Arrays, NGS and Epigenetics Flashcards
exam 2
method to screen specimens for genome wide variation
Arrays
identify difference between the test DNA and the control DNA
Comparative Genomic Hybridization array
velocardial facial syndrome
DiGeorge syndrome
Di George is a
microdeletion disorder 22q11.2
SNP array asks
which SNPs are present
measure changes in gene regulation via gene expression levels
expression arrays
characterize tumors; used to guide tx. based on resistance or response of tumors with similar expression patterns
expression arrays
when do we use arrays?
used pretty often when we don’t have a clear clinical picture and can be used to identify genes
limitations of arrays (3)
(1) may not detect low level mosaicism
(2) only look at quantity, not location
(3) can not detect: translocations or inversion
known translocation or inversion should be followed up with an
array
gold standard for validation of variants found in NGS
sanger sequencing
sequencing:
I Kb read length
sanger
sequencing:
30-400 bp read length
Next generation sequencing (NGS)
predominantly on a research basis, but is coming to clinical practice
WGS
capture DNA fragments which contain exons prior to sequencing
Whole Exome sequencing (WES)
sequencing for a specific list of genes associated with the clinical phenotype
panel
NGS potential results: what is it and what sign is it?
Benign
(-)
- does not affect gene function
- not included in clinical report
NGS potential results: what is it and what sign is it?
variant of uncertain significance (VUS)
(?)
- must meet threshold of evidence
- not enough evidence to determine if change is pathogenic or benign
NGS potential results: what is it and what sign is it?
Pathogenic
(+)
- disrupts gene function
- potential to cause health effects
what are medically actionable genes?
pathogenic mutations
can patients opt-out of receiving this information of secondary findings?
yes
medically actionable genes are those that have
- high penetrance
- established interventions
Potential results:
focused (4)
(1) mutations definitely related to phenotype
(2) variants possibly related to phenotype
(3) medically actionable mutations (secondary findings)
(4) carrier status for Mendelian disorders (AR or X-linked)
limitation of NGS;
can not detect (4)
(1) triplet repeat expansions
(2) methylation /imprinting
(3) structural rearrangements
(4) copy number variation- not as reliable as other methods
True or False:
WES/WGS is a “one size fits all” tests
false, it is not
modification of gene expression without alteration of underlying DNA sequence
epigenetics
Epigenetics changes (3)
(1) methylation
(2) nucleosome positioning
(3) Histone Modification
evidence for epigenetic modifications
concordance (or not) of disease between monozygotic twins
evidence for epigenetic modifications
concordance (or not) of disease between monozygotic twins
high throughout sequencing
Next Generation Sequencing
modification of gene expression without changing DNA sequence
Epigenetics
Level of resolution:
2-3 Mb
karyotype
Level of resolution:
120-400 kb
FISH
Level of resolution:
500bp
Array
Level of resolution:
1 bp
NGS
may or may not result in a change of the aa sequence
SNP
SNPs observed in groups =
haplotype
can be used for gene mapping
SNP
CGH array:
Red=more of the patient DNA
duplication
CGH array:
Green= more of the control
deletion
one thing we need to assume with SNPs
that all SNPs occur with similar frequency
for SNP array we should expect _____ and to have ____ copies at each position
for SNP array we should expect heterozygosity and to have two copies at each position
How can we determine UPD/IBD vs deletion?
Both have drop out of the AB trace and we need to see the log-ratio data
provide more information than CGH arrays
SNP
SNP arrays reports on ___________, with ___________ being more easily recognized
SNP arrays reports on amount of DNA with deletions being more easily recognized
SNP arrays can identify _____ of heterozygosity or _______
SNP arrays can identify loss of heterozygosity or uniparental disomy
with SNP arrays we can only identify _______ (meiosis 2 error) and _____can’t be identified (meiosis 1 error)
with SNP arrays we can only identify isodisomy (meiosis 2 error) and heterodisomy can’t be identified (meiosis 1 error)
why do we care about loss of heterozygosity? (4)
(1) Uniparental disomy UPD
(2) Imprinting
(3) consaguinity
(4) autosomal recessive conditions
Arrays are valuable for assessing for _______ in apparently ________ rearrangements found on karyotype
Arrays are valuable for assessing for small deletions in apparently balanced rearrangements found on karyotype
NGS that takes into about 180,00 exons, 3% of the genome
WES
NGS that takes in from one to a few thousand genes
Panels
secondary findings
when you find something that you were not looking for
ACMG recomendations (3)
(1) 1 of the 59 genes
(2) high penetrance
(3) interventions in place
Potential Results: Expanded (3)
(1) mutations in genes unrelated to phenotype
(2) variants in genes unrelated to phenotype
(3) deleterious mutations in genes with no disease association
what is a variant of uncertain significance (VUS)
A change in a gene for which there is not enough information to determine its health effect
epigenetic modifications lead to changes in the _______ of genes
expression
Epigenetic modifications _____ over time and are ______
Epigenetic modifications change over time and are reversible
can affect the adult human methylome
early gestation changes in methylation
