Alterations in the long QT syndrome genes KVLQT1 and SCN5A and methods for detecting same

Abstract

Long QT Syndrome (LQTS) is a cardiovascular disorder characterized by prolongation of the QT interval on electrocardiogram and presence of syncope, seizures and sudden death. Five genes have been implicated in Romano-Ward syndrome, the autosomal dominant form of LQTS. These genes are KVLQT1, HERG, SCN5A, KCNE1 and KCNE2. Mutations in KVLQT1 and KCNE1 also cause the Jervell and Lange-Nielsen syndrome, a form of LQTS associated with deafness, a phenotypic abnormality inherited in an autosomal recessive fashion. Mutational analyses were used to screen 262 unrelated individuals with LQTS for mutations in the five defined genes. A total of 134 mutations were observed of which eighty were novel.

1 . An isolated DNA comprising a sequence of SEQ ID NO:1 as altered by one or more mutations selected from the group consisting of C1172T, C1343G, C 1588T, C1697T, C1747T and G1781A.  
     
     
         2 . An isolated nucleic acid probe which hybridizes to the isolated DNA of  claim 1  under conditions at which it will not hybridize to wild-type KVLQT1 DNA.  
     
     
         3 . A method for detecting a mutation in KVLQT1 said mutation selected from the group consisting of C1172T, C1343G, C1588T, C1697T, C1747T and G1781A which comprises analyzing a sequence of said KVLQT1 DNA or RNA from a human sample or analyzing the sequence of cDNA made from mRNA from said sample for said mutation.  
     
     
         4 . The method of  claim 3  wherein said mutation is detected by a method selected from the group consisting of: 
 a) hybridizing a probe specific for one of said mutations to RNA isolated from said human sample and detecting the presence of a hybridization product, wherein the presence of said product indicates the presence of said mutation in the sample;  
 b) hybridizing a probe specific for one of said mutations to cDNA made from RNA isolated from said sample and detecting the presence of a hybridization product, wherein the presence of said product indicates the presence of said mutation in the sample;  
 c) hybridizing a probe specific for one of said mutations to genomic DNA isolated from said sample and detecting the presence of a hybridization product, wherein the presence of said product indicates the presence of said mutation in the sample;  
 d) amplifying all or part of said KVLQT1 DNA in said sample using a set of primers to produce amplified nucleic acids and sequencing the amplified nucleic acids;  
 e) amplifying part of said KVLQT1 DNA in said sample using a primer specific for one of said mutations and detecting the presence of an amplified product, wherein the presence of said product indicates the presence of said mutation in the sample;  
 f) molecularly cloning all or part of said KVLQT1 DNA in said sample to produce a cloned nucleic acid and sequencing the cloned nucleic acid;  
 g) amplifying said KVLQT1 DNA to produce amplified nucleic acids, hybridizing the amplified nucleic acids to a DNA probe specific for one of said mutations and detecting the presence of a hybridization product, wherein the presence of said product indicates the presence of said mutation;  
 h) forming single-stranded DNA from a KVLQT1 DNA fragment of said gene from said human sample and single-stranded DNA from a corresponding fragment of a wild-type gene, electrophoresing said single-stranded DNAs on a non-denaturing polyacrylamide gel and comparing the mobility of said single-stranded DNAs on said gel to determine if said single-stranded DNA from said sample is shifted relative to wild-type and sequencing said single-stranded DNA having a shift in mobility;  
 i) forming a heteroduplex consisting of a first strand of nucleic acid selected from the group consisting of a genomic DNA fragment isolated from said sample, an RNA fragment isolated from said sample and a cDNA fragment made from mRNA from said sample and a second strand of a nucleic acid consisting of a corresponding human wild-type gene fragment, analyzing for the presence of a mismatch in said heteroduplex, and sequencing said first strand of nucleic acid having a mismatch;  
 j) forming single-stranded DNA from said KVLQT1 DNA of said human sample and from a corresponding fragment of an allele specific for one of said mutations, electrophoresing said single-stranded DNAs on a non-denaturing polyacrylamide gel and comparing the mobility of said single-stranded DNAs on said gel to determine if said single-stranded DNA from said sample is shifted relative to said allele, wherein no shift in electrophoretic mobility of the single-stranded DNA relative to the allele indicates the presence of said mutation in said sample; and  
 k) forming a heteroduplex consisting of a first strand of nucleic acid selected from the group consisting of a genomic DNA fragment of said KVLQT1 DNA isolated from said sample, an RNA fragment isolated from said sample and a cDNA fragment made from mRNA from said sample and a second strand of a nucleic acid consisting of a corresponding gene allele fragment specific for one of said mutations and analyzing for the presence of a mismatch in said heteroduplex, wherein no mismatch indicates the presence of said mutation.  
 
