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Revision as of 07:21, 18 April 2017
, 07:21, 18 April 2017→Student Presentations
== Scheduling ==
== Scheduling ==
For Winter 2015, classes are scheduled for Tuesdays and Thursday, 8:30 - 10 am.
For Winter 2017, classes are scheduled for Tuesdays and Thursdays, 8:30 - 10 am in SPH II, room 1152.
== Grading ==
== Grading ==
The final grade will take into account your performance in problem sets and worksheets as well as your participation in class.
The final grade will take into account your performance in problem sets and worksheets as well as your participation in class.
== Class Worksheets ==
=== Hidden Markov Models ===
Week of January 8 - [[Media:Question_Sheet_-_Li_et_al_(2010)_Gen_Epid.pdf|Li et al (2010)]]
Week of January 15 - [[Media:Question_Sheet_-_Howie_et_al_(2012)_Nat_Genet.pdf|Howie et al (2012)]] (and, [[Media:866_-_Slides_for_Hyun.pdf|Discussion slides for January 19]])
Week of January 22 - [[Media:Question_Sheet_-_Delaneau_et_al_(2013)_Nature_Methods.pdf|Delaneau et al (2013)]]
Week of January 29 - [[Media:Question_Sheet_-_Boehnke_and_Cox_(1997)_AJHG.pdf|Boehnke and Cox (1997)]]
=== Short Read Sequencing ===
February 12 - [[Media:Question_Sheet_-_Li_et_al_(2008)_Genome_Research.pdf|Li et al (2008)]]
February 19 - [[Media:Question_Sheet_-_Li_and_Durbin_(2009)_Bioinformatics.pdf|Li and Durbin (2009)]]
March 5 - [[Media:Question_Sheet_-_Zerbino_and_Birney_(2008)_Bioinformatics.pdf|Zerbino and Birney (2008)]]
March 12 - [[Media:Question_Sheet_-_Iqbal_et_al_(2012)_Nature_Genetics.pdf|Iqbal et al (2012)]]
=== Association Analysis ===
March 19 - [[Media:Question_Sheet_-_2017_-_Kang_et_al_(2010)_Nature_Genetics_.pdf|Kang et al (2010)]]
March 26 - [[Media:Question_Sheet_-_2017_-_Wu_et_al_(2011)_American_Journal_of_Human_Genetics.pdf|Wu et al (2011)]]
April 2 - [[Media:Question_Sheet_-_2017_-_Liu_et_al_(2013)_Nature_Genetics.pdf|Liu et al (2014)]]
=== Adventures in Statistical Genetics ===
April 9 - [[Media:2017.04_-_Adventures_in_Human_Genetics.pdf|Goncalo's Adventure in Human Genetics]]
== Student Presentations ==
*[[Media:Zajac_Journey_Lecture.pdf | Greg]]
*[https://www.dropbox.com/sh/9buuwbojq3tmp1f/AAADGOK-0yyKTfLiwG984QCHa?dl=0 Dropbox]
== Standards of Academic Conduct ==
== Standards of Academic Conduct ==
== Planned Reading ==
== Planned Reading ==
* Abecasis GR, Cherny SS, Cookson WO, Cardon LR (2002) Merlin--rapid analysis of dense genetic maps using sparse gene flow trees. ''Nat Genetics'' '''30''':97-101
* Boehnke M and Cox N (1997) Accurate Inference of Relationships in Sib-Pair Linkage Studies. ''Am J Hum Genet'' '''61''':423-429
* Coventry A, Bull-Otterson LM, Liu X, Clark AG, Maxwell TJ, Crosby J, Hixson JE, Rea TJ, Muzny DM, Lewis LR, Wheeler DA, Sabo A, Lusk C, Weiss KG, Akbar H, Cree A, Hawes AC, Newsham I, Varghese RT, Villasana D, Gross S, Joshi V, Santibanez J, Morgan M, Chang K, Iv WH, Templeton AR, Boerwinkle E, Gibbs R, Sing CF (2010) Deep resequencing reveals excess rare recent variants consistent with explosive population growth. ''Nat Commun.'' '''1''':131. PMID: 21119644
* Coventry A, Bull-Otterson LM, Liu X, Clark AG, Maxwell TJ, Crosby J, Hixson JE, Rea TJ, Muzny DM, Lewis LR, Wheeler DA, Sabo A, Lusk C, Weiss KG, Akbar H, Cree A, Hawes AC, Newsham I, Varghese RT, Villasana D, Gross S, Joshi V, Santibanez J, Morgan M, Chang K, Iv WH, Templeton AR, Boerwinkle E, Gibbs R, Sing CF (2010) Deep resequencing reveals excess rare recent variants consistent with explosive population growth. ''Nat Commun.'' '''1''':131. PMID: 21119644
