reverse dot blot for human mutation detection dr pupak derakhshandeh, phd ass prof of medical...
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Reverse Dot Blot for Human Mutation
Detection
Dr Pupak Derakhshandeh, PhD
Ass Prof of Medical Science of Tehran University
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Introduction
Reverse dot blot (RDB) or reverse allele specific
oligonucleotide (Reverse ASO) hybridization important method for genotyping
common human mutations
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Commonly used in:
a high mutation spectrum high frequency disorders such as:
cystic fibrosis hemoglobin C (HbC) hemoglobin E (HbE) hemoglobin S (HbS) ß-thalassemias
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Location of mutations in the -globin gene
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Oligonucleotides used for reverse dot blot (RDB)
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RDB
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Reverse dot (RDB) blot hybridization for detection of 10 common β-thalassaemia mutations
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-thalassemia Patients
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Molecular genetic analyses of -thalassemia
Hereditary hemoglobinopathies heterogeneous autosomal recessive
disorders -thalassemia: the most prevalent
single-gene disorder > 200 mutations in the -globin gene
located at 11p15.5 characterized by hypochromic micro
cyclic hemolytic anemia
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Blood parameters of the patients and their family members
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EVALUATION OF BONE INVOLVEMENT IN BETA THALASSEMIA MAJOR
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Beta thalassemia minor A few oval, elliptocytes and basophilic stippling
Image 1C - Beta thalassemia minor (400 X Magnification)
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Thalassemia major, untreatedlaboratory values are hbg <6.7 hgb,20 hct, 62 MCV
Thalassemia major, untreated (250 X Magnification)
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Pedigree of the b-Thalassemia family
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Therapy
no viable forms of treatment a chronic course requiring repeated
blood transfusions that usually leads to iron overload no other effective therapy is presently
available the best course: prevention through
prenatal diagnosis
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a woman having amniocentesis
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Untreated Patient
affected individuals manifest failure to thrive
Shortened life expectancy
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Screening for causal mutations
genomic DNA from patient blood samples
reverse dot blot (RDB) amplification refractory mutation
system-polymerase chain reaction (ARMSPCR)
DNA sequencing
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PCR from genomic DNA
720 bp
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Strips
N M
1
2
3
4
5
6
7
8
9
1 2 3 4 5 6 7 8 9 10
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The Blots
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RDB procedure
exons (or other regions of interest) amplified by the polymerase chain
reaction (PCR) using labeled oligonucleotide primers 5' biotin label on PCR primers
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Amplicons Amplification products denatured hybridized
with mutation specific DNA probes covalently bound to solid membran
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Incubation nucleic acids: incubated with an
enzyme conjugated to streptavidin. enzyme-conjugated, streptavidin-
biotin-nucleic acid complex is then washed
incubated with a chromogenic or luminogenic substrate, which allows
visualization of hybridized spots
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Materials and Methods
Total genomic DNA extracted from peripheral blood
leukocytes Amniotic fluid cells (AF) chorionic villi (CVS)
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Oligonucleotide probes
A C6-amino-link phosphoramidite amino moiety on the 5' end of the
product
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In vitro amplification of DNA by PCR
Reaction mixture: 5 µl template DNA 5 µl forward primer (B-F27, 5 pmol/µl) 5 µl reverse primer (R518, 5 pmol/µl) 2.5 µl dNTP’s (2.5 mM of each dNTP) 5 µl 10x PCR buffer 1.5 µl 50 mM MgCl 0.25 µl Taq polymerase 23.75 µl water
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PCR program:
Our forward primer is biotinylated 94°C for 5 min 1 cycle 94°C for 1 min 50-55°C for 1 min 72°C for 1 min 30 cycles 72°C for 5 min 1 cycle 4°C hold
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Remarks
Repeated freeze thawing of the biotin labeled oligo or PCR products may damage the biotin label
Preferably the membrane should be stripped as soon as possible, but this can also be done a few days after the hybridization.
