Genetic testing of Tay-Sachs disease by PCR and Restriction Digest

Transcription

1 Genetic testing of Tay-Sachs disease by PCR and Restriction Digest ESC102-PRA0103 Submitted to: Elizabeth Berndl 18 February, 2009 Submitted by: Laila Hulbert ( ) Maria Yancheva ( )

2 Scientific and Medical Justification Tay-Sachs disease is a progressive neurodegenerative disorder, which causes large quantities of the GM2 ganglioside fatty acid to accumulate in the nerve cells of the brain [1]. The presence of gangliosides in the retinal cells results in the appearance of a red spot in the retinae of patients with Tay-Sachs disease. Other consequences caused by the excess presence of gangliosides in the nerve cells are a loss of mental and physical abilities in infants, leading to blindness and deafness [2]. The atrophy of muscles causes paralysis and eventual death at an early age. In its classic form, the disease is found in infants and is typically fatal by the age of 2 or 3. Tay-Sachs is a genetic disorder caused by a mutation in the hexosaminidase A (HEXA) gene [1], and is inherited in an autosomal recessive pattern [2]. There are a number of genetic mutations which can cause the disease. The Arg170Gln mutation was found to be one of the wide-spread mutations causing Tay-Sachs among the Moroccan Jewish population [1]. There is currently no cure for the disease, and infantile Tay-Sachs disease results in death by the age of 5 at best. The methods of treatment currently being researched include enzyme replacement therapy which aims to replace a missing enzyme in patients; gene therapy which aims to replace defective genes through the brain; and substrate reduction therapy which aims to control the metabolism of GM2 gangliosides in the brain [2]. This proposal describes a diagnostic which tests for the Arg170Gln mutation caused by the substitution of glutamine in place of arginine-170, resulting in a G-to-A change at nucleotide 509 [1]. See Appendix A for transcript and genomic region. The primers used to amplify the region are as follows: (see Appendix B for primer design details) Tay-Sachs F: CTTGAGGCCACACTGCTTTGAA Tay-Sachs R: TGTATCCCTGGAAACAGCCTGA The restriction enzyme HpaII will be used to cleave these sites (see Appendix C for cleave sites). The following bands will be produced. Homozygous Wild Type: 346, 614 Heterozygous: 346, 614, 960 Homozygous Mutant: 960 Protocol (Modified from Labs 2 & 3) Step One: Obtaining DNA See Lab 2, step1. Step Two: PCR Amplification of DNA See Lab 2, step 2, except: After 3, each group member transfers the remaining Instagene liquid (without beads) to a 1.5 ml tube, labeled with her name on a removable label. The TA removes the label with the name and replaces it with a number, and selects three random samples to test. Transfer 20 μl of master mix into each PCR tube, mix by pipetting up and down two to three times. Avoid bubbles. Cap the tubes and keep them on ice. Continue from step 6 in protocol. Step Three: Restriction Digest and Electrophoresis See Lab 3, except: Add 10 μl PCR product and 10 μl HpaII master mix to microtubes, and incubate at 37C for 1 hour (do this before preparing gel). Continue from 1.

3 Concentration of agarose gel should be 2% (from RFP) After incubation, add 5 μl loading dye to one undigested sample and to all digested samples. Continue from step 6. Step Four: Staining with Sybr Green See Lab 3.

4 References [1] OMIM. (2009). Tay-Sachs Disease. Retrieved February 17, 2009, from [2] Wikipedia. (n.d.). Tay-Sachs Disease. Retrieved February 17, 2009, from

