PKD MUTATIONS AND EVALUATION OF SAME

- Athena Diagnostics, Inc.

The present invention relates to methods of detecting novel mutations in a PKD1 and/or PKD2 gene that have been determined to be associated with autosomal dominant polycystic kidney disease (ADPKD) in order to detect or predict the occurrence of ADPKD in an individual.

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Description
RELATED APPLICATION

This application is a Divisional of U.S. patent application Ser. No. 17/008,385, filed Aug. 31, 2020, which is a Divisional of U.S. patent application Ser. No. 14/289,160, filed May 28, 2014, now U.S. Pat. No. 10,760,128, which is a continuation of U.S. patent application Ser. No. 12/309,337, filed Sep. 2, 2009, now U.S. Pat. No. 8,771,946, which is a National Phase of International Patent Application No. PCT/US2007/016705, filed Jul. 24, 2007, which claims priority from U.S. Provisional Patent Application No. 60/832,890, filed Jul. 24, 2006. The contents of these applications are incorporated herein by reference in their entirety.

GOVERNMENT SUPPORT

This invention was made with government support under DK0706 1 7, DK057325, and DK048006, awarded by the National Institutes of Health. The government has certain lights in the invention.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. The ASCII copy, created on Jan. 28, 2014, is named 103779-0367 SL.txt and is 171,496 bytes in size.

BACKGROUND OF THE INVENTION

Autosomal dominant polycystic kidney disease (ADPKD) is an exceptionally common inherited disorder in humans, affecting approximately one in every 600 to 1000 individuals (Gabow P. A., N Engl J Med 329(5):332-342, 1993). The disease is characterized by age dependent growth of renal cysts such that end-stage renal disease (ESRD) typically ensues during mid-adulthood. ADPKD may alternatively, or in addition, involve cysts in other organs including liver and spleen, as well as gastrointestinal, cardiovascular, and musculoskeletal abnormalities (Gabow P. A., N Engl J Med 329(5):332-342, 1993; Gabow P et al., Adv Nephrol 18:19-32, 1989). Both ADPKD type 1 and type 2 share the entire range of renal and extrarenal manifestations, but type 2 appears to have a delayed onset relative to type 1. The common phenotypic complications observed for ADPKD which include hypertension, hematuria and urinary tract infection, seem to be clinically milder in type 2 patients.

Approximately 85 percent of ADPKD cases are caused by mutations in the PKD1 gene [MIM 601313], which is located on chromosome 16, while the remainder are due to mutations in the PKD2 gene [MIM 173910] located on chromosome 4 (Peters et al., Contrib Nephrol 97:128-139, 1992; European Polycystic Kidney Disease Consortium, Cell, 77(6):881-894, 1994; International Polycystic Kidney Disease Consortium, Cell 81(2):289-298, 1995; Hughes J. et al, Nat Genet 10(2):151-160, 1995; Mochizuki T. et al., Science 272(5266):1339-1342, 1996). However, genetic testing for ADPKD has posed a unique set of challenges in terms of DNA diagnostics. PKD1 analysis in particular has been complicated because the 5′ portion of the gene (exons 1-34) is replicated in at least five highly homologous copies (with less than 2% divergence) elsewhere on chromosome 16 (Hughes J. et al, Nat Genet 10(2):151-160, 1995). Further complicating PKD1 mutant analysis, PKD1 has a high rate of potentially non-pathogenic DNA variation; thus the nature of each change detected must be verified. Several techniques have been used to detect mutations in the PKD1 gene including using gene-specific primers to amplify large products screened via nested PCR techniques, denaturing high-performance liquid chromatography (DHPLC) to screen nested PCR products for mutations and direct sequencing of the entire PKD1 coding sequence (Watnick T J et al., Hum Mol Genet 6(9):1473-1481, 1997; Watnick T J et al., Mol Cell 2(2):247-251, 1998; Watnick T. et al., Am J Hum Genet 65(6):1561-1571, 1999; Phakdeekitcharoen B. et al., Kidney Int 58(4):1400-1412, 2000; Phakdeekitcharoen B. et al., J Am Soc Nephrol 12:955-963, 2001; Thomas R. et al., Am J Hum Genet 65(1):39-49, 1999; Perichot R. A., Hum Genet 105(3):231-239, 1999; Perichot R. et al., Eur J Hum Genet 8(5):353-359, 2000; Afzal A. R. et al., Genet 4(4):365-370; Rossetti S. et al., Lancet 361(9376):2196-2201, 2003; Rossetti S. et al., Kidney Int 61:1588-1599, 2002; Rossetti S. et al., Am J Hum Genet 68(1):46-63, 2001, Inoue S. et al., Hum Mutat 19(6):622-628, 2002; Burtey S. et al., J Med Genet 39(6):422-429, 2002; Mizoguchi M. et al., J Hum Genet 46(9):511-517, 2001; Zhang D. Y. et al., Zhonghua Yi Xue Yi Chuan Xue Za Zhi 21(3):211-214, 2004). However, some of these strategies may not be cost effective for routine clinical sample analysis and/or their mutation detection rate has not been established or is inadequate. For example, direct DNA sequencing of the entire coding regions of PKD1 and PKD2 is considered necessary because no mutational hot spots have been identified in either PKD1 or PKD2. Although several pathogenic mutations in PKD1 and PKD2 have been identified, the known mutations do not account for all those individuals with ADPKD. Thus, to accurately diagnose and treat the disease, there remains a need to identify other mutations of PKD1 or PKD2 which are linked to ADPKD.

SUMMARY OF THE INVENTION

Several novel nucleotide sequence alterations in the PKD1 and PKD2 genes have been identified that are associated with ADPKD. The mutations in PKD1 and PKD2 were found by direct sequencing of the genes and the pathogenicity of the mutations determined using a combination of various analyses and algorithms. The mutations in the PKD1 and PKD2 genes identified as pathogenic can be used to detect and/or predict the occurrence of ADPKD in an individual. This is important clinically in diagnostic and prognostic analysis of the genes for ADPKD.

Accordingly, the invention relates to methods of detecting or predicting the occurrence of ADPKD in an individual. In one aspect, the present invention relates to a method of detecting or predicting the occurrence of autosomal dominant polycystic kidney disease (ADPKD) in an individual comprising detecting the presence of one or more nucleotide sequence alterations in a PKD1 gene having the nucleotide sequence of SEQ ID NO:1 or SEQ ID NO:7 in a nucleic acid sample obtained from said individual, wherein said one or more alterations are selected from the group consisting of: a deletion of TTTAA at nucleotide positions 559 to 563 of SEQ ID NO:1, an insertion of CT at nucleotide position 1124 of SEQ ID NO:1, an insertion of an A, T, G, or C at nucleotide position 2291 of SEQ ID NO:1, an insertion of an A, T, G, or C at nucleotide position 2297 of SEQ ID NO:1, an insertion a T at nucleotide position 5365 of SEQ ID NO:1, an insertion of a G at nucleotide position 6666 of SEQ ID NO:1, an insertion of an A at nucleotide position 6881 of SEQ ID NO:1, a deletion of a T at nucleotide position 8713 of SEQ ID NO:1, an insertion of an A, T, G, or C at nucleotide position 9134 of SEQ ID NO:1, an insertion of 5 nucleotides at nucleotide position 9536 of SEQ ID NO:1, a deletion of a T at nucleotide position 10239 of SEQ ID NO:1, a change of a C to an A at nucleotide position 483 of SEQ ID NO:1, a change of a C to a T at nucleotide position 4517 of SEQ ID NO:1, a change of a C to an A at nucleotide position 7006 of SEQ ID NO:1, a change of a C to T at nucleotide position 8267 of SEQ ID NO:1, a change of a G to a T at nucleotide position 8639 of SEQ ID NO:1, a change of a G to an A at nucleotide position 20168 of SEQ ID NO:7, a change of a G to a T at nucleotide position 31025 of SEQ ID NO:7, a change of a G to a C at nucleotide position 33415 of SEQ ID NO:7, a deletion of CAA between nucleotide positions 508 to 516 of SEQ ID NO:1, a deletion of TGG at nucleotide positions 1848 to 1850 of SEQ ID NO:1, a deletion of CCAACTCCG at nucleotide positions 8892 to 8900 of SEQ ID NO:1, a deletion of AAG at nucleotide positions 9905 to 9907 of SEQ ID NO:1, a deletion of CTC at nucleotide positions 10070 to 10072 of SEQ ID NO:1, a deletion of TGG at nucleotide positions 12597 to 12599 of SEQ ID NO:1, a change of a C to an A at nucleotide position 1023 of SEQ ID NO:1, a change of a G to an A at nucleotide position 385 of SEQ ID NO:1, a change of an A to a G at nucleotide position 1470 of SEQ ID NO:1, a change of a C to a T at nucleotide position 4262 of SEQ ID NO:1, a change of a T to an A at nucleotide position 8855 of SEQ ID NO:1, a change of an A to a G at nucleotide position 1794 of SEQ ID NO:1, a change of a G to an A at nucleotide position 6036 of SEQ ID NO:1, a change of a C to a Tat nucleotide position 2042 of SEQ ID NO:1, a change of a C to a Tat nucleotide position 3351 of SEQ ID NO:1, a change of an A to a Gat nucleotide position 6756 of SEQ ID NO:1, a change of a C to a T at nucleotide position 5793 of SEQ ID NO:1, a change of a C to a T at nucleotide position 6707 of SEQ ID NO:1, a change of a G to a Cat nucleotide position 10187 of SEQ ID NO:1, a change of a C to a G at nucleotide position 7116 of SEQ ID NO:1, a change of an A to a G at nucleotide position 10311 of SEQ ID NO:1, a change of a T to a Cat nucleotide position 7554 of SEQ ID NO:1, a change of a C to a T at nucleotide position 7757 of SEQ ID NO:1, a change of a T to a Cat nucleotide position 8067 of SEQ ID NO:1, a change of a C to a Tat nucleotide position 8138 of SEQ ID NO:1, a change of a C to a Tat nucleotide position 8509 of SEQ ID NO:1, a change of a C to an A at nucleotide position 10096 of SEQ ID NO:1 and a change of a C to a T at nucleotide position 12658 of SEQ ID NO:1. The detection of one or more of the listed nucleotide sequence alterations indicates that the individual has ADPKD or will develop ADPKD. In one embodiment, at least one nucleotide sequence alteration other than the one or more nucleotide sequence alterations listed above is also detected in SEQ ID NO:1 and/or SEQ ID NO:4, wherein the at least one nucleotide sequence alteration which is also detected is associated with ADPKD. In another aspect, the one or more nucleotide sequence alterations are detected by sequencing, polymerase chain reaction (PCR), DHPLC or combinations of the foregoing.

The present invention also relates to a method of detecting or predicting the occurrence of autosomal dominant polycystic kidney disease (ADPKD) in an individual comprising detecting the presence of one or more nucleotide sequence alterations in a PKD2 gene having the nucleotide sequence of SEQ ID NO:4 in a nucleic acid sample obtained from said individual, wherein said one or more alterations are selected from the group consisting of: an insertion of an A at nucleotide position 2226 of SEQ ID NO:4, a deletion of AG at nucleotide positions 2422 to 2423 of SEQ ID NO:4, a change of a C to a T at nucleotide position 2680 of SEQ ID NO:4, IVS7-1G>A, IVS8+5G>A, a deletion of TGG at nucleotide positions 374-376 of SEQ ID NO:4 and a deletion of TTC between nucleotide positions 1876-1881 of SEQ ID NO:4, wherein detection of the one or more nucleotide sequence alterations indicates that the individual has ADPKD or will develop ADPKD. In one embodiment, at least one nucleotide sequence alteration other than the one or more nucleotide sequence alterations listed above is also detected in SEQ ID NO:1 and/or SEQ ID NO:4, wherein the at least one nucleotide sequence alteration also detected is associated with ADPKD. In yet another embodiment, the one or more nucleotide sequence alterations are detected by sequencing, PCR, DHPLC or combinations thereof.

