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  • C12Q—MEASURING 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
  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
  • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
  • C12Q1/6879—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for sex determination
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  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Q—MEASURING 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
  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
  • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
  • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
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  • C12Q2600/00—Oligonucleotides characterized by their use
  • C12Q2600/156—Polymorphic or mutational markers
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  • C12Q2600/00—Oligonucleotides characterized by their use
  • C12Q2600/172—Haplotypes

Definitions

• STDDT syndrome is a previously undescribed disease that presents with a variety of clinical symptoms including respiratory arrest leading to death by six months of age, ambiguous genitalia, and cranial nerve palsy.
• the disorder has only been seen in the Old Order Amish population, and is inherited in an autosomal recessive fashion. Historically the syndrome has been unexplained, no diagnostic tests were available, and clinical recognition in the neonate was difficult, particularly in affected females.
• SUMMARY OF THE INVENTION A method of identifying individuals who are carriers of a mutation associated with STDDT syndrome and individuals who are likely to be affected by SIDDT syndrome are disclosed.
• TSPYL Testis Specific- Protein Y-Like gene
• the isolated nucleic acid molecule comprises a sequence selected from the group consisting of: a nucleotide sequence that encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 2 or the complement of said nucleotide sequence; a nucleotide sequence comprising SEQ ID NO: 4 or its complement; and, an oligonucleotide comprising at least 16 contiguous nucleotides of SEQ ID NO: 3 or its complement, wherein the oligonucleotide includes an insertion of a nucleotide at position 457_458.
• the mutation identified has an insertion of a guanine at this position, 457_458insG, but in other embodiments the insertion may be another base, for example, adenine, cytosine or thymine. Any single base insertion at this position, or at another position in the coding- region upstream of amino acid 169, would result in the in frame stop codon at amino acid position 169, resulting in a truncated protein. Any mutation in the coding region that would result in a non-functional protein or a mutation in a regulatory region that alters the expression of the gene, for example, by altering transcription levels, mRNA stability or mRNA processing may also have a disease phenotype.
• the mutation may be detected, for example, by hybridizing an isolated nucleic acid sequence described above to a nucleic acid sample and detecting hybridization.
• the isolated nucleic acid sequence may be labeled or the nucleic acids in the nucleic acid sample may be labeled.
• One or more of the nucleic acids may be attached to a solid support such as an array, a membrane or a bead.
• the methods may be used to determine if a subject carries a mutant TSPYL gene associated with SIDDT syndrome by detecting a TSPYL 457_458insG gene or gene product in a biological sample from the subject.
• the step of determining may comprise performing an in vitro nucleic acid assay, for example PCR.
• the PCR may be with allele specific probes so that amplification is present if the allele is present and absent if the allele is absent. Hybridization with allele specific probes may also be used to detect the mutant allele.
• a nucleic acid probe spanning the 457_458insG mutation in the TSPYL gene is hybridized to a nucleic acid sample from an individual and if hybridization is detected this is an indication that the 457_458insG mutation is present.
• the probe may be directed to either strand of the double stranded DNA or to the mRNA.
• the absence of the mutation could also be detected, for example, by a probe that hybridizes to the 457_458 region only in the absence of the mutation, i.e. only hybridizes to the wild type. Since the deleterious effect of the mutation seems to result from the introduction of a downstream stop condon, any single base insertion at that position would be expected to have the same phenotype.
• the mutation to be detected in one aspect is 457_458insN where N can be A, G, C, T or U.
• the probe may have a degenerate base at the position corresponding to the insertion so that it will hybridized specifically to all possible single base insertions at the insertion position.
• the presence or absence of a mutant TSPYL polypeptide is detected.
• the TSPYL polypeptide may be detected, for example, using an antibody to a TSPYL polypeptide.
• the antibody may be capable of distinguishing between the mutant (SEQ TD NO: 2) and wild type (SEQ ID NO: 1) proteins or the antibody may be directed to an epitope present in both the mutant and wild type proteins.
• Differences in size may be used to distinguish the mutant and wild type proteins, for example, by differences in mobility on a gel.
• Screening for the mutation may be performed on an individual to determine if the individual is a carrier. Individuals who are heterozygous for the 457_458insG mutation are carriers. Testing may also be performed in utero to determine if the offspring of a known or suspected carrier will be affected with STDDT syndrome. Testing may be done on a human conceptus or fetus and may be done in utero or in vitro. Neonates may also be tested to determine if the mutation is present and if it is present if the individual is homozygous or heterozygous.
• kits that may be used for assaying for the presence of a mutant TSPYL gene are disclosed.
• Components of the kit may include one or more oligonucleotide probes which specifically bind to a mutant TSPYL gene; and one or more reagents that may be used for detecting the hybridization of the oligonucleotide probe to the mutant, for example, the TSPYL 457_458insG gene or gene product; wherein the probe and reagents are present in amounts effective to perform the hybridization assay.
• a kit for assaying for the presence of a 457_458insN mutation in a TSPYL gene is disclosed.
• the kit may contain primers for allele specific PCR amplification or allele specific hybridization.
• the kit comprises a first primer that is specific for the 457_458insN mutation, a second primer that is specific for the wild type allele and a third primer that hybridizes to both alleles in a region outside of the 457_458insN region.
• the primers may be used in separate PCR reactions so that if the mutant allele is present, an amplification product is generated in a reaction with the first and third primers and if the wild type allele is present an amplification product is generated in a reaction with the second and third primers.
• kits may also contain one or more thermally stable polymerases, dNTPs and mixtures thereof, one or more buffers and instructions for use of the kit for genotyping the TSPYL gene.
• Any method known in the art for mutation detection may be used to detect a TSPYL mutation associated with STDDT or another disease. Methods that may be used include, for example, single base extension, oligonucleotide ligation assay, molecular inversion probe assays, allele specific primer extension with sequence coded identity tags and allele specific hybridization.
• an antibody to a wild type or mutant TSPYL protein is disclosed. In one aspect of the invention, an antibody that binds to the mutant TSPYL protein and not the wild type TSPYL protein is disclosed.