     
     
         5 . A method according to  claim 4  wherein hybridization is performed in situ.  
     
     
         6 . A method of assessing a risk in a human subject for long QT syndrome which comprises screening said subject for a mutation in KVLQT1 selected from T3911 , P448R, Q530X, S566F, R583C and R594Q by comparing the sequence of said KVLQT1 or its expression products isolated from a tissue sample of said subject with a wild-type sequence of said KVLQT1 or its expression products, wherein a mutation selected from T3911, P448R, Q530X, S566F, R583C and R594Q in the sequence of the subject indicates a risk for long QT syndrome.  
     
     
         7 . The method of  claim 6  wherein said expression product is selected from mRNA of KVLQT1 DNA or a polypeptide encoded by said gene.  
     
     
         8 . The method of  claim 6  wherein one or more of the following procedures is carried out: 
 (a) observing shifts in electrophoretic mobility of single-stranded DNA from said sample on non-denaturing polyacrylamide gels;  
 b) hybridizing a probe to genomic DNA isolated from said sample under conditions suitable for hybridization of said probe to said gene;  
 (c) determining hybridization of an allele-specific probe to genomic DNA from said sample;  
 (d) amplifying all or part of said KVLQT1 DNA from said sample to produce an amplified sequence and sequencing the amplified sequence;  
 (e) determining by nucleic acid amplification the presence of a specific mutant allele in said sample;  
 (f) molecularly cloning all or part of said KVLQT1 DNA from said sample to produce a cloned sequence and sequencing the cloned sequence;  
 (g) determining whether there is a mismatch between molecules (1) said KVLQT1 DNA or mRNA isolated from said sample, and (2) a nucleic acid probe complementary to the human wild-type gene DNA, when molecules (1) and (2) are hybridized to each other to form a duplex;  
 (h) amplification of said KVLQT1 DNA sequence in said sample and hybridization of the amplified sequence to nucleic acid probes which comprise wild-type gene sequences;  
 (i) amplification of said KVLQT1 DNA sequence in said tissue and hybridization of the amplified sequence to nucleic acid probes which comprise mutant gene sequence;  
 (j) screening for a deletion mutation;  
 (k) screening for a point mutation;  
 (l) screening for an insertion mutation;  
 (m) determining in situ hybridization of said KVLQT1 DNA in said sample with one or more nucleic acid probes which comprise said KVLQT1 DNA sequence or a mutant sequence of said KVLQT1 DNA;  
 (n) immunoblotting;  
 (o) immunocytochemistry;  
 (p) assaying for binding interactions between said protein isolated from said tissue and a binding partner capable of specifically binding the polypeptide expression product of a mutant allele and/or a binding partner for the polypeptide and assaying for the inhibition of biochemical activity of said binding partner.  
 
     
     
         9 . A method for diagnosing a mutation which causes long QT syndrome comprising hybridizing a probe which hybridizes to isolated DNA comprising a sequence of SEQ ID NO:1 as altered by one or more mutations selected from the group consisting of C1172T, C1343G, C1588T, C1697T, C1747T and G1781A and not to wild-type KVLQT1 DNA, to a patient's sample of DNA or RNA, the presence of a hybridization signal being indicative of long QT syndrome.  
     
     
         10 . A method according to  claim 9  wherein the patient's DNA or RNA has been amplified and said amplified DNA or RNA is hybridized with said probe.  
     
     
         11 . A method according to  claim 9  wherein said hybridization is performed in situ.  
     
     
         12 . A method according to  claim 9  wherein said assay is performed using nucleic acid microchip technology.  
     
     
         13 . A method for diagnosing a mutation which causes long QT syndrome comprising amplifying a region of gene or RNA for KVLQT1 and sequencing the amplified gene or RNA wherein long QT syndrome is indicated by any one or more mutations selected from the group consisting of C1172T, C1343G, C1588T, C1697T, C1747T and G1781A.  
     
     
         14 . A method for diagnosing a mutation which causes long QT syndrome comprising identifying a mismatch between a patient's DNA or RNA and a wild-type DNA or RNA probe wherein said probe hybridizes to a region of DNA or RNA wherein said region comprises a mutation of SEQ ID NO:1 selected from the group consisting of C1172T, C1343G, C1588T, C1697T, C1747T and G1781A.  
     
     
         15 . The method of  claim 14  wherein the mismatch is identified by an RNase assay.  
     
     
         16 . An isolated DNA encoding a KVLQT1 polypeptide of SEQ ID NO:2 having a mutation selected from the group consisting of T3911, P448R, Q530X, S566F, R583C and R594Q.