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WO1993016197A1 - Materiaux et sequences de nucleotides et procedes pour le diagnostic de la myotonie dystrophique - Google Patents

Materiaux et sequences de nucleotides et procedes pour le diagnostic de la myotonie dystrophique Download PDF

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Publication number
WO1993016197A1
WO1993016197A1 PCT/GB1993/000253 GB9300253W WO9316197A1 WO 1993016197 A1 WO1993016197 A1 WO 1993016197A1 GB 9300253 W GB9300253 W GB 9300253W WO 9316197 A1 WO9316197 A1 WO 9316197A1
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WIPO (PCT)
Prior art keywords
sequence
dna
repeats
probe
risk diagnosis
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PCT/GB1993/000253
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English (en)
Inventor
Duncan James Shaw
Helen Grace Harley
Keith Jack Johnson
John David Brook
David E. Housman
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University Of Wales College Of Medicine
Massachusetts Institute Of Technology
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Publication date
Application filed by University Of Wales College Of Medicine, Massachusetts Institute Of Technology filed Critical University Of Wales College Of Medicine
Priority to JP51388793A priority Critical patent/JP4205158B2/ja
Priority to EP93904174A priority patent/EP0625210A1/fr
Publication of WO1993016197A1 publication Critical patent/WO1993016197A1/fr

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    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K14/00Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • C07K14/4701Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
    • C07K14/4707Muscular dystrophy
    • C07K14/471Myotonic dystrophy
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00Oligonucleotides characterized by their use
    • C12Q2600/112Disease subtyping, staging or classification
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00Oligonucleotides characterized by their use
    • C12Q2600/156Polymorphic or mutational markers