The present invention further relates to a method for detecting in an individual the presence or absence of a mutant PKD gene comprising obtaining a nucleic acid sample from the individual and detecting the presence or absence of one or more nucleotide sequence alterations in a PKD1 or PKD2 gene of the individual, wherein the one or more alterations are selected from the group consisting of: a deletion of TTTAA at nucleotide positions 559 to 563 of SEQ ID NO: 1, an insertion of CT at nucleotide position 1124 of SEQ ID NO:1, an insertion of an A, T, G, or C at nucleotide position 2291 of SEQ ID NO:1, an insertion of an A, T, G, or C at nucleotide position 2297 of SEQ ID NO:1, an insertion of a Tat nucleotide position 5365 of SEQ ID NO:1, an insertion of a G at nucleotide position 6666 of SEQ ID NO:1, an insertion of an A at nucleotide position 6881 of SEQ ID NO:1, a deletion of a T at nucleotide position 8713 of SEQ ID NO:1, an insertion of an A, T, G, or C at nucleotide position 9134 of SEQ ID NO:1, an insertion of 5 nucleotides at nucleotide position 9536 of SEQ ID NO:1, a deletion of a Tat nucleotide position 10239 of SEQ ID NO:1, a change of a C to an A at nucleotide position 483 of SEQ ID NO:1, a change of a C to a T at nucleotide position 4517 of SEQ ID NO:1, a change of a C to an A at nucleotide position 7006 of SEQ ID NO:1, a change of a C to T at nucleotide position 8267 of SEQ ID NO:1, a change of a G to a T at nucleotide position 8639 of SEQ ID NO:1, a change of a G to an A at nucleotide position 20168 of SEQ ID NO:7, a change of a G to a T at nucleotide position 31025 of SEQ ID NO:7, a change of a G to a C at nucleotide position 33415 of SEQ ID NO:7, a deletion of CAA between nucleotide positions 508 to 516 of SEQ ID NO:1, a deletion of TGG at nucleotide positions 1848 to 1850 of SEQ ID NO:1, a deletion of CCAACTCCG at nucleotide positions 8892 to 8900 of SEQ ID NO:1, a deletion of AAG at nucleotide positions 9905 to 9907 of SEQ ID NO:1, a deletion of CTC at nucleotide positions 10070 to 10072 of SEQ ID NO:1, a deletion of TGG at nucleotide positions 12597 to 12599 of SEQ ID NO:1, a change of a C to an A at nucleotide position 1023 of SEQ ID NO:1, a change of a G to an A at nucleotide position 385 of SEQ ID NO:1, a change of an A to a G at nucleotide position 1470 of SEQ ID NO:1, a change of a C to a T at nucleotide position 4262 of SEQ ID NO:1, a change of a T to an A at nucleotide position 8855 of SEQ ID NO:1, a change of an A to a G at nucleotide position 1794 of SEQ ID NO:1, a change of a G to an A at nucleotide position 6036 of SEQ ID NO:1, a change of a C to a T at nucleotide position 2042 of SEQ ID NO:1, a change of a C to a Tat nucleotide position 3351 of SEQ ID NO:1, a change of an A to a Gat nucleotide position 6756 of SEQ ID NO:1, a change of a C to a T at nucleotide position 5793 of SEQ ID NO:1, a change of a C to a T at nucleotide position 6707 of SEQ ID NO:1, a change of a G to a C at nucleotide position 10187 of SEQ ID NO:1, a change of a C to a G at nucleotide position 7116 of SEQ ID NO:1, a change of an A to a G at nucleotide position 10311 of SEQ ID NO:1, a change of a T to a Cat nucleotide position 7554 of SEQ ID NO:1, a change of a C to a T at nucleotide position 7757 of SEQ ID NO:1, a change of a T to a Cat nucleotide position 8067 of SEQ ID NO:1, a change of a C to a Tat nucleotide position 8138 of SEQ ID NO:1, a change of a C to a Tat nucleotide position 8509 of SEQ ID NO:1, a change of a C to an A at nucleotide position 10096 of SEQ ID NO:1, a change of a C to a Tat nucleotide position 12658 of SEQ ID NO:1, a change of a C to an A at nucleotide position 7476 of SEQ ID NO:1, a change of a C to a G at nucleotide position 3527 of SEQ ID NO:1, a change of a C to an A at nucleotide position 1947 of SEQ ID NO:1, a change of an A to a G at nucleotide position 3312 of SEQ ID NO:1, a change of a C to a G at nucleotide position 4391 of SEQ ID NO:1, a change of a T to an A at nucleotide position 11040 of SEQ ID NO:1, a change of a G to a T at nucleotide position 840 of SEQ ID NO:1, a change of a G to an A at nucleotide position 7197 of SEQ ID NO:1, a change of a G to a C at nucleotide position 351 of SEQ ID NO:1, a change of a G to an A at nucleotide position 4757 of SEQ ID NO:1, a change of an A to a C at nucleotide position 1023 of SEQ ID NO:1, an insertion of: an A at nucleotide position 2226 of SEQ ID NO:4, a deletion of AG at nucleotide positions 2422 to 2423 of SEQ ID NO:4, a change of a C to a T at nucleotide position 2680 of SEQ ID NO:4, IVS7-1G>A, IVS8+5G>A, a deletion of TGG at nucleotide positions 374-376 of SEQ ID NO:4, a deletion of TTC between nucleotide positions 1876-1881 of SEQ ID NO:4 and a change of a G to an A at nucleotide position 634 of SEQ ID NO:4, wherein detection of the one or more nucleotide sequence alterations is indicative of a mutant PKD gene. In one embodiment, the presence or absence of the one or more nucleotide sequence alterations in the PKD1 or PKD2 gene of the individual indicates that the individual has ADPKD. In another embodiment, the presence or absence of one or more nucleotide sequence alterations in the PKD1 or PKD2 nucleic acid sequence is detected by sequencing, PCR and/or DHPLC.

The identification of mutations associated with ADPKD provides conclusive diagnostic information, allows the blood relatives of an individual to be pre-symptomatically and inexpensively evaluated for counseling and planning using targeted PKD gene analysis and allows prospective living-related kidney donors to be tested and subsequently accepted or rejected for donation with greater certainty. Pre-symptomatic testing for ADPKD may be particularly relevant not only in the evaluation of living kidney donors from ADPKD families, but also in the early detection for treatment with new agents that may be indicated for use early in the course of the disease (e.g., before cystic disease is apparent), family planning, the detection of ADPKD in young individuals (e.g., those under 30) for whom ultrasound imaging may not be accurate and/or adequate or in those families with PKD2-associated ADPKD, a clinically milder disease. In addition, clinicians may encounter patients with atypical cystic disease in whom the diagnosis is not obvious. Thus, using the novel, pathogenic mutations identified in the PKD1 and PKD2 genes, the methods of the invention help to better assist in the diagnosis and management of existing ADPKD and/or predict the likelihood of the occurrence of ADPKD in an individual.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1E depict the PKD1 coding sequence (GenBank Accession No. L33243) (SEQ ID NO:1).

FIGS. 2A-2B depict the PKD2 coding sequence (GenBank Accession Nos. AF004859-AF004873) (SEQ ID NO:4).

FIGS. 3A-3T depict wild-type PKD1 cDNA coding sequence according to one embodiment of the invention. Exon and PCR product junctions are depicted above the nucleotide sequence and amino acids are positioned under the center of each codon.

FIGS. 4A-4D depict wild-type PKD2 cDNA coding sequence according to one embodiment of the invention. Exon and PCR product junctions are depicted above the nucleotide sequence and amino acids are positioned under the center of each codon.

FIG. 5A illustrates missense mutations affecting the PKD1 repeats and C-lectin domain. Changes that disrupt the consensus sequence are red (dark-shaded) those that do not are yellow (light-shaded). Consensus sequence code: 1 (aliphatic), a (aromatic), c (charged), s (small residue), p (polar residue), b (big residue), h (hydrophobic), capital letters represent the corresponding amino acid codon. FIG. 5A discloses SEQ ID NOS 8-23, respectively, in order of appearance.

FIGS. 5B and 5C illustrate ribbon diagrams of the PKD repeat (5B) and C-lectin domain (5C) with potential pathogenic missense changes indicated.

FIG. 6 illustrates a schematic of PKD1 mutant polypeptides with the location of each amino acid substitution indicated, M (missense) or P (polymorphism) and a photograph of a western blot of the full-length, flagged-tagged PKD1 constructs for each mutant protein and any cleavage products. FL: full-length, NTF: PKD1 N-terminal cleavage fragment, CTF; PKD1 C-terminal cleavage fragment.

FIGS. 7A-7B are schematics illustrating all the PKD1 (5A) and PKD2 (5B) mutations identified. Numbers 1-113 refer to identifiers of the mutations in Table 8.

FIGS. 8A and 8B are schematic representations of polycystin-1 (PC-1) (8A) and polycystin-2 (PC-2) (8B). The location of pathogenic (Class I and Class II, see Example) mutations are indicated.

 DETAILED DESCRIPTION OF THE INVENTION

The PKD genes are genomic DNA sequences that map to chromosomal position 16p13.3 (PKD1) or chromosomal position 4q21-23 (PKD2) and give rise to messenger RNA molecules encoding PKD1 and PKD2 proteins. The PKD1 and PKD2 genes comprise the sequences of SEQ ID NO:1 and SEQ ID NO:4, respectively, which include introns and putative regulatory sequences. Like many other genes, PKD1 and PKD2 gene sequences, when compared among individuals, show sequence variations that do not affect gene expression or expression and/or function of the gene product.

The PKD1 gene (e.g., GenBank Accession Number L39891, SEQ ID NO:7) spans about 54 kb of genomic DNA on chromosome 16 (16p13.3) and contains a 12,906 basepair coding sequence divided into 46 exons from which a 14 kb mRNA is transcribed. The protein product of PKD1, polycystin-1 (PC-1) (GeneBank Accession No. AAC37576, SEQ ID NO:3), is a 4303 amino acid protein with a predicted mass of 460 kDa which forms multiprotein complexes at the cell membrane and is thought to function in cell-cell and cell-matrix signal regulation. (Arnould T et al., J Biol. Chem 273:6013-6018, 1992; Parnell S. C. et al., J Biol Chem, 277:19566-19572, 2002; Bhunia A. K. et al., Cell, 109:157-168, 2002; Nauli S. M. et al., Nat Genet 33:129-137, 2003). Approximately 75% of the PKD1 gene is duplicated and shares about 97% identity with its homologous copies. The reiterated region encompasses a 50 kb (5′) portion of the gene containing the first 34 exons. Only the most 3′, 5.7 kb of the gene, containing exons 35-46, is unique to PKD1. Another notable feature of the PKD1 gene is a polypyrimidine tract in intron 21 that is 2.5 kb long, the longest described in the human genome.

The PKD2 gene (see e.g., GenBank Accession Numbers AF004859 (exon1)-AF004873 (exon 15), SEQ ID NO:4) (see also GenBank Accession Number V50928) spans 68 kb of genomic DNA and is located on chromosome 4 (4q21-23). PKD2 contains 15 exons and encodes a 5.4 kb transcript (see e.g., GenBank Accession Number NM000297) from which a 968-amino acid protein product, polycystin-2 (PC-2) of approximately 110 kDa is generated (SEQ ID NO:6) (see also GenBank Accession Number NP00288). Polycystin-2 has been shown to interact with the carboxy-terminus of PC-1 and functions as a cation channel in complex with PC-1. (Gonzalez-Perrett S. et al., Proc Natl Acad Sci USA 98:1182-1187, 2000; Vassilev P. M. et al, Biochem Biophys Res Commun 282:341-350, 2001; Koulen P. et al., Nat Cell Biol 4:191-197, 2002; Hanaoka K. et al., Nature 408:990-994, 2000). Unlike PKD1, PKD2 is a single copy gene, making its analysis much more straight-forward. See Table 1 for a summary of the PKD genes. Further discussion of PKD1 and PKD2 genes, gene and protein alterations and methods of detecting the same can be found in US 2006/0246504, US 2003/0008288, WO 2002/006529, US 2005/017399, U.S. Pat. Nos. 7,083,915, 6,031,088, 6,228,591, US 2007/0166755, US 2005/0100898, U.S. Pat. Nos. 6,916,619, 6,656,681, 6,485,960, 6,380,360 and WO 1995/018225, which are all herein incorporated by reference.

TABLE 1 PKD gene description Gene Description PKD1 PKD2 Chromosome 16p13.3 4q21-23 Genomic length 54 kb 68 kb Exons 46 15 Base pairs 12,909 2,904 Codons 4,303 968 Protein Polycystin-1 Polycystin-2 Analysis: Total Long Range PCRs 8 — 8 Amplicons 54 17 71 Base Pairs evaluated 13,830 3,204 17,034 (including adjacent intronic sequence)

PKD Gene Analysis

Genomic DNA obtained from a sample from a subject can be used as the template for generating one or more PKD-specific amplification products (e.g., long-range PKD amplification products). DNA testing is advantageous as it has the potential to provide genetic information to an isolated individual (e.g., when family members are unavailable for linkage studies. Both copies of the PKD genes in an individual should be analyzed/sequenced to identify bona fide gene mutations, as mutations have been detected on a normal haplotype and/or in combination with other amino acid truncating mutations.

