8 - Polymorphisms and Genetic Markers

Question 1

What are some goals of personalized medicine?

Answer 1

To use genetic information to cater healthcare on an individual basis.

Question 2

What does the human genome consist of?

Answer 2

nuclear DNA and mitochondrial DNA

Question 3

Define exome?

Answer 3

Isolation and sequencing of only the coding portions of a gene, the exons.

This is a faster and cheaper analysis of a patients relevant genetic makeup.

Question 4

What is a transcriptome?

Answer 4

The quantitation and/or sequencing of mRNA expressed in an individual’s tissue.

Question 5

What is an epigenome?

Answer 5

An analysis of the epigenetic changes found in a parson’s genome.

Patterns of chemical modifications to both DNA (methylation) and histones (acetylation, methylation, phosphorylation)

Question 6

When was the human genome project launched and what was its goal?

Answer 6

1990.

Construct a physical map of entire human genome, map ~22,000 genes, and help identify genetic roots of disease.

Consensus sequence, the first draft being a composite of multiple individuals.

Question 7

How similar are humans genetically? What are the majority of the differences? How different are men and women?

Answer 7

99.9% - DNA sequence contains exactly same nucleotides in the same order for 99.9% of the sequence.

Majority of differences are single bp changes.

Males and females are 98.5% identical, most of the differences originating on the Y chrom.

Question 8

How many genes does the nuclear genome encode for? What about the mitochondrial genome?

Answer 8

Nuclear: ~22,000 genes

Mitochondrial: ~37 genes

Question 9

How much of the nuclear genome is coding DNA (exons)? What is the rest of it?

Answer 9

~1.5%.

Rest is introns, repetitive sequences, regulatory elements, long-interspersed elements (LINES), and short-interspersed elements (SINEs).

Question 10

How many amino acids does the average protein have?

What is the length of the average gene?

Answer 10

~450 amino acids.

Avg gene is between 14 kb and 27 kb (including introns, exons, and promoters.)

Question 11

How is DNA in the human genome organized? Describe what falls into each category

Answer 11

1. Unique sequence DNA: pseudogenes, simple repeats, and duplications
2. Middle repetitive DNA: rRNA, histone genes, transposons
3. Highly repetitive DNA: telomeres and centromeres

Question 12

Is middle repetitive DNA transcribed/translated into proteins?

Answer 12

Most are not; only ribosomal sequences and histone genes are.

The rest that are not transcribed/translated are those that resemble transposons.

Question 13

What was the goal of the ENCODE project published in 2012?

Answer 13

Identify all the functional elements within the human genome including:

1. coding and non-coding transcripts
2. marks of accessible chromatin
3. Protein-binding sites

Question 14

What revelation was made from the ENCODE project?

Answer 14

Only about ~1.5% of the genome represents protein-coding sequences.

They reported that at least 80% of the human genome has likely functional role, which remains controversial.

Question 15

What are five examples of non-coding RNA (ncRNA)?

Answer 15

1. MicroRNA: regulate gene expression
2. siRNA: silence transcription
3. snRNAs: processing of pre-RNA
4. piRNAs: epigenetic and post-transcript gene silencing
5. long ncRNAs: involved in transcription, translation, and epigenetics

Question 16

What are some things responsible for genetic variation?

Answer 16

Single nucleotide variants (“SNP”)

Insertions and deletions (“indels”)

Block substitution

Inversion variants

Copy number variants (increase or decrease in # of bases)

Question 17

What is a genetic marker?

Answer 17

Physical location on a chromosome whose inheritance can be determined.

Question 18

What do genetic markers allow us to do?

Answer 18

Distinguish the two copies (alleles) of a chromosome

Determine which allele is inherited from a parent

Identify regions of the genome that harbor disease-causing mutations

Question 19

What is a restriction fragment length polymorphism? How are they detected?

Answer 19

A genetic marker: restriction enzyme that cuts DNA at recognition sequence.

Can be caused by single base changes, Indels, or other changes.

Differences detected via southern blot or digestion after PCR.

(one of the first tools for genetic fingerprinting)

Question 20

What are single nucleotide polymorphisms (SNPs)? What function do they have?

Answer 20

Most common sequence variation (~1 every 1000 bp)

Most have no discernible function, those with functional effects are called mutations.

Question 21

What are the types of coding SNPs?

Answer 21

Synonymous: do not change aa sequence

Non-synonymous: change the aa sequence

Promoter SNPs: alter gene expression

Splice site SNPs: alter RNA processing

Question 22

What is the purpose of genome-wide association studies (GWAS)?

Answer 22

Linking the transmission of a specific SNP along with the transmission of a genetic trait or disorder.

SNPs can be used as genetic markers.

Question 23

How can SNPs be used as genetic markers? How do you know if the individual is heterozygous or homozygous?

Answer 23

Because they are biallelic, it’s easier to genotype. All you need to do is look for presence or absence of an allele.

If one allele is present in a sample, the individual is homozygous.

If both alleles are present, they are heteroxygous.

Question 24

What are microsatellites? What are other names for microsatellites?

Answer 24

Genetic markers that contain repeats of only a few bps.

Can be called short tandem repeats (STR), simple sequence length polymorphisms (SSLPs), or simple sequence repeats (SSRs).

Question 25

What are minisatellites? What can these be used for?

Answer 25

Genetic markers (>6 bps) that are somewhat longer than micro-satellites also found as tandem repeats.

Number of repeats can vary by individual, and variable number of tandem repeats (VNTR’s) can be used in forensics for paternity testing.

Question 26

How can variable number of tandem repeats (VNTRs) be visualized?

Answer 26

Using PCR followed by gel electrophoresis.

Different number of repeats will result in a size difference in the PCR products.

Question 27

What are copy number variants? How large are they and? How common are they?

Answer 27

Genetic markers that are changes in the number of copies of a gene.

Range from 50 to >1 Mbp in size.

15% of human genome affected by them. ~12 per individual.

Linked to multiple diseases.

Question 28

What is Cantu syndrome associated with?

Answer 28

Copy number variations.

Duplication encompassing three genes that are highly expressed in cardiac muscle and hair follicle.

Result: large heart, bone abnormalities, hypertrichosis.

Question 29

What is linkage analysis used for?

Answer 29

Associating genetic markers with genetic conditions.

Question 30

What is the limitation of genetic markers?

Answer 30

They are not as useful for rare diseases, particularly if there’s not a large pedigree to test.

Question 31

What is a better way (as opposed to using genetic markers) to determine the genetic cause of a rare disease?

Answer 31

Using whole genome/exome sequencing.