For chemiluminescent detection, the Solution A+B should be warmed to roomtemperature for at least 30 min
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MATERIALS AND METHODS
PCR from 150 ng of genomic DNA
Preparation of membrane strips
Allele-specific hybridization and color development
Preparation of membrane strips
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Preparation of membrane strips
Biodyne C (Pall Biomedical, U.S.A.) membrane Membrane : activated briefly in 0·1 N HCl Rinsed with water and soaked in 16% 1-ethyl-3-
[3-dimethylaminopropyl] carbodiimide (EDC) for 15 min it was rinsed in water and air dried overnight Oligonucleotide probes were diluted with 0·5 M
NaHCO3/Na2CO3 buffer, pH 8·4 (0.5 pmol/ml) for application onto the membrane.
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Allele-specific hybridization and colour development
50–60 l of biotinylated-PCR product Hybridized with the filter strips containing
the normal and mutant probes in 0·8 ml hybridization buffer (2 ´ SSC,
0·1% sodium dodecyl sulphate) (1 ´ SSC¼0·3 M NaCl, 0·03 M sodium citrate)
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Allele-specific hybridization and color development
sealed in a cooking pouch The pouch of reactants was denatured
in boiling water for 5 min. Hybridized at 428C ´ 1 h Membrane strips were then washed in
0·4 ´ SSC,0·1% SDS at 428C for 10 min
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Allele-specific hybridization and color development
The strips were then reacted at room temperature for15 min with 20 ml streptavidin horse-radish peroxidase(Gibco BRL, as conjugate for the biotin-labelled hybridization signal) in 20 ml 2 ´ SSC, 0·1% SDS
washes (5 min ´ 2) in 2 ´ SSC, 0·1% SDS and (2 min ´ 2) in 0·1 M sodium citrate pH 5·0
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Allele-specific hybridization and color development
Color development was carried out: with 0·1% 3,30,5,50-tetramethylbenzidine
dihydrochloride in 0·1 M sodium citrate and 80 ml of 3%
hydrogen peroxide for 30 min at room temperature
The reaction was stopped :
rinsing once with 0·1 M sodium citrate and several times with water
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Preparation of membrane strips
Approximately 4 ml was applied to each spot allowed to dry for 15 min before fixation in
0·5 N NaOH for 1 min The membrane was then rinsed thoroughly
with water and air dried overnight Membrane strips: stored at room
temperature in adesiccator for up to 6 months.
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Automated DNA sequencing
Cd 2C>G
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ARMS-PCR
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Haplotype analysis of the β-globin gene cluster from the patient's family.
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PCR-RFLP1 2 3 M 4 5 6 7
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Direct genomic sequencing of the β-globin gene (ATG→AGG substitution of initiation codon)(a) The sequence of sense stranded sequence using Ex1 forward (b) The sequence of antisense stranded sequence using 3' reverse
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Comparison of different factors determining the efficiency of ARMS and reverse hybridization in beta thalassemia diagnosis
ARMS Reverse hybridization
Turnover time several days 6-8 hours
Equipment Expensive (large PCR machine, gel electrophoresis, photodocumentation system)
Less expensive (small PCR machine, agarose gel, small shaking water bath)
Number of PCR reactions
per sample 8-88 1
Documentation Requires documentation process after experiment
Self-documented
Technician time (number of patients: time in days)
1:1 10:1
Starting material Depending on the number of PCR reactions
0.5 μg genomic DNA for just one PCR reaction
Toxic materials Ethidium bromide (carcinogen)
None
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Reference Iranian J Publ Health, Vol. 32, No. 1, pp.11-14 (2003)
Detection of Rare and Unknown Mutations in ß- tathalassemia Traits in Iran
M Habibi Roudknar, H Najmabadi, P Derakhshandeh-Peykar, DD Farhud
Ian J Pub Heal. Spectrum of b-thalassemia Mutations in Isfahan Province of Iran (2007, in press)P Derakhshandeh-Peykar, H Hourfar, M Heidari, M Kheirollahi, M Miryounesi, and DD Farhud Haemoglobin (2007) Distribution of ß-thalassemia mutations in
Northern provinces of Iran. Derakhshandeh-Peykar P, Akhavan-Niaki H, Tamaddoni A,
Ghawidel-Parsa S, Holakouie Naieni K, Rahmani M, Babrzadeh F, Dilmaghani-Zadeh M, Farhud DD (2007).
