

Presenters: Michael Goldberg and Priyanka Murali (Matthew Conomos)