PP #2 - mtDNA to Nuclear DNA Ratio as Biomarker of Human Embryo Implantation Potential

omarys's version from 2017-08-03 14:23

Section 1: Background - general and terminology

Question Answer
mt genome size16.6k BPs
The mt genome has its owntRNA
How many protein-coding genes does the mt genome approx. have?37
The mt genome is ____ in shapecircular
Fate of sperm mt after fertilization?marking by ubiquitin = doomed
Which enzyme is responsible for the elimination of paternal mt?Mt endonuclease G
Gene for mt endonuclease GGPS-6
The mtDNA in a mature oocyte expands (from 10 to 105 copies) during which stage?metaphase II
T or F- There is some mtDNA replication happening between fertilization and (early) post-implantationFalse.
T or F- Oocyte mtDNA content is related to fertilization success rate.True, but there's conflicting evidence as to more or less mtDNA improves fertilization rates.
High mt/nDNA in day ______ (___ stage) correlates with _____ ____.3 (cleavage) ; better morphology
High mt/nDNA in the ______ stage (day 5) correlates withbastocyst ; WORSE morphology
High mt/nDNA combined with advanced maternal age correlates withaneuploidy
In general (?), high mt/nDNA correlates withdecreased success in implantation

Section 2: Previous research - Correlation between mtDNA/nDNA ratio (in TE cells of D5-6 embryos) and embryonic ploidy and viability

Question Answer
Illumina is used forrapid and large-scale sequencing
The illumina sequencing approach is built around a massive quantity of sequences read in ___parallel
Deep ____ and uniform ____ are used to generate a consensus and ensure high confidence in determination of genetic differences.sampling ; coverage
Example of software used very widely in PGS/D data analysis BlueFuse Multi
BlueFuse Multi analyzes ___-based molecular cytogenetic data as well as ___-based IVF data.array ; NGS
BioLinux is a system forhandling and analyzing biological data; it's a bioinformatics workstation platform
Workflow during this project was: PGS >> _________-_________ (#) TE cells for ___ >> ____ library preparation >> sequencing and processing.3-5 ; WGA ; VeriSeq
To analyze ploidy, _____ ___ was used.BlueFuse Multi
The aim of the study was both to find a new way to ____ the ___/___ ____ and to determine the usefulness of this ____ for ____ _____.calculate ; mtDNA/nDNA ratio ; ratio ; embryo selection.

Section 2.5: Previous research, cont. - Methodology and results

Question Answer
DNA from ___ biopsies was tested using ____ PGS kit on ____ (illumina).TE ; VeriSeq ; MiSeq
____-_____ mtDNA and nDNA reads were used to calculate the ratio.quality-filtered
Around ___ of the embryos were ___.half ; euploid
In women ___ 36 years old, a higher mt/nDNA ratio correlated with ____ implantation rates.over ; increased
Correction factors used to accurately calculate mt/nDNA ratio included correction by ____ of ____ by ____, ____ _____ (gain/loss), and level of _____, if present.size of nDNA by gender ; chromosomal aberrations ; mosaicism.
The purpose of the 3 correction factors used (CNV, size of segmental aberration, % of mosaicism) was toaccount for variability to provide more concise results
In terms of culture conditions, there was ____ (a difference/no difference?) in implantation rate bwn ES-cultured and incubator-cultured difference
It was found that mt/nDNA ratio has a ___ (strong/weak) correlation with _____ level.strong ; aneuploidy

Section 3: Current 2017 research

Question Answer
Aim #1 is to evaluate mt/nDNA ratio ____ bwn _____ _____variations ; sibling embryos
Aim #2 is to determine the clinical significance of the ratio, by evaluating its effect on _____ ____ outcome.cumulative pregnancy
Methodology includes clinical ___ ____ of 384 ____ _________ (OD) and ____ ____ (GC) patients.chart review ; ovum donor ; gestational carrier.
Other than the data collection, there was also ____ ____ via ____ _____ to determine factors associated with different ratios.statistical analysis ; logistic regression