A sample can be a biological material which is isolated from its natural environment containing target nucleic acid (e.g., a nucleic acid comprising a PKD gene), and may consist of purified or isolated nucleic acid, or may comprise a biological sample such as a tissue sample, a biological fluid sample, or a cell sample comprising the target nucleic acid. Collecting a tissue sample also includes in vitro harvest of cultured human cells derived from an individual's tissue or any means of in vivo sampling directly from a subject, for example, by blood draw, spinal tap, tissue smear or tissue biopsy. Optionally, tissue samples can be stored before analysis by well known storage means that preserve a sample's nucleic acid(s) in an analyzable condition, such as quick freezing, or a controlled freezing regime, in the presence of a cryoprotectant, for example, dimethyl sulfoxide (DMSO), glycerol, or propanediol-sucrose. Tissue samples can also be pooled before or after storage for purposes of amplifying them for analysis. In some embodiments, the sample contains DNA, tissue or cells from two or more different individuals. In another embodiment, the amount of sample necessary to analyze a PKD gene is dependent on the type of sample (e.g., more than 5 milliliters of blood) and this amount is best assessed by one of skill in the art. Preferably, aseptic techniques are used to obtain these samples to avoid their contamination.

Methods of isolating genomic DNA from a particular sample are well known and routine (see Sambrook et al., supra, 1989). In a particular embodiment, amplification of the genomic PKD DNA has advantages over the cDNA amplification process, including, for example, the allowance of the analysis of exons and introns of the PKD gene. As such, a target sequence of interest associated with either an intron or exon sequence of a PKD gene can be amplified and characterized. A target sequence of interest is any sequence or locus of a PKD gene that contains or is thought to contain a nucleotide sequence alteration, including those alterations that correlate with a PKD-associated disorder or disease (e.g., ADPKD).

Mutations in a PKD gene can be detected by amplification, including, for example, by polymerase chain reaction (PCR), ligase chain reaction, self sustained sequence replication, a transcriptional amplification system, Q-Beta Replicase, or any other nucleic acid amplification method, followed by the detection of the amplification products. Accordingly, in one embodiment, genomic DNA extracted from whole blood serves as a template for highly specific PKD1 gene amplification by long-range amplification of 8 segments encompassing the entire PKD1 duplicated region. The specific long-range amplification prevents the spurious amplification of PKD1 homologs that would otherwise confound the analysis. These PKD1 homologs are sequences which are closely related to PKD1, but which do not encode an expressed PKD1 gene product. In fact, analysis of the PKD1 gene had not been amenable to genetic analysis largely because of the presence of at least three highly homologous copies of the gene that map proximal to PKD1 along chromosome 16 (16p13.1). The sequence of these PKD1 gene homologs are contained in GenBank Accession Nos. AC002039, AC010488, AC040158, AF320593 AND AF320594 (each of which is incorporated herein by reference). Several examples of such homologs that map to chromosomal location 16p13.1 or 4q21-23 have been identified and sequenced. A PKD1 homologue may share more than 95% sequence identity to an authentic PKD gene.

In some embodiments of the invention, a nested amplification is performed using amplified products in a preceding amplification reaction as templates. Preferably, the nested amplification reaction is a nested PCR using PCR amplified products from a preceding PCR reaction as templates. In addition to optimizing the annealing temperature of the primers, “nested” amplification can be used to increase the specificity and sensitivity of the PKD-specific amplification assay. For example, a method comprising a nested PCR can involve two sequential PCR reactions. After multiple cycles of PCR (e.g., 10 to 40, or 10 to 30 or 10 to 20 cycles) with the first pair of primers comprising at least one PKD-specific primer (e.g., a PKD-specific primer and a control primer or two PKD-specific primers), a small amount aliquot of the first reaction (e.g., 1 μl of a 50 μl reaction) serves as the template for a second round comprising multiple cycles of PCR reaction (e.g., 10 to 40, or 10 to 30 or 10 to 20 cycles) with a new set of primers comprising at least one PKD-specific primer (e.g., a PKD-specific primer and a control primer or two PKD-specific primers) that anneal to sequences internal to, or nested between, the first pair.

In a particular embodiment, the 8 long range PCR products described above serve as template for 43 nested PCR reactions and cover exons 1-34 of the PKD1 gene. The unique region of the PKD1 gene (exons 35-46) and the entire PKD2 gene are amplified from genomic DNA as 28 additional gene segments. Using the nested PCR procedure, the template that is successfully amplified is selected twice for PKD-specificity. The use of nested PCR can also greatly enhance the yield of the species-specific product and, therefore, the sensitivity of the assay, when a single primer pair fails by itself.

Methods for designing primers and for performing PCR are known in the art (see Current Protocols in Molecular Biology, supra). The general criteria for selecting primers applies to primers for both the long-range PCR and nested PCR. With regard to primer for the nested PCR, both nested primers should anneal to sequences internal to (e.g., within) the first pair of primers and at least one of the nested primers. Some PKD1-specific primers which eliminate unintended amplification of PKD1 homologs have been developed (see, e.g., U.S. 2003/0008288, which is incorporated herein by reference). Other such primers can be designed, where a “PKD-specific” primer would be a nucleic acid sequence which anneals to a sequence within a PKD gene (including introns and exons) under specific stringent conditions. A PKD-specific primer, anneals to a unique site present in the authentic expressed PKD1 gene, and not to PKD1 homologs or other sequences under specific stringent conditions. Thus, PKD-specific primers can be designed using these unique PKD sites. The length of a unique site may vary from several nucleotides to thousands of nucleotides. Most of unique sites that have been identified comprises less than or equal to 100 nucleotides, e.g., less than or equal to 50 nucleotides, or less than or equal to 30 nucleotides. Amplification using PKD-specific primers increases the specificity of the amplification reaction and reduces the amount of by-products amplified from PKD homologs. The primers may be 10 to 60 nucleotides in length, for example, 18-52 nucleotides in length.

The 71 PCR products are bi-directionally sequenced to detect nucleotide sequence alterations. In a particular embodiment, all PCR primers comprise a tag (e.g., M13 forward and reverse primer sequences) to permit bi-directional sequencing of all fragments with the same primers. Methods of sequencing DNA are well-known in the art and are dependent on the primer position and/or fragment length. For example, in one embodiment, sequencing is performed using ABI Big Dye terminator chemistry followed by electrophoresis on an ABI 3730 capillary sequencer. Nucleotide alterations of the invention can be detected in a PKD sequence to assess existing or potential ADPKD. Novel alterations identified can be clinically interpreted as disease-associated mutations, for example, frameshift or nonsense mutations or invariant splice site changes. Benign polymorphisms would include silent or conservative missense mutations, intronic variants and synonymous codon changes.

Sequence alterations in a PKD gene can also be detected using denaturing high performance liquid chromatography (DHPLC). DHPLC has been used to detect sequence variants by separating a heteroduplex (resulting from the presence of a mutation) and a homoduplex having the same basepair length. This separation is based on the fact that a heteroduplex has a lower melting temperature (Tm) than a homoduplex. DHPLC can separate heteroduplexes that differ by as little as one base pair under certain conditions. The “heteroduplex site separation temperature” or “midpoint temperature” or “Tm” is defined herein to mean, the temperature at which one or more base pairs denature, i.e., separate, at the site of base pair mismatch in a heteroduplex DNA fragment. When DHPLC is carried out at a partially denaturing temperature, i.e., a temperature sufficient to denature a heteroduplex at the site of a base pair mismatch, homoduplexes can be separated from heteroduplexes having the same base pair length and detected by various methods (e.g., gel electrophoresis). DHPLC can also be used to separate duplexes having different basepairs in length.

Evaluation of Identified PKD Nucleotide Alterations

Numerous novel nucleotide alterations in PKD have been identified (see Tables 4-7). These sequence alterations were then evaluated to determine whether they were pathogenic, this is, resulted in an altered PKD gene product (e.g., protein, polypeptide). A “nucleotide sequence alteration” or “nucleotide alteration” or “mutation” refers to a nucleotide sequence modification including one or more substitutions (transitions or transversions), deletions (including loss of locus), insertions (including duplications), translocations, inversions and/or other modifications relative to a normal PKD gene (e.g., SEQ ID NO:1, SEQ ID NO:7 or SEQ ID NO:4). Thus, a nucleotide alteration/change in a PKD1 or PKD2 nucleotide sequence (e.g., DNA or mRNA) can be a deletion, insertion, substitution or inversion, or can be silent such that there is no change in the reading frame of a polypeptide encoded by the PKD polynucleotide. Pathogenic mutations are those nucleic acid alterations that result in an amino acid change (e.g., a non-silent or non-conservative change) and/or introduces a STOP codon into the nucleotide sequence, or changes nucleotide sequence involved in transcription or translation of the PKD1 or PKD2 nucleotide sequence; for example, a change that results in altered splicing of a PKD1 or PKD2 gene transcript into an mRNA (see FIGS. 7A and 7B). An “amino acid alteration” refers to an amino acid modification including a substitution, a frameshift, a deletion, a truncation and an insertion, and/or other modifications relative to the normal PKD amino acid sequence (e.g., SEQ ID NO:3 or SEQ ID NO:6). Thus, a mutation in a PKD gene sequence can result in the expression of a truncated PKD polypeptide, or even a complete loss of expression of the PKD polypeptide.

In contrast, polymorphic mutations or variants are those nucleic acid alterations that do not alter and/or are not expected to alter a PKD protein/polypeptide in the above-described manner and/or do not correlate with the signs or symptoms of a PKD-associated disorder such as ADPKD (see Tables 8 and 9). These mutations include, for example, nucleotide substitutions that do not result in a change in the encoded amino acid, i.e., silent mutations, in which the wild type (see, e.g., SEQ ID NOs:1, 7 or 4) and mutant codons both encode the same amino acid; those that do not segregate with the disease or those that are found in a panel of unaffected individuals. Nucleic acid alterations that cause conservative amino acid substitutions in which a wild-type amino acid (see, e.g., SEQ ID NOs:3 or 6) is substituted for another amino acid with similar properties, may also be non-pathogenic polymorphic mutations, as it would be expected that the secondary structure and hydropathic nature of the PKD polypeptide would be substantially unchanged by these mutations. In general, the following groups of amino acid substitutions are thought to be conservative: (1) ala, pro, gly, glu, asp, gln, asn, ser, thr; (2) cys, ser, tyr, thr; (3) val, ile, leu, met, ala, phe; (4) lys, arg, his; and (5) phe, tyr, trp, his. With respect to PKD mutations, polymorphisms are then defined as: (i) sequence variants not predicted to alter an amino acid; (ii) missense changes found in homozygosity in at least one individual; (iii) intronic sequences of unknown significance; or (iv) changes in the 3′ UTR of unknown significance. Accordingly, polymorphic mutations would be expected to result in a PKD protein/polypeptide that is still properly expressed and/or fully functional; that is, these variants would not be expected to be associated with ADPKD.

Nucleotide sequence alterations identified in PKD1 and PKD2 genes can be evaluated for pathogenicity in a number of ways. Mutant PKD nucleotide sequence can be compared to wild-type PKD sequence (SEQ ID NOs:1 and 4) and the effect of the nucleic acid sequence alterations on amino acid codon(s) assessed. For example, a change in nucleotide sequence that produces a stop codon (e.g., UGA, UAA, UAG) or a frameshift, which generally results in a nonsensical polypeptide and/or also produces a stop codon, or that alters a consensus donor/acceptor splice site would result in a non-functional PKD protein, a truncated PKD protein, or obliterate its expression altogether. These mutations would be expected to be pathogenic and thus correlates with ADPKD.

PKD nucleic acid sequence alterations that do not result in the production of a stop codon, frameshift or splice site mutation can also be assessed by comparing the mutant PKD amino acid sequence to the wild-type PKD amino acid sequence from various species to determine if the alteration affects an amino acid residue that is conserved across several species. In particular, an amino acid change (i.e., a missense mutation) or a deletion of several adjacent nucleotide residues (e.g., a deletion of 3, 6 or 9 nucleotides) which would cause a complete deletion of one or more amino acid residues (i.e., an in-frame deletion; see also Table 5) would result in a PKD polypeptide that is still expressed. The change or loss of an amino acid residue conserved across several species (e.g., human, canine, mouse, fish, fruit fly, nematode, etc), where a “conserved” amino acid residue is one that is identical or has similar properties (e.g., ala, pro, gly, glu, asp, gln asn, ser, thr), would strongly indicate that the amino acid residue is important/critical to PKD protein function. Accordingly, such PKD mutations might also be expected to be associated with and/or predictive of ADPKD.