• Figure IA shows the wild type protein. An asterisk marks the location of the insertion in the mutant protein.
• Figure IB shows the truncated mutant protein resulting from the 457_458insG mutation.
• Figure 2A shows a wild type mRNA sequence for TSPYL. The coding region is underlined and the initiator AUG and stop codon are shown in bold.
• Figure 2B shows a mutant mRNA sequence for TSPYL carrying the 457_458insG mutation. The initiator AUG, the inserted G and the now in-frame stop codon at position 169 of the protein are shown in bold and underlined.
• Figure 3 shows the 457_458insG mutation including 70 additional bases of upstream and downstream flanking sequence.
• the practice of the present invention may employ, unless otherwise indicated, conventional techniques and descriptions of organic chemistry, polymer technology, molecular biology (including recombinant techniques), cell biology, biochemistry, and immunology, which are within the skill of the art.
• Such conventional techniques include polymer array synthesis, hybridization, ligation, and detection of hybridization using a label. Specific illustrations of suitable techniques can be had by reference to the example herein below. However, other equivalent conventional procedures can, of course, also be used.
• Such conventional techniques and descriptions can be found in standard laboratory manuals such as Genome Analysis: A Laboratory Manual Series (Vols. I-IV), Using Antibodies: A Laboratory Manual, E. Harlow et al.
• a STDDT syndrome carrier is an individual in apparent health whose chromosomes contain a mutant TSPYL1 gene that may be transmitted to that person's offspring.
• a STDDT syndrome patient is an individual who is homozygous for the 457_458insG mutation in the TSPYL gene.
• a genome is all the genetic material of an organism. In some instances, the term genome may refer to the chromosomal DNA. Genome may be multichromosomal such that the DNA is cellularly distributed among a plurality of individual chromosomes.
• genomic DNA derived from the genetic material in the chromosomes of a particular organism is genomic DNA.
• genome may also refer to genetic materials from organisms that do not have chromosomal structure.
• genome may refer to mitochondria DNA.
• a genomic library is a collection of DNA fragments representing the whole or a portion of a genome.
• a genomic library is a collection of clones made from a set of randomly generated, sometimes overlapping DNA fragments representing the entire genome or a portion of the genome of an organism.
• the term "chromosome” refers to the heredity-bearing gene carrier of a cell which is derived from chromatin and which comprises DNA and protein components (especially histones).
• the conventional internationally recognized individual human genome chromosome numbering system is employed herein.
• the size of an individual chromosome can vary from one type to another within a given multi-chromosomal genome and from one genome to another. In the case of the human genome, the entire DNA mass of a given chromosome is usually greater than about 100,000,000 bp.
• the size of the entire human genome is about 3 x 10 9 bp.
• the largest chromosome, chromosome no. 1 contains about 2.4 x 10 8 bp while the smallest chromosome, chromosome no. 22, contains about 5.3 x 10 7 bp.
• a "chromosomal region" is a portion of a chromosome. The actual physical size or extent of any individual chromosomal region can vary greatly. The term
• region is not necessarily definitive of a particular one or more genes because a region need not take into specific account the particular coding segments (exons) of an individual gene.
• An allele refers to one specific form of a genetic sequence (such as a gene) within a cell, an individual or within a population, the specific form differing from other forms of the same gene in the sequence of at least one, and frequently more than one, variant sites within the sequence of the gene. The sequences at these variant sites that differ between different alleles are termed "variances", “polymorphisms", or "mutations”.
• an individual At each autosomal specific chromosomal location or "locus" an individual possesses two alleles, one inherited from one parent and one from the other parent, for example one from the mother and one from the father.
• An individual is "heterozygous” at a locus if it has two different alleles at that locus.
• An individual is "homozygous” at a locus if it has two identical alleles at that locus.
• Polymorphism refers to the occurrence of two or more genetically determined alternative sequences or alleles in a population.
• a polymorphic marker or site is the locus at which divergence occurs.
• Preferred markers have at least two alleles, each occurring at a frequency of preferably greater than 1%, and more preferably greater than 10%) or 20% of a selected population.
• a polymorphism may comprise one or more base changes, an insertion, a repeat, or a deletion.
• a polymorphic locus may be as small as one base pair.
• Polymorphic markers include restriction fragment length polymorphisms, variable number of tandem repeats (VNTR's), hypervariable regions, minisatellites, dinucleotide repeats, trinucleotide repeats, tetranucleotide repeats, simple sequence repeats, and insertion elements such as Alu.
• the first identified allelic form is arbitrarily designated as the reference form or allele and other allelic forms are designated as alternative or variant alleles.
• the allelic form occurring most frequently in a selected population is sometimes referred to as the wild type form.
• a diallelic polymorphism has two forms.
• a triallelic polymorphism has three forms.
• a polymorphism between two nucleic acids can occur naturally, or be caused by exposure to or contact with chemicals, enzymes, or other agents, or exposure to agents that cause damage to nucleic acids, for example, ultraviolet radiation, mutagens or carcinogens.
• Single nucleotide polymorphisms (SNPs) are positions at which two alternative bases occur at appreciable frequency (>1%) in a given population.
• SNPs are the most common type of human genetic variation. A polymorphic site is frequently preceded by and followed by highly conserved sequences (e.g., sequences that vary in less than 1/100 or 1/1000 members of the populations). A SNP may arise due to substitution of one nucleotide for another at the polymorphic site. A transition is the replacement of one purine by another purine or one pyrimidine by another pyrimidine. A transversion is the replacement of a purine by a pyrimidine or vice versa. SNPs can also arise from a deletion of a nucleotide or an insertion of a nucleotide relative to a reference allele.
• genotyping refers to the determination of the genetic information an individual carries at one or more positions in the genome.
• genotyping may comprise the determination of which allele or alleles an individual carries for a single SNP or the determination of which allele or alleles an individual carries for a plurality of SNPs.
• a particular nucleotide in a genome may be an A in some individuals and a C in other individuals. Those individuals who have an A at the position have the A allele and those who have a C have the C allele.
• the individual will have two copies of the sequence containing the polymorphic position so the individual may have an A allele and a C allele or alternatively two copies of the A allele or two copies of the C allele.
• a polymorphic location may have two or more possible alleles and the array may be designed to distinguish between all possible combinations.
• Linkage disequilibrium or allelic association means the preferential association of a particular allele or genetic marker with a specific allele, or genetic marker at a nearby chromosomal location more frequently than expected by chance for any particular allele frequency in the population.
• locus X has alleles a and b, which occur at equal frequency
• linked locus Y has alleles c and d, which occur at equal frequency
• linkage disequilibrium may result, for example, because the regions are physically close, from natural selection of certain combination of alleles or because an allele has been introduced into a population too recently to have reached equilibrium with linked alleles.
• a marker in linkage disequilibrium can be particularly useful in detecting susceptibility to disease (or other phenotype) notwithstanding that the marker does not cause the disease.
• a marker (X) that is not itself a causative element of a disease, but which is in linkage disequilibrium with a gene (including regulatory sequences) (Y) that is a causative element of a phenotype can be detected to indicate susceptibility to the disease in circumstances in which the gene Y may not have been identified or may not be readily detectable.
• LOD scores are calculated by estimating a linkage distance of specific genes or markers, and, given that estimate, calculating the probability of a given birth sequence. That value is divided by the probability of a birth sequence if the genes or markers (SNPs) are unlinked. The log of this value is calculated by iterating this process over several estimated linkage distances.
• LOD score log(probability of birth with a given linkage value/P of birth with no linkage).
• STDS Sudden Infant Death Syndrome
• SIDDT Sudden Infant Death with Dysgenesis of the Testes Syndrome
• OMTM Mendelian Inheritance in Man accession no. 608800
• Clinical recognition of the syndrome has historically been difficult, particularly in affected females. Infants with STDDT syndrome appear normal at birth, develop signs of visceroautonomic dysfunction early in life, and die before 12 months of age of abrupt cardiorespiratory arrest. Caretakers of affected infants say that at birth the infants often have an unusual cry, which is a staccato sound, similar to the cry of a goat. Affected newborns appear to be normal but are difficult to feed and usually require nasogastric tube alimentation.
• Signs of abnormal autonomic and visceral nerve regulation manifest within the first months of life and include neonatal bradycardia, hypothermia, severe gastoresophageal reflux, laryngospasm, bronchospasm, and abnormal cardiorespiratory patterns during sleep.
• the infants typically have a pathological startle reflex that includes obstructive apnea and appears similar to breath- holding. The startle can be provoked by loud noise, bright light, movement or tactile stimulation and is unresponsive to clonazepam.
• seizure like movements have been described by parents, EEGs were normal for several cases. Bulbar and cervical anterior horn cell dysfunction or degeneration may be part of the neurological basis for abnormal airway control and dysphagia.
• the region that received the highest 2-point LOD score (4.7) was on chromosome 6q22.1c-q22.2d and extended from bases 113744706 to 115890416 (Build 34 of the NCBI human genome sequence).
• the individual genotypes for 13 homozygous SNPs in affected individuals are shown in Table 1.
• the homozygous segment spanned 3.6 Mb corresponding to roughly 1.1 cM.
• Genetic and physical map of the SIDDT syndrome locus including the TSPYL gene may be found in Puffenberger et al. PNAS 101 : 11689-11694 (2004), which is incorporated herein by reference in its entirely for all purposes.
• the SNP autozygous haplotype was comprised of 13 homozygous SNPs bounded by rs 1388219 and rs 1321370 across 1.1Mb. Thirty seven known and hypothetical genes reside within the interval, including TSPYL and TSPYL4. TSPYL4 showed no coding region SNPs upon sequencing the gene in affected individuals.
• the STDDT phenotype included testicular dysgenesis, so TSPYL was analyzed because it has a sequence similarity of 38-40% homology compared to the Y-linked testis-specific protein (TSPY), which maps to chromosome Ypl 1. This homology indicates that TSPYL may have a function related to sexual differentiation and testicular development.
• TSPYL is broadly expressed in the testis, ovaries, prostates, brain, spleen kidney, lung, heart and liver and contains a domain common to nucleosome assembly proteins (NAPs) and a domain that has homology to DNA binding domains.
• the coding sequence of the TSPYL gene is 1314 bases in length (Genbank accession number BC048969 which is incorporated herein in its entirety by reference) and lacks introns (Genbank accession number AL050331 which is incorporated herein in its entirety by reference).
• the TSPYL protein is a 437 amino acid protein, Figure 1 A (SEQ ID NO: 1).
• the GenBank accession number for the protein is XP_371844.
• Figure IB shows the mutant protein resulting from the 457_458insG mutation.
• An mRNA with the wild type sequence is shown in Figure 2 A, SEQ TD NO: 3.
• complete sequencing of the TSPYL gene revealed a homozygous single base insertion at position 457 of the coding region in affected individuals, Figure 2B, SEQ TD NO: 4.
• the 457_458insG causes a missense mutation at amino acid 153 and results in premature truncation of the protein at amino acid 169.
• the sequence of the truncated protein is shown in Figure IB, SEQ ID NO: 2. This change was not seen as a polymorphic variant in the SNP database or in GenBank.
• Truncation of the TSPYL protein at amino acid 169 results in inappropriate subcellular targeting of TSPYL and loss of the NAP domain, suggesting that the protein is nonfunctional. Loss of the NAP functional domain may affect the ability of the protein to shuttle histones from the cytoplasm to the nuclease and disrupts the nuclear localization signal on the tertiary surface of the peptide.
• Example 3 below demonstrated that the truncated mutant protein, lacking the NAP domain, has altered subcellular localization compared to the wild type protein. The mutant shows diffuse cytoplasmic staining in contrast to the wild type which shows punctate staining and localization to the nucleus.
• This protein is predicted to be involved in the male sexual differentiation pathway, and the truncation may result in aberrant male sexual differentiation, neurological dysfunction, and fatal sleep apnea.
• male sexual differentiation see, Olaf Hiort and Paul-Martin Holterhus, Eur J. Endo. 142 : 101 - 110, (2000).
• sequencing control samples a known nonsynonymous SNP 541 G/A (A181T, rs3749894) and a unique in-frame short tandem repeat [523(GTG) 2-3 ] that codes for either two or three adjacent valine residues at positions 175-177 in the peptide.
• the 541 A allele had a frequency of 7.8% whereas the 523(GTG) 2 allele had a frequency of 30.2% on control chromosomes.
• the position of the two wild type valines is underlined in Fig. 1 A.
• Other nonsynonymous SNPs that have been identified in TSPYL include A74P (rs3749895) and P62S (rs3828743).
• Embryos that are not affected with the disease can be selected for implantation.
• a fetus may be tested and the parents can choose to seek counseling to make informed decisions.
• Parents who are carriers or suspect that they may be carriers may elect to have a child tested for the mutation soon after birth. The disease has been very difficult to diagnose and children were frequently subjected to numerous, costly tests and treatments in an effort to diagnose. Many of those tests can be avoided and replaced with a simple genetic test to determine if the child is homozygous for the mutation. In addition, accurate diagnosis will facilitate improved treatment regimens that are directed to the disease.
• the invention relates to isolated nucleic acid molecules comprising all or a fragment of a variant allele of TSPYL (e.g., wherein reference or wild type TSPYL is exemplified by SEQ TD NOs: 1 and 3).
• preferred fragments are at least 10, 12 or 15 contiguous nucleotides and comprise a polymorphic site, e.g.
• the invention further relates to isolated gene products, e.g., polypeptides or proteins, which are encoded by a nucleic acid molecule comprising all or at least a portion of the variant allele of TSPYL.
• isolated nucleic acid molecules which hybridize to the variant allele identified herein (or its complement) and not to the wild type allele under stringent hybridization conditions.
• the insertion detected is an insertion of a G nucleotide at a position that in the wild type already has two G nucleotides, therefore the insertion results in the presence of three G nucleotides in the mutant instead of two.
• the mutation may be used to define a haplotype.
• the haplotype may be associated with STDDT syndrome.
• Haplotype refers to a particular set of alleles at linked loci that are found together on a single chromosome and tend to be inherited together as a unit.
• the presence of a first mutation that is tightly linked to a second mutation can be determined by genotyping the second mutation.
• the second mutation can be genotyped and the presence of the 457_458insN mutation can be inferred from the genotype of the second mutation.
• TSPYL Testis-Specific Protein, Y-encoded
• TSPYL (TSPY-Like) differs from TSPY in at least two important ways: (1) TSPY is found on the Y chromosome, whereas TSPYL is found on an autosomal chromosome and (2) TSPY is only found to be expressed in the testis, whereas TSPYL is broadly expressed in the testis, ovaries, prostates, brain, spleen kidney, lung, heart and liver. The biochemical and cellular function for TSPYL was previously unknown. TSPYL contains a Nucleosome Assembly Protein (NAP) domain preceded by a region of low complexity.
• NAP Nucleosome Assembly Protein
• NAPs are a family of proteins that function as chaperones, shuttling histones from the cytosol to the nucleosome, and then shuttling unbound back to the cytosol. Consistent with this molecular function, studies of yeast NAP proteins show that NAPs are critical to nucleosome assembly, mitotic progression and chromatin formation. NAP domains may also function as transcription factors or gene regulators during embryogenesis. For example, during the development of Xenopus embryos, the NAP-containing protein NAP1L is broadly expressed at its highest level during development of hematopoietic tissue.
• TSPYL When NAP1L is over expressed, genes involved in tissue development are up-regulated, specifically GATA-2, a gene essential for hematopoiesis (Steer, Mech Dev. 120(9): 1045-57 (2003)). TSPYL may play a specific role in testicular development by altering regulation of other development genes and contributing to chromatin stability during cell division. Genotypic females are also affected by the mutation in TSPYL, suggesting that the gene, unlike TSPY, is expressed in other tissues. TSPYL may play a role in development by altering regulation of specific developmental genes and contributing to region-specific chromatin remodeling. TSPYL is highly expressed in fetal brain (GEO no. GSM14799).
• TSPYL has been shown to be negatively regulated in the hippocampus in a linear does-dependent fashion by corticosteroids (GEO no. GSM12543), sensitively negatively regulated by TNK2 (GEO no. GSM1514) and positively regulated by testosterone (GEO no. GSM6733).
• TSPYL may play a fundamental role in embryogenesis of the human nervous and reproductive systems. TSPYL expression and function in the developing brain may provide new insight into the genetic basis of apnea, dysphagia, cardiac arrests and sudden unexplained deaths in infancy. Present clinical evidence suggests that in STDDT, sudden death may result from dysregulation of the autonomic brainstem systems that control cardiac and pulmonary protective reflexes.
• the lethal event may be profound vagally mediated laryngobronchospasm or asystole.
• Methods are disclosed for detecting the presence of the 457_458insG allele.
• Samples that contain the mutant allele or mutant gene product may be identified by analysis of the TSPYL gene or gene product. Samples may be identified as being homozygous or heterozygous for the mutation.
• the genetic material to be assessed may be obtained from any nucleated cell from the individual.
• assay of genomic DNA virtually any biological sample (other than pure red blood cells) is suitable.
• convenient tissue samples include whole blood, semen, saliva, tears, urine, fecal material, sweat, skin and hair. Buccal and blood samples are used in some embodiments.
• Samples may also be derived from archived tissue samples.
• the sample may be obtained from chord blood.
• the tissue sample is preferably obtained from an organ in which the target nucleic acid is expressed.
• genomic DNA may be obtained, for example, from amniotic fluid or from chorionic villus sampling (CVS).
• Amniotic fluid may be obtained, for example, by amniocentesis, where a needle is inserted through the mother's abdomen into the uterus (womb) and a small amount of fluid is withdrawn.
• CVS is performed by removing a small sample of the placenta from the uterus. It may be removed with a catheter or a needle.
• the sample may be obtained through the cervix or by insertion of a needle into the abdomen.
• Many of the methods described herein require amplification of DNA from target samples. This can be accomplished by e.g., PCR. See generally PCR Technology: Principles and Applications for DNA Amplification (ed. H. A. Erlich, Freeman Press, N.Y., N.Y., 1992); PCR Protocols: A Guide to Methods and Applications (eds. Innis. et al, Academic Press, San Diego, Calif., 1990); Mattila et al, Nucleic Acids Res. 19, 4967 (1991); Eckert et al, PCR Methods and Applications 1, 17 (1991); PCR (eds.
• ligase chain reaction LCR
• LCR ligase chain reaction
• NASBA nucleic acid based sequence amplification
• the latter two amplification methods involve isothermal reactions based on isothermal transcription, which produce both single stranded RNA (ssRNA) and double stranded DNA (dsDNA) as the amplification products in a ratio of about 30 or 100 to 1 , respectively.
• ssRNA single stranded RNA
• dsDNA double stranded DNA
• the presence of the insertion at position 457 of TSPYL can be identified by a variety methods, such as Southern analysis of genomic DNA; Northern analysis of RNA; denaturing high pressure liquid chromatography (DHPLC); gene isolation and sequencing; hybridization of an allele-specific oligonucleotide with amplified gene products; single base extension (SBE) including SBE-FRET (see, U.S. Patent No.
• TSPYL 6,642,001
• PCR-OLA amplification refractory mutation system
• ARMS amplification refractory mutation system
• determination of the allelic form of TSPYL is carried out using allele-specific probes, or using chip-based oligonucleotide arrays. A sampling of suitable procedures is discussed below. Allele-Specific Probes. The design and use of allele-specific probes for analyzing polymorphisms is described by e.g., Saiki et al, Nature 324, 163-166 (1986); EP 235,726, and WO 89/11548.
• Allele-specific probes can be designed that hybridize to a segment of target DNA from one individual but do not hybridize to the corresponding segment from another individual due to the presence of different polymorphic forms in the respective segments from the two individuals.
• Hybridization conditions should be sufficiently stringent that there is a significant difference in hybridization intensity between alleles, and preferably an essentially binary response, whereby a probe hybridizes to only one of the alleles.
• Hybridizations are usually performed under stringent conditions, for example, at a salt concentration of no more
• mM NaCl 50 mM NaPhosphate, 5 mM EDTA, pH 7.4
• a temperature of 25-30°C, or equivalent conditions are suitable for allele-specific probe hybridizations.
• Equivalent conditions can be determined by varying one or more of the parameters given as an example, as known in the art, while maintaining a similar degree of identity or similarity between the target nucleotide sequence and the primer or probe used.
• Some probes are designed to hybridize to a segment of target DNA such that the polymorphic site aligns with a central position (e.g., in a 15-mer at the 7 position; in a 16-mer, at either the 8 or 9 position, in a 25-mer at the 13 position) of the probe.
• Allele-specific probes are often used in pairs, one member of a pair showing a perfect match to a reference form of a target sequence and the other member showing a perfect match to a variant form.
• Several pairs of probes can then be immobilized on the same support for simultaneous analysis of multiple polymorphisms within the same target sequence.
• multiple probe pairs may be used for each polymorphism.
• the probe pairs may differ in the position of the polymorphic allele. See, for example, U.S. Patent Application No. 10/681,773.
• the polymorphisms can also be identified by hybridization to nucleic acid arrays, some examples of which are described in WO 95/11995.
• WO 95/11995 also describes subarrays that are optimized for detection of a variant form of a pre- characterized polymorphism.
• a subarray contains probes designed to be complementary to a second reference sequence, which is an allelic variant of the first reference sequence.
• the second group of probes is designed by the same principles, except that the probes exhibit complementarity to the second reference sequence.
• the inclusion of a second group (or further groups) can be particularly useful for analyzing short subsequences of the primary reference sequence in which multiple mutations are expected to occur within a short distance commensurate with the length of the probes (e.g., two or more mutations within 9 to 21 bases). Allele-Specific Primers.
• An allele-specific primer hybridizes to a site on target DNA overlapping a polymorphism and only primes amplification of an allelic form to which the primer exhibits perfect complementarity. See Gibbs, Nucleic Acid Res. 17, 2427-2448 (1989). This primer is used in conjunction with a second primer which hybridizes at a distal site. Amplification proceeds from the two primers, resulting in a detectable product which indicates the particular allelic form is present. A control is usually performed with a second pair of primers, one of which shows a single base mismatch at the polymorphic site and the other of which exhibits perfect complementarity to a distal site. The single-base mismatch prevents amplification and no detectable product is formed.
• ARMS amplification refractory mutation system
• a pair of primers is used in which one primer is complementary to a known mutant sequence. If the DNA sample is amplified, the presence of the mutant sequence is confirmed. Lack of amplification indicates that the mutant sequence is not present.
• the primers are complementary to wild type sequences. Amplification of the DNA sample indicates that the DNA has the wild type sequence complementary to the primers. If no amplification occurs, the DNA likely contains a mutation at the sequence where hybridization should have occurred.
• a description of ARMS can be found in Current Protocols in Human Genetics, Chapter 9.8, Tohn Wiley & Sons, ed by Dracopoli et ⁇ /. (1995). Direct-Sequencing.
• the direct analysis of the sequence of polymorphisms of the present invention can be accomplished using either the dideoxy chain termination method or the Maxam-Gilbert method (see Sambrook et al, Molecular Cloning, A Laboratory Manual (2nd Ed., CSHP, New York 1989); Zyskind et al., Recombinant DNA Laboratory Manual, (Acad. Press, 1988)).
• Denaturing Gradient Gel Electrophoresis Amplification products generated using the polymerase chain reaction can be analyzed by the use of denaturing gradient gel electrophoresis. Different alleles can be identified based on the different sequence- dependent melting properties and electrophoretic migration of DNA in solution. Erlich, ed., PCR Technology, Principles and Applications for DNA Amplification, (W.H.
• the different electrophoretic mobilities of single- stranded amplification products can be related to base-sequence differences between alleles of target sequences.
• Single-Base Extension Another method for identifying and analyzing polymorphisms is based on single-base extension (SBE) of a fluorescently-labeled primer coupled with fluorescence resonance energy transfer (FRET) between the label of the added base and the label of the primer.
• SBE single-base extension
• FRET fluorescence resonance energy transfer
• the method such as that described by Chen et al, (PNAS 94:10756-61 (1997), incorporated herein by reference) uses a locus-specific oligonucleotide primer labeled on the 5' terminus with 5- carboxyfluorescein (FAM).
• FAM 5- carboxyfluorescein
• This labeled primer is designed so that the 3' end is immediately adjacent to the polymorphic site of interest.
• the labeled primer is hybridized to the locus, and single base extension of the labeled primer is performed with fluorescently labeled dideoxyribonucleotides (ddNTPs) in dye-terminator sequencing fashion, except that no deoxyribonucleotides are present.
• ddNTPs dideoxyribonucleotides
• An increase in fluorescence of the added ddNTP in response to excitation at the wavelength of the labeled primer is used to infer the identity of the added nucleotide. Immunological Assays.
• An immunological assay such as an Enzyme Linked Immunoassay (ELISA) can be used as a diagnostic tool to determine whether or not an individual carries a mutation in TSPYL.
• ELISA Enzyme Linked Immunoassay
• One of skill in the art is familiar with the procedure for performing an ELISA. Briefly, antibodies are generated against native or mutant TSPYL. This can be accomplished by administering a native or mutant protein, or a peptide derived from a wild type or mutant protein, to an animal, such as a rabbit. The anti- TSPYL antibodies are purified and screened to determine specificity.
• wells of a microtiter plate are coated with the specific anti-TSPYL antibodies. An aliquot of a sample from a patient to be analyzed for TSPYL protein is added in serial dilution to each antibody coated well.
• labeled anti-TSPYL antibodies such as biotinylated anti-TSPYL antibodies
• labeled anti-TSPYL antibodies can be added to the microtiter plate as secondary antibodies. Detection of the label is correlated with the specific TSPYL antigen assayed.
• suitable secondary antibody labels include radioactive isotopes, enzymes, fluorophores or chromophores.
• the presence of bound labeled (biotinylated) antibody is determined by the interaction of the biotin with avidin coupled to peroxidase. The activity of the bound peroxidase is easily determined by known methods.
• Antibodies that bind to the wild type but not the mutant, the mutant but not the wild type or the mutant and the wild type may be generated.
• an antibody that binds to the mutant but not the wild type may be generated by administering to the animal a peptide that is in the mutant but not the wild type.
• a wild type specific antibody may be raised to a peptide that is in the wild type but not the mutant and an antibody that binds to both mutant and wild type may be raised to a peptide that is present in both the mutant and wild type proteins.
• the antigenic agent may also be administered in a transfected cell.
• Antibodies may be polyclonal or monoclonal. Polyclonal antibodies are made by immunizing an animal with a selected antigen.
• the blood will contain a variety of antibodies to the antigen, each binding the antigen in a slightly different way.
• the immune-sera can be used in its crude form where high levels of specific antibodies are present, or the specific antibodies can be isolated from sera components by affinity purification.
• To produce monoclonal antibodies the same immunization protocol may be used and all antibody forming cells may be removed. These are fused with immortal cells to become hybridomas, which are screened for antibody production. The hybridomas that produce antibodies are given clone names, which are uniquely assigned to permit identification.
• the antibody producing hybridomas are cloned and then the antibodies are isolated for cultivation by tissue culture. Unlike polyclonal antibodies these are homogeneous antibodies with defined specificity.
• the tissue culture supernatant can also be used in its crude form, or it can be further purified by affinity purification.
• Production of TSPYL protein The nucleic acid sequence encoding wild type or mutant TSPYL can be used to produce TSPYL in cells transformed with the sequence.
• cells can be transformed by known techniques with an expression vector containing the TSPYL sequence operably linked to a functional promoter. Expression of TSPYL in transformed cells is useful in vitro to produce large amounts of the protein. Examples of suitable host cells include bacterial or yeast cells, for example.
• mammalian cells such as Chinese hamster ovary (CHO) cells can be used. Due to degeneracy of the genetic code, most amino acids are encoded by more than one codon. Therefore, applicants recognize, and include within the scope of the invention, variations of the sequence shown in SEQ TD NOs: 3 and 4. For example, codons in a DNA sequence encoding TSPYL can be modified to reflect the optimal codon frequencies observed in a specific host. Rare codons having a frequency of less than about 20% in known sequences of the desired host are preferably replaced with higher frequency codon.
• Transgenic Animals The nucleic acid sequences encoding TSPYL, both wild type and mutant, provided in this application are useful for the development of transgenic animals expressing TSPYL.
• transgenic animals may be used, for example, to screen compounds for treating STDDT syndrome.
• Useful variations of a transgenic animal are “knock out” or “knock in” animals.
• a known gene sequence such as the sequence encoding TSPYL
• Experiments can be performed on the animal, for example a mouse, to determine what effect the absence of the gene has on the animal.
• the wild type gene is deleted and a mutant version or a gene from another organism is inserted, for example, a mutant or wild type human TSPYL gene.
• kits The invention is also directed towards a kit for detecting mutation in the TSPYL gene.
• a diagnostic kit may include a nucleic acid sequence encoding wild type TSPYL and at least one nucleic acid sequence encoding mutant TSPYL.
• a kit includes at least one anti-TSPYL antibody which binds to mutant TSPYL and optionally an anti-TSPYL antibody which binds to wild type TSPYL. The antibody to the mutant may or may not bind to the wild type and the antibody to the wild type may or may not bind to the mutant.
