# *Genome 2 Phenome 4 Non-Biologists Workshop*: Quantitative Genetics, March 25 2021

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## Quantitative Genetics
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### Learning Objectives:

* Understand how to quantify differences in genomes by looking for quantitative trait loci markers (like SNPs)

* SNP data in genome-wide association studies to estimate correlations between DNA sequence information and observed phenotypes

* Cellular and organismal responses to the environment can be quantified with gene expression studies

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### Question 1:
**What are some of the pros and cons of sequence information to describe traits?**

* Breakout Room 1:
* Cons: Sequencing errors, phenotypes not always at the DNA level (epigenetic level), get lots of SNPs and may not easily figure out which SNP is associate with the trait, may not take into account environmental influence, may not get all the SNPs/gene targets for a quantitative trait
* Pros: Highly useful in many cases (rare diseases), pedigree information prior to having children, easy to collect SNPs

* Breakout Room 2:
* Pro: Enables understanding of inheritance and genetic control of traits
* Con: need an appropriate reference population that may or may not be available

* Breakout Room 3:
Pros: Can see genotypes of the traits via sequencing.This means that you can also select for these SNPs when breeding. Cons: The SNP(s) may be heritable, but the trait may not be. Some SNP(s) can be located in hard to sequence areas, and can therefore be difficult to genotype. A lot fo variation at the sequence level may be meaningless.

* Breakout Room 4:
pros: associate SNP to phenotype with GWAS;
cons: having errors in sequencing data that would skew the description of the trait

* Breakout Room 5:
* pro: if you know for sure a sequence matches with a trait, this can be beneficial
* con: sequence may not tell us exactly what the trait will be; multiple sequences for the same trait; doesn't tell you environmental effects on the trait

* Breakout Room 6:
* ?
* Breakout Room 7:
* Pros: we can study inheritance of traits better
* Cons: hard to comprehend environment interactions

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### Question 2:
**Why is the selection of a reference set (genome or population of organisms) so important for generating SNP data sets?**

* Breakout Room 1:
* Can't map SNPs without a reference genome. If too divergent, will get a lot of SNPs. If making a SNP chip, need to know a refence for getting variants.

* Breakout Room 2:

* Breakout Room 3:
A reference set needs to represent the population in order to map SNP data. A reference genome is required to select locations of SNPs across the genome in order to generate SNP datasets that are representative of the entire genome.
* Breakout Room 4:
SNP datasets for different populations in different SNP chip; if the population that we are working with is too deviant from the reference than the genotypes that are being called will be inaccuarte

* Breakout Room 5:
* the reference population has to be all different or the results won't be beneficial
* Breakout Room 6:
*
* Breakout Room 7:
* If the refrences aren't clear, you cannot interpret data.

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### Question 3:
**What other molecules may be useful to quantify in cells/organisms aside from mRNA transcripts?**

* Breakout Room 1:
* Proteins (proteomics), pre-mRNAs and other RNAs, metabolites
* Breakout Room 2:

* Breakout Room 3:
Proteins and metabolites
* Breakout Room 4:
proteins
* Breakout Room 5:
* proteins
* Breakout Room 6:

* Breakout Room 7:
* proteins, metabolites

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### Comments:

* Breakout Room 1:

* Breakout Room 2:

* Breakout Room 3:

* Breakout Room 4:

* Breakout Room 5:

* Breakout Room 6:

* Breakout Room 7:

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**Resources for Further Learning:**

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