Furthermore, there are also several algorithms that can be used to predict/evaluate alterations to a PKD nucleic acid sequence, particularly those that result in a missense mutation. These algorithms include, for example, the Miller/Kumar matrix (Miller M. P. and Kumar S., Hum Mol Genet 10(21):2319-2328, 2001); Grantham's chemical difference matrix; Online Mendelian Inheritance in Man (OMIM), //www.ncbi.nlm.nih.gov/Omim/; Splice Site Prediction by Neural Network (SSPNN) (see also Reese M. G. et al., J Comput Biol 4(3):311-323, 1997), fruitfly.org.seqtools/splice.html; Automated Splice Site Analyses (ASSA) (see also, Nalla V. K. et al., Hum Mutat 25(4):334-342, 2005 and Rogan P. K. et al., Hum Mutat 12(3)153-171, 1998), //splice.cmh.edu/; Simple Modular Architecture Research Tool (SMART), //smart.embl.de; Pfam, www.sanger.ac.uk/Software/Pfam.; MDRD equation: //nephron.com/cgi-bin/MDRDSI.cgi; Prediction of Protein Sorting Signals and Localization Sites in Amino Acid Sequences II (PSORT II) (see also Krogh A. et al., J Mol Biol 305:567-580, 2001), //psort.ims.u-tokyo.ac.jp/form2.html; and Transmembrane Helices Prediction (TMHMM), (see also Grimm D. H. et al, J Biol Chem 278:36786-36793, 2003), //www.cbs.dtu.dk.services/TMHMM/. By predicting mRNA and/or protein structure, function and motifs, these and other algorithms can help determine the likelihood that a mutation (e.g., a missense mutation) represents a pathogenic change as opposed to a polymorphism.

Further assessment of PKD mutations not clearly pathogenic could also be aided with a dataset comprising complete sequence information from a population of unaffected, ethnically diverse individuals. Normal or wild-type PKD1 and PKD2 sequence information from such a population would be a useful control for comparison to novel PKD mutations identified to both evaluate the presence or absence of a sequence variant in the control population and expand the spectrum of known non-pathogenic sequence variants. Having such a dataset to compare to PKD mutations that have been identified would be advantageous diagnostically and prognostically, especially in the analysis of individuals having less than a 50% probability of having ADPKD (e.g., individuals not the progeny and/or siblings of an individual with ADPKD).

The effect of mutations in a PKD gene on a PKD gene product can be assessed and/or confirmed by expressing a polynucleotide having or constructed (e.g., a recombinant polynucleotide) to have the identified mutation(s). The polynucleotide can comprise the mutant PKD polypeptide or a portion of a recombinant nucleic acid molecule, which, for example, can encode a fusion PKD protein (e.g., a tagged PKD protein). The mutant polynucleotide or recombinant nucleic acid molecule can be inserted into a vector, which can be an expression vector, and can be derived from a plasmid, a virus or the like. The expression vector generally contains an origin of replication, a promoter, and one or more genes that allow phenotypic selection of transformed cells containing the vector. Expression vectors suitable for use are well-known in the art e.g., a T7-based expression vector for expression in bacteria, a pMSXND expression vector for expression in mammalian cells or baculovirus-derived vectors for expression in insect cells and the like. The choice of a vector will depend on the size of the polynucleotide sequence and the host cell to be employed. Thus, the vector used in the methods of the invention can be plasmids, phages, cosmids, phagemids, viruses (e.g., retroviruses, parainfluenzavirus, herpesviruses, reoviruses, paramyxoviruses, and the like), or selected portions thereof (e.g., coat protein, spike glycoprotein, capsid protein). For example, cosmids and phagemids are typically used where the specific nucleic acid sequence to be analyzed or modified is large because these vectors are able to stably propagate large polynucleotides. Cosmids and phagemids are particularly suited for the expression or manipulation of a PKD polynucleotide (e.g., SEQ ID NO:1) or a mutant PKD1 polynucleotide.

A variety of host-expression vector systems can be utilized to express wildtype PKD polynucleotide sequence (e.g., SEQ ID NO:1 or SEQ ID NO:4), the PKD coding sequence (e.g., SEQ ID NO:2 or SEQ ID NO:5) and a variant or mutant PKD1 or PKD2 polynucleotide. In a particular embodiment, the PKD polynucleotide(s) is tagged (e.g., FLAG, Myc, biotin, streptavadin, avadin and the like) to aid in purification and/or visualization of the PKD polypeptide after it has been exposed. Such host-expression systems represent vehicles by which the nucleotide sequences of interest can be produced and subsequently purified, and also represent cells that, when transformed or transfected with the appropriate nucleotide coding sequences, can express a PKD protein, including a PKD variant or mutant polypeptide or peptide portion thereof in situ. Such cells include, but are not limited to, microorganisms such as bacteria (e.g., E. coli, B. subtilis) transformed with recombinant bacteriophage DNA, plasmid DNA or cosmid DNA expression vectors containing a PKD1 polynucleotide, or oligonucleotide portion thereof (wild type, variant or other mutant); yeast (e.g., Saccharomyces, Pichia) transformed with recombinant yeast expression vectors containing a PKD polynucleotide, or oligonucleotide portions thereof (wild type, variant or other PKD mutant); insect cell systems infected with recombinant virus expression vectors (e.g., baculovirus) containing a PKD polynucleotide, or oligonucleotide portion thereof (wild type, PKD variant or other mutant); plant cell systems infected with recombinant virus expression vectors (e.g., cauliflower mosaic virus or tobacco mosaic virus) or transformed with recombinant plasmid expression vectors (e.g., Ti plasmid) containing a mutant PKD polynucleotide, or oligonucleotide portion thereof; or mammalian cell systems (e.g., HEK293, COS, CHO, BHK, 3T3) harboring recombinant expression constructs containing promoters derived from the genome of mammalian cells (e.g., metallothionein promoter) or from mammalian viruses (e.g., the adenovirus late promoter; the vaccinia virus 7.5K promoter). Further discussion of vectors and expressions systems for PKD polynucleotides can be found, for example, in US 2003/0008288.

For instance, the PKD1 gene product, polycystin-1 (PC-1), which is believed to function as a cell surface signaling receptor at cell-cell and cell-matrix junctions and as a mechano-sensor in renal cells, is an 11-transmembrane glycoprotein with a long N-terminal extracellular region and short cytoplasmic tail (Boletta A. and Germino G. G., Trends Cell Biol 13(9):484-492, 2003; Harris P. C. and Tones V. E., Curr Opin Nephrol Hypentens 15(4):456-463, 2006; Nauli S. M. et al., Nat Genet 33(2):129-137, 2003; Hughes J. et al., Nat Genet 10(2):151-160, 1995) (see also FIG. 8A). PC1 has several amino acid sequence motifs of interest (e.g., receptor for egg jelly (REJ) domain, G-protein coupled receptor proteolytic site (GPS), C-type lectin domain, leucine rich repeat (LRR), polycystic kidney disease repeat (PKD-R), transmembrane domain (TM), coiled-coil domain (CC)) (see also FIG. 4). A site useful for evaluation of PC-1 function/activity is the GPS domain, a site at which the PC-1 protein undergoes cleavage (Qian F. et al., Proc Natl Acad Sci USA 99(26):16981-16986, 2002). Cleavage of PC1 at this site produces an N-terminal fragment (NTF) and a C-terminal fragment (CTF) and this cleavage is critical for normal PC-1 function (Qian F. et al., Proc Natl Acad Sci USA 24:99(26):16981-16986). Thus, expression and cleavage of the PKD1 gene product can be used to assess the pathogenicity of identified PKD1 mutations, particularly missense mutations. PKD1 mutants can be constructed (e.g., in an expression vector) and expressed (as, e.g., a recombinantly tagged fusion protein) in the above-described manner and the cleavage of the PKD1 mutant gene products assayed (e.g., by immunoprecipitation and/or western blot, fluorescence of a tag, radioactivity or the like).

One or more of the above-described methods to assess/evaluate PKD mutations can be used to determine whether PKD1 or PKD2 gene mutations that have been identified are benign polymorphisms or pathogenic, such that the mutations can be associated with ADPKD and, subsequently used to diagnose or predict ADPKD in, for instance, the methods of the invention.

Methods of the Invention

The PKD mutations identified and determined to be pathogenic are listed in Tables 4-7. These mutations are used in the methods of the invention to detect or predict the occurrence of ADPKD in an individual or detect the presence or absence of a mutant PKD gene in an individual. Specifically, ADPKD is detected or the occurrence of ADPKD is predicted by detecting the presence of one or more of the identified nucleotide sequence alterations in a PKD1 gene having the nucleotide sequence of SEQ ID NO:1 or SEQ ID NO:7 in a nucleic acid sample obtained from an individual. Similarly, ADPKD can be detected or predicted in an individual using the methods of the invention by detecting the presence of one or more of the identified nucleotide sequence alterations in a PKD2 gene having the nucleotide sequence of SEQ ID NO:4 in a nucleic acid sample obtained from an individual. As several mutations in the PKD genes that are associated with ADPKD have been detected in just a single individual/family (see e.g., Table 7), these other nucleotide sequence alterations in a PKD1 gene (e.g., SEQ ID NO:1 or 7) and/or PKD2 gene (SEQ ID NO:4) not listed above (see Summary of Invention and Tables 4-7) can also be detected in the methods of the invention. The methods can be performed by obtaining a sample (e.g., biological fluid, tissue, cell) from an individual by one or more procedures (e.g., DNA isolation method/kit) and/or one or more methods (e.g., sequencing, PCR, DHPLC) as described above.

In addition, the invention relates to methods of detecting the presence or absence of a mutant PKD gene in an individual by obtaining a nucleic acid sample from the individual (e.g., biological fluid, tissue or cell sample), by the above-described methods (e.g., DNA isolation method/kit) and detecting the presence or absence of one or more of the identified nucleotide sequence alterations in a PKD1 or PKD2 gene, by using one or more of the above-described processes (e.g., sequencing, PCR, DHPLC or the like). In a particular embodiment, detection of one or more of the identified PKD nucleotide sequence alterations indicates that the individual has ADPKD or may develop ADPKD.

Exemplification Patient Recruitment and Clinical Evaluation

Eighty-two unrelated ADPKD patients were recruited from outpatient nephrology clinics. The Johns Hopkins Institutional Review board approved the study and informed consent was obtained from each patient. A diagnosis of ADPKD was based on established ultrasound criteria described (Ravine et al., Lancet 2:343(8901):824-7, 1994). A detailed medical history was obtained from each participant at the time of entry into the study. A coded blood sample was collected from each proband and sent to Athena Diagnostics, Inc. for mutation analysis. In most cases routine laboratory data were obtained as part of the standard medical evaluation.

Baseline characteristics of the study population are summarized in Table 2. The average age of the study participants was 46.5 years of age. Only 22% had reached ESRD at the time that mutation analysis was performed. The average glomerular filtration rate (GFR) for those that had not reached ESRD was 68 ml/min. Family history was either unknown or was negative for ADPKD in 34% of the patients.

Mutation Analysis

DNA sequence analysis of patient samples was performed using methods described in detail previously and optimized at Athena Diagnostics, Inc (Watnick T J et al., Hum Mol Genet 6(9):1473-1481, 1997; Watnick T J et al., Mol Cell 2(2):247-251, 1998; Watnick T. et al., Am J Hum Genet 65(6):1561-1571, 1999; Phakdeekitcharoen B. et al., Kidney Int 58(4):1400-1412, 2000; Phakdeekitcharoen B. et al., J Am Soc Nephrol 12:955-963, 2001), which references are incorporated in entirety herein. For example, genomic DNA is derived from whole blood using a Puregene® DNA extraction kit (Gentra Systems, Inc. Minneapolis, MN) or other suitable extraction method. Amplified DNA product served as a template for highly specific long-range PCR amplification of the 8 segments encompassing the entire PKD1 duplicated region, to prevent the amplification of PKD1 homologs that would confound the analysis. The 8 long range PCR products served as template for 43 nested PCR reactions while the unique region of the PKD1 gene and the entire PKD2 gene were amplified from genomic DNA as 28 additional gene segments. PCR primers were tagged with M13 forward and reverse primer sequences to permit bi-directional sequencing of all fragments with the same primers.

