4.6./ Self-assessment questions (5) For each of the following sequence changes o

Question

4.6./ Self-assessment questions (5) For each of the following sequence changes or effects, choose possible testing methods from the list below that could be used to check for the presence of the change or effect (more than one method may be appropriate for some cases). a G>A change in exon 2 of the PAX3 gene that results in replacement of valine 60 by methionine in the gene product. a heterozygous 3 bp deletion in exon 6 of the BRCA1 gene. . an A>T nucleotide substitution that changes the codon for arginine 214 (AGA) into a stop codon (TGA) in exon 7 of the MITF gene. a GTGA change in the donor splice site at the end of exon 4 of the PAH gene, which encodes the liver enzyme phenylalanine hydroxylase. a C>A change in an intron near a splice site in the ubiquitously expressed actin gene: the question is whether or not it affects splicing of the primary transcript. deletion of several contiguous genes on one copy of chromosome 17 in a child with suspected Smith-Magenis syndrome. a duplication of one or more exons in the dystrophin gene in a boy with Duchenne muscular dystrophy deletion of one or more exons of the HYP gene in a boy with hypophosphatemia (an X-linked dominant condition). insertion of three nucleotides in the promoter of a gene - the question is whether this affects expression of the gene. any material extra or missing on a copy of chromosome 7 in a patient - the cytogeneticist reported that the banding pattern on one copy of chromosome 7 was abnormal but could not work out exactly what events had produced the change. * - . Options: lal PCR amplification, check for the presence / absence of product Ib] PCR amplification, check the size of the product Icl PCR amplification followed by sequencing (see Chapter 5 for detail) (d) PCR amplification followed by hybridization to an allele-specific oligonucleotide (see Chapter 5 for detail) le) RT-PCR If) Real-time quantitative PCR gl Southern blotting hl FISH lil Chromosome painting jl Array-CGH. lHints on questions la and 4 are provided in the Guidance section at the back. of the book.]

Explanation / Answer

1. C
A single nucleotide change can be detected by PCR followed by sequencing.

2. B and C
If we use high percentage gels, we can distinguish a 3-bp size difference.

3. C
A single nucleotide change can be detected by PCR followed by sequencing.

4. B, C and D
Intron retention can increase the PCR product size.

5. B, C and D
Intron retention can increase the PCR product size.

6. A, B, C, D, E, F and G
Loss of several genes can be detected by PCR, sequencing and Southern blotting

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