Definitions

  • NUCLEOTIDE SEQUENCES AND MATERIALS AND METHODS
  • DM Myotonic dystrophy
  • the onset and degree of severity of the disease is highly variable, ranging from very mildly affected adult cases whose only symptoms are a type of lens cataract occuring in later life, to a life-threatening neonatal form of the disease found in some affected infants who have inherited the genetic defect from their mother.
  • the type of symptoms is also very variable and can involve a wide range of tissues including muscle, brain, heart, and endocrine organs.
  • DM is characterised by myotonia and progressive muscle weakness and wasting. To date this disease has been untreatable and its biochemical basis is not understood.
  • the gene responsible for DM has been mapped by family studies to a small region on the long arm of chromosome 19 (Harley HG et al, American Journal of Human Genetics 49, pp68-75 (1991)). Further studies have shown that the gene lies between the markers D19S63 and D19S95.
  • SEQ ID NO:l DNA sequence that identifies the precise site in the DNA of DM patients that causes their disease. The sequence was obtained from a collection of DNA fragments that represent the genes expressed in human brain. It is just over 2700 bases in length and is unique. Its biochemical function is the subject of further investigation.
  • the sequence includes, at a particular point along its length, a run of repeats of a 3-base unit (CTG) .
  • CCG 3-base unit
  • the number of times this triplet is repeated is variable between individuals. In normal unaffec ⁇ ted people, the number is between 5 and about 40. In DM patients the number is between 50 and at least 2000. Generally speaking, the greater the number, the more severe the disease. We have not yet found any individual with between 40 and 50 repeats and this suggests that the population divides into two distinct groups; those having less than 50 repeats being unaffected and those having 50 or more repeats being affected.
  • the number of repeats of the 3- base sequence appears to be the basic underlying genetic difference between DM patients and normal individuals.
  • this invention provides a nucleotide sequence, comprising:- a DNA sequence derived from human chromosome 19q including a variable number of repeats of the three-base unit CTG or its complement, wherein said number is greater than about 50 in individuals affected by DM; a DNA sequence which hybridises under standard condi ⁇ tions to said first mentioned sequence over a region containing said variable number of repeats; an RNA sequence transcribed from or corresponding to either of said aforementioned DNA sequences, or a fragment containing one of said sequences.
  • the nucleotide sequence is substantially as given in SEQ ID NO:l
  • this invention provides a nucleic acid hybridisation probe useful for determining the number of repeats of said three-base unit in a sample nucleotide sequence as defined above, said probe including a nucleotide sequence capable of hybridising to said sample sequence, or its complementary sequence or to a fragment of either of these, said probe having associated therewith a detectable label.
  • this invention provides a method of DM risk diagnosis which comprises directly or indirectly observing monitoring or determining the number of repeats of the base sequence CTG or its complement in the DNA from chromosome 19q, or the number of repeats of the equivalent three-base unit in RNA transcribed from or corresponding to said DNA sequence, or observing monitoring or determining the length of the region containing said repeats.
  • Said method of DM risk diagnosis preferably involves hybridising a sample of genomic DNA or RNA from an individ ⁇ ual with one or more probes as defined above, said sample preferably initially being exposed to a restriction enzyme before hybridisation with said probe or probes.
  • Suitable restriction enzymes are EcoRI, EcoRV, P ⁇ tl and PvuII, although many other enzymes which, with the appropri ⁇ ate probe, provide fragments which differ in length between DM patients and unaffected adults, may be used.
  • An important feature of this aspect of the invention is that the number of repeats or the length of the repeat region may be used to predict the severity of DM of the individual.
  • the invention also extends to primers for use in a nucleic acid amplification technique (for example the PCR or polymerase chain reaction) for amplifying at least the variable repeat region of a nucleotide sequence as defined above.
  • the primers preferably comprise first and second oligonucleotides closely flanking said repeat region (e.g. each spaced between about 5 and 75 bases therefrom) .
  • Said first and second oligonucleotides preferably each comprise respective sequences of from 8 to 32 bases and in one embodiment are substantially as identified by primer references 101 and 102 in Figure 1 (SEQ ID NO: 2) , or complements thereof.
  • this invention provides a diagnos ⁇ tic kit for carrying out a method of DM risk diagnosis which involves hybridising a sample of genomic DNA or RNA from an individual with one or more hybridisation probes, wherein the kit includes a hybridisation probe and one or more other components for carrying out the method, characterised in that said hybridisation probe is as defined above, and optionally including PCR primers.
  • the techniques disclosed herein have the capability to distinguish between normal unaffected people and carriers of the DM gene, even when these cannot be diagnosed by clinical examination alone. This can be done by standard methods of DNA or RNA analysis, including Southern or Northern blotting and hybridisation, and/or PCR (polymerase chain reaction) . There is always a risk to gene carriers that their offspring may be severely affected, and therefore there is a demand from DM families for carrier detection by DNA or RNA testing. When a pregnancy at risk for DM is already under way, the family will often request prenatal diagnosis of the foetus by means of chorionic villus sampling or amniocentesis and DNA analysis, following which a decision may be made regarding termination or continuation.
  • the DNA diagnosis is done indirectly using DNA sequences that are not themselves part of the DM gene; this is often technically unsatisfactory and requires the cooperation of other family members than those directly involved. Furthermore it gives no indication of the severity of the symptoms, only that the disease gene is or is not present.
  • the techniques disclosed herein will overcome these limitations since they allow diagnosis of the presence of the disease gene in a sample of DNA or RNA from just the person in question, without the need for a full family analysis. This increases the speed of the procedure (an important consideration when a pregnancy is ongoing) and reduces the risk of misdiagnosis considerably. More significantly, these techniques will enable a prediction to be made concerning the severity of the disease in the person or pregnancy at risk.
  • DM is a highly variable condition, ranging from a trivial adult complaint to a potentially lethal congenital illness, it is important for the family and their counsellors to know how severe a form is involved, so that informed choices may be made. Whilst the invention has been described above, it extends to any inventive combination of the features set out above or in the following description.
