8 - Polymorphisms and Genetic Markers Flashcards
What are some goals of personalized medicine?
To use genetic information to cater healthcare on an individual basis.
What does the human genome consist of?
nuclear DNA and mitochondrial DNA
Define exome?
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.
What is a transcriptome?
The quantitation and/or sequencing of mRNA expressed in an individual’s tissue.
What is an epigenome?
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)
When was the human genome project launched and what was its goal?
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.
How similar are humans genetically? What are the majority of the differences? How different are men and women?
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.
How many genes does the nuclear genome encode for? What about the mitochondrial genome?
Nuclear: ~22,000 genes
Mitochondrial: ~37 genes
How much of the nuclear genome is coding DNA (exons)? What is the rest of it?
~1.5%.
Rest is introns, repetitive sequences, regulatory elements, long-interspersed elements (LINES), and short-interspersed elements (SINEs).
How many amino acids does the average protein have?
What is the length of the average gene?
~450 amino acids.
Avg gene is between 14 kb and 27 kb (including introns, exons, and promoters.)
How is DNA in the human genome organized? Describe what falls into each category
- Unique sequence DNA: pseudogenes, simple repeats, and duplications
- Middle repetitive DNA: rRNA, histone genes, transposons
- Highly repetitive DNA: telomeres and centromeres
Is middle repetitive DNA transcribed/translated into proteins?
Most are not; only ribosomal sequences and histone genes are.
The rest that are not transcribed/translated are those that resemble transposons.
What was the goal of the ENCODE project published in 2012?
Identify all the functional elements within the human genome including:
- coding and non-coding transcripts
- marks of accessible chromatin
- Protein-binding sites
What revelation was made from the ENCODE project?
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.
What are five examples of non-coding RNA (ncRNA)?
- MicroRNA: regulate gene expression
- siRNA: silence transcription
- snRNAs: processing of pre-RNA
- piRNAs: epigenetic and post-transcript gene silencing
- long ncRNAs: involved in transcription, translation, and epigenetics
What are some things responsible for genetic variation?
Single nucleotide variants (“SNP”)
Insertions and deletions (“indels”)
Block substitution
Inversion variants
Copy number variants (increase or decrease in # of bases)
What is a genetic marker?
Physical location on a chromosome whose inheritance can be determined.
What do genetic markers allow us to do?
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
What is a restriction fragment length polymorphism? How are they detected?
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)
What are single nucleotide polymorphisms (SNPs)? What function do they have?
Most common sequence variation (~1 every 1000 bp)
Most have no discernible function, those with functional effects are called mutations.
What are the types of coding SNPs?
Synonymous: do not change aa sequence
Non-synonymous: change the aa sequence
Promoter SNPs: alter gene expression
Splice site SNPs: alter RNA processing
What is the purpose of genome-wide association studies (GWAS)?
Linking the transmission of a specific SNP along with the transmission of a genetic trait or disorder.
SNPs can be used as genetic markers.
How can SNPs be used as genetic markers? How do you know if the individual is heterozygous or homozygous?
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.
What are microsatellites? What are other names for microsatellites?
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).
What are minisatellites? What can these be used for?
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.
How can variable number of tandem repeats (VNTRs) be visualized?
Using PCR followed by gel electrophoresis.
Different number of repeats will result in a size difference in the PCR products.
What are copy number variants? How large are they and? How common are they?
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.
What is Cantu syndrome associated with?
Copy number variations.
Duplication encompassing three genes that are highly expressed in cardiac muscle and hair follicle.
Result: large heart, bone abnormalities, hypertrichosis.
What is linkage analysis used for?
Associating genetic markers with genetic conditions.
What is the limitation of genetic markers?
They are not as useful for rare diseases, particularly if there’s not a large pedigree to test.
What is a better way (as opposed to using genetic markers) to determine the genetic cause of a rare disease?
Using whole genome/exome sequencing.
