In general, the resources listed here for the computational test will be somewhat helpful, but never as helpful as the materials covered in miRcore MVP meetings. We list most of the MVP meeting dates that cover each topic in hopes that you can refer to your notes/slides from those lectures.
Conceptual Test (40 minutes, multiple choice)
Neurodegenerative Diseases: (link to slides)
Conceptual Slides Review for Genes and Health ContestBrain Anatomy and Function
https://mayfieldclinic.com/pe-anatbrain.htm
Cell Death
https://my.clevelandclinic.org/health/articles/cell-death
Diseases Tested
Parkinson’s Disease
Alzheimer’s Disease
Multiple Sclerosis
Frontotemporal dementia
Amyotrophic Lateral Sclerosis (ALS)
Refer to the pamphlets you all made during the beginning of MVP (e.g. ALS, Alzheimer’s, Parkinson’s)!
Generic symptoms, known treatments, genes and environments, social impact
https://www.kaizenbraincenter.com/about-neurodegenerative-disease
Meetings:
Aug. 26, 2023 (1st)
Sept. 9, 2023 (2nd): Central Dogma and Biomarkers– SEE GROUP WORK
Statistics
P-values/logFC, t-tests, enrichment
Meetings:
Sept. 30, 2023 (5th): t-test, log in RNA expression data analysis
Genetics
DNA base pairing, replication, and transcription
RNA processing (editing and splicing) and translation
The Central Dogma
Amino acids and codon relationships (no need to memorize specifics)
Basic knowledge of technologies measuring DNA sequences, RNA expression
Microarray analysis and electrophoresis
Meetings:
Sept. 9, 2023 (2nd): Central Dogma and Biomarkers
Other resources
Lecture slides from “Computational Biology Camp for High School Students”
DNA RNA Proteins from August 21, 2012
Gene Expressions from August 22, 2012
Additional lecture slides from the one-day camp on January 29, 2013
DNA-RNA-Protein measurement from January 29, 2013
Genes in Diseases from January 29, 2012
Computational Test (40 minutes, multiple choice + free response)
Examples of tasks for the computational test:
- Identify a gene related to the increased risk of developing late-onset Alzheimer’s with specific DNA sequences. This gene is on chromosome 19 and one of the four forms of this gene accounts for about 40 percent of all cases of late-onset Alzheimer’s. Write its general gene symbol, not differentiating the four forms.
- Identify the function of the gene (helpful sites: http://www.genecards.org, http://www.ncbi.nlm.nih.gov/gene)
- Find its genome position (helpful sites: http://genome.ucsc.edu/cgi-bin/hgGateway, http://www.ncbi.nlm.nih.gov/gene)
- What is the total number of transcribed sequences?
- Find the mRNA sequences* (helpful sites: http://genome.ucsc.edu/cgi-bin/hgGateway,http://www.ncbi.nlm.nih.gov/nuccore).
- Find only coding sequences among the mRNA sequences* (helpful sites: http://genome.ucsc.edu/cgi-bin/hgGateway: use “Genomic Sequence” rather than “mRNA” sequence for this task, http://www.ncbi.nlm.nih.gov/nuccore).
*No need to worry about U/T conversion or upper/lower cases (i.e. T will be considered as U).
GEO2R About Page: Explanations on defining groups, volcano plots, and boxplots. Analyzing datasets with GEO2R
Meetings:
Sept. 23, 2023 (4th): microarray | GEO | GEO2R for quick understanding samples
Oct. 7, 2023 (6th): GEO2R
String About Page: Explanations on creating String maps, interpreting String maps and enrichment analysis (GO, KEGG), and navigating the platform. Goes a bit too in-depth though, would not recommend spending much time studying this.
Meetings:
Oct. 14, 2023 (7th): String analysis
KEGG About Page: Explanations on KEGG sidebar functions and includes a great diagram of KEGG map notations. Would definitely at least have a look at the map notations.
Meetings:
Oct. 21, 2023: Enriched function | GO, KEGG
Oct. 28, 2023: Enriched function | GO, KEGG
Meetings:
Sept. 16, 2023 (3rd): OMIM and SNP in UCSC genome browser, DNA to RNA
Meetings:
Dec. 10, 2022 (13th): GO KEGG Pathways GeneCards
Meetings:
Sept. 16, 2023 (3rd): OMIM and SNP in UCSC genome browser, DNA to RNA
R
Meetings:
Nov. 4, 2023 (10th): R: basics
Nov. 11, 2023 (11th): R: data frame
Nov. 18, 2023 (12th): R: read table and graph
Other resources
UCSC Genome Browser Demo (prepared by a student)
Genes in general (from the One-day camp on January 29, 2013)
Using GEO2R to find biomarkers (from Saturday miRcore volunteer meetings)
Disease of focus: Neurodegenerative Diseases
General Topics
Symptoms
Treatment
Genes and Environments
Social impact