PCR products were then bi-directionally sequenced, for example, using ABI Big Dye™ terminator chemistry (versions 3.1 and 1.1 depending upon primer position and/or fragment length) followed by electrophoresis on an ABI 3730 capillary sequencer (Applera Corporation, Norwalk, CT). This process provides sequence data for the entire coding region of the PKD1 and PKD2 genes including the highly conserved exon-intron splice junctions.

Analysis of Normal Samples

A normal population was selected from anonymized samples, older than 65, submitted to Athena Diagnostics, Inc for ataxia testing. PCR products from a minimum of 171 individuals were sequenced to determine the frequency of certain common variants in either PKD1 or PKD2. Complete DNA analysis was not performed for these samples.

Generation of PC-1 Variant Constructs for Cleavage Testing

Missense variants were generated, for example using the QuickChange™ Site-Directed Mutagenesis Kit (Stratagene). The full-length wild type PKD1 cDNA construct and three of the constructs have been previously described (Q3016R, F3064L, F2853S) (Hanaoka K. et al., Nature 408:990-994, 2000; Qian F. et al., Proc Natl Acad Sci USA 24:99(26):16981-16986, 2002), incorporated in entirety herein.

Cleavage Assay

Constructs were transfected into HEK293 cells using Lipofectamine Plus™ (Life Technologies, Rockville, MD). After transfection, the cells were lysed in buffer [20 mM sodium phosphate, pH 7.2, 150 mM NaCl, 1 mM EDTA, 10% (vol/vol) glycerol, 0.5% Triton X-100] for 1 hr on ice in the presence of protease inhibitor (Roche Molecular Biochemicals). The cell lysates were immunoprecipitated (IP) using ANTI-FLAG® M2 beads Affinity Gel Freezer-Safe (SIGMA) and then resolved on a NuPAGE® 3-8% Tris-Acetate Gel (Invitrogen). The IP products were electro-blotted onto an Immobilon™ transfer membrane (MILLIPORE) and probed with α-Leucine-rich-repeat (LRR) and α-C-terminus (CT) antibodies for PC1. These antibodies have been previously described (Boletta A. et al., Mol Cell 6:1267-1273, 2000; Qian F. et al., Proc Natl Acad Sci USA 24:99(26):16981-16986, 2002).

Results

DNA sequence variance analysis identified three categories of variants. Class I variants were defined as those having definitive pathogenic sequence variants, including stop codons, frameshift and splice site alterations, that are diagnostic without additional information (Tables 3, 4). Class II variants included those demonstrating in-frame deletions or amino acid substitutions determined likely to be pathogenic based on various algorithms, as described in detail below. Class III variants included those where no pathogenic changes were confirmed.

Class I Variants

Forty-two percent (N=34) of the study population had stop codons, frameshift or splice site alterations (Tables 3, 4). Twenty-four of these alterations occurred in PKD1 (29% of total sample) and 10 in PKD2 (12% of total sample). The mutations found in Class I variants were expected to result in premature truncation of a PKD1 or PKD2 protein and therefore segregate with ADPKD.

Class II Variants

Thirty participants had either an in-frame deletion or at least one amino acid substitution deemed likely to be pathogenic (Tables 5 and 6). A total of 8 unique in-frame deletions (6 in the PKD1 gene and 2 in PKD2 gene) were detected (Table 5). In each case, the deletion affected one or more residues fully or highly conserved between Fugu rubripes (Fugu fish) and Mus musculus (mouse) polycystin proteins.

There were 10 individuals with no other truncating PKD mutations who had unique intronic variants. Two of the predicted splice site mutations did not directly affect a consensus splice donor/acceptor site; JHU573 and JHU595 had an intronic change at the 5th base pair from the intron 24 splice donor site (IVS24+5 G>C) that affected a residue that is highly conserved as a guanine in 84% of donor splice sites. Both the Neural Network Splice Site prediction program (SSPN) and Automated Splice Site Analyses (ASSA) predicted that these variants resulted in improper splicing, as such an alteration would severely disrupt the architecture of the splice donor site at the exon 24/intron 24 boundary. JHU105 had a similar alteration (IVS8+5, G>A) at the 5th basepair from the end of PKD2 exon 8 splice donor site (i.e., the 5th nucleotide base counted from left to right after nucleotide residue 1964 of SEQ ID NO:5 into the following intron (intron 8)), in which the highly conserved guanine residue was replaced by an adenine. In addition, IVS37-10C>A (JHU 604), was previously reported to segregate with ADPKD in a European family (Bogdanova, M. et al., Hum Mutat 16(2):166-174, 2000). JHU562 also had a PKD2 pathogenic mutation that affected a splice site, IVS7-1G>A (i.e., a change from a guanine to an adenine at the 1st nucleotide residue counted right to left from the beginning of exon 8 (e.g., nucleotide residue 1783 of SEQ ID NO:5) into the previous intron (intron 7)), which resulted in the loss of the acceptor site for exon 7.

Most of the remaining participants had a combination of amino acid substitutions, primarily in PKD1. Three major criteria were used to judge the pathogenicity of each missense variant. Conservation of the altered residue between human polycystin-1 and Fugu fish and mouse proteins was examined. Amino acids that were considered “fully conserved” were those that were identical in all three species, while amino acids with similar properties (i.e. belonging to the same class) were deemed to be “highly conserved” residues. In addition, a pathogenicity score for each missense variant was assigned using the matrix of Miller and Kumar (Miller M. P. and Kumar S., Hum Mol Genet 12(21):2319-2328, 2001), which defines the relative likelihood that a missense change represents a pathogenic alteration versus a polymorphism. This algorithm was developed by using interspecies sequence comparisons coupled with Grantham's chemical difference matrix to determine the common attributes of amino acid replacement mutations across 7 disease genes (including tuberous sclerosis and cystic fibrosis). Other investigators have used this strategy to assist in characterizing amino acid substitutions (Sharp A. M. et al., J Med Genet 42(4):336-349, 2005). Finally, literature was reviewed to determine whether any of the variants had been reported by others to occur in unaffected individuals. Several amino acid substitutions (N=13, Table 9), detected in homozygosity in one or more individuals, were classified as polymorphisms. Since germ line ADPKD mutations are heterozygous, one of these changes would have to be associated with a wild type allele, presumably inherited from an unaffected parent.

Analysis of individual amino acid substitutions, grouped by patient, is summarized in Table 6. An amino acid substitution was deemed to be pathogenic, if it occurred at a fully or highly conserved amino acid residue and if it was also predicted to have a higher pathogenic potential using the matrix of Miller and Kumar (Table 6, shaded in Gray). Using these strict criteria, 24 of 30 patients had one or more pathogenic amino acid substitutions. Six of these missense changes were predicted to disrupt structural determinants of either the C-type lectin (Y420C, Y528C) or one of the PKD repeats (51047L, R1340W, R1351W, T18611) (FIGS. 5A and 5B). Three of the missense changes (Q3016R, E2771K, F2853S) were previously shown to disrupt polycystin-1 cleavage, a property that is critical for normal polycystin-1 function (see FIG. 6) (Qian F. et al., Proc Natl Acad Sci USA 24:99(26):16981-16986, 2002).

Recurrent PKD1 variants (R2200C, Q739R, G2814R, Q2182R, G2309R, R1340W) that met the criteria for pathogenicity were observed in 7 individuals and were also present in other individuals who harbored either chain terminating mutations or other predicted pathogenic amino acid substitutions (Tables 4, 6 and 7). For example, R2200C was present in 4 patients, JHU584, JHU606, JHU111 and JHU573. The latter two individuals had a PKD1 frame shift mutation and a splice site mutation, respectively. This association suggested that these changes represented polymorphisms. To further characterize the missense mutations, 342 normal chromosomes were sequenced to identify polymorphisms and the R2200C sequence alteration was seen in a small (1.4%) fraction but greater than the polymorphism threshold of 1%. Likewise Q739R (this study 6.4%) and G2814R (Rossetti et al., 0.9%) have also been reported in a small percentage of the unaffected population and are or may be polymorphisms, respectively (Thomas T. et al., Am J Hum Genet 65(1):39-49, 1999 and Rossetti S. et al., Kidney Int 61(5):1588-1599, 2002).

If patients with only these pathogenic recurrent variants (without additional chain terminating mutations or other pathogenic amino acid substitution) were eliminated, then approximately 21% of the sample (N=17/82 patients) would be predicted to harbor a pathogenic PKD1 missense mutation.

Five participants JHU 602 (N=2), JHU100 (N=3), JHU588 (N=2), JHU411 (N=2), JHU114 (N=2) had more than one PKD1 amino acid variant that met the criteria for pathogenicity. This observation raises the possibility that a combination of missense changes in cis might cooperatively result in a diminished level of functional PKD1 protein (Reiterova J. et al., Hum Mutat 19(5):573, 2002).

In contrast with PKD1, only two PKD2 amino acid substitutions were detected among the 37 patients lacking chain-terminating mutations. One change (M800L in JHU559, Table 6), was not considered pathogenic by the criteria of the present system and did not segrate with disease in a PKD2 family. A second PKD2 substitution, A190T, was found in 3 patients and, likewise, did not meet the criteria for pathogenicity as it was identified in 3.2% of normal chromosomes (Table 6).

In assessing Class II variants, detection of in-frame deletions was a useful predictor of pathogenicity. Also amino acid substitutions resulting in loss of polycystin-1 cleavage were predictive of pathogenicity.

Class I and Class II amino acid changes in the PKD-1 protein (polycystin-1) and PKD-2 protein (polycystin-2) are depicted in a schematic in FIG. 8.

Class III Variants

Eighteen subjects in the study lacked definitive pathogenic sequence alterations (Tables 6 and 9). Of these, 9 had clear and extensive family history of polycystic kidney disease (Table 9). The other 9 had enlarged kidneys with cysts, with 4 of these individuals suffering from significant renal dysfunction (GFR<40) at the time of DNA testing.

Failure to detect pathogenic or potentially pathogenic changes in a subset of individuals with polycystic kidney disease may be due to several reasons. Mutational events in individuals with Class III tests could involve introns or other regulatory regions that were not assayed by the methodology that was used. Direct sequencing might also miss deletions or duplications, which would appear as an area of homozygous normal sequence. Alternatively, the stringent criteria used may have identified some missense changes as benign when they are in fact pathogenic. For example, JHU617, with an extensive family history of ADPKD, was found to have a unique leucine to valine change in PKD repeat 4 that was judged more likely to be a polymorphism by the matrix of Miller/Kumar. Nevertheless, this change does disrupt the structure of PKD repeat 4 and could be pathogenic (see FIGS. 5A and 5B). In addition, as reported by Reynolds, missense variants may unexpectedly activate cryptic splice sites, thereby reducing the level of normal transcript (Reynolds D. M. et al., J Am Soc Nephrol 10(11):2342-2351, 1999).

Functional Analysis of Missense Changes

To confirm that a subset of PKD1 amino acid substitutions predicted to be pathogenic disrupted the functional properties of the protein, full-length mutant constructs were generated and transiently expressed in HEK293 cells. FIG. 6 demonstrates that E2771K, Q3016R and F2853S disrupt cleavage, as do three additional missense changes, R2643C, R2767C and L2619P.

Polymorphism and Variability in PKD Genes

In addition to the sequence alterations described in Tables 4-7, a large number of polymorphisms were detected (Table 9) (see also FIGS. 7A and 7B). Polymorphisms are defined as: (i) sequence variants not predicted to alter an amino acid; (ii) missense changes found in homozygosity in at least one patient; (iii) intronic sequences of unknown significance; or (iv) changes in the 3′ UTR of unknown significance.

Further discussion of the above example can be found in M. A. Garcia-Gonzalez et al., Evaluating the clinical utility of a molecular genetic test for polycystic kidney disease, Mol. Genet. Metab (2007) in press, doi:10.1016/j.ymgme.2007.05.004, which is herein incorporated by reference.

The teachings of all patents, published applications and references cited herein are incorporated by reference in their entirety.

While this invention has been particularly shown and described with references to example embodiments thereof, it will be understood by those skilled in the art that various changes in form and details may be made therein without departing from the scope of the invention encompassed by the appended claims.

TABLE 2 Cohort characteristics. % Female*  50% Average Age at time of Test* 46.5 (range 1-73 y)  % ESRDE€, * 20.7% Average GFR (ml/min)¥ 68.7 (range 14-126) % Liver cysts* 74.3% % Vascular complications*  9.8% % Unknown or no Family history* 30.5% *N = 82 subjects. €ESRD defined as transplant, dialysis or MDRD GFR <10 ml/minute. ¥N = 80 patients.

TABLE 3 PKD mutations definitively pathogenic. Truncation and Splicing Gene Stop Codon Frameshift Splicing Total % PKD1 8 (9.8%) 14 (17.1%) 4 (4.9%) 31.7% PKD2 6 (7.3%) 3 (3.7%) 2 (2.4%) 13.4% Total % 17.1% 20.8% 7.3% 45.1%

TABLE 4 Truncating and Splice site mutations. Leucine Rich Repeat (LRR), Polycystic Kidney Disease Repeat (PKD-R), Receptor for Egg Jelly domain (REJ), Transmembrane (TM), Coiled Coil (CC), Novel change (N). See Full Reference List for mutation references. Mutation Mutation Effect ID cDNA Protein Stop Codon Splice Site Exon Domain Rate Ref. PKD1 gene Frameshift: JHU111 559delTTTAA N116fsX 117 3 LRR2 1/164 N. JHU568 1124insCT W305 fsX 334 5 PKDR1 1/164 N. JHU582 2291ins1 P694 fsX 713 10 1/164 N. JHU585 2297ins1 A696 fsX 713 10 1/164 N. JHU15  5225delAG R1672 fsX 1721 15 PKDR11 1/164 1, 8, 23 JHU508 5365insT V1718 fsX 1770 15 PKDR12 1/164 N. JHU613 6666insG D2152 fsX 2174 15 REJ 1/164 N. JHU611 6881insA P2224 fsX 2261 15 REJ 1/164 N. JHU577 8713delT F2834 fsX 2874 23 1/164 N. JHU600 9134ins1 P2975 fsX 3068 24 1/164 N. JHU579 9536ins5 I3109 fsX 3317 26 2/164 N. JHU609 9536ins5 I3109 fsX 3317 26 2/164 N. JHU599 10239delT L3343 fsX 3395 30 TM3 1/164 N. JHU104 11587delG G3792 fsX 3824 40 1/164 26 Nonsense: JHU605  483 C>A S91X 91 2 LRR1 1/164 N. JHU567 4517 C>T R1436X 1436 15 PKDR8 1/164 N. JHU108 7006 C>A Y2265X 2265 15 REJ 1/164 N. JHU563 7499 C>T R2430X 2430 18 REJ 1/164 2, 3 JHU593 7877 C>T Q2556X 2556 19 REJ 1/164 N. JHU083 8267 C>T Q2686X 2686 22 REJ 1/164 N. JHU574 8639 G>T E2810X 2810 23 REJ 1/164 N. JHU620 12243 G>A W4011X 4011 44 TM9 1/164 N. Splicing: JHU572 IVS4 + 1G>A. Loss of donor site 4 1/164 N. JHU580 IVS19 + 1G>T. Loss of donor site 19 REJ 1/164 N. JHU573 IVS24 + 5G>C. Loss of donor site 24 2/164 N. JHU595 IVS24 + 5G>C. Loss of donor site 24 2/164 N. PKD2 gene Frameshift: JHU586 2226insA 720fsX 11 2/164 N. JHU116 2226insA 720fsX 11 2/164 N. JHU591 2422delAG 786fsX 12 CC 1/164 N. Nonsense: JHU578  982 C>T R306X 4 TM1 2/164 5 JHU583  982 C>T R306X 4 TM1 2/164 5 JHU607 2224 C>T R742X 11 1/164 6 JHU594 2680C>T R872X 14 3/164 N. JHU566 2680C>T R872X 14 3/164 N. JHU608 2680C>T R872X 14 3/164 N. Splicing: JHU562 IVS7 − 1G>A Loss of acceptor site 7 1/164 N. JHU105L2 IVS8 + 5G>A Loss of donor site 8 1/164 N.

TABLE 5 In-Frame Deletions. Leucine rich repeat-2 (LRR2), polycystic kidney disease repeat (PKD-R), receptor for egg jelly domain (REJ), Transmembrane (TM), coiled coil (CC), Novel change (N),* Disrupts the Consensus sequence for the Domain. Mutation Conservation ID CDNA Protein Exon Domain Fugu Mouse Level Variant Ref. PKD1 gene JHU115 514-551delCAA N101del  3 LRR2 N N Fully 1/164 N. JHU107L1 1848-1851delTGG V546del  8 V V Fully 1/164 N. JHU560 8892- ANS2894del 23 AGA VGS Highly 1/164 N. 8898delCCAACTCCG JHU592 9905-9909delAAG K3232del 28 PLAT I K Highly 1/164 N. JHU571 10070-10074delCTC L3287del 29 TM2 L L Fully 1/164 N. JHU112 12597-12600delTGG V4129del 45 V V Fully 1/164 N. PKD2 gene JHU 596 374-378delTGG V103del  1 Poly- — V Highly 1/164 N. Glu JHU416L2 1879-1882delTTC F605del  8 TM5 — F Highly 1/164 N.

TABLE 6 Families with One or More Amino Acid Changes. Families underlined are those with one or more amino acid change that meets criteria of pathogenicity (grey shadow) and not found in patients with definitive pathogenic sequence variants. Total # of Mutation Conservation variants. ID Gene CDNA Protein Exon Domain Graham Fugu Mouse Level Rate Ref. PKD1 PKD2 JHU612 PKD1 1023C>A A271D 5 WSC Path.H. A A Fully 1/164 N. 4 0 PKD1  385G>A A92T 2 Equal F A Highly 1/164 N. JHU602 PKD1 1470A>G Y420C 6 C-LECT* Path.H. F Y Highly 1/164 N. 25 1 PKD1 4262C>T R1351W 15 PKDR7* Path.H. R R Fully 1/164 N. PKD1 8855T>A W2882R 23 Path.H. G Q No 1/164 N. PKD1 9109G>C E2966    24 Poly. H. G E Highly 1/164 10, 3, 24, 27 JHU103 PKD1 1794A>G Y528C 7 C-LECT* Path.H. Y Y Fully 1/164 N. 28 1 PKD1 6036G>A R1942H 15 PKDR14 Equal R R Fully 1/164 N. JHU001 PKD1 2042C>T R611W 9 Path.H. R R Fully 1/164 N. 6 0 PKD1 8651G>A G2814R 23 REJ Path.H. A G Highly 6/164 8, 9 JHU411 PKD1 3351C>T S1047L 13 PKDR4* Path.H. M S Highly 1/164 N. 60 1 PKD1 6756A>G Q2182R 15 REJ Path.H. G Q Highly 2/164 N. PKD2  634G>A A190T 1 Equal — A Highly 3/164 N. JHU100 PKD1 5793C>T T1861I 15 PKDR13* Path.H. T S Highly 1/164 N. 8 1 PKD1 6707C>T R2166C 15 REJ Path.H. P R Highly 1/164 N. PKD1 4229C>T R1340W 15 PKDR6* Path.H. H H Fully 3/164 8 JHU564 PKD1 10187G>C  G3326R 30 TM3 Path.H. G G Fully 1/164 N. 4 1 PKD1 7116C>G A2302G 15 REJ Equal S A Highly 1/164 N. PKD1 10311A>G  I3367V 31 Poly. H. I V Highly 1/164 N. JHU588 PKD1 7554T>C L2448P 18 REJ Path.H. L L Fully 1/164 N. 39 0 PKD1 4229C>T R1340W 15 PKDR6* Path.H. H H Highly 3/164 8 JHU603 PKD1 7757C>T R2516C 19 REJ Path.H. R R Fully 1/164 N. 4 0 JHU569 PKD1 8067T>C L2619P 20 REJ Path.H. L L Fully 1/164 N. 22 2 PKD1 8411C>A P2734T 23 REJ Equal P P Fully 1/164 3 PKD1 8415A>T Q2735L 23 REJ Equal S Q Highly 1/164 3 JHU597 PKD1 8138C>T R2643C 21 REJ Path.H. R R Fully 1/164 N. 3 1 JHU101 PKD1 8509C>T R2767C 23 REJ Path.H. R R Fully 1/164 N. 4 2 JHU109 PKD1 8522G>A E2771    23 REJ Path.H. E E Fully 1/164 3, 24, 23 3 0 JHU589 PKD1 8769T>C F2853    23 Path.H. F F Fully 1/164 4, 24 22 2 JHU 576 PKD1 10096C>A  N3295K 29 TM2 Path.H. N N Fully 1/164 N. 3 0 JHU114 PKD1 12658C>T  R4149C 46 Path.H. R R Fully 1/164 N. 22 1 PKD1 4229C>T R1340W 15 PKDR6* Path.H. H H Highly 3/164 8 JHU601 PKD1 9258A>G Q3016    25 GPS Path.H. Q Q Fully 1/164 4, 3, 27, 24 43 1 B PKD1 2427A>G Q739R 11 Path.H. R Q Highly 11/164  21 JHU565 PKD1 7476C>A T2422K 18 REJ Equal T T Fully 1/164 N. 24 0 PKD1 3527C>G L1106V 15 PKDR4 Poly. H. S V No 1/164 N. PKD1 3713C>T P1168S 15 PKDR5 Equal — P Highly 2/164 8 JHU570 PKD1 1947C>A P579Q 9 Equal P P Fully 1/164 N. 5 1 PKD1 2427A>G Q739R 11 Path. H. R Q Highly 11/164  21 JHU575 PKD1 3312A>G N1034S 13 PKD R4 Poly. H. G S No 1/164 N. 17 1 JHU178 PKD1 3713C>T P1168S 15 PKDR5 Equal — P Highly 2/164 8 2 1 PKD2  634G>A A190T 1 Equal — A Highly 3/164 N. JHU610 PKD2  634G>A A190T 1 Equal — A Highly 3/164 N. 40 2 JHU617 PKD1 4391C>G L1394V 15 PKDR8* Poly. H. V L Highly 1/164 N. 5 1 PKD1 11040T>A L3730Q 39 Equal F L Highly 1/164 N. JHU587 PKD1  840G>T C210F 5 Equal C C Fully 1/164 N. 6 2 PKD1 7197G>A R2329Q 16 REJ Equal E R Highly 1/164 N. PKD1 2427A>G Q739R 11 Path. H. R Q Highly 11/164  21 JHU559 PKD1  351G>C C47S 1 LRR-N Poly. H. W C Highly 1/164 N. 24 3 PKD2 2464A>C M800L 13 Poly. H. — M Highly 1/164 JHU606 PKD1 6809C>T R2200C 15 REJ Path. H. R R Fully 4/164 23 5 2 JHU584 PKD1 6809C>T R2200C 15 REJ Path. H. R R Fully 4/164 23 20 1 JHU106 PKD1 8651G>A G2814R 23 REJ Path. H. A G Highly 6/164 3, 8 4 1 JHU614 PKD1 4757G>A A1516T 15 PKDR9 Equal T I No 2/164 N. 10 0 PKD1 1973A>C E586D 9 Equal A E Highly 1/164 N. PKD1 2427A>G Q739R 11 Path. H. R Q Highly 11/164  21 Fp = do not disrupt cleavage; Fm = disrupt cleavege. See Full Reference List for mutation references.

