Next Gen Sequencing Flashcards
what is the key idea underlying next-generation DNA sequencing?
parallel observation of spatially separated sequencing reactions
what are the 2 main types of sequencing today?
short read and long read (both optical)
how to microarrays measures gene expression?
intensity
how do next gen sequencing measure gene expression?
sequences
what is the process that microarrays rely on?
hybridization of DNA to probe
what are some of the downsides of microarray?
no sequence level information, can miss mutations, search space is limited to probes on the array
which system is best for RNA sequencing?
microarray
what is the point of mutation detection?
detect single nucleotide variants compared to a reference genome
what are 3 problems that affect SNP calling?
- coverage (how many times you sequence the same strand with different reads)
- error rates (if error rate low, coverage reportings with be correct)
- ploidy
what is exome sequencing?
build sequence library based solely on genes that are expressed
why is exome sequencing helpful in the clinical setting?
can detect SNPs among patient with the same genetic disorder
what is the best way to perform exome sequencing?
microarrays with hybridization
what is the best way to detect mendelian diseases?
exome sequencing
what does methotrexate do?
inhibits parts of de novo pyrimidine biosynthesis
how many mutations are created each generation?
about 60
what is the paternal contribution to mutation rate?
90%
what is the main way to non-invasively sequence a babies genome?
sequence mom and then dad’s genome, moms blood contains 13% babies genome
how much percentage of a mother’s blood is cell-free DNA from baby?
13%
what is a genome?
all genetic information from a single organism
what is a metagenome?
all genetic information from a group of organisms
what can the extended genotype influence?
obesity, disease susceptibility, decision making
what is the extended genotype influenced by?
sex and body polarity
what is a variant of unknown significance?
coding variant without an associated functional cause (disrupt protein function, stabilize mRNA)
why is error rate so much higher in long read version of DNA sequencing?
because it is just focusing on one molecule instead of an entire genome
