Trigger 9: Genomic technologies Flashcards
which is the oldest genomic technology
sanger sequencing (1977)
which is the newest genomic technology
single- molecular real time (SMRT) sequencing
name 6 forms of genomic technology
- high microscope - G-banded karyotype - Array- CGH - SNP- array - Exome sequencing - genome sequencing
what is G banded karyotype testing
a technique used in cytogenetics to produce a visible karyotype by staining condensed chromosomes.
resolution of G banded karyotype
5-10Mb
number of loci probed in G banded karyotype
around 500
how large do the variants have to be to be to be detected
over 5Mb
how many variants detected per person using G banded karyotype
0 to 1
diagnostic yield and incidental findings in G banded karyotype
low
Array CGH
has the ability to explore all 46 chromosomes in a single test and to detect any DNA imbalance including extra or missing chromosomes and loss or gain of chromosome material much more precisely than conventional chromosome analyses (e.g. G banded karyotype)
resolution of Array- CGH
50-100kb
number of loci probed in Array- CGH
0.05- 2 million
What sort of variants detected in Array- CGH
copy number variants
copy number variants
a phenomenon in which sections of the genome are repeated
variants per person in Array- CGH
10-100s
diagnostic yield and incidential findings in Array-CGH
medium ability
resolution of light miroscope
entirre genome
number of probed loci in ligh microscopy
N/A
variants detected in light microscopy
aneuploidy / polyploid
how many variants per person detected by ligh microspcy
0 to 1
diagostic yiled and incidental finding ability of lght microscopy
low!
outline the Array CGH process
- Patient and control DNA are labeled with fluorescent dyes and applied to the microarray
- patient and control DNA compete to attach to the microarray
- the microarray scanner measures the fluorescent signal
- computer softwar analyses the date and generated plot (e.g. can see where copy number variant is different
example of array CGH result
shows differences between the amount of DNA (e.g. number of CNVs) in controls vis signature
copy number variants are largest in what sorts of mutations
craniofacial and then autism
SNP array
is a type of DNA microarray which is used to detect polymorphisms within a population.
resolution of SNP array
10kb
number of loci probed in SNP-array
0.1- 2 million
variant detected in SNP array
common SNVs
how many variants detected per person using SNP array
4 million
diagnostic yield and incidental finding ability of SNP-array
medium high
resolution of exome sequencing
1bp
number of loci probed in exome seuquencing
50 million
variants detected using exome sequencing
coding variants
variants per person in exome seqeuncing
20,000
diagnostic yeild and incidental findings of exome sequencing
high
resolution of genome sequencing
1bp
number of loci probed in genome sequencing
3 billion
variants detected in genome sequencing
most variants
variants per person in genome sequencing
4-5 million
diagnostic yield and incidental finding ability of genome sequencing
highhhhh
strongest genome technology
genome sequecing
example of a light microscope
G-banded karyotype
Array-CGH
SNP- array
exome sequencing
genome sequencing
genotyping
determining which genetic variants are present in an individual genome
genotyping uses
arrays
array
only assay specific type of variants
SNP-chip
determines genotype of specific SNPs on microarray
array-CGH
determine copy number of scpeific regions on microarray
Sequencers
only assay variants within sequenced regions
role of sequencing
determining the order of baseparis in a region of DNA
sanger sequencing
targets specific exons or a single genome
next generation sequencing
targets multiple genes or whole genome