TABLE 7 Families with multiple PKD mutations associated with ADPKD. Occasionally, families with a mutation associated to the disease had other change that could be classified also as associated to the disease by meeting our criteria or disrupting the consensus sequence of the Domain*. Mutations Disease Amino acid changes # of Changes Associated highly pathogenic per patient Pedigree PKD1 PKD2 PKD1 PKD2 PKD1 PKD2 JHU605 S91X 4 0 JHU 567 R1436X 24 0 JHU108 Y2265X Q739R 5 1 JHU563 R2430X Q739R R807Q 19 1 JHU593 Q2556X 3 2 JHU083 Q2686X 5 0 JHU574 E2810X G2814R 4 0 JHU620 W4011X 22 0 JHU568 W305 fsX W305C* 4 1 JHU582 P694 fsX 1 0 JHU585 A696 fsX 6 2 JHU508 V1718 fsX 5 2 JHU613 D2152 fsX E624K 21 0 JHU611 P2224 fsX 29 1 JHU600 P2975 fsX Q739R 25 2 JHU609 I3109 fsX 41 1 JHU579 I3109 fsX G2814R 23 2 JHU577 F2834fsX Q739R 4 1 JHU111 N116 fsX R2200C 7 1 S1619F JHU15 R1672 fsX 5 1 JHU599 L3343 fsX R1312Q 20 1 JHU104 G3792 fsX 4 2 JHU115 N101del 20 0 JHU107 V546del R1142W 25 1 JHU560 ANS2894del 21 1 JHU592 K3232del 3 1 JHU571 L3287del 10 0 JHU112 V4129del S4053F 19 2 JHU580 IVS19 + G2814R 5 1 1G > T. JHU573 IVS24 + R2200C 5 0 5G > C JHU595 IVS24 + 16 2 5G > C JHU572 IVS4 + 17 1 1G > A JHU578 R306X 3 3 JHU583 R306X 5 1 JHU607 R742X 21 1 JHU594 R872X 22 3 JHU566 R872X 1 3 JHU608 R872X G2814R 4 2 JHU596 V103del Q2182R 35 1 JHU416 F605del 2 3 JHU591 786fsX 4 2 JHU562 IVS7 − 3 2 1G > A JHU105 IVS8 + T1773I* 3 2 5G > A JHU116 720 fsX Q739R 3 2 JHU586 720 fsX T1773I* 22 1

TABLE 8 Families without disease-associated PKD mutations. Non-pathogenic Intronic # of missense Changes Family Changes ID PKD1 PKD2 PKD1 PKD2 history PKD1 PKD2 JHU565 L1106V Yes 24 0 P1168S T2422K JHU570 Q739R Yes 5 1 P579Q JHU575 N1034S No 17 1 JHU178 P1168S A190T Yes 2 1 JHU610 A190T No 40 2 JHU617 L1394V* Yes 5 1 L3730Q JHU587 C210F No 6 2 Q739R R2329Q JHU559 C47S M800L Yes 24 3 JHU604 Q739R IVS37 − Yes 2 0 10C> A{circumflex over ( )}{circumflex over ( )} JHU606 R2200C No 5 2 JHU584 R2200C No 20 1 JHU590 IVS24 + Yes 3 1 28G> T{circumflex over ( )}{circumflex over ( )} JHU106 G2814R Yes 4 1 JHU614 E586D No 10 0 Q739R A1516T JHU102L1 Yes 21 0 JHU616 Yes 17 0 JHU615 No 0 1 JHU110L3 Yes 3 0 JHU113 No 2 1 JHU598 No 19 0 *disrupts the consensus sequence. {circumflex over ( )}{circumflex over ( )}predicted to generate a new splice site.

TABLE 9 Polymorphisms Identified. See Full Reference List for mutation references. ID# Designation cDNA Change (s) Location Domain Frequency Ref. PKD1 Polymorphisms. — T263S(H) 1004C>T Exon 5 2/164 N. — P572S(H) 1925C>T Exon 8 4/164 8 — M1092T(H) 3486T>C  Exon 14 PKD R4 30/164  8 — W1399R(H) 4406T>G  Exon 15 PKD R8 22/164  1, 8, 16 — V1943I(H) 6038G>A  Exon 15 PKD R14 5/164 8 — E2548Q(H) 7853G>C  Exon 19 REJ 4/164 1 — H2638R(H) 8124A>G  Exon 21 REJ 32/164  1 — P2674S(H) 8231C>T  Exon 21 REJ 2/164 3, 8 — F3066L (H) 9407T>C  Exon 25 38/164  3, 17, 34 — V3408L(H) 10433G>C  Exon 33 5/164 N. — A3511V(H) 10743C>T  Exon 35 13/164  3, 8 — I4044V(H) 12341A>G  Exon 44 TM10 42/164  3, 8, 17, 18, 14, 10 — A4058V(H) 12386C>T  Exon 45 12/164  8, 10 1 104C>T Exon 1 5′UTR 1/164 N. 2 145C>T Exon 1 5′UTR 2/164 N. 3 160C>T Exon 1 5′UTR 1/164 N. 4 210C>T Exon 1 5′UTR 1/164 N. 5 L72L 425C>T Exon 1 LRR1 2/164 N. 6 G109G 538A>T Exon 3 LRR2 1/164 N. 7 IVS4 + 1G>A(H) Intron 4 1/164 N. 8 S196S 799C>T Exon 5 2/164 N. 9 A341A 1234C>T Exon 5 PKD R1 5/164 3 10 L373L(H) 1330T>C Exon 5 36/164  3, 8, 15 11 G441G 1534G>A Exon 6 C-LECT 1/164 N. 12 H570H 1921C>T Exon 8 1/164 3, 8 13 IVS9 + 2del7 Intron 9 12/164  N. 14 IVS9 + 2 T>A Intron 9 1/164 N. 15 IVS9 + 28del7 (H) Intron 9 4/164 8 16 ISV9 − 44G>C Intron 9 1/164 8 17 IVS9 − 4A>G Intron 9 42/164  8 18 IVS10 − 4G>A  Intron 10 1/164 N. 19 P738P(H) 2425C>G  Exon 11 4/164 N. 20 A745A 2448C>G  Exon 11 1/164 N. 21 A898A 2905A>C  Exon 11 PKD R2 4/164 8, 9 22 P900P 2911G>A  Exon 11 PKD R2 10/164  8, 16, 9 23 D910D 2941C>T  Exon 11 PKD R2 10/164  8, 16, 9 24 IVS11 − 5C>T  Intron 11 2/164 8 25 IVS11 + 23C>T(H)  Intron 11 4/164 N. 26 IVS12 − 15C>T  Intron 12 5/164 N. 27 G1021G(H) 3274T>C  Exon 13 PKD R4 30/164  8, 16, 9 28 L1037L 3392A>G  Exon 13 PKD R4 15/164  9 29 E1061E 3394G>A  Exon 14 PKD R4 1/164 N. 30 P1076P 3439G>A  Exon 14 PKD R4 1/164 N. 31 A1124A 3583C>T  Exon 15 PKD R4 25/164  8, 9 32 S1125S 3586C>T  Exon 15 PKD R5 25/164  8, 9 33 F1163F 3700C>T  Exon 15 PKD R5 1/164 N. 34 T1171T 3724C>G  Exon 15 PKD R5 1/164 N. 35 D1310D 4141C>T  Exon 15 PKD R7 1/164 N. 36 L1357L 4282G>T  Exon 15 PKD R7 1/164 N. 37 S1373S 4330C>T  Exon 15 PKD R7 1/164 N. 38 S1452S 4567T>C  Exon 15 PKD R8 1/164 N. 39 P1511P 4744G>A  Exon 15 PKD R9 1/164 N. 40 A1555A(H) 4876A>C  Exon 15 Extracellular 42/164  16, 1, 9 41 T1558T 4885G>A  Exon 15 Extracellular 9/164 2 42 S1603S 5020C>T  Exon 15 Extracellular 1/164 N. 43 T1724T(H) 5383C>T  Exon 15 PKD R12 40/164  8, 9, 21 44 A1818A(H) 5665G>A  Exon 15 PKD R13 5/164 8, 9 45 G1860G 5791C>A  Exon 15 PKD R13 1/164 N. 46 A1894A 5893C>T  Exon 15 PKD R14 1/164 8, 9 47 L1921L 5974G>A  Exon 15 PKD R14 2/164 8, 9 48 V2026V 6289C>T  Exon 15 PKD R15 1/164 N. 49 R2121R 6574C>T  Exon 15 PKD R16 1/164 N. 50 T2180T 6751C>T  Exon 15 REJ 1/164 N. 51 A2202A 6817G>A  Exon 15 REJ 1/164 N. 52 V2257V 6982G>A  Exon 15 REJ 1/164 N. 53 G2309G 7138C>T  Exon 16 REJ 4/164 8, 9 54 IVS16 + 10 G>A  Intron 16 REJ 1/164 N. 55 R2359R 7289G>C  Exon 17 REJ 3/164 N. 56 L2389L(H) 7376T>C  Exon 17 REJ 46/164  1, 2, 8, 9. 57 G2425G 7486C>T  Exon 18 REJ 1/164 N. 58 L2481L(H) 7652C>T  Exon 18 REJ 39/164  1, 8 59 IVS19 + 24 C>A  Intron 19 REJ 2/164 N. 60 L2570L(H) 7919T>C  Exon 20 REJ 31/164  1, 9 61 IVS20 + C>A  Intron20 REJ 1/164 N. 62 ISV20 − 16C>G  Intron20 REJ 2/164 N. 63 T2708M 8334C>T  Exon 22 REJ 1/164 3, 8 64 IVS22 + 8G>A (H)  Intron 22 REJ 1/164 1, 8 65 S2729S 8398G>A  Exon 23 REJ 2/164 N. 66 A2749A 8458G>A  Exon 23 REJ 1/164 N. 67 S2766S 8509C>T  Exon 23 REJ 1/164 13 68 D2789D 8578C>T  Exon 23 REJ 2/164 N. 69 S2813S 8650C>T  Exon 23 REJ 2/164 3, 8, 24 70 S2893S 8890C>G  Exon 23 2/164 3 71 A2971A(H) 9124T>C  Exon 24 2/164 N. 72 IVS24 − 20G>A (H)  Intron 24 3/164 N. 73 IVS24 − 17A>G(H)  Intron 24 6/164 N. 74 IVS24 + 17A>G  Intron 24 32/164  N. 75 S3007S 9232C>T  Exon 25 1/164 N. 76 V3065V(H) 9406G>C  Exon 25 38/164  24 77 V3090V 9481C>T  Exon 26 TM1 3/164 N. 78 P3110P(H) 9543T>C  Exon 26 37/164  6 79 IVS26 + 76C>A  Intron26 1/164 N. 80 IVS27 − 13T>C(H)  Intron27 15/164  8 81 T3223T 9880G>A  Exon 28 PLAT 2/164 6, 3, 8 82 S3265S 10006C>T  Exon 29 1/164 N. 83 IVS29 − 4 C>T  Intron29 1/164 N. 84 A3455A 10576C>T  Exon 34 1/164 N. 85 L3589L 10976C>T  Exon 36 TM5 5/164 N. 86 IVS37 − 4C>T  Intron 37 1/164 N. 87 IVS38 + 11G>A  Intron 38 4/164 N. 88 R3752R 11385C>A  Exon 39 Polycystin motif 1/164 N. 89 L3753L 11465G>C  Exon 39 Polycystin motif 1/164 N. 90 IVS39 − 25del72bp  Intron 39 1/164 7, 3 91 IVS41 + C>T  Intron 41 1/164 N. 92 IVS41 + 5insGGG  Intron 41 2/164 8 93 IVS41 − 11C>T C>T  Intron 41 2/164 N. 94 S3893S(H) 11890C>T  Exon 42 3/164 8 95 IVS43 + 42C>A  Intron 43 6/164 N. 96 R3971R 12124C>T  Exon 43 3/164 N. 97 L4025L 12286C>T  Exon 44 1/164 N. 98 L4035L 12316C>T  Exon 44 TM10 1/164 N. 99 IVS44 + 22delG  Intron44 4/164 N. 100 L4089L 12478C>G  Exon 45 TM11 1/164 N. 101 A4091A(H) 12484A>G  Exon 45 TM11 43/164  8, 3, 17, 18, 7 102 L4136L(H) 12617C>T  Exon 45 13/164  8, 14 103 V4152V 12667C>T  Exon 46 2/164 N. 104 P4161P 12696C>A  Exon 46 1/164 N. 105 S4189S 12778C>T  Exon 46 1/164 6 106 P4209P(H) 12838T>C  Exon 46 40/164  8, 6, 3 107 L4221L 12874C>T  Exon 46 COILED COIL 1/164 N. 108 A4255A 12978C>T  Exon 46 1/164 N. 109 13135G>A 3′UTR 2/164 8 PKD2 Polymorphisms. — R28P(H) 149C>T Exon 1 50/164  8, 10, 22 110 R60R 246G>A Exon 1 1/164 N. 111 G140G(H) 486G>A Exon 1 22/164  N. 112 IVS6 − 4C>T Intron 6 1/164 N. 113 L539L 1683G>C Exon 7 1/164 N.

