Notes in LE009 DNA Diagnostics: Principles of Cytogenetics and Genome Analysis

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Status	Last Update	Fields
Published	10/04/2024	Deletions result in {{c1::partial}} monosomy for lost segment.Deletions can be {{c1::Terminal}} (end of chromosome) or {{c1::interstitial}} (along chr…
Published	10/04/2024	Giemsa banding:{{c1:: 300 - 400 bands}}Reverse banding:{{c2:: heat treatment, reverse the pattern in R-banding. For distal ends of chromosomes}}High-r…
Published	10/04/2024	Basic Types of Genetic DiseaseChromosomal: Effects of {{c1::many contiguous genes}}Single gene: {{c1::One gene with a major effect}}Multifactorial: {{…
Published	10/04/2024	Cytogenetic location: Xp22.3{{c1::X}} chromosome{{c1::p}} armRegion {{c1::2}}Band {{c1::2}}Sub-band {{c1::3}}
Published	10/04/2024	Locus specific probes - bind to {{c1::specific region}} of chromosomesKey question: {{c1::Is gene there or not?}}Alphoid or centromeric repeat probes …
Published	10/04/2024	FISH is TARGETED and employs a {{c1::fluorescently labeled probe}} to detect and localize the presence or absence of a {{c1::specific D…
Published	10/04/2024	Duplication copy number analysis:{{c1::New values}} generated because of new possible genotypes in area of duplication
Published	10/04/2024	What do the allele peaks and copy number tracks look like for deletions?
Published	10/04/2024	Uniparental disomy: inheriting {{c1::2}} copies of chromosomes from one parent and {{c1::no}} copies from the other parentMechanis…
Published	10/04/2024	Robertsonian (nonreciprocal) translocations: {{c1::fusion of 2 acrocentric chromosomes}}Resulting karyotype has {{c1::45}} chromosomes
Published	10/04/2024	Karyogram looks at {{c1::entire chromosomes}}DNA probes are {{c1::targetted and catpure target sequence}}
Published	10/04/2024	Common autosomal chromosome disorders: - trisomy {{c1::13, 18. Severe, multisystem with frequent neonatal death}}
Published	10/04/2024	To visualize chromosomes, arrest in {{c1::metaphase}}
Published	10/04/2024	Types of chromosomal aberrations{{c1::Numerical: change in number of chromosomesUnbalanced by definitionTurner (XO)Klinefelter (XXY)Autosomies include…
Published	10/04/2024	Whole genome arrays: Oligo + SNP combinationOligo provides {{c1::copy number}} info throughout genomeSNPs provide both {{c1::copy number and genotype…
Published	10/04/2024	Next-gen sequencing:Advantages:{{c1::Unbiased look at the whole genomeàmore likely to find previously unknown genes contributing to disease}}Disadvant…
Published	10/04/2024	Estimated 1 in {{c1::150}} births have chromosomal aberrations and are the leading cause of {{c2:: intellectual disability}}These can be present in a…
Published	10/04/2024	Segregation of balanced translocation during meiosis may result in {{c1::an unbalanced translocation in the gametes}}
Published	10/04/2024	Meiotic nondisjunction can happen in {{c1::Meiosis I or meiosis II}}
Published	10/04/2024	FISH with break-apart probes measure {{c1::gene disruption by translocation}}
Published	10/04/2024	Turn around time for karyotyping is {{c1::7 to 10 days}}
Published	10/04/2024	To analyze SNP profile, for each SNP assign {{c1::a value to signal from the allele A probe and the signal from the allele B probe}}
Published	10/04/2024	Oligo arrays: cells are ground and {{c1::location lost}}Labelling allows for the {{c1::quantification}} of DNA binding to each probe Labelling with {{…
Published	10/04/2024	Oligos: {{c1::Selected DNA probes}}
Published	10/04/2024	FISH summary:FISH will detect:{{c1::Changes in number of chromosomesLarge insertions, deletions, translocations (>500kb - 2Mb)Mosaicism}}FISH will …
Published	10/04/2024	Oligo array/aCGH advantages and disadvantages:ADVANTAGES{{c1::Detection of abnormalities at multiple loci in the genomeVery small amounts of starting …
Published	10/04/2024	Isochromosomes: {{c1::abnormal chromosomes with 2 identical arms, either two p or 2 q}}
Published	10/04/2024	Robertsonian translocations result in high frequencies of {{c1::trisomy births}} due to generation of {{c1::unbalanced gametes }}
Published	10/04/2024	Chromosomal stains developed to produce {{c1::chromosome banding}}Cytogeneticists can use these to determine {{c2:: insertions and deletions}}
Published	10/04/2024	Hemizygosity copy number signal {{c1::New values}} generated in copy number track
Published	10/07/2024	Large insertions: type of {{c1::non-reciprocal translocation}}{{c1::A segment of DNA moved from one chromosome and inserted into a different chromosom…
Published	10/04/2024	Chromosomal duplication results in {{c1::partial trisomy }}
Published	10/04/2024	Approximately 4% of Down syndrome patients have {{c1::46 chromosomes, one of which is a Robertsonian translocation between chromosome 21q and the long…
Published	10/04/2024	FISH resolution{{c1::depends on probe length >500 Kb to 2 Mb}}
Published	10/04/2024	Chromosmal translocation: {{c1::rearrangement of part between nonhomologous chromosomes}}
Published	10/04/2024	{{c1::DNA probes}} are stretches of single-stranded DNA used to detect the presence of {{c2::complementary nucleic acid sequences (target sequences)}}…
Published	10/04/2024	A balanced karyotype is not always {{c1::cytogenetically normal}}
Published	10/04/2024	Isodisomy: {{c1::two identical copies from 1 parent}}Heterodisomy: {{c1::2 different chromosomes from 1 parent}}