5 Appendix A Wild Type and Tay-Sachs cell variants of the HEXA gene from Ensembl Wild Type Transcript: 961 ACATTCTTTATCAACAAGACTGAGATTGAGGACTTTCCCCGCTTTCCTCACCGGGGCTTG 153 -T--F--F--I--N--K--T--E--I--E--D--F--P--R--F--P--H--R--G--L- Mutant Transcript: 961 ACATTCTTTATCAACAAGACTGAGATTGAGGACTTTCCCCGCTTTCCTCACCaGGGCTTG 153 -T--F--F--I--N--K--T--E--I--E--D--F--P--R--F--P--H--R--G--L- Wild Type Genomic Region: ACCCAGGCTCCTTGGAAACCCAAGCTTATGATCACTTTCTCACAATTTATTCTGGGACCC CTTTTCTCAGCTCTCTTAGCTCCTGATAGGGGTTATCCATGAAAAGTCCAACTCTTGCAG GCTGAGTTGTCTCTGTGTCTGTCCTCATGAGTATATGTCTTGGCCTCTCTTCTCAATATT CTTGTGAAGGCACAGGAAATATAGATAAGAGGTATGTGGGTTTTGAAGGTTAGTATGTTG TAAGGAAGGGCACTAAAACCCTTACTCTGACATCTCCCAAAATGAAATACAGAAGTAAAG ATGGATAGTGGCTTCCTAATATCCCCTTTTCATCAGTGTTAAAAATCGTCAAGCCTACAC TACATCCATTTTCCCTGTGTACCCAAATGTTATGCTCTGCTACATTGAGAACCTTCCAAA TAGAGACATCTCTTTTTCCACTCCCTGAGTCTTTACTCTGCCTCTCTACATCTTCCTAGG TCTGGAGACTTTTAGCCAGCTTGTTTGGAAATCTGCTGAGGGCACAGTAAGTGTGGACCC TCAAAAAGGGCTCCTTTTTCATCTCTGGGGTTGGATCCCAATATTGAGAATCCTAGAAAA ATCTTGTTTTGCCTTAGGATCCTGGTGGCTTGAGATAGCCCCAGTAGAAATGGAAGAGGA GATGTGAGTGGAAAACTGGTTTGGTAGATTTGGTCTGTTTGGAATCACTGTAATTTGGTC CCCCTGAGTCATCATTTAGTAATGACCTTGAGGCCACACTGCTTTGAAGAAAATAAACTA TGTTAACAGGAAAATCCAGAATTTGTAGGCTGAGTGGTGTTTGGGACAGTTGTATTAGGC TGGCGTTGGACAATTGCTCTCTGGGAAGGTGGCTGCTTATGGTCATTTATAGAGGTGGGG AGCATTTAGGGAGAGAGCGACCCTGAGAACAGTCACAGATTGGCTTTTTAAGAATCCTGG GAGAGTTGTCTTCATCTCCCTGTGCCCCCATAGTAAGCTTCCTTTGAAACTGACATGTTC AATGTTTGTTCTGCACAGTTCTTTATCAACAAGACTGAGATTGAGGACTTTCCCCGCTTT CCTCACCGGGGCTTGCTGTTGGATACATCTCGCCATTACCTGCCACTCTCTAGCATCCTG GACACTCTGGTAACCAGGCCTTAAGGCCTTCTTCACACTTAAGAGTTCTAGGGTGATGGA GCAACGGACAGACCAAGTTCCAAATTCTTAAAGAGTTAGAGAGGGAATGTATGGACTGGG TGTGGTGGCTCATGCCTGTAATCCCAACACTTTGGGAGGCCGAGGTGGGCGGATCACCTG AAGTCAGAAGTTCAAGGCCAGCCTGGCCAACATGGTGAAACTCTGTCTCTACTAAAAATA CAAAAATTAGCTGGGCATGGTGGTGCATGCTTGTAATCCCAGCTACCTGGGAGGCTGAGG CAGGAGAATCGCATGAACCCAGGAGGCAGAGGTTGCAGTGGGTGGAGATCACGCCACTGC ACTCCAGCCTGGGTGAAAGAGTGAGACGCTGTCTCAAAAAAAAAAAAAAAAATTGTATGT AATTCTATGAGCTCCTGGGAAAAATGTAGAAGATGAGCTGCTCCAAGACTCAAAAAATAA CAGAGTGACTTAAATCTACCTTACAGGCTACTGTAGATCAATGTTCAGGCTGTTTCCAGG GATACAAATGTTTAGGGGAATTGGCTTCATTGGCAGAGCTAACTATATTTGTTTTTGAGA CAGCGTCTCAATTTTTTTTTTTTTTTTTTGTATTTTTTGTAGAGCTGGGGTTTCGTCATG TTACCCAGGCTGGTCTTGAACTCCTGGGCTCAAGCAATCTGCCCACCTTGGCCTGCCAGA GTGGTAGAATTACAGGCATGAGTCACTACACCTGGCCGGCAGAGCTAACTTTAGTTAGAA CAAGGTCATAGGAGAGAGACGTTCAAAGCCTTAACTTGGGGCCAGGTGCAGTGGCTCACA CCTGTAATCCTAGCACTCTGGGAGGCCAAGGCGGGTGGATTGCCCGAGCTCAGGAGTTTG AGACTAACCTGGCCAAGACGGTGAAACCCCATCTCTACTGAAAATACAAAAAATTAGCCA GGCGCGATGGCGCAAACCTGTAGTCCCAGCTACTCAGGAGTCTGTGATGGGAGAATCACC TGAGCCTGGGGAGATCAAGGATGCATGAACTGTGATTGCACCACTGCACTCCAGCCTGGA Mutant Genomic Region: ACCCAGGCTCCTTGGAAACCCAAGCTTATGATCACTTTCTCACAATTTATTCTGGGACCC CTTTTCTCAGCTCTCTTAGCTCCTGATAGGGGTTATCCATGAAAAGTCCAACTCTTGCAG GCTGAGTTGTCTCTGTGTCTGTCCTCATGAGTATATGTCTTGGCCTCTCTTCTCAATATT CTTGTGAAGGCACAGGAAATATAGATAAGAGGTATGTGGGTTTTGAAGGTTAGTATGTTG 23100