  • the invention may be performed in various ways and certain experimental data will now be disclosed to illus- trate examples in accordance with the invention.
  • Figure 1 is a restriction map of the 10 kb EcoRI fragment which undergoes expansion in DM patients
  • Figures 2(a) and (b) are autoradiographs showing the variation of fragment lengths for a number of individuals
  • Figure 2(c) is a family tree for the individuals of Figure 2(b) .
  • the DM gene has been mapped to a 200 kilobase (kb) interval at 19q, presently believed to be at 19ql3.3.
  • Construction of a radiation reduced hybrid 2F5, containing 2 megabases of human chromosome 19 including the closest flanking markers facilitated cloning of this entire region in phage ⁇ .
  • Clones were further localised using radiation reduced hybrids and pulsed-field gel electrophoresis.
  • Clone ⁇ M9C showed strong inter-species conservation, and a sub- clone (pBB0.7) identified an RFLP with EcoRV and EcoRI.
  • a series of phage clones derived from libraries of radiation-reduced hybrid 2F5 were used to span the interval between D19S63 and D19S95, the loci in linkage disequilib ⁇ rium with DM. Intensive screening of this interval led to the identification of clones designated as ⁇ MlOM, ⁇ M8L and ⁇ SM2 (which contain sub-clone pBB0.7). These clones span the lOkb EcoRI fragment that is increased in size in DM patients. Clone ⁇ MlOM was one such clone, and was found to have the ability to distinguish between DM patients and normal individuals, as follows. A fragment of the DNA from clone ⁇ MlOM was radioactively labelled to make a "DNA probe".
  • a series of DNA samples from DM patients and normal individuals were digested into specific small fragments using a bacterial enzyme called EcoRI.
  • the fragments were separated according to their length by electrophoresis in an agarose gel, and transferred to a nylon membrane to which they adhere (Southern blotting) .
  • the radioactive probe from ⁇ MlOM was then incubated with the membrane, which allows it to find its corresponding sequence in each of the samples of human DNA (DNA hybridisation) .
  • the positions of these fragments on the membrane are then visualised by exposure to X-ray film (autoradiography) . This experiment revealed that the fragments corresponding to M10M are always larger (by varying amounts) in DM patient DNAs than in DNAs from normal individuals.
  • ⁇ MlOM contained a copy of the DNA sequence responsible for myotonic dystrophy.
  • the original ⁇ MlOM clone was derived from DNA of complete human chromosomes. Because only part of this DNA is "expressed" (i.e. functions as genes by making proteins) , a second cloned sequence was obtained using M10M as a probe. This second clone came from a collection of cDNAs represent- ing most of the genes expressed in human brain. The clone, which we have designated C28, contains 2726 bases of human DNA. The entire DNA sequence was determined and is shown in (SEQ ID NO: 1) .
  • the position of the 3-base repeat that undergoes expansion in DM patients is indicated and lies at a position approximately 500bp from the poly(A) tract of a mRNA expressed in many of the tissues affected in DM.
  • the RNA in which the repeat resides encodes a polypeptide with strong a ino acid homology to members of the protein kinase gene family .
  • the first method is based on Southern blotting and hybridisation, and is most effective in detecting expanded sequences towards the upper end of the size range.
  • Samples (5-10 ⁇ g) of DNA from people to be tested, together with normal controls, are digested by incubation with the restriction enzyme EcoRI or PstI for 2-4 hours at 37°C, The samples are then separated by electrophoresis in 0.8% agarose gels for 16-18 hours at 45 volts, and the DNA transferred to a nylon membrane by overnight capillary action (Southern blotting) . The membrane is removed from the agarose gel, dried, and the DNA fixed to it by ultraviolet radiation.
  • a probe consisting of a part of the C28 sequence (SEQ ID NO: 1) is made by incorporation of a radioactive tracer into the DNA sequence. This is then incubated overnight at 65°C with the membrane in an aqueous buffer solution, allowing the probe to hybridise to the DNA samples on the membrane. The excess unbound probe is then washed off with dilute salt solution at 65°C, and the membrane exposed to X-ray film in the dark at -70°C for 1 to 4 days. The film is developed and aligned with the original mem ⁇ brane, allowing identification of the various samples and the size of the DNA fragments containing the 3-base repeat sequence.
  • the second procedure is based on PCR (polymerase chain reaction) and is best suited to the detection of DM muta ⁇ tions that are only slightly larger than normal.
  • a pair of small, unique DNA sequences called "primers", which are derived from the C28 sequence (SEQ ID NO: 1) and flank closely the site of the 3-base repeat, are used.
  • Small samples (0.1-0.5 ⁇ g) of DNA from individuals to be tested, along with normal controls, are mixed with 20 pmoles of each primer, 1 unit of a bacterial enzyme (Taq polymerase) , individual bases for DNA synthesis, and buffer salts, in a volume of 20 ⁇ L. The mixtures are then subjected to a cyclical, 3-phase incubation protocol.
  • the mixture is heated to 94°C for 90 seconds to separate the two strands of the DNA sample.
  • the second phase is for 60 seconds at 62°C and allows the primers to bind to their complementary sites on the sample DNA.
  • the Taq polymerase enzyme synthesises a new complementary DNA strand on each of the sample strands, starting from the primer.
  • the whole 3-phase procedure is repeated 30 times, using an automatic programmable heating/cooling device. Because each cycle causes a doubling of the number of molecules, the net result is to specifically amplify the sequence delimited by the two primers. In our procedure this represents the 3-base repeat region which is expanded in DM patients.
  • the products of the PCR reactions are separated by agarose gel electrophore- sis (3% agarose gel, 2 hours at 80 volts) and visualised by staining the DNA with a fluorescent dye.
  • the sizes of the amplified fragments are estimated by comparison with known standards, separated on the same electrophoresis gel.
  • SEQ ID NO: 1 is a cDNA (RNA derived) sequence, and there are flanking and interven ⁇ ing sequences mixed in with this in genomic DNA. Suitable PCR primers which flank the CTG repeat region in genomic DNA may also be used which may differ from those described above.
  • lanes 2,4 and 8 are normal, unrelated individuals; lanes 1,5 and 7 are unrelated affected individ- uals; lanes 3, 6 and 9 are affected offspring of individuals 1 and 2, 4 and 5, 7 and 8 respectively.
  • Lane 1 shows one of the smallest size changes detectable, and lane 6 one of the largest. Two distinct bands can clearly be seen on the autoradiograph. Lanes 5 and 7 illustrate the smearing of bands seen in some individuals.
  • the restriction map shown in Figure 1 was derived from overlapping genomic phage clones from unaffected individ ⁇ uals. Restriction sites for BamHI(B), EcoRI(E), Hindi(C), Hind ⁇ II(H), Pst ⁇ (P), and SacI(S) are indicated. The subcloned 1.4kb BamHI fragment (pM10M-6) is shown enlarged with the PstI and Hindi sites, which flank the expanded region. The positions of PCR primers 96, 98, 100, 101, 102 and 103 and the sequence between primers 101 and 102 is shown SEQUENCE LISTING
  • CTTCCTGGGG CTGGAGCCCC TGCTCGACCT TCTCCTGGGC GTCCACCAGG AGCTGGGCGC 240
  • MOLECULE TYPE DNA (genomic)