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References
J Clin Microbiol. 2001 March; 39(3): 871–878. Reverse Dot Blot Assay (Insertion Site Typing) for Precise Detection of Sites of IS6110 Insertion in the Mycobacterium tuberculosis GenomeLauren M. Steinlein and Jack T. Crawford*
Lee GR, Forester J, Lukens J, Paraskovas F, Greer JP, Rodgers GM. The Wintrobe’s Clinic Hematology. Vol 1. 10th ed. Baltimore: Lippincott, Williams and Wilkins; 1999.
Huisman THJ, Carver MFH. The beta- and delta-thalassemia repository. Hemoglobin. 1998; 22: 169-95.
Lorey FW, Arnopp J, Cunningham GC. Distribution of hemoglobinopathy variants by ethnicity in multiethnic
states. Genet Epidemiol. 1996; 13: 501-25. Vetter B, Schwarz C, Kohne E, Kulozik AE. Beta- thalassemia in
the immigrant and non-immigrant German populations. Br J Haematol. 1997; 97: 266-72.
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Habibzadeh F, Yadollahie M, Merat A, Haghshenas M. Thalassemia in Iran: an overview. Arch Irn Med. 1998; 1: 27-34.
Mahboudi F, Zeinali S, Merat A, et al. The molecular basis of ß-thalassemia mutations in Fars province, Iran. Irn J Med Sci. 1996; 21: 104.
Najmabadi H, Karimi-Nejad R, Sahebjan S, et al. The ß-thalassemia mutation spectrum in Iranian population. Hemoglobin. 2000. [Accepted for publication].
Newton CR, Graham A, Hepatinstall LE, et al. Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acid Res. 1989; 17: 2503-16.
Old JM, Varawalla NY, Weatherall DJ. Rapid detection and prenatal diagnosis of beta-thalassemia: studies in Indian and Cypriot populations in UK. Lancet. 1990; 336: 834-7.
Vienna Laboratories. ß-Globin Strip Assay. 1998.
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Kaufhold A, Podbielski A, Baumgarten G, Blokpoel M, Top J, Schouls L. Rapid typing of group-a
streptococci by the use of dna amplification and nonradioactive allele-specific oligonucleotide probes. FEMS
Microbiology Letters 119: 19-25 (1994) [reverse line blot hybridization]
Rapid Hla-Dpb Typing Using Enzymatically Amplified Dna And Nonradioactive Sequence-Specific
Oligonucleotide Probes Bugawan Tl, Begovich Ab, Erlich Ha Immunogenetics 32 (4): 231-241 Oct 1990 Dattagupta N, Rae PMM, Huguenel ED, Carlson E, Lyga A,
Shapiro JA, Albarella JP. Rapid identification of microorganisms by nucleic-acid hybridization after labeling the
test sample. Analytical Biochemistry 177: 85- 89 1989
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Saiki RK, Walsh PS, Levenson CH, Erlich HA. Genetic-analysis of amplified dna with immobilized sequence-
specific oligonucleotide probes. Proc Nat Acad Sci USA 86: 6230-6234 (1989).
Kamerbeek J, Schouls L, Kolk A, vanAgterveld M, vanSoolingen D, Kuijper S, Bunschoten A, Molhuizen H,
Shaw R, Goyal M, vanEmbden J. Simultaneous detection and strain differentiation of Mycobacterium
tuberculosis for diagnosis and epidemiology. JOURNAL OF CLINICAL MICROBIOLOGY 35 (4): 907-914
APR 1997 Aranaz A, Liebana E, Mateos A, Dominguez L, Vidal D, Domingo
M, Gonzolez O, Rodriguez Ferri EF,
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Bunschoten AE, Van Embden JDA, Cousins D. Spacer oligonucleotide typing of Mycobacterium bovis
strains from cattle and other animals: A tool for studying epidemiology of tuberculosis. JOURNAL OF
CLINICAL MICROBIOLOGY 34 (11): 2734-2740 NOV 1996 (According to our literature search Dattagupta et al. and Saiki et
al. were the first to apply reverse dot blot, Kaufhold et al. introduced reversed line blotting).