Genomics Flashcards
what is high throughput sequencing
technology that quickly generates large volumes of sequence data
quantitative and qualitative
what are sequence census assays
use quantitative data from high throughput sequencing to understand genome function
- RNA-seq for transcriptome
- PCR- seq for metagenomics
define genomics
the study of whole sets of genes, their products and their interactions
encompasses a bunch of -omics
define bioinformatics
application of computational methods of storage and analysis of bio data
define gene annotation
identifying protein encoding genes and their functions
T/F: majority of our DNA consists of repetative DNA
T
what % of human genes are conserved in other organisms
50%
what do genomes vary in
size, density, and number of genes
diff between euk and prok genomes
1) prok genomes have higher density
2) euk larger, more genes
what are the 3 kinds of variation
1) SNPs
2) Various types of chormosomal structural rearrangements
3) CNVs
explain SNPs
a single bp substitution at a particular site, must occur in pop at least > 1%
most do not have ptypes or cause disease
can be used as bio markers associated with disease causing genes
some directly causes disease
-ex FGFR3 gene in achondroplasia
can vary in freq
minor allele freq- freq at which least common allele occurs in a pop
common/freq variants >5%
rare variants < 1%
various chromosomal structural rearrangements
genetic rearranement between diff chromosome or same one
balanced translocation are harmless
unbalanced translocations have lots of health affects
CNVs
due to segmental duplication and deletion
loci w/ diff numbers of copies between indiv in pop; some indiv have >=1 copies of a particular gene rather than standard 2 copies
can be 50 bp to whole chromosome
may or may not cause phenotype or disease
cover large part of genome
4 types of repetitive DNA?
1) STR
2) TR
3) Interspersed repeats (DNA transposons and retretransposons)
4) segmental duplications (large blocks of 10,000-300,000 bp that have been copied to another region of genome)
STR
duplications of simple sets of 1-5 bp
directly involved in ptype variation
TR
normally found at centromeres and telomeres
duplications of more complex, 100-200 bp
variation in number of TR in FLO1 gene in yeast can make cells stick to each other or be loose in liquid culture
when was TE first observed/experimented on
color of corn kernels
how do DNA transposons work
transposon in DNA is copied and moves to region of insertion
moves through DNA intermediate
BOTH cut-paste and copy-paste mechanism
how do retrotransposons work
ss RNA intermediate synthesized from retrotransposon in DNA, reverse transcriptase uses RNA intermediate to synthesize ss DNA which is copied and moved to insertion region
RNA intermediate
ONLY copy-paste
most abundant
T/F: TE content is relatively the same between species
false
T/F: TE have not contributed to human proteins
F
T/F: TE are a source of ptypic variation
T
an ex of TE being a source of ptypic variation
carbernet has no retrotransposon
retrotransposon inserted leads to color loss–> chardonay
rearrangment of retrotransposon leads to red color
diversity through gene duplication
duplication of ancestral gene–> mutation in both copies–> transposition to diff chromosomes-> further duplications and muts
ex. fetal hgb
diversity through changes in gene regulation
Ubx Hox gene 7 suppressed legs in crustacean ancestor but are expressed in present day insects
diversity through gene loss
humans have 3 pseudogenes for yolk, so no yolk
chickens have all 3 genes for yolk
monotremes have 1 yolk gene, 2 pseudos
