Genetics E1- Diagnostic Methods

Which cytogenetic test creates a visible karyotype to identify chromosome pairs & banding patterns for detecting structural and numerical abnormalities?

G banding

What testing would be used for a Down syndrome diagnosis?

Karyotyping

What kind of tissue can G (Giemsa) banding be used on?

Any tissue containing nucleated cells that under go division: lymphocytes (MC), skin, BM, chorionic villi, amniotic fluid

Which cytogenetic test is more specific, targeting known/suspected chromosomal or gene abnormalities, and maps gene locations on chromosomes?

ex: use for suspected DiGeorge syndrome where karyotype looks normal

FISH

How does fluorescence in situ hybridization (FISH) work?

Short sequences of single stranded DNA (probes) match a portion of the gene of interest & form complementary sequences of nucleic acids to determine degree of sequence identity

What are examples of medical applications for FISH cytogenetic testing?

Detect aneuploidy (faster than karyotype, ideal for rapid prenatal screening)

Test of choice for loss of chromosome or region (microdeletion)

Detection of specific cancers (HER2, bladder, leukemia) & monitoring success of BM transplantation

What type of DNA testing amplifies DNA sequences by rapidly producing billions of copies to look for genetic variants known to cause certain diseases?

PCR

How does polymerase chain reaction (PCR) work?

Short DNA sequences (primers) used to select portion of the genome to amplify→ temp is raised & lowered repeatedly to help a DNA replication enzyme copy the target sequence

What DNA testing technique uses a special chemical that marks each DNA nucleotide with a different colored fluorescent dye depending on the base it carries?

Sanger sequencing

What is the limitation of Sanger sequencing?

Can only read one short section of DNA at a time

What type of DNA sequencing test is much faster & sequences millions of small DNA fragments simultaneously?

Next generation sequencing (NGS)

What are indications for DNA analysis (PCR, NGS)?

Diagnostic confirmation of Huntington’s or PKD or screening for CF, thalassemias, familial polyposis, or X linked conditions such as Duchenne muscular dystrophy & hemophilia A/B

Which type of testing analyzes proteins rather than genes to determine the presence or absence of specific proteins and identify enzymatic defects?

Biochemical analysis

What can biochemical analysis be used to detect?

Inborn errors of metabolism (PKU, CF), protein activity, level of metabolites, & size/quantity of protein

Which test uses comparative genomic hybridization to detect gains/losses across the genome, including microdeletions & duplications too small for karyotyping or large rearrangements in genes like BRCA1/2?

Microarray

What genetic testing is best for multiple congenital abnormalities, unexplained intellectual disability, or autism evaluation?

Microarray

What risks does microarray carry?

Possibility of not detecting triploidy & finding variants of uncertain significance

What are benefits of direct-to-consumer genetic testing?

Provides info about risk/carrier states, better sense of personal health agency/motivation to screen, less expensive & faster

What are limitations to direct-to-consumer testing?

May not detect all pathogenic variants, reports on conditions w/o confirmed medical utility (ex-which vitamins to take), false + & -, results may be misunderstood or reveal distressing ancestral relationship, & may be accessed by law enforcement

How is direct-to-consumer testing limited when evaluating BRCA genes?

Only examines 3 genetic variants, but there are more than 1000 mutations known to affect risk of breast & ovarian cancer