PP #1 - NGS Panel for PGD

omarys's version from 2017-08-01 16:01

Section 1: Background - General and terminology

Question Answer
Tests for overall chromosomal normalcy in embryos (i.e. not specific to a certain condition)PGS
Tests for specific genetic diseases and chromosomal disordersPGD
Examples of genetic diseases dx'ed by PGD (=waGhD =bastard) - (TFThMC)Tay sachs, Fragile X, Thalassemia, Myotonic dystrophy, Cystic fibrosis
Other than genetic mutations, PGD dx'esChromosomal translocations
HbSSickle hemoglobin allele (as opposed to the normal HbA allele)
HbCabnormal hemoglobin allele; there is substitution of a glutamic acid with a lysine at the 6th position of the β-globin chain (E6K substitution)
Robertsonian translocations are _____ and GENERALLY* occur between two _____ chromosomes.non-reciprocal ; acrocentric ; (*Other Robertsonian translocations can occur, but they don't lead to a viable fetus)
acrocentric chromosomes?13, 14, 15, 21, 22
A haplotype is a _____ _____haploid genotype (a group of genes in an organism that are inherited TOGETHER from a SINGLE parent)
PGHPreimplantation genetic haplotyping
Definition #2 of a haplotypea set of single-nucleotide polymorphisms (SNPs) on one chromosome that tend to always occur together (i.e. are associated statistically)
Common PGD methods?aCGH, FISH, qfPCR, qPCR (WGA is used as well)
An advantage of PGH over other PGD methodsmore accurate than certain (more common) PGD methods...been found to reduce risk of misdiagnoses (it's often used to reinforce other methods of genetic testing)
Rather than searching merely for a mutation or focusing on the genetic makeup of the embryo, PGH -compares the genome of affected and unaffected members of PREVIOUS GENERATIONS, i.e. examines generational variation and allows for the HAPLOTYPING of genetic MARKERS statistically ASSOCIATED WITH the target disease
SNaPshot system is used toscreen and confirm SNPs, detect minor sequence variations, assess DNA methylation, fingerprint bacterial artificial chromosomes (BACs) or general labeling of restriction fragments
STRs are
SNPs are
aCGH cannot detect ____ translocations.reciprocal
Which PGD method detects gain or loss of DNA relative to a reference sample?aCGH
a piece of DNA or RNA that is the source and/or product of natural or artificial amplification or replication events (i.e. can be formed via PCR or natural gene duplication)amplicon

Section 2: Background - Balanced translocations and segregation in meiosis

Question Answer
In the quadrivalent formation in meiosis, which segregation type yields 1 normal and 1 balanced gamete?alternate
In the quadrivalent formation in meiosis, which segregation type yields 2 unbalanced gametes?adjacent
In the quadrivalent formation in meiosis, which segregation type is most common?alternate
Balanced chromosomal rearrangements are detectable ONLY viaGenome-wide haplotyping

Section 3: Background - Nonreciprocal translocations

Question Answer
In nonreciprocal translocations, the karyotype is considered to be ___ despite the chromosome number being ____balanced ; 45

Section 4: Previous research at CReATe - Clinical utilization of NGS in PGD for chromosomal rearrangements

Question Answer
To improve implantation and pregnancy outcome rates in ART, selection of euploid embryos is done via _____aCGH
The NGS VeriSeq kit was shown to behighly consistent with aCGH
A ____ biopsy of D__/_________ blastocyst is performed for use in PGS/PGD.trophoectoderm ; 5;6
The product of ____ is what is actually assessed via VeriSeq and aCGH.WGA
NGS was shown to have more ____ and ____, and it ___ the ____ ____ and the ____.precision ; accuracy ; reduced ; hands-on time ; costs

Section 5: Current research - Aim and methodology

Question Answer
The 3 PGD methods compared in the current research areNGS, aCGH and qfPCR
The NGS panel to be designed for PGD contains ___ genes50
INTEGRATED NGS includes both ____ and ___ methodsdirect ; indirect
The gene may have ___ ____ located ____ or ____ to it.informative markers ; upstream ; downstream
Examples of informative markers that can be used in the research areSNPs and STRs
SNPs and STRs can be identified bySNP array and qfPCR utilizing STR markers, respectively
aCGH is used directly (i.e. on the gene itself) or indirectly (on informative markers)?indirectly
The gene can be worked with via _____ sequencing (___), _____ analysis, ____ ____ restriction analysis, and ____ (for which we're trying to design a 50-gene panel)direct ; (Sanger) ; SNaPshot ; fragment length ; NGS
Integrated NGS allows simultaneous detection of mutations and _____.haplotype
The next step after designing an NGS panel is ______ of _____ (via _____) and of ______.validation ; specificity ; (Sanger) ; sensitivity