deck_2782448 Flashcards
Chromosome classification terminology in Clinical Genetics
1-22 numbered by length1 = longest2 = shortestCentromere = centerTelomeres = endsp arm = petit arm = short armq arm = long armInternationally accepted system of chromosome classification: -Chromosome number -Arm -Region -Band -Sub-band**Capital letters & italicizedSpectrum of testing modalities:DNA sequencing (coding)Cytogenetics: - the study of the structure and function of the cell, especially the chromosomes - can detect both numerical and structural abnormalities in chromosomes - specimens must be fresh, so the cells can be cultured
Down Syndrome
Trisomy 21 -> 3x chromosome 21Mental retardationAbundant Neck skinCongenital heart defects - Majority of childhood deaths - Endocardial cushion defects (cells that make up spetum & divide A/V & L/Rintestinal stensosisEpicanthic folds (upper eyelid folds)Flat facial profileSimian crease (only 1 crease in palms)Umbilical herniaHypotoniaIncreased leukemia risk +10-20% Acute megakaryoblastic leukemia
Nucleic Acid Hybridization
• Detects the presence of a specific sequence• Based on the principle of complementary base pairing between a target nucleic acid and a labeled probeProcess: - Label probe with fluorescent dye - Denature DNA - Hybridize - Look for fluorscence***Always limitations
Patau Syndrome
Trisomy 13Microphthalmia - small eyesPolydactyly - extra fingersCardiac defectsUmbilical herniasRenal defectsMicrocephaly - small headMental retardationCleft lip & PalateOcker bottom feet - rounded arches**Most often fatal- Some have Robertsonian translocations
Robertsonian Translocation
Fusion long arms of Chromosome 13 & Chromosome 14 between acrocentric (long arms have all information)Not detectable with a centromeric FISH probe
Comparative Genomic Hybridization (CGH) Array
A hybridization technique that can assess the entire genome for copy number changesLabel all patient’s DNA with 1 color (green) & control DNA (red)Control color (red) appears where there are gains/losses in genetic material-> any difference = extra/lack of genetic material
Edwards Syndrome
Trisomy 18Low set earsShort NeckCongenital Heart defects - Vent Septal DefectRenal malformations - Horseshoe kidneyLimited HIp AbductionOcker bottom feetMental retardationMicrognathia - small jawProminent OcciputClenched Fist with overlapping fingers
Single Nucleotide Polymorphism (SNP) Array
Detect copy number variations like CGH, but they can also detect zygosityCopy Number - 0 is normal - below = lost - above = gainedZygosity- mixtures are in the middle- only 1 parental contribution will be gap in midline -> will be at poles (indicates lack of mutual contribution)
Angelman SyndromePrader Willi Syndrome
Angelman = MaternalPrader Wili = Paternal Need SNP Array to tell who contributed what
Polymerase Chain Reaction (PCR)
Method for selectively amplifying target nucleic acids up to a million foldReagents:– Template DNA– Two oligonucleotide primers (15-22 bp long)– Thermostable polymerase– Mixture of four deoxynucleotides dATP, dCTP, dGTP, dTTP– Buffers containing magnesiumMechanism:1. Denaturation (95°)2. Hybridization/annealing (55°-72°)3. Synthesis/extension (72°)
Amplicon Length Analysis
Gel electrophoresis: - DNA is separated in a gel matrix using an electrical fieldDiagnose triplet repeat disorders - Fragile X syndrome - Huntington disease
Restriction fragment length analysis or Restriction Endonucleases
Used to identify point mutations in PCR productsRestriction enzymes are bacterially-derived enzymes that cut DNA at specific recognition sequencesDesign Assays to take advantage of this & target mutant sequences that are differentially recognized by the enzymesRestriction fragment length analysis in the diagnosis of hereditary hemochromatosis
Direct DNA sequencing
Sanger sequencing - Gold standard1) All 4 building blocs of deoxynucleotides in same tube & fluorescently labeled2) Capillary electrophoreisis - creates peaks that correlate to where nucleotide is3) Transpose from graph to DNA sequencePyrosequencing - PCR with Luciferase (firefly tail light enzyme)-Probe is specific sequence searching forUseful when testing specific sequence variants - missense mutation of Sickle Cell
Huntington disease
Autosomal dominantProgressive movement disorders and dementia Caused by CAG repeats in coding region of the the first exon of HTT (4p16.3) -> toxic gain of function in proteinPolyglutamine expansionCharacterized by: - Dementia - Jerky movements/motor neuron- Toxic protein kills brain
Fragile X syndrome
Most common cause of mental retardationCGG repeats in promoter region of FMR1 genePCR primers on either side of promoter region & amplifyNormal = baselinePremutation = elevatedFull Mutation = nothing - because too long to amplify**limitation of test - but also diagnositc to be CONCLUSIVELarge, protruding ears (one or both)Long face (vertical maxillary excess)High-arched palate (related to the above)Hyperextensible finger jointsHyperextensible (‘Double-jointed’) thumbsFlat feetSoft skinPostpubescent macroorchidism (Large testes in men after puberty)Hypotonia (low muscle tone)
Real-Time PCR
• DNA template amplification and detection steps occur simultaneously, allowing quantification of the template• A fluorescent reporter emits light in direct proportion to the amount of the PCR product.• Requires a special thermal cycler that can measure fluorescence.Several techniques:TaqMan probe- labeled with quencher & reporter molecules when cleaved - reporter emits lightUse a LOT to quantify - Viral - Hep B - Hep C - Minimal residual disease amount
Sickle Cell Anemia
Misssense Mutation6th Codon in Beta HbDNA = T-A -> A-TRNA = A-U-> U-AAA = Glutamic Acid -> ValineSymptomatic: Stoke
Next-Generation sequencing
Involves high-throughput sequencing technologies that parallelize the sequencing process, producing thousands or millions of sequences at onceMassive parallel sequencing- Can produce upwards of 1 billion sequences per instrument on 1 run- Multiple genes in one assay- Same genes multiple times Cost/nucleotide sequence is FAR CHEAPERTremendously powerful
Marfan Syndrom
Autosomal dominantDefect in extracellular glycoprotein fibrillin-1 due to mutations in FBN1 (15q21.1) or FBN2 (5q23.31)Characterized by:Skeletal abnormalities Very tall & Thin Long arms/legs & Feet/Fingers *Think Michael Phelps bodyChest pectus excavatum - indentation pectus carinatum - protrusionScoliosisEctopia lentis - eye problemsCardiovascular lesions mitral valve prolapse, dilated ascending aorta due to cystic medionecrosis)Cystic medionecrosis in Aorta:- Typically regular dense CT- Elastic is disrupted & CT becomes irregular**Next Generation sequencing - because mutations are interspersed through the span the FBN1 and FBN2 genes - need broad net
Non-invasive prenatal testing
Fetal cell free DNA in Maternal blood - Sequence with Next generation sequencing from that
Turner syndrome
Monosomy X or 45, XShort statusLower posterior hairlineWebbing of neckLymphangioma in posterior neckPigmented neviCoarctation of aortaShield chest - broad chest with wide nipplesStreak ovaries, infertility, amenorrheaPeripheral edema at birthCubitus valgus - deformity where forearm is angled more angled away from the body when fully extended
