Compositions and methods for detecting noonan syndrome

Abstract

Diagnostic and therapeutic applications for Noonan Syndrome are described. The diagnostic and therapeutic applications are based on certain mutations in a RAS-specific guanine nucleotide exchange factor gene SOS1 or its expression product. The diagnostic and therapeutic applications are also based on certain mutations in a serine/threonine protein kinase gen RAF1 or its expression product thereof. Also described are nucleotide sequences, amino acid sequences, probes, and primers related to RAF1 or SOS1, and variants thereof, as well as host cells expressing such variants.

1 . An isolated oligonucleotide comprising at least about 20 consecutive nucleotides of SEQ ID NO: 1, wherein the oligonucleotide has a substitution selected from the group consisting of:
 (a) a G to T substitution at position 1161 of SEQ ID NO:1;   (b) a C to T substitution at position 1163 of SEQ ID NO:1;   (c) a C to T substitution at position 1169 of SEQ ID NO:1;   (d) a C to G substitution at position 1172 of SEQ ID NO:1;   (e) a C to T substitution at position 1174 of SEQ ID NO:1;   (f) a C to T substitution at position 1175 of SEQ ID NO:1;   (g) a G to A substitution at position 1849 of SEQ ID NO:1;   (h) an A to G substitution at position 1850 of SEQ ID NO:1;   (i) a C to T substitution at position 1865 of SEQ ID NO:1;   (j) a C to G substitution at position 1865 of SEQ ID NO:1; and   (k) a T to A substitution at position 2227 of SEQ ID NO:1.   
     
     
         2 . An isolated oligonucleotide comprising at least about 20 consecutive nucleotides complementary to SEQ ID NO: 1, wherein the oligonucleotide has a substitution selected from the group consisting of:
 (a) a G to T substitution at position 1161 of the complement of SEQ ID NO:1;   (b) a C to T substitution at position 1163 of the complement of SEQ ID NO:1;   (c) a C to T substitution at position 1169 of the complement of SEQ ID NO:1;   (d) a C to G substitution at position 1172 of the complement of SEQ ID NO:1;   (e) a C to T substitution at position 1174 of the complement of SEQ ID NO:1;   (f) a C to T substitution at position 1175 of the complement of SEQ ID NO:1;   (g) a G to A substitution at position 1849 of the complement of SEQ ID NO:1;   (h) an A to G substitution at position 1850 of the complement of SEQ ID NO:1;   (i) a C to T substitution at position 1865 of the complement of SEQ ID NO:1;   (j) a C to G substitution at position 1865 of the complement of SEQ ID NO:1; and   (k) a T to A substitution at position 2227 of the complement of SEQ ID NO:1.   
     
     
         3 . A solid phase surface comprising a set of oligonucleotides affixed to the surface, wherein the set of oligonucleotides comprises:
 (a) an oligonucleotide of at least about 20 consecutive nucleotides of SEQ ID NO: 1 having a C to A substitution at position 1161 of SEQ ID NO:1;   (b) an oligonucleotide of at least about 20 consecutive nucleotides of SEQ ID NO: 1 having a G to A substitution at position 1163 of SEQ ID NO:1;   (c) an oligonucleotide of at least about 20 consecutive nucleotides of SEQ ID NO: 1 having a G to A substitution at position 1169 of SEQ ID NO:1;   (d) an oligonucleotide of at least about 20 consecutive nucleotides of SEQ ID NO: 1 having a G to C substitution at position 1172 of SEQ ID NO:1;   (e) an oligonucleotide of at least about 20 consecutive nucleotides of SEQ ID NO: 1 having a G to A substitution at position 1174 of SEQ ID NO:1;   (f) an oligonucleotide of at least about 20 consecutive nucleotides of SEQ ID NO: 1 having a G to A substitution at position 1175 of SEQ ID NO:1;   (g) an oligonucleotide of at least about 20 consecutive nucleotides of SEQ ID NO: 1 having a C to T substitution at position 1849 of SEQ ID NO:1;   (h) an oligonucleotide of at least about 20 consecutive nucleotides of SEQ ID NO: 1 having a T to C substitution at position 1850 of SEQ ID NO:1;   (i) an oligonucleotide of at least about 20 consecutive nucleotides of SEQ ID NO: 1 having a G to A substitution at position 1865 of SEQ ID NO:1;   (j) an oligonucleotide of at least about 20 consecutive nucleotides of SEQ ID NO: 1 having a G to C substitution at position 1865 of SEQ ID NO:1;   (k) an oligonucleotide of at least about 20 consecutive nucleotides of SEQ ID NO: 1 having an A to T substitution at position 2227 of SEQ ID NO:1; and   the oligonucleotides complementary to oligonucleotides (a)-(k).   
     
     
         4 . A solid phase surface of  claim 3 , wherein the solid phase surface comprising a set of oligonucleotides affixed to the surface is a microarray. 
     
     
         5 . An isolated nucleic acid that encodes a RAF1 polypeptide with an amino acid substitution, wherein the nucleic acid has a substitution selected from the group consisting of:
 (a) a G to T substitution at position 1161 of SEQ ID NO:1;   (b) a C to T substitution at position 1163 of SEQ ID NO:1;   (c) a C to T substitution at position 1169 of SEQ ID NO:1;   (d) a C to G substitution at position 1172 of SEQ ID NO:1;   (e) a C to T substitution at position 1174 of SEQ ID NO:1;   (f) a C to T substitution at position 1175 of SEQ ID NO:1;   (g) a G to A substitution at position 1849 of SEQ ID NO:1   (h) an A to G substitution at position 1850 of SEQ ID NO:1   (i) a C to T substitution at position 1865 of SEQ ID NO:1   (j) a C to G substitution at position 1865 of SEQ ID NO:1; and   (k) a T to A substitution at position 2227 of SEQ ID NO:1.   
     
     
         6 . The isolated RAF1 nucleic acid of  claim 5 , wherein the nucleic acid has a substitution that results in an RAF1 polypeptide comprising an amino acid substitution at a position selected from the group consisting of:
 (a) an R to S substitution at position 256 of SEQ ID NO:2;   (b) an S to L substitution at position 257 of SEQ ID NO:2;   (c) an S to F substitution at position 259 of SEQ ID NO:2;   (d) a T to R substitution at position 260 of SEQ ID NO:2;   (e) a P to S substitution at position 261 of SEQ ID NO:2;   (f) a P to L substitution at position 261 of SEQ ID NO:2;   (g) a D to N substitution at position 486 of SEQ ID NO:2   (h) a D to G substitution at position 486 of SEQ ID NO:2   (i) a T to I substitution at position 491 of SEQ ID NO:2   (j) a T to R substitution at position 491 of SEQ ID NO:2; and   (k) an S to T substitution at position 612 of SEQ ID NO:2.   
     
     
         7 . A kit for diagnosing Noonan syndrome, comprising at least one of the oligonucleotides of  claim 1 ; and instructions for use. 
     
     
         8 . A kit for diagnosing Noonan syndrome, comprising at least one of the oligonucleotides of  claim 2 ; and instructions for use.