Nucleic acid size detection method

• US 8,697,399 B2
• Filed: 04/11/2007
• Issued: 04/15/2014
• Est. Priority Date: 10/05/2006
• Status: Active Grant

• Current Assignee: Quest Diagnostics Investments Incorporated (Quest Diagnostics Incorporated), U.S. Genomics, Inc (Toxic Reports LLC)
• Original Assignee: Quest Diagnostics Investments Incorporated (Quest Diagnostics Incorporated), U.S. Genomics, Inc (Toxic Reports LLC)
• Inventors: Huang, Donghui, Strom, Charles M., Rooke, Jenny Ellen, Potts, Steven J.
• Primary Examiner(s): Pande, Suchira
• Application Number:
  US12/444,361
• Publication Number:
  US 20100167284A1
• Time in Patent Office: 2,561 Days
• Field of Search: None
• US Class Current: 435/91.2
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 2525/151 repeat or repeated sequences, e.g. VNTR, microsatellite, concatemer
• CPC Class Codes: C12Q 2565/125 Electrophoretic separation
• CPC Class Codes: C12Q 2565/629 being a microfluidic device
• CPC Class Codes: Y10T 436/17 Nitrogen containing

Abstract

The present invention provides methods of determining the size of a particular nucleic acid segment of interest in a sample of nucleic acids through fragmentation of DNA, size fractionation, an optional second fragmentation, and identification using a marker sequence. In particular aspects, an expansion or reduction of tandem repeat sequences can be detected. In further aspects, carriers and individuals afflicted with fragile X syndrome or other diseases associated with tandem repeats can be distinguished from normal individuals.

Claims

1. A method for screening human male and female individuals for carrier status of mutations in the tandem repeat region of the FMR1 gene, said method comprising

assaying nucleic acids from an individual to determine gender;

and

assaying nucleic acids from said individual to determine the length of the tandem repeat region of the FMR1 gene wherein said determining comprises

separating fragments of a nucleic acid, said fragments prepared from a nucleic acid containing sample of the individual, wherein said fragments include some which contain a tandem repeat segment of the FMR1 gene and a marker sequence, wherein the marker sequence is not contained within the tandem repeat segment, said separating into fractions according to size under conditions in which a fragment containing the tandem repeat segment having a normal number of repeats will be located in a first fraction; and

a fragment containing a tandem repeat segment having a premutation will be located in a second fraction; and

a fragment having a tandem repeat region having a full mutation will be located in a third fraction,

subjecting said separated fragments from each of said fractions to a second fragmentation such that all or a portion of the tandem repeat segment is cleaved from said marker sequence, and

identifying those fraction(s) containing the segment by detecting the marker sequence, wherein the number of repeats in the tandem repeat segment is determined by the fraction in which it is identified, wherein

in male individuals;

a positive result in the first fraction indicates the individual is not a carrier,

a positive result in the second fraction indicates the individual is a premutation carrier,

a positive result in the third fraction indicates the individual is affected; and

in female individuals;

a positive result in only the first fraction indicates the individual is homozygous for the a normal allele;

a positive result in the second fraction indicates the individual is a premutation carrier; and

a positive result in the third fraction indicