Materials and methods for identifying spinal muscular atrophy carriers

Patent metadata

Field	Value
Publication number	US-2018340227-A1
Application number	US-201815984659-A
Country	US
Kind code	A1
Filing date	May 21, 2018
Priority date	Jun 7, 2011
Publication date	Nov 29, 2018
Grant date	—

Abstract

Materials and methods for identifying carriers of genetic determinants of spinal muscular atrophy are disclosed. In particular, polymorphisms in linkage disequilibrium are associated as markers of spinal muscular atrophy alleles detectable by various techniques, including multiplex ligation-dependent probe analysis, sequence analysis, and RFLP detection. The materials and methods of the disclosure are particularly useful in identifying silent (2+0) carriers of spinal muscular atrophy in which two copies of the SMN1 gene are located on a single human chromosome 5 and no copies of the gene are located on the chromosome 5 homolog.

First claim

1 . A method of identifying a human subject as a carrier of a SMN1 duplication allele comprising:
(a) obtaining a nucleic acid sample from a human subject; (b) screening the nucleic acid by determining
(i) the identity of the nucleotide corresponding to position 11678 of SEQ ID NO:1;
(ii) the identity of the nucleotide corresponding to position 15774 of SEQ ID NO:1;
(iii) the identity of the nucleotide corresponding to position 22804 of SEQ ID NO:1;
(iv) the identity of the nucleotide corresponding to position 26190 of SEQ ID NO:1;
(v) the identity of the nucleotide corresponding to position 27134 of SEQ ID NO:1, or
(vi) whether the A-T dinucleotide corresponding to positions 27706-27707 of SEQ ID NO:1 has been deleted; and
(c) identifying the human subject as a carrier of the SMN1 duplication allele if
(i) the nucleotide corresponding to position 11678 of SEQ ID NO:1 is not G or there is a nucleotide inserted between nucleotides corresponding to positions 11678 and 11679 of SEQ ID NO:1;
(ii) the nucleotide corresponding to position 15774 of SEQ ID NO:1 is not G or there is a nucleotide inserted between nucleotides corresponding to positions 15774 and 15775 of SEQ ID NO:1;
(iii) the nucleotide corresponding to position 22804 of SEQ ID NO:1 is not G or there is a nucleotide inserted between nucleotides corresponding to positions 22804 and 22805 of SEQ ID NO:1;
(iv) the nucleotide corresponding to position 26190 of SEQ ID NO:1 is not A or there is a nucleotide inserted between nucleotides corresponding to positions 26190 and 26191 of SEQ ID NO:1;
(v) the nucleotide corresponding to position 27134 of SEQ ID NO:1 is not a T or there is at least one nucleotide inserted between nucleotides corresponding to positions 27134 and 27125 of SEQ ID NO:1; or
(vi) the A-T dinucleotide corresponding to positions 27706-27707 of SEQ ID NO:1 is deleted.

2 . The method according to claim 1 wherein the human subject is identified as a carrier of a SMN1 duplication allele based on the presence of a nucleotide structure selected from the group consisting of a T corresponding to the nucleotide at position 11678 or 11679 of SEQ ID NO:1, an A corresponding to the nucleotide at position 15774 or 15775 of SEQ ID NO:1, an A corresponding to position 22804 or 22805 of SEQ ID NO:1, a G corresponding to the nucleotide at position 26190 or 26191 of SEQ ID NO:1, a G corresponding to the nucleotide at position 27134 or 27135 of SEQ ID NO:1 and an AT deletion corresponding to the nucleotides at positions 27706-27707 of SEQ ID NO:1.

3 . A method of identifying a human Spinal Muscular Atrophy (SMA) silent (2+0) carrier comprising:
(a) screening nucleic acid from a human subject by determining
(i) the identity of the nucleotide corresponding to position 27134 of SEQ ID NO:1, or
(ii) whether the A-T dinucleotide corresponding to positions 27706-27707 of SEQ ID NO:1 has been deleted; and
(b) identifying an individual as a silent (2+0) carrier of SMA if the nucleotide corresponding to position 27134 of SEQ ID NO:1 is not a T or the A-T dinucleotide corresponding to positions 27706-27707 of SEQ ID NO:1 is deleted, or both.

4 . The method according to claim 3 further comprising obtaining a sample of nucleic acid from the human subject.

