Tissues appropriate for conventional cytogenetic study

That can undergo cell division (during mitosis is best)

• Chorionic villi, amniotic fluid, peripheral blood (lymphocytes), skin (fibroblasts), bone marrow
   After culturing in vitro, a proportion of cells are arrested in mitosis, and are then ‘harvested’ for
  chromosome analysis
  o MOST COMMON tissue used to search for a constitutional abnormality is peripheral blood
   After harvesting, the cell preparations are dropped onto glass slides and stained. For most chromosome
  analysis, a G-banding technique is utilized for staining
   Each chromosome has a unique G-banding pattern that is constant from individual to individual
  ISCN (International System for Cytogenetic Nomenclature):
• P=short arm
• Q=long arm
• Centromeres= p10 and q10
• Telomeres = 6 bp sequence repeat at ends of chromosomes: pter, qter
• Band numbers increase as move from the centromere to the telomere
  A single G-band typically contains more than 3 MB of DNA
• Therefore, most constitutional chromosome abnormalities are associated with multiple congenital anomalies
• Therefore, deletion of a single gene cannot be detected by G-banding
  Clinical findings in Down Syndrome:
• Recurrent respiratory infections, GI tract anomalies, increased risk for leukemia, mental retardation, Alzheimer’s
  disease
  o Phenotype Mapping for Down Syndrome:
   APP = amyloid beta precursor
   RUNX1 = leukemia
   Dyrk = neurogenisis
  Pregnant women in 19 weeks gestation showing abnormal findings: FISH is done because it is faster
  Fluorescence-in-situ hybridization (FISH): get results in 24 hrs (G-banding takes a week for culture of amniotic fluid)
• Probe DNA, label with fluorescent due, and denature and hybridize
  Down Syndrome can also result from structural chromosomal abnormalities:
• Trisome 21:
  o 95% due to meiotic nondisjunction
  o 4% due to Robertsonian translocation
  o 1% due to mosaicism
  In general, TRANSLOCATIONS may be classified as BALANCED or UNBALANCED:
• Balanced: no net gain/loss of essential genetic info
• Unbalanced: net loss or gain of essential genetic material
• Carriers of balanced translocations are typically phenotypically normal, but are at risk for generating gametes
  with unbalanced translocations
  LECTURE 3: CYTOGENETICS 2
  Gain of an extra sex chromosome:
• XXY and XYY (1:1000 males)
• XXX (1:1000 females)
• Most do not cause clinical suspicion in the newborn period
  47, XXY
• 6 yr old presenting with behavior issues, 15 hr old presenting with gynecomnastia (large mammary glands in
  men), 30 yr old male presenting with history of infertility
• Taurodontism: enlarged pulp chamber at expense of roots in the molar teeth
  “Micro” deletion Syndromes:
• Involve the loss of a very small amount of material from the chromosome
• Typically associated with a specific clinical syndrome
• Can be very difficult to detect by G-banding therefore, typically characterized by FISH or microarray
  Di George Syndrome and Velocardiofacial Syndrome
• 85% have a deletion of gene 22q11.2
• VCFS: cleft palate, cardiac anomalies, characteristic faces
• Di George: developmental defects of the 3rd and 4th pharyngeal pouches, resulting in thymic and parathyroid
  hypoplasia and cardiac defects
  Congenital anomalies in 22q deletion syndrome:
• Cardiac: 74%
• Hearing impairments: 39%
• Hypocalcemia: 49%
• T-cell immune deficiency
  The most recent advance in cytogenetic technology: Array based-comparative Genomic Hybridization (a-CGH):
• You take a patient genomic DNA and a control genomic DNA: restrict and quantify them and label each with
  different fluorochromes and combine in a 1:1 ratio.
• Then hybridize to “chip”onto which DNA probes have been “spotted”
• Ratio equals 0: no copy number gains or losses
  o Less than -0.3 = deletion
  o More than 0.3 = gain (duplication)
  Two data bases that are most informative:
• UCSC Genome Browser
• TCAG: Toronto Center for Applied Genomics: Database for Genomic Variants
  Acquired Chromosomal Abnormalities:
  Most cancer cells have associated chromosomal abnormalities:
• The abnormalities are acquired
• The abnormalities are clonal (2 or more cells have the same abnormality)
• The abnormalities are limited to the tissues involved in the malignancy
  Identification of these abnormalities is important for:
• Differential diagnosis
• Determining therapy
• Providing info about prognosis