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Abstract

On a détecté chez des patients atteints de myotonie dystrophique (MD) une séquence d'ADN ayant une longueur variable. La région de longueur variable renferme un certain nombre de répétitions d'une unité à trois bases (CTG). On a découvert que le nombre de répétitions chez des patients atteints de MD est supérieur à 50 alors que ce nombre chez des sujets sains est inférieur à 40. On peut diagnostiquer le risque de développer la myotonie dystrophique en détectant la longueur de la région variable et en déterminant par conséquent le nombre de répétitions.
PCT/GB1993/000253 1992-02-06 1993-02-05 Materiaux et sequences de nucleotides et procedes pour le diagnostic de la myotonie dystrophique WO1993016197A1 (fr)

Priority Applications (2)

Application Number Priority Date Filing Date Title
JP51388793A JP4205158B2 (ja) 1992-02-06 1993-02-05 筋緊張性ジストロフィー診断用ヌクレオチド配列,材料および方法
EP93904174A EP0625210A1 (fr) 1992-02-06 1993-02-05 Materiaux et sequences de nucleotides et procedes pour le diagnostic de la myotonie dystrophique

Applications Claiming Priority (2)

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GB929202485A GB9202485D0 (en) 1992-02-06 1992-02-06 Dna sequences and materials and methods for the diagnosis of myotonic dystrophy
GB9202485.0 1992-02-06

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Cited By (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1994028175A1 (fr) * 1993-05-28 1994-12-08 Massachusetts Institute Of Technology Detection directe d'unites recurrentes nucleotidiques expansees dans le genome humain
FR2718753A1 (fr) * 1994-04-15 1995-10-20 Pasteur Institut Procédé de comptage de mono-, di- et trinucléotides répétés dans un génome eucaryote et trousse permettant la mise en Óoeuvre de ce procédé.
WO1997030178A2 (fr) * 1996-02-15 1997-08-21 Fondation Jean Dausset-Ceph Diagnostic des maladies a repetition trinucleotidique et genes impliques dans ces maladies
US5874215A (en) * 1995-01-16 1999-02-23 Keygene N.V. Amplification of simple sequence repeats
EP0956365A1 (fr) * 1996-08-28 1999-11-17 The Johns Hopkins University School Of Medicine Procede de detection de dereglements proliferatifs cellulaires
US6218119B1 (en) 1996-01-16 2001-04-17 Keygene, N. V. Amplification of simple sequence repeats

Non-Patent Citations (5)

* Cited by examiner, † Cited by third party
Title
AMERICAN JOURNAL OF HUMAN GENETICS vol. 49, no. 1, July 1991, US pages 68 - 75 HARLEY, H G. ET AL. 'detection of linkage disequilibrium between the myotonic dystrophy locus and a new polymorphic DNA marker.' cited in the application *
GENOMICS vol. 9, no. 2, February 1991, SAN DIEGO US pages 257 - 263 SMEETS H. ET AL. 'identification of variable simple motifs in 19q13.2-qter: markers for the myotonic dystrophy locus' *
LANCET vol. 338, no. 8762, August 1991, LONDON GB pages 289 - 291 SUTHERLAND G R ET AL 'heriditary unstable DNA: a new explanation for some old genetic questions?' *
NATURE vol. 335, 6 February 1992, LONDON GB pages 545 - 546 HARLEY, H G ET AL. 'Expansion of an unstable DNA region and phenotypic variation in myotonic dystrophy' *
NATURE vol. 355, 6 February 1992, LONDON GB pages 547 - 548 BUXTON J. ET AL 'detection of an unstable fragment of DNA specific to individuals with myotonic dystrophy' *

Cited By (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1994028175A1 (fr) * 1993-05-28 1994-12-08 Massachusetts Institute Of Technology Detection directe d'unites recurrentes nucleotidiques expansees dans le genome humain
US5695933A (en) * 1993-05-28 1997-12-09 Massachusetts Institute Of Technology Direct detection of expanded nucleotide repeats in the human genome
FR2718753A1 (fr) * 1994-04-15 1995-10-20 Pasteur Institut Procédé de comptage de mono-, di- et trinucléotides répétés dans un génome eucaryote et trousse permettant la mise en Óoeuvre de ce procédé.
US5874215A (en) * 1995-01-16 1999-02-23 Keygene N.V. Amplification of simple sequence repeats
US6218119B1 (en) 1996-01-16 2001-04-17 Keygene, N. V. Amplification of simple sequence repeats
WO1997030178A2 (fr) * 1996-02-15 1997-08-21 Fondation Jean Dausset-Ceph Diagnostic des maladies a repetition trinucleotidique et genes impliques dans ces maladies
FR2745007A1 (fr) * 1996-02-15 1997-08-22 Fondation Jean Dausset Ceph Diagnostic des maladies a repetition trinucleotidique et genes impliques dans ces maladies
WO1997030178A3 (fr) * 1996-02-15 1997-10-16 Fondation Jean Dausset Ceph Diagnostic des maladies a repetition trinucleotidique et genes impliques dans ces maladies
EP0956365A1 (fr) * 1996-08-28 1999-11-17 The Johns Hopkins University School Of Medicine Procede de detection de dereglements proliferatifs cellulaires
EP0956365A4 (fr) * 1996-08-28 2004-08-25 Univ Johns Hopkins Med Procede de detection de dereglements proliferatifs cellulaires

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JPH07506246A (ja) 1995-07-13
GB9202485D0 (en) 1992-03-25
AU3505993A (en) 1993-09-03
JP4205158B2 (ja) 2009-01-07
EP0625210A1 (fr) 1994-11-23

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