6 23101 TAAGGAAGGGCACTAAAACCCTTACTCTGACATCTCCCAAAATGAAATACAGAAGTAAAG ATGGATAGTGGCTTCCTAATATCCCCTTTTCATCAGTGTTAAAAATCGTCAAGCCTACAC TACATCCATTTTCCCTGTGTACCCAAATGTTATGCTCTGCTACATTGAGAACCTTCCAAA TAGAGACATCTCTTTTTCCACTCCCTGAGTCTTTACTCTGCCTCTCTACATCTTCCTAGG TCTGGAGACTTTTAGCCAGCTTGTTTGGAAATCTGCTGAGGGCACAGTAAGTGTGGACCC TCAAAAAGGGCTCCTTTTTCATCTCTGGGGTTGGATCCCAATATTGAGAATCCTAGAAAA ATCTTGTTTTGCCTTAGGATCCTGGTGGCTTGAGATAGCCCCAGTAGAAATGGAAGAGGA GATGTGAGTGGAAAACTGGTTTGGTAGATTTGGTCTGTTTGGAATCACTGTAATTTGGTC CCCCTGAGTCATCATTTAGTAATGACCTTGAGGCCACACTGCTTTGAAGAAAATAAACTA TGTTAACAGGAAAATCCAGAATTTGTAGGCTGAGTGGTGTTTGGGACAGTTGTATTAGGC TGGCGTTGGACAATTGCTCTCTGGGAAGGTGGCTGCTTATGGTCATTTATAGAGGTGGGG AGCATTTAGGGAGAGAGCGACCCTGAGAACAGTCACAGATTGGCTTTTTAAGAATCCTGG GAGAGTTGTCTTCATCTCCCTGTGCCCCCATAGTAAGCTTCCTTTGAAACTGACATGTTC AATGTTTGTTCTGCACAGTTCTTTATCAACAAGACTGAGATTGAGGACTTTCCCCGCTTT CCTCACCaGGGCTTGCTGTTGGATACATCTCGCCATTACCTGCCACTCTCTAGCATCCTG GACACTCTGGTAACCAGGCCTTAAGGCCTTCTTCACACTTAAGAGTTCTAGGGTGATGGA GCAACGGACAGACCAAGTTCCAAATTCTTAAAGAGTTAGAGAGGGAATGTATGGACTGGG TGTGGTGGCTCATGCCTGTAATCCCAACACTTTGGGAGGCCGAGGTGGGCGGATCACCTG AAGTCAGAAGTTCAAGGCCAGCCTGGCCAACATGGTGAAACTCTGTCTCTACTAAAAATA CAAAAATTAGCTGGGCATGGTGGTGCATGCTTGTAATCCCAGCTACCTGGGAGGCTGAGG CAGGAGAATCGCATGAACCCAGGAGGCAGAGGTTGCAGTGGGTGGAGATCACGCCACTGC ACTCCAGCCTGGGTGAAAGAGTGAGACGCTGTCTCAAAAAAAAAAAAAAAAATTGTATGT AATTCTATGAGCTCCTGGGAAAAATGTAGAAGATGAGCTGCTCCAAGACTCAAAAAATAA CAGAGTGACTTAAATCTACCTTACAGGCTACTGTAGATCAATGTTCAGGCTGTTTCCAGG GATACAAATGTTTAGGGGAATTGGCTTCATTGGCAGAGCTAACTATATTTGTTTTTGAGA CAGCGTCTCAATTTTTTTTTTTTTTTTTTGTATTTTTTGTAGAGCTGGGGTTTCGTCATG TTACCCAGGCTGGTCTTGAACTCCTGGGCTCAAGCAATCTGCCCACCTTGGCCTGCCAGA GTGGTAGAATTACAGGCATGAGTCACTACACCTGGCCGGCAGAGCTAACTTTAGTTAGAA CAAGGTCATAGGAGAGAGACGTTCAAAGCCTTAACTTGGGGCCAGGTGCAGTGGCTCACA CCTGTAATCCTAGCACTCTGGGAGGCCAAGGCGGGTGGATTGCCCGAGCTCAGGAGTTTG AGACTAACCTGGCCAAGACGGTGAAACCCCATCTCTACTGAAAATACAAAAAATTAGCCA GGCGCGATGGCGCAAACCTGTAGTCCCAGCTACTCAGGAGTCTGTGATGGGAGAATCACC TGAGCCTGGGGAGATCAAGGATGCATGAACTGTGATTGCACCACTGCACTCCAGCCTGGA 25080

7 Appendix B Primer design details from PrimerQuest

8 Appendix C Cutting patterns of HpaII for wild type and mutant HEXA WILD TYPE: MUTANT: