lect 24 Detection of CNVs using Multiplex QF-PCR

Flashcards covering the vocabulary and core concepts of CNV detection via multiplex QF-PCR, including STR analysis, interpretation ratios, and clinical aneuploidy examples.

Short tandem repeats (STRs)

Highly polymorphic DNA sequences consisting of $2-9\,bp$ repeating motifs, usually repeated between $5$ and $50$ times, that serve as unique allele identifiers.

Copy Number Variants (CNVs)

Genomic deletions and amplifications, such as trisomy or hemizygosity, associated with specific diseases or phenotypes.

Quantitative Fluorescence – PCR (QF-PCR)

A quantitative assessment of STRs using primers complementary to flanking regions to identify and quantitate specific alleles via capillary electrophoresis and fluorescent tags.

Hemizygosity

A condition where an individual has only one allele at a locus when there should be two, indicating a deletion.

Multiplex QF-PCR

A technique using multiple primer pairs labeled with different fluorophores in a single reaction to investigate multiple genomic regions or chromosomes simultaneously.

Electrophoretogram

The visual output of capillary electrophoresis where DNA fragments are identified based on their size (base pairs) and color (fluorescence).

Normal Heterozygous Allele Ratio

The expectation of two peaks in a $1:1$ ratio, typically defined by an area ratio between $0.8$ and $1.4$.

Trisomy (QF-PCR Detection)

An aberrant result characterized by either three peaks in a $1:1:1$ ratio or two peaks in a $2:1$ ($1.8-2.4$) or $1:2$ ($0.45-0.65$) ratio.

Nomenclature: rsa(13,18)x2,(21)x3

A Region Specific Assay notation indicating two copies of chromosomes $13$ and $18$ and three copies of chromosome $21$ (Down syndrome).

Maternal cell contamination (MCC)

The presence of maternal DNA (tissue or blood) within a fetal sample (such as chorionic villi) that can complicate the interpretation of the fetal genotype.

Digynic triploidy

A condition identified as $rsa(13,18,21) \times 3$, characterized by the presence of an extra haploid set of chromosomes inherited from the mother.

DNA polymerase slippage

The molecular process that results in the formation and variation of short tandem repeat (STR) sequences throughout the genome.

Karyotyping

A whole chromosome detection method with a resolution of approximately $5\,Mb$ and a turnaround time (TAT) of $7-14$ days.

Capillary electrophoresis

A process where amplicons are separated on the basis of size using an electric current in thin tubes containing a matrix, resolved via light emitted from fluorescent dyes.

FAM-6

A type of fluorescent label attached to the $5'$ end of a primer that does not require intercalation between DNA strands to fluoresce.

Turner syndrome

A sex chromosome aneuploidy characterized by a $45,X$ (also known as $45XO$) genotype, where there is an abnormal copy number of the X chromosome.

Inconclusive (Intermediate) Ratio Range

Allele peak area ratios falling between $1.4-1.8$ or $0.65-0.8$ that do not clearly indicate a normal or aberrant result.

Single Peak Result Limitations

A pattern that can represent two copies of an identical allele, monosomy, loss of a primer binding site, or a mutation at the binding site.