5 . The method according to claim 3 further comprising providing genetic counseling to the human subject based on the results of the method of identifying a human Spinal Muscular Atrophy (SMA) silent (2+0) carrier.

6 . A method of identifying a human Spinal Muscular Atrophy (SMA) silent (2+0) carrier comprising:
(a) screening nucleic acid from a human subject by determining the identity of the nucleotide corresponding to position 27134 of SEQ ID NO:1; (b) determining if the A-T dinucleotide corresponding to positions 27706-27707 of SEQ ID NO:1 has been deleted; and (c) identifying an individual as a silent (2+0) carrier of SMA if the nucleotide corresponding to position 27134 of SEQ ID NO:1 is G and the A-T dinucleotide corresponding to positions 27706-27707 of SEQ ID NO:1 is deleted.

7 . The method according to claim 6 further comprising obtaining a sample of nucleic acid from the human subject.

8 . The method according to claim 6 further comprising providing genetic counseling to the human subject based on the results of the method of identifying a human Spinal Muscular Atrophy (SMA) silent (2+0) carrier.

9 . The method according to claim 6 wherein the identity of the nucleotide corresponding to position 27134 of SEQ ID NO:1, and the identities of the nucleotides corresponding to positions 27706 and 27707 of SEQ ID NO:1 are determined by restriction fragment length polymorphism.

10 . The method according to claim 6 wherein a G is identified at the position corresponding to position 27134 of SEQ ID NO:1 by restriction fragment length polymorphism using restriction endonuclease HpyCH4III.

11 - 23 . (canceled)

24 . The method according to claim 1 , comprising screening the nucleic acid by determining the identity of the nucleotide corresponding to position 11678 of SEQ ID NO:1; and identifying the human subject as a carrier of a SMN1 duplication allele if the nucleotide corresponding to position 11678 of SEQ ID NO:1 is not G or there is a nucleotide inserted between nucleotides corresponding to positions 11678 and 11679 of SEQ ID NO:1.

25 . The method according to claim 1 , comprising screening the nucleic acid by determining the identity of the nucleotide corresponding to position 15774 of SEQ ID NO:1; and identifying the human subject as a carrier of a SMN1 duplication allele if the nucleotide corresponding to position 15774 of SEQ ID NO:1 is not G or there is a nucleotide inserted between nucleotides corresponding to positions 15774 and 15775 of SEQ ID NO:1.

26 . The method according to claim 1 , comprising screening the nucleic acid by determining the identity of the nucleotide corresponding to position 22804 of SEQ ID NO:1; and identifying the human subject as a carrier of a SMN1 duplication allele if the nucleotide corresponding to position 22804 of SEQ ID NO:1 is not G or there is a nucleotide inserted between nucleotides corresponding to positions 22804 and 22805 of SEQ ID NO:1.

27 . The method according to claim 1 , comprising screening the nucleic acid by determining the identity of the nucleotide corresponding to position 26190 of SEQ ID NO:1; and identifying the human subject as a carrier of a SMN1 duplication allele if the nucleotide corresponding to position 26190 of SEQ ID NO:1 is not A or there is a nucleotide inserted between nucleotides corresponding to positions 26190 and 26191 of SEQ ID NO:1.

28 . The method according to claim 1 , comprising screening the nucleic acid by determining the identity of the nucleotide corresponding to position 27134 of SEQ ID NO:1; and identifying the human subject as a carrier of a SMN1 duplication allele if the nucleotide corresponding to position 27134 of SEQ ID NO:1 is not a T or there is at least one nucleotide inserted between nucleotides corresponding to positions 27134 and 27125 of SEQ ID NO:1.

29 . The method according to claim 1 , comprising screening the nucleic acid by determining whether the A-T dinucleotide corresponding to positions 27706-27707 of SEQ ID NO:1 has been deleted; and identifying the human subject as a carrier of a SMN1 duplication allele if the A-T dinucleotide corresponding to positions 27706-27707 of SEQ ID NO:1 is deleted.

Assignees

• Icahn School Med Mount Sinai

Inventors

• Edelmann Lisa
• Desnick Robert J

Classifications

• C12Q2600/156

  Polymorphic or mutational markers · CPC title

• C12Q1/6827

  for detection of mutation or polymorphism · CPC title

• C12Q1/6883 Primary

  for diseases caused by alterations of genetic material · CPC title

• C12Q2600/172

  Haplotypes · CPC title