Vocabulary
Contents
Glossary words (A - Z):
#
5mCpG: A methylated CpG site (CpG is short for 5’—C—phosphate—G—3’)
A
Androgenic hydatidiform mole: An abnormal pregnancy with grossly swollen chorionic villi, but without an embryo, cord, or amniotic membranes. It is diploid with paternal chromosomes because of a failure of the female pronucleus during fertilization. The two sets of paternal chromosomes come from a diploid sperm or haploid sperm which has duplicated.
B
Bisulfite conversion: A method providing single nucleotide resolution information about DNA methylation status. Treating DNA with bisulfite converts cytosine to uracil, but will not convert methylcytosine. Bisulfite treated DNA is then sequenced and compared to the original sequence to assess methylation status.
C
Capillary electrophoresis: a technique that separates DNA fragments amplified by PCR according to their electrophoretic mobility
CpG Islands/Sites: CpG sites are regions of the DNA where a cytosine is followed by a guanine in the linear sequence of bases (5' --> 3'). CpG Islands are short interspersed DNA sequences that deviate significantly from the average genomic pattern by being GC-rich, CpG-rich, and predominantly nonmethylated. Most, CGIs are sites of transcription initiation, including thousands that are remote from currently annotated promoters.
D
DMR: (differentially methylated region) stretches of DNA in an organism’s genome that have different DNA methylation patterns compared to other samples
E
F
G
gDMR: (Germline differentially methylated region) These differentially methylated regions are present immediately after fertilization and are contributed by the gametes.
H
hESC: (human embryonic stem cells) generated by growing cells from a preimplantation-stage embryo in a culture medium; pluripotent
HhaI: a methylation sensitive restriction enzyme that won’t cleave DNA in methylated region.
I
ICR: (imprinting control region) imprinting is an epigenetic process which the methylation of a parental gene is inherited and replicated by the offspring. ICRs are non-coding RNAs and DMRs that control the imprinting of one or more genes
J
K
L
MSRE-PCR: (methylation sensitive restriction enzyme polymerase chain reaction) It can determine methylation status at a given CpG island
MT21: nuclear family trio with Down syndrome of maternal origin
N
N21: "normal" nuclear family trio without Down syndrome
NCBI GEO: a genomics data repository supporting array- and sequence-based data. da Silva et al. queried GEO to obtain RNAseq data for SNPs neighboring the WRB locus.
Nondisjunction: is the failure of homologous chromosomes or sister chromatids to separate properly during cell division. There are three forms of nondisjunction:
- ailure of a pair of homologous chromosomes to separate in meiosis I
- failure of sister chromatids to separate during meiosis II, and
- failure of sister chromatids to separate during mitosis. Nondisjunction results in daughter cells with abnormal chromosome numbers (aneuploidy). This is the non-lethal form of nondisjunction that can result in Down's syndrome.
O
Oogenesis: The development of a mature egg cell (ovum) from the primary oocyte.
P
Proband: A person that is used as the starting point for a family in a genetic study. A term used especially in medicine or psychiatry.
PT21: nuclear family trio with Down syndrome of paternal origin
Q
R
rs#: (Reference SNP) - way to reference specific SNPs (Single Nucleotide Polymorphisms)
S
SNP: (single nucleotide polymorphisms) difference in a single nucleotide at a specific position; the most common type of genetic variation among people
SNuPE: (single-nucleotide primer extension) A molecular biology technique in which an oligo flanking a target site is extended and terminated by a ddNTP complementary to the following base.
SRA: (sequence read archive) large database online which stores high-throughput sequencing data for researchers to compare and contrast
STR: (Short tandem repeats) A region of the DNA two-thirteen bases long that is repeated up to hundreds of times. These regions can be used to trace lineage
T
TSS: (Transcription Start Site) location where transcription starts in the genome. These occur on the 5' end a number of base pairs away from the promoter
U
V
W
WRB: (Tryptophan Rich Basic Protein coding gene) This gene codes for a nuclear protein of unknown function. Known as a critical region for Down Syndrome because it is linked to congenital heart disease and heart disease.