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  • 15. Bogdanova N, McCluskey M, Sikmann K, et al. Screening the 3′ region of the polycystic kidney disease 1 (PKD1) gene in 41 Bulgarian and Australian kindreds reveals a prevalence of protein truncating mutations. Hum Mutat 16(2):166-74, 2000.
  • 16. Watnick T J, Torres V E, Gandolph M A, et al. Somatic mutation in individual liver cysts supports a two-hit model of cystogenesis in autosomal dominant polycystic kidney disease. Mol Cell 2(2):247-51, 1998.
  • 17. Perrichot R, Mercier B, Quere I, et al. Novel mutations in the duplicated region of PKD1 gene. Eur J Hum Genet 8(5):353-9, 2000.
  • 18. Boletta, A., Qian, F., Onuchic, L. F., et al. Polycystin-1, the gene product of PKD1, induces resistance to apoptosis and spontaneous tubulogenesis in MDCK cells. Mol. Cell 6, 1267-1273, 2000.
  • 19. Aguiari G, Savelli S, Garbo M, et al. Novel splicing and missense mutations in autosomal dominant polycystic kidney disease 1 (PKD1) gene: expression of mutated genes. Hum Mutat 16(5):444-5, 2000.
  • 20. Bycroft M, Bateman A, Clarke J, et al. The structure of a PKD domain from polycystin-1: implications for polycystic kidney disease. EMBO J. 15; 18(2):297-305, 1999.
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  • 26. Qian F, Boletta A, Bhunia A K, Xu H, et al. Cleavage of polycystin-1 requires the receptor for egg jelly domain and is disrupted by human autosomal-dominant polycystic kidney disease 1-associated mutations. Proc Natl Acad Sci USA 24; 99(26):16981-6, 2002.
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Claims

1. A method of detecting or predicting the occurrence of autosomal dominant polycystic kidney disease (ADPKD) in an individual comprising detecting the presence of one or more nucleotide sequence alterations in a PKD1 gene having the nucleotide sequence of SEQ ID NO:1 or SEQ ID NO:7 in a nucleic acid sample obtained from said individual, wherein said one or more alterations are selected from the group consisting of: an insertion of CT at nucleotide position 1124 of SEQ ID NO:1, an insertion of an A, T, G, or C at nucleotide position 2291 of SEQ ID NO:1, an insertion of an A, T, G, or C at nucleotide position 2297 of SEQ ID NO:1, an insertion of a T at nucleotide position 5365 of SEQ ID NO:1, an insertion of a G at nucleotide position 6666 of SEQ ID NO:1, an insertion of an A at nucleotide position 6881 of SEQ ID NO:1, a deletion of a T at nucleotide position 8713 of SEQ ID NO:1, an insertion of an A, T, G, or C at nucleotide position 9134 of SEQ ID NO:1, an insertion of 5 nucleotides at nucleotide position 9536 of SEQ ID NO:1, a deletion of a T at nucleotide position 10239 of SEQ ID NO:1, a change of a C to an A at nucleotide position 483 of SEQ ID NO:1, a change of a C to an A at nucleotide position 7006 of SEQ ID NO:1, a change of a C to T at nucleotide position 8267 of SEQ ID NO:1, a change of a G to a Tat nucleotide position 8639 of SEQ ID NO:1, a change of a G to an A at nucleotide position 20168 of SEQ ID NO:7, a change of a G to a T at nucleotide position 31025 of SEQ ID NO:7, a change of a G to a C at nucleotide position 33415 of SEQ ID NO:7, a deletion of CAA between nucleotide positions 508 to 516 of SEQ ID NO:1, a deletion of TGG at nucleotide positions 1848 to 1850 of SEQ ID NO:1, a deletion of CCAACTCCG at nucleotide positions 8892 to 8900 of SEQ ID NO:1, a deletion of AAG at nucleotide positions 9905 to 9907 of SEQ ID NO:1, a deletion of CTC at nucleotide positions 10070 to 10072 of SEQ ID NO:1, a deletion of TGG at nucleotide positions 12597 to 12599 of SEQ ID NO:1, a change of a C to an A at nucleotide position 1023 of SEQ ID NO:1, a change of a G to an A at nucleotide position 385 of SEQ ID NO:1, a change of an A to a G at nucleotide position 1470 of SEQ ID NO:1, a change of a C to a T at nucleotide position 4262 of SEQ ID NO:1, a change of an A to a G at nucleotide position 1794 of SEQ ID NO:1, a change of a G to an A at nucleotide position 6036 of SEQ ID NO:1, a change of a C to a T at nucleotide position 2042 of SEQ ID NO:1, a change of a C to a Tat nucleotide position 3351 of SEQ ID NO:1, a change of an A to a G at nucleotide position 6756 of SEQ ID NO:1, a change of a C to a T at nucleotide position 5793 of SEQ ID NO:1, a change of a C to a T at nucleotide position 6707 of SEQ ID NO:1, a change of a G to a C at nucleotide position 10187 of SEQ ID NO:1, a change of a C to a G at nucleotide position 7116 of SEQ ID NO:1, a change of an A to a G at nucleotide position 10311 of SEQ ID NO:1, a change of a T to a Cat nucleotide position 7554 of SEQ ID NO:1, a change of a C to a T at nucleotide position 7757 of SEQ ID NO:1, a change of a T to a C at nucleotide position 8067 of SEQ ID NO:1, a change of a C to a Tat nucleotide position 8138 of SEQ ID NO:1, a change of a C to a T at nucleotide position 8509 of SEQ ID NO:1, a change of a C to an A at nucleotide position 10096 of SEQ ID NO:1 and a change of a C to a Tat nucleotide position 12658 of SEQ ID NO:1,

wherein detection of said one or more nucleotide sequence alterations indicates that said individual has ADPKD or will develop ADPKD.

2. The method of claim 1, wherein at least one nucleotide sequence alteration other than said one or more nucleotide sequence alterations listed in claim 1 is also detected in a sequence selected from the group consisting of SEQ ID NO:1 and SEQ ID NO:4, wherein said at least one nucleotide sequence alteration is associated with ADPKD.

3. The method of claim 2, wherein the presence of said one or more nucleotide sequence alterations in said nucleic acid sequence is detected by a method selected from the group consisting of sequencing, polymerase chain reaction (PCR), denaturing high performance liquid chromatography and combinations thereof.

4. The method of claim 2, further comprising assessing the effect of said one or more nucleotide sequence alterations on a PKD1 gene product by assaying for at least one activity selected from the group consisting of expression of said PKD1 gene product and cleavage of said PKD1 gene product.

5. A method of detecting or predicting the occurrence of autosomal dominant polycystic kidney disease (ADPKD) in an individual comprising detecting the presence of one or more nucleotide sequence alterations in a PKD2 gene having the nucleotide sequence of SEQ ID NO:4 in a nucleic acid sample obtained from said individual, wherein said one or more alterations are selected from the group consisting of: an insertion of: an A at nucleotide position 2226 of SEQ ID NO:4, a deletion of AG at nucleotide positions 2422 to 2423 of SEQ ID NO:4, a change of a C to a T at nucleotide position 2680 of SEQ ID NO:4, IVS7-1G>A, IVS8+5G>A, a deletion of TGG at nucleotide positions 374-376 of SEQ ID NO:4 and a deletion of TTC between nucleotide positions 1876-1881 of SEQ ID NO:4,

wherein detection of said one or more nucleotide sequence alterations indicates that said individual has ADPKD or will develop ADPKD.

6. The method of claim 5 wherein at least one nucleotide sequence alteration other than said one or more nucleotide sequence alterations listed in claim 5 is also detected in a sequence selected from the group consisting of SEQ ID NO:1 and SEQ ID NO:4, wherein said at least one nucleotide sequence alteration is associated with ADPKD.

7. The method of claim 5, wherein the presence of said one or more nucleotide sequence alterations in said nucleic acid sequence is detected by a method selected from the group consisting of sequencing, polymerase chain reaction (PCR), denaturing high performance liquid chromatography and combinations thereof.

8. The method of claim 5, further comprising assessing the effect of said one or more nucleotide sequence alterations on a PKD2 gene product by assaying for expression of said PKD2 gene product.

9. A method for detecting in an individual the presence or absence of a mutant PKD gene comprising:

a) obtaining a nucleic acid sample from said individual; and
b) detecting the presence or absence of one or more nucleotide sequence alterations in a PKD1 or PKD2 gene of said individual, wherein said one or more alterations are selected from the group consisting of: an insertion of CT at nucleotide position 1124 of SEQ ID NO:1, an insertion of an A, T, G, or C at nucleotide position 2291 of SEQ ID NO:1, an insertion of an A, T, G, or C at nucleotide position 2297 of SEQ ID NO:1, an insertion of a T at nucleotide position 5365 of SEQ ID NO:1, an insertion of a G at nucleotide position 6666 of SEQ ID NO:1, an insertion of an A at nucleotide position 6881 of SEQ ID NO:1, a deletion of a Tat nucleotide position 8713 of SEQ ID NO:1, an insertion of an A, T, G, or C at nucleotide position 9134 of SEQ ID NO:1, an insertion of 5 nucleotides at nucleotide position 9536 of SEQ ID NO:1, a deletion of a T at nucleotide position 10239 of SEQ ID NO:1, a change of a C to an A at nucleotide position 483 of SEQ ID NO:1, a change of a C to an A at nucleotide position 7006 of SEQ ID NO:1, a change of a C to T at nucleotide position 8267 of SEQ ID NO:1, a change of a G to a T at nucleotide position 8639 of SEQ ID NO:1, a change of a G to an A at nucleotide position 20168 of SEQ ID NO:7, a change of a G to a Tat nucleotide position 31025 of SEQ ID NO:7, a change of a G to a C at nucleotide position 33415 of SEQ ID NO:7, a deletion of CAA between nucleotide positions 508 to 516 of SEQ ID NO:1, a deletion of TGG at nucleotide positions 1848 to 1850 of SEQ ID NO:1, a deletion of CCAACTCCG at nucleotide positions 8892 to 8900 of SEQ ID NO:1, a deletion of AAG at nucleotide positions 9905 to 9907 of SEQ ID NO:1, a deletion of CTC at nucleotide positions 10070 to 10072 of SEQ ID NO:1, a deletion of TGG at nucleotide positions 12597 to 12599 of SEQ ID NO:1, a change of a C to an A at nucleotide position 1023 of SEQ ID NO:1, a change of a G to an A at nucleotide position 385 of SEQ ID NO:1, a change of an A to a G at nucleotide position 1470 of SEQ ID NO:1, a change of a C to a T at nucleotide position 4262 of SEQ ID NO:1, a change of an A to a G at nucleotide position 1794 of SEQ ID NO:1, a change of a G to an A at nucleotide position 6036 of SEQ ID NO:1, a change of a C to a T at nucleotide position 2042 of SEQ ID NO:1, a change of a C to a T at nucleotide position 3351 of SEQ ID NO:1, a change of an A to a G at nucleotide position 6756 of SEQ ID NO:1, a change of a C to a T at nucleotide position 5793 of SEQ ID NO:1, a change of a C to a Tat nucleotide position 6707 of SEQ ID NO:1, a change of a G to a Cat nucleotide position 10187 of SEQ ID NO:1, a change of a C to a G at nucleotide position 7116 of SEQ ID NO:1, a change of an A to a G at nucleotide position 10311 of SEQ ID NO:1, a change of a T to a C at nucleotide position 7554 of SEQ ID NO:1, a change of a C to a T at nucleotide position 7757 of SEQ ID NO:1, a change of a T to a Cat nucleotide position 8067 of SEQ ID NO:1, a change of a C to a T at nucleotide position 8138 of SEQ ID NO:1, a change of a C to a Tat nucleotide position 8509 of SEQ ID NO:1, a change of a C to an A at nucleotide position 10096 of SEQ ID NO:1 and a change of a C to a T at nucleotide position 12658 of SEQ ID NO:1, an insertion of: an A at nucleotide position 2226 of SEQ ID NO:4, a deletion of AG at nucleotide positions 2422 to 2423 of SEQ ID NO:4, a change of a C to a T at nucleotide position 2680 of SEQ ID NO:4, IVS7-1G>A, IVS8+5G>A, a deletion of TGG at nucleotide positions 374-376 of SEQ ID NO:4 and a deletion of TTC between nucleotide positions 1876-1881 of SEQ ID NO:4,
wherein detection of said one or more nucleotide sequence alterations is indicative of a mutant PKD gene.

10. The method of claim 9, wherein the presence of one or more nucleotide sequence alterations in said PKD1 or PKD2 gene of said individual indicates that the individual has autosomal dominant polycystic kidney disease (ADPKD) or may develop ADPKD.

11. The method of claim 10, wherein the presence or absence of said one or more nucleotide sequence alterations in said nucleic acid sequence is detected by a method selected from the group consisting of sequencing, polymerase chain reaction (PCR), denaturing high performance liquid chromatography and combinations thereof.

Patent History
Publication number: 20230374593
Type: Application
Filed: Apr 5, 2023
Publication Date: Nov 23, 2023
Applicants: Athena Diagnostics, Inc. (Marlborough, MA), The Johns Hopkins University (Baltimore, MD)
Inventors: Terry J. Watnick (Chevy Chase, MD), Miguel Garcia-Gonzales (Brion), Gregory G. Germino (Chevy Chase, MD), Jeffery G. Jones (Wilbraham, MA)
Application Number: 18/131,204
Classifications
International Classification: C12Q 1/6883 (20180101);