• kits containing at least one pair of amplification primers capable of amplifying a at least part of the TSPYL DNA or RNA may contain one or more allele specific primers that bind to the wild type and not to the mutant allele to be detected or one or more allele specific primers that bind to the mutant allele to be detected but not to the wild type.
• the kit contains one or more primer pairs for detection of a TSPYL mutation associated with disease, using an oligonucleotide ligation assay (OLA).
• OLA oligonucleotide ligation assay
• An example of a pair of primers for OLA may include a first primer that binds to the region that is just 3' of the mutation and contains at the 3' end of the first primer the complement of the mutation, and a second primer that binds to the region that is immediately 5' of the mutation. If the mutation is present the primers when hybridized will be juxtaposed and can be ligated together, and the presence of the ligated product can be detected. If the mutation is not present the primers may still bind to the wild type form but there will be a mismatch at the 3' end of the first primer and ligation will be blocked. OLA is described in greater detail in U.S. Patent No. 5,521,065. In another aspect the kit may include one or more primers for single base extension detection (SBE).
• SBE single base extension detection
• SBE primers may include a 5' tag sequence for detection and a 3' locus specific region that hybridizes to the target immediately 3' of the mutation.
• the SBE primer can be extended by one or more bases, including a base that is complementary to the mutation. The presence of the mutation can be detected by analyzing the extended SBE primer. In some embodiments the extended SBE primer is detected by detection of the tag sequence.
• Methods of mutation detection using SBE and an array of tag probes has been described in Fan et al, Gen. Res. 10(6):853-60 (2000).
• the kit comprises one or more molecular inversion probes (MIPs) as described in Hardenbol et al, Nat Biotechnol. 21(6):673f-678 (2003).
• MIPs molecular inversion probes
• MTPs based genotyping uses MIPs to produce inverted sequences, which undergo a unimolecular rearrangement and are then amplified by PCR using common primers and analyzed using universal sequence tag DNA microarrays.
• the MTJP is a single probe that has a region that binds upstream of the polymorphism and a region that binds downstream of the polymorphism.
• the probe is gap filled with a base that is complementary to the polymorphism and ligated to form a circle.
• Circularized MTPs are amplified using universal priming sequences in the probe, more than 1,000 different MT s can be amplified in parallel in a reaction.
• the probe also contains a tag sequence.
• the amplified tag sequence is labeled and detected to determine the presence of the mutation.
• the mutation can be detected by allele specific extension with sequence-coded identity tags as described in US Patent No. 6,287,778.
• the region containing the mutation can be amplified, for example, by PCR using a pair of primers that are specific for the locus.
• One or more allele specific primers that terminate at the 3' end with a base that is complementary to the polymorphic allele are hybridized to the amplification product and extended by one or more bases, incorporating a label.
• the allele specific primers also have a 5' tag sequence that is unique for each allele specific primer.
• the extended primers are hybridized to a solid support, for example, a bead, with a probe complementary to the tag sequence. Hybridization is detected by detecting the presence of label.
• Other methods for detection of a mutation include, amplification of all or part of the TSPYL DNA in the sample using a set of primers to produce amplified nucleic acids and sequencing the amplified nucleic acids; amplifying part of said TSPYL DNA in the sample using a primer specific for the mutation and detecting the presence of an amplified product, molecularly cloning all or part of the TSPYL DNA in the sample to produce a cloned nucleic acid and sequencing the cloned nucleic acid; amplifying the TSPYL DNA to produce amplified nucleic acids, hybridizing the amplified nucleic acids to a DNA probe specific for the mutation and detecting the presence of a hybridization product, forming single-stranded DNA from a gene fragment of said TSPYL DNA from
• the 457_458insG mutation results in a protein that does not perform the function of the wild type protein. Treatments may be developed to supplement the affected individual with functional protein. This may be done in utero or immediately after birth.
• methods for identification of individuals at risk for Sudden Infant Death syndrome STDS, OMTM #272120 are disclosed.
• STDS Sudden Infant Death syndrome
• the demonstrated association of the 457_458insG mutation with STDDT and the similarity of the disease with STDS make the TSPYL gene a candidate for a gene in which mutations that may be associated with one or more forms of STDS may be identified.
• TSPYL and the surrounding region are candidates for STDS associated mutations.
• the gene and sunounding regions may be sequenced in a collection of samples obtained from individuals who have died from STDS. Such collections are available and could be sequenced to identify mutations in TSPYL that are present in individuals whose death was attributed to STDS. Samples from STDS victims may be sequenced in the TSPYL and TSPYL4 regions to identify novel mutations associated with the disease. Once mutations are identified larger sample populations can be genotyped at those SNPs.
• the present invention may be better understood with reference to the following examples. These examples are intended to be representative of specific embodiments of the invention, and are not intended as limiting the scope of the invention. EXAMPLES
• Example 1 Mapping STDDT All DNA samples used in mapping and sequencing studies of STDDT syndrome were acquired from patients and their families at the Clinic for Special Children, Strasburg, PA. Over the past two generations, nine families from the Old Order Amish community of Mifflin and Tuniata counties have lost twenty-one infants to a disorder locally known as Swarey syndrome. Samples were collected from affected individuals, their parents, and siblings, addition, samples from other sibships were collected based on medical records and family interviews which indicated that affected children had been born into these families. Comprehensive genealogies for all affected individuals were prepared from private and published family records. SNP Genotyping was done using the GeneChip ® Mapping 10K Mapping Anay and Assay Kit (Affymetrix, Inc., Santa Clara, CA).
• Ligated products were amplified in quadruplicate using a concentration of 0.5 ⁇ M of the supplied generic primer Xbal (Affymetrix) in PCR Buffer II (Applied Biosystems) with 2.5 mM MgCl 2 , 250 ⁇ M each dNTP and 10 units of AmpliTaq Gold polymerase (Applied Biosystems) under the following PCR conditions: 95 °C for 5 min, followed by 35 cycles of 95 °C for 20 sec, 59 °C for 15 sec, 72 °C for 15 sec, and a final extension at 72 °C for 7 min. Fragments in the 250 to 1,000 base pair size range are preferentially amplified under these conditions.
