Biostatistics 830: Fall 2013 Edition

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This is an archive of the Biostatistics 830 class page, as taught in the Fall of 2013. For the current edition of the course see Biostatistics 830: Main Page.

Objective

Gene mapping studies study the relationship between genetic variation and susceptibility to human disease. These studies are changing rapidly with the availability of techniques for very large scale genetic analysis, whether based on sequencing or on genotyping. Biostatistics 830 is a Ph.D. level course that dissects some recently developed methods and the principles behind their implementation. It is meant to provide students with a toolkit to facilitate development and implementation of new statistical methods.

For additional information, see also Core Competencies in Biostatistics Program covered by this course.

Target Audience

It is highly recommended that students registering for Biostatistics 830 should have previously completed Biostatistics 666 and Biostatistics 615/815, which are courses introducing methods for genetic analysis and programming principles, respectively.

Scheduling

For Fall 2013, classes are scheduled for Wednesdays and Fridays, 3:00 - 4:30 pm room M4318 SPH II.

The final grade will take into account your performance in problem sets and worksheets as well as your participation in class.

Dates

The green dates below indicate when we will be meeting.

September     October     November     December
Mon Wed Fri Mon Wed Fri Mon Wed Fri Mon Wed Fri
2 4 6 2 4 1 2 4 6
9 11 13 7 9 11 4 6 8 9 11
16 18 20 14 16 18 11 13 15
23 25 27 21 23 25 18 20 22
30 28 30 25 27 29

Class Worksheets

September 6 - Li et al (2010)

September 20 - Howie et al (2012)

September 27 - Browning and Browning (2007)

October 16 - Li et al (2008)

November 1 - Li and Durbin (2009)

November 8 - Zerbino and Birney (2008)

November 13 - Iqbal et al (2012)

November 22 - Li and Durbin(2011)

November 27 - Liu et al (2013)

December 6 - Wu et al (2011)

December 9 - Jun et al (2012)

Standards of Academic Conduct

The following is an extract from the School of Public Health's Student Code of Conduct [1]:

Student academic misconduct includes behavior involving plagiarism, cheating, fabrication, falsification of records or official documents, intentional misuse of equipment or materials, and aiding and abetting the perpetration of such acts. The preparation of reports, papers, and examinations, assigned on an individual basis, must represent each student’s own effort. Reference sources should be indicated clearly. The use of assistance from other students or aids of any kind during a written examination, except when the use of books or notes has been approved by an instructor, is a violation of the standard of academic conduct.

In the context of this course, any work you hand-in should be your own and any material that is a transcript (or interpreted transcript) of work by others must be clearly labeled as such.

Required Reading

  • Albers CA, Lunter G, MacArthur DG, McVean G, Ouwehand WH, Durbin R (2010) Dindel: accurate indel calls from short-read data. Genome Res. 21:961-73
  • Browning SR, Browning BL (2007) Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet. 81:1084-97. PMID: 17924348
  • 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
  • Delaneau O, Zagury JF, Marchini J (2013) Improved whole-chromosome phasing for disease and population genetic studies. Nat Methods. 10:5-6. PMID: 23269371
  • Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR (2012) Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nat Genet. 44:955-9. PMID: 22820512 [Code Snippets]
  • 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
  • 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
  • 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 [Code Snippets]
  • 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 [Code Snippets]
  • Lin DY, Zeng D (2010) Meta-analysis of genome-wide association studies: no efficiency gain in using individual participant data. Genet Epidemiol. 34:60-6. PMID: 19847795
  • 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

This course is an ad-hoc course, first taught by Goncalo Abecasis in the Fall of 2013.