PSYC 7102 – Statistical Genetics. Final Exam
Due: December 17 2015 @ 5pm.
There are 5 questions, each worth 8 points, for a total of 40 possible points. The exam is “open book”. Use whatever online sources are helpful to you. All questions contain multiple parts – please read the questions carefully and answer all components.
Complete this exam on your own, without help from others.
For this final exam I ask that you conduct all requested analyses on the following files, each of which contains a single person from 1000 Genomes. There's no need to copy any of these files. Just use them out of my directory.
Aligned reads /Users/scvr9332/final_exam_files/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam /Users/scvr9332/final_exam_files/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.bai
Annotated VCFs /Users/scvr9332/final_exam_files/chrALL.filtered.PASS.beagled.HG00096.rsID.anno.vcf.gz /Users/scvr9332/final_exam_files/chrALL.filtered.PASS.beagled.HG00096.rsID.anno.vcf.gz.tbi
Interpret the phenotypic effects of variant rs16969968.
Here is an example samtools visualization command:
samtools tview -p chr:pos -d C in.bam /Users/scvr9332/reference_data/gotcloud.ref/hs37d5.fa
This section will draw from the quality control plots of a bad Illumina run here: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/bad_sequence_fastqc.html
What do genetic ancestry PCA estimates, such as those you generated in this course, represent (3 points)? In your opinion how is genetic ancestry different from/related to race/ethnicity (3 points)? List and discuss two reasons why ancestry is crucial to consider in genetic association studies (2 points).
Describe the difference between coding and regulatory variation and summarize their relative roles in complex traits and diseases. (8 points)
On a conceptual level, how does imputation work (2 points)? List and discuss three advantages of conducting imputation in genetic association studies (6 points).