Genomics in Modern Medicine Flashcards
what is next generation sequencing
technologies that permit rapid interrogation of DNA, up to and including entire genomes via massively parallel sequencing
what is the prevalence of common single nucleotide variants and rare single nucleotide variants? and what are they
- Common: greater than 1% of population- can be advantageous, silent, risk associated
- rare ones are less than 1% of population- can be advantageous, silent, risk associated and pathogenic
single nucleotide variants account for about ____ of all DNA changes
75%
single nucleotide variants are found in about 1 in every _____ nucleotides
100 to 300 nucleotides
describe insertion and deletion mutations
occur from 50-100 nucleotides
how often do insertion deletion mutations occur compared to single nucleotide variants
1/10th as often
90% of insertion deletion mutations are ____ nucleotides in length
1-10
Describe CNV mutations
least frequent but large so affect the most nucleotides
what is the purpose of library prep for NGS
add primers and barcodes to identify individuals
what does library prep for NGS involve
fragmenting DNA called shotgun sequencing
what is sanger PCR
gene by gene, exon by exon sequencing
how many base pairs are in the human genoe
3.2 bilion
how many nucelotides are in the human genome
6.4 billion
______ genes (1-2% of genome) which encode _____ proteins
19,000; 100,000
in a completed library, each DNA fragment has:
-sequencing primer
-adapters
-barcode
what does enrichment involve
selecting out specific regions of interest for sequencing using capture probes
what are the cost and time considerations for enrichment
-pooling allows for samples to be mixed together before enrichment
- allows for more sequencing of targeted regions
- decreases cost and time per sample
what is sequencing by synthesis (SBS)
-fluorescent nucleotides are incorportated one at a time
-lasers excite fluorescence which is read by the instrument
what is variant detection
the analysis of sequence data to find the differences between an individuals DNA and the human reference genome
what are the typical variant counts for small panel, exome, and whole genome
- small panel: 8000
- exome: 300,000
whole genome: 4,000,000
what are the sensitivity and specificity for SNPs in CPGM NGS variant detection
> 99%
CPGM NGS variant detection can detect insertion deletion mutations up to _____ base pairs
40
how fast can 6 sequel Ile sequence
1 genome in 90 hours
what genes affect mineralization
PHEX, DMP1, FGF23
what genes affect hypo/oligodontia
PAX9
what gene affects amelogenesis imperfecta
ENAM
what is the average diagnosis rate of NGS
about 30%
what genes are involved in amelogenesis imperfecta
- AMELX (amelogenin)
-AMTN (amelotin) - ENAM (enamelin)
what is the prevalence of amelogenesis imperfecta
1/700 to 1/14,000