Published	10/04/2024	FISH basics:A labeled {{c1::ssDNA fragment (probe)}} is exposed to denatured {{c1::metaphase, prophase, or interphase}} chromosomesThe probe undergoes…
Published	10/04/2024	Large insertions result from unequal {{c1::crossover}} during meiosis
Published	10/04/2024	Interphase FISH: {{c1::faster}} (no need to wait for metaphase), {{c1::cleaner}} (more compact), diffuse signal, {{c1::harder}}
Published	10/04/2024	Metacentric: {{c1::centromere in the middle}}Submetcentric: {{c2::centromere somewhere between the middle of the tip}}Acrocentric: {{c3::centromere ne…
Published	10/04/2024	Paracentric inversion: inversion does not include the centromere.{{c1::Inviable}} gametes
Published	10/04/2024	{{c1::Insertional mutagenesis}}: when a transposon inserts into or near a gene, it can disrupt the normal function of the gene
Published	10/04/2024	{{c1::4900}} out of {{c1::27000}} human genes cause disease or other known phenotype
Published	10/04/2024	UPD isodisomy is also known as {{c1::copy neutral loss of heterozygosity }}
Published	10/04/2024	An inversion occurs when a {{c1::single chromosome undergoes two breaks and is reconstituted with the segment between the breaks inverted. }}
Published	10/04/2024	Inversions:Paracentric: {{c1::both breaks occur in one arm (the centromere is not involved)}}Pericentric: {{c1::there is a break in each arm (the cent…
Published	10/04/2024	Dual fusion probes were designed to capture {{c1::translocations}}
Published	10/04/2024	SNP + Oligo:Will detect:{{c1::Changes in the number of chromosomes Relatively small (as small as 1Kb) insertions ordeletionsCopy neutral LOH (like uni…
Published	10/04/2024	Meiosis in the presence of a balances translocation: must adopt a {{c1::quadrivalent formation}} to ensure proper alignment {{c1::3 possible patterns …
Published	10/04/2024	Oligo arrays: Each “spot” or “feature” contains {{c1::millions of identical single-stranded DNA molecules}} termed {{c1::“oligos”}} or {{c1::“probes”.…
Published	10/04/2024	Congentical heart disease occurs in about {{c1::0.7%}} of all live- born childrenA genetic cause can be identified in approximately {{c1::35%}} of th…
Published	10/04/2024	Uniparental disomy can be problematic when 1. {{c1::the wrong genes are imprinted and}} 2. {{c1::when there is a disease allele on the inherited chro…
Published	10/04/2024	Conventional Karyotype:Will detect:{{c1::Changes in the number of chromosomes ✓Deviations from normal banding patterns Large (>5-10Mb) insertions o…
Published	10/04/2024	The 5 acrocentric chromosomes are {{c1::13, 14, 15, 21, 22}}
Published	10/04/2024	Array comparative genomic hybridization (CGH):The resolution depends on {{c1::the number of probes used}} and {{c1::their distribution through the gen…
Published	10/04/2024	This is a {{c1::translocation trisomy 21}} and may not always cause a phenotype because {{c2::all the genetic information is present, jsut organized d…
Published	10/04/2024	Pericentric inversion: {{c1::duplication and deficiency of chromosome}}Child with unbalanced karyotype estimated to be {{c1::5% - 10%}}
Published	10/04/2024	Single nucleotide polymorphisms (SNPs): {{c1::a sequence variation such that 2 chromosomes may differ by a single nucleotide}}
Published	10/04/2024	SNP arrays: design {{c1::One oligonucleotide probe per known sequence variant (SNP allele) (one for allele A and one probe for allele B)}}
Published	10/04/2024	Cytogenetics is {{c1::the study of chromosomes, their structure, and their role in heredity}}
Published	10/04/2024	Normal CGH:No losses or gains of {{c1::currently known clinical significance}}Does not rule out {{c2::1. mosaicism2. areas of the genome not covered b…
Published	10/04/2024	What will Oligo array/aCGH tell you?Will detect:{{c1::Changes in the number of chromosomes Relatively small (as small as 1Kb) insertions ordeletions(U…
Published	10/04/2024	Karyogram: banded {{c1::methaphase}} chromosome pairs arranged according to {{c1::length}}
Published	10/04/2024	Array resolution: how many {{c1::probes}} there are relative to the {{c1::region of interest}}
Published	10/04/2024	Aneuploidy results from mistakes in {{c1::meiosis, nondisjunction}}
Published	10/04/2024	Microarray technology:1. Identify {{c1::area of interest}}2. Design {{c1::1 probe}} for each area of interest3. {{c1::Array the probes onto a solid su…
Published	10/04/2024	Consequence of large insertions (4):{{c1::cytogenetically normaloffspring with same non-reciprocal translocation offspring with partial trisomy for in…
Published	10/04/2024	What is the function of DNA methylation in mammalian systems?{{c1::• Imprinting• X chromosome inactivation• Heterochromatin maintenance, chromosome st…
Published	10/04/2024	Balanced chromosmal translocation if (3):{{c1::1. No material lost2. Breaks not within a gene3. Rearrangement does not move gene away from regulator o…
Published	10/04/2024	Most trismoy 21 caused by {{c1::full aneuploidy }}- {{c1::95}}%- {{c1::meiotic nondisjunction}}
Published	10/04/2024	What does a SNP profile look like?
Published	10/04/2024	What does a normal allele peak and copy number track look like?
Published	10/04/2024	What do the allele peaks and copy number tracks look like for loss of heterozygosity?
Status	Last Update	Fields