* Iqbal Z, Caccamo M, Turner I, Flicek P, McVean G (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nat Genet.'' '''44''':226-32. PMID: 22231483
* Iqbal Z, Caccamo M, Turner I, Flicek P, McVean G (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nat Genet.'' '''44''':226-32. PMID: 22231483
* Field Y, Boyle EA, Telis N, Gao Z, Gaulton KJ, Golan D, Yengo L, Rocheleau G, Froguel P, McCarthy MI, Pritchard JK (2016) Detection of human adaptation during the past 2000 years. ''Science'' '''354''':760-764
* Jun G, Flickinger M, Hetrick KN, Romm JM, Doheny KF, Abecasis GR, Boehnke M, Kang HM (2012) Detecting and estimating contamination of human DNA samples in sequencing and array-based genotype data. ''Am J Hum Genet.'' '''91''':839-48. PMID: 23103226
* Kang HM, Sul JH, Service SK, Zaitlen NA, Kong SY, Freimer NB, Sabatti C, Eskin E (2010) Variance component model to account for sample structure in genome-wide association studies. ''Nat. Genet.'' '''42''':348-354
* Kang HM, Sul JH, Service SK, Zaitlen NA, Kong SY, Freimer NB, Sabatti C, Eskin E (2010) Variance component model to account for sample structure in genome-wide association studies. ''Nat. Genet.'' '''42''':348-354
* Kircher 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. ''Nat. Genet.'' '''46''' 310–315
* Kircher 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. ''Nat. Genet.'' '''46''' 310–315
* Kruglyak L, Daly MJ, Reeve-Daly MP, Lander ES (1996) Parametric and non-parametric linkage analysis: a unified multipoint approach. ''Am J Hum Genet'' '''58''':1347-63
* Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. ''Genome Res.'' '''18''':1851-8. PMID: 18714091
* Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ''Bioinformatics.'' '''25''':1754-60. PMID: 19451168
* Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ''Bioinformatics.'' '''25''':1754-60. PMID: 19451168
* Li H, Durbin R (2011) Inference of human population history from individual whole-genome sequences. ''Nature.'' '''475''':493-6. PMID: 21753753
* Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR (2010) MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. ''Genet Epidemiol.'' '''34''':816-34. PMID: 21058334 [[Biostatistics 830 - Code Snippets|[Code Snippets]]]
* Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR (2010) MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. ''Genet Epidemiol.'' '''34''':816-34. PMID: 21058334 [[Biostatistics 830 - Code Snippets|[Code Snippets]]]
* Wen X, Stephens M (2010) Using linear predictors to impute allele frequencies from summary or pooled genotype data. ''Ann Appl Stat.'' '''4''':1158-1182. PMID: 21479081
* Wen X, Stephens M (2010) Using linear predictors to impute allele frequencies from summary or pooled genotype data. ''Ann Appl Stat.'' '''4''':1158-1182. PMID: 21479081
* Wu MC, Lee S, Cai T, Li Y, Boehnke M, Lin X (2011) Rare-variant association testing for sequencing data with the sequence kernel association test. Am J Hum Genet. 89:82-93
* Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. ''Genome Res.'' '''18''':821-9. PMID: 18349386
== Course History ==
== Course History ==
This course is offered occasionally. Typically, Mike Boehnke has taught it. Each instructor gives the course a different flavor, so you may find it worthwhile -- even if you have taken the course with Mike previously.
This course is offered occasionally. Typically, Mike Boehnke has taught it. Each instructor gives the course a different flavor, so you may find it worthwhile -- even if you have taken the course with Mike previously.
