Genetic Technology Flashcards

1
Q

CMA

A
  • chromosome microarray
  • detects CNVs (missing or extra DNA/ “microduplications/microdeletions” 500 bp to 30 kb)
  • Usually either aCGH and/or a microarray
  • Can’t detect balanced rearrangements, SNVs, small indels
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2
Q

aCGH

A
  • array comparative genomic hybridization
  • detects CNVs/indels as small as 100bp
  • cannot determine locus or orientation of duplications
  • can’t detect point mutations or balanced translocations
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3
Q

WES

A
  • whole exome sequencing genes and their introns
  • can rarely detect balanced translocations
  • unable to determine the phase of sequence variants (e.g., when two likely causative mutations for recessive disorders are found, cannot be certain that the mutations are on different alleles)
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4
Q

WGS

A

whole genome seq

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5
Q

Sanger seq

A
  • sequences predetermined regions with primers
  • can detect most SNVs within the sequenced region
  • can detect insertions up to 300bp
  • Can’t detect CNVs
  • doesn’t sequence regulatory regions outside of genes
  • Slippage can be an issue with runs of mononucleotide repeats
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6
Q

SNP chip

A
  • Often only used in DTC testing (e.g., for ancestry estimates)
  • Usually looks at only 1% of genome
  • Not “sequencing”
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7
Q

MLPA

A
  • Multiplex Ligation-Dependent Probe Amplification Assay
  • Del/dup
  • Detects small indels within a single exon of a given gene or within an entire gene
  • The peak heights of the amplification products of the target DNA sequence is compared to the peak heights in reference samples
    • A del/dup is inferred from the relative decrease or increase in peak height
  • Can’t detect point mutations
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8
Q

karyotype

A
  • can only detect large structural chromosomal rearrangements
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9
Q

FISH

A
  • Flourescence in-situ hybridization
  • detects ploidy and larger CNVs
  • Can’t detect locus of CNVs
  • Can’t detect balanced rearrangements
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10
Q

methylation analysis

A

e.g., for PWS/Angelman, etc.

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11
Q

mtDNA seq

A

sequences mtDNA

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12
Q

ms-MLPA

A
  • Methylation-specific MLPA (MS-MLPA)
  • Used to detect both the copy number and methylation status of DNA sequences in a single multiplex PCR-based reaction
  • Target DNA sequences recognized by the MS-MLPA probes contain restriction sites for enzymes such a HhaI or HpaII that are sensitive to cytosine methylation of one CpG site in their recognition sequence
    • When target DNA is digested with these enzymes, the probe will amplify if theCpG site is methylated
    • The level of methylation is determined by the ratio of the relative peak area for each target probe from digested vs undigested DNA sample.
  • Used for imprinting disorders like Prader-Willi syndrome /Angelman syndrome, Beckwith-Widemann syndrome, Russell-Silver syndrome, Lynch syndrome and Albright hereditary osteodystrophy.
  • MS-MLPA has several advantages over other assays such as MS-PCR based on bisulphite sequencing, southern blotting, and methylation analysis including PCR following restriction digestion with methylation sensitive enzyme.
  • Can’t detect point mutations
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13
Q

repeat-primed PCR

A

uses specific primers amplify full-length PCR products from each allele, for disorders associated with presence or absence of a nucleotide repeat expansion (e.g., Fragile X, HD, etc.)

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14
Q

Methylation specific PCR

A

pairs methylation sensitive DNA digestion with repeat-specific PCR amplification of the a repeat region to determine the methylation status of full mutation alleles

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