• PCR products were purified with the QIAaquick PCR purification kit (Qiagen) according to the manufacturer's recommendations with the exception of the elution procedure. DNA from each of 4 PCR replicate samples was bound to separate columns and washed. The eluant collected from column 1 was used to elute the remaining 3 columns in series. The final purified product is the combination of 4 purified PCR product samples. 18-20 ⁇ g of purified PCR products were fragmented with 0.24 units of the supplied GeneChip ® Fragmentation Reagent (Affymetrix) for 30 min at 37 °C followed by a heat inactivation for 15 min at 95 °C.
• GeneChip ® Fragmentation Reagent Affymetrix
• Samples were then labeled with 15-20 units of terminal deoxytransferase (Affymetrix) and 0.143 mM of supplied GeneChip ® DNA Labeling Reagent in TdT buffer (Affymetrix) for 2 hr at 37 °C followed by heat inactivation for 15 min at 95 °C. After end-labeling, the fragments were hybridized to a GeneChip ® Human Mapping 10K Anay for 16-18 hr at 48 °C while rotating at 60 rpm. Microanays were then washed using the Fluidics Station 450 (Affymetrix) in 0.6 x SSPE (sodium chloride, sodium phosphate, EDTA), followed by a three-step staining protocol.
• Affymetrix terminal deoxytransferase
• SSPE sodium chloride, sodium phosphate, EDTA
• LOD scores were calculated for each SNP individually, representing the ratio of the likelihood of observing the measured SNPs given autozygosity at that locus in the affected individuals relative to the likelihood of observing the individual SNPs given no autozygosity at that locus.
• One hyndred seventy Old Order Amish Control chromosomes (including 6 untransmitted chromosomes from the SIDDT syndrome parents and 38 from the three mapping validation sibships) were used as controls to estimate SNP allele frequencies. Genomic regions of contiguous markers that exhibited the highest sum of individual LOD scores were identified and ranked. Cumulative two-point LOD scores for a block of SNPs were considered the LOD score for the region.
• the calculated LOD scores were used to ascertain genomic regions worthy of further investigation. Analyses were repeated using haplotype blocks defined in a similar manner to Daly et al. Nat Genet 29:229-232 (2001). The haplotype blocks were then treated as individual genetic markers. The results were very similar to the two-point LOD score approach used for microsatelhte marker mapping where they are assumed to be in linkage equilibrium with respect to one another.
• the three regions of the genome having the highest location scores were 6q22.1-q22.31 with a location score of 8.11, 9q32-q33.1 with location score of 6.18 and 1 lq22.2 with location score of 5.94.
• the four affected individuals are homozygous for 13 adjacent S ⁇ Ps at the 6q22 locus.
• the region is bounded by S ⁇ Ps rsl388219 and rsl321370.
• the gene content of the interval contained 18 characterized and 9 hypothetical genes.
• the characterized genes in the interval are: MARCKS, FLT34503, HDAC2, HS3ST5, FRK, ⁇ T5C2L1, COL10A1, TSPYL4, RPS5P1, TSPYL, SART2, C6orfl88, C6orf78, RWDD1, C6orfll3, KPNA5, GPRC6A, and RFXDCl.
• TSPYL and TSPYL4 (Genbank # AL050331 contains both genes).
• the exon of each target gene was amplified using specific oligonucleotide primers and 30-50 ng of genomic DNA from affected and unaffected family members.
• the TSPYL gene lacks introns and contains a coding region of 1,314 bases (GenBank accession no. AL050331).
• the mRNA is about 3200 bases in length (GenBank
• TSPYL PCR amplification was (forward) 5'-AGATCTCCAGTCCTGACGACAC-3' (SEQ TD NO: 6) and (reverse) 5'-AGGAAACAGGGTGCAGAAAAGT-3' (SEQ TD NO: 7).
• Primer sequences for PCR amplification of TSPYL4 were AAAACTCCCCTTCCAGACTGAC (SEQ TD NO: 8) and CACAATGCAGAAAAGCATGAAG (SEQ ID NO: 9).
• TSPYL sequencing primers were TSPYL1036-F: GGCCGAGTGGTGTCTCTTTCTA (SEQ ID NO: 10); TSPYL618-F: GGAGGATAGATTGGAGGAGGAG (SEQ ID NO: 11); TSPYL237-F: TACTCCCCAGATCCGAGTTGTT (SEQ TD NO: 12).
• TSPYL4 sequencing primers were: TSPYL4C277-F: ACACAGGTGATGGCGAACACAG (SEQ TD NO: 13); TSPYL4C776-F: CCATCGATCAAGAGTTGTCAAA (SEQ TD NO: 14); TSPYL4C1165-F: CAGGCTCATATCCACAGAAACC (SEQ TD NO: 15); TSPYL4C889-R: TAATGAAACTTCTGCGCTGCAT (SEQ TD NO: 16). Extension products were subsequently size-fractionated on an ABI 310 Genetic
• Cycling conditions were an initial denaturation step of 94 °C for 2 min followed by 30 cycles of 94 °C for 15 sec, 68 °C for 1 min, and 72 °C for 1 min, with a final extension step at 72 °C for 10 min with AmpliTaq or 94 °C for 2 min followed by 9 cycles of (94 °C for 15 sec, 68 °C for 1 min, and 68 °C for 105 sec) followed by 94°C for 15 sec and then 24 cycles of (68°C for 1 min, 72°C for 3 min), with a final extension step at 72 °C for 12 min for Expand.
• PCR products were cloned directionally into entry vector pENTR-D-TOPO Gateway vector (Invitrogen) and then into the Gateway destination vector pcDNA- DEST47 (Invitrogen) containing a C-terminal GFP tag. All clones were sequence verified. 10 5 HeLa F2 cells (10 5 ) were grown in DMEM supplemented with 10% FBS (Gibco) and then switched to opti-MEM medium (Invitrogen) and transfected with 2-4

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