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Flashcards in Genomics Deck (15):
1

The study of an entire genome or genomes

Genomics

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Two major subfields of genomics:

1. Functional Genomics
2. Comparative Genomics

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The global analysis of the function of sequences in a genome.
-Understand genome and phenotype of an organism
-Useful when considering complex traits.

Functional genomics

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Comparison of entire genomes from different species, individuals, or groups.
-Studies genetic variation, evolutionary relatedness
-Asks "what sequences are different and what are similar?"

Comparative Genomics

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An example of genomics: identification of genes linked to drought tolerance in plants:
-Tomato plants grown in high vs. low water conditions
-Performed microarray to identify genes that are differentially transcribed in these conditions

An example of genomics: identification of genes that make us human:
-HAR-1= Human Accelerated Region 1
-Chicken and chimp HAR-1 nearly identical
-Chimp and human HAR-1 a lot different
-HAR-1 encodes a small noncoding RNA (fxn unknown)
-Expressed in a region of the brain that undergoes a unique deelopmental process in humans
-Other genes: FOXP2 (speech) and ASPM (brain size)

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An example of genomics: identification of genes hat make certain cancers aggressive

-Sequence DNA from different breast cancers, some with good prognosis (less aggressive and easily treatable) and some from patients with poor prognosis (from highly aggressive tumors)
-Identify and compare mutations and copy number variants between the two groups
-Compare genome from your patient's tumor to the known genomes
-Why is this beneficial?

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Selected techniques used in genomics:

1. Whole genome sequencing
2. Bioinformatics
3. Transcriptomics
-RNAseq

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Combines biology and computer science.

Bioinformatics

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Bioinformatics examples

-Find DNA with a sequence of interest.
-Align sequences for similarities.
-Predict structure, therefore function of RNA and protein
-Describe gene interactions (interacto maps)
-Map phylogenetic relationships

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Part of the promoter region; transcription factors will bind to for transcription to proceed.

Response element

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Compare the sequence of a gene product with unknown function to a similar gene product with known function.
-Analyze a region of sequence that might encode a particular protein function.
-Goal: to assign a predictive function for a gene (or a set of genes) of interest.

Sequence Similarity Searches

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The study of the complete set transcripts that are produced by a genome under a specific condition.
-Uses RNAseq

Transcriptomics

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Method provides the sequences of all transcripts in a sample.
-Transcriptome= all transcripts

RNAseq

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Method of RNAseq

1. extract RNA
2. Make cDNA
3. Sequence cDNA using Next Gen. sequencing technology

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What can RNAseq tell you?

The relative amounts of each transcript and different splice variants.