Omics Lecture 16

Question 1

Types of Pseudogenes

Answer 1

1) Vestigial (now dormant); eg: Vit C
2) Duplicated that are not expressed; e.g.- beta globin
3) Processed (genes without introns typical not expressed)

Question 2

50% of genome is repetitive sequence

Answer 2

1) STR and VNTR
2) Transposons (LINES and SINES)
3) Pseudogenes

Question 3

what’s the most repetitive DNA in the genome?

Answer 3

transposon sequence

• LINES
• SINES

Question 4

How do transposons sequence lead to disease? (name 2 ways)

Answer 4

1) Transposons may integrated into a critical spot and disrupt a gene –>disease
2) May lead to misalignment during meiosis and gene disruption

Question 5

Name 3 types of microarray

Answer 5

1) CGH (chromosomal microarray analysis)
2) SNP (chromosomal microarray analysis)
3) cDNA (gene expression analysis)

Question 6

define haplotype

Answer 6

A combination of alleles at different chromosomal loci that are transmitted together.
May be 1 locus, several loci, or an entire chromosome depending on number of recombination events

Question 7

What is the HapMap

Answer 7

A resource describing common patterns of human genetic variation.
Involved SNP Chip as an important data collection tool

Question 8

GWAS

Answer 8

Genome wide association studies;
An attempt to uncover genetic determinants of multifactorial diseases.
Created by scanning 1000’s of SNP among 1000’s of people

Question 9

Problems with GWAS

Answer 9

Rare variants (data no complete)
Correlation does not mean causation
Raises new questions regarding hereditary factors
DTC genetic testing (direct to consumer)

Question 10

Epigenomics

Answer 10

the study of the epigenetic component of cells (DNA methylation/silencing)

Question 11

Transcriptomics

Answer 11

The total mRNA component of cells/tissues

Question 12

Variomics

Answer 12

The study of all variations that exists in the human genome btwn different people

Question 13

Proteomics

Answer 13

The total protein component of the cell.

Note: number of genes does not equal the number of proteins

Question 14

The number of genes does not equal the number of proteins. Why?

Answer 14

1) multiple start sites
2) alternate splicing
3) RNA editing
4) proteins may work as complexes
5) most proteins are modified (phosphorylated, glycosylated etc)

Question 15

Name some Proteomics Tools

Answer 15

1) 2-d Gel

2) Mass Spectrometry

Question 16

Fragile X

Answer 16

Reduced expression of FMR1 gene
expansion of CGG (gets methylated)
Mental retardation

Question 17

Genomic Annotation

Answer 17

Identifying the location of genes and their function
Based on:
1) ORFs

Question 18

Problems with genomic annotation

Answer 18

1) very small ORFs (ex-ubiquitin)
2) smalle gene within larger genes
3) genes on opposing DNA strands
4) genes not translated into proteins
5) unknown RNA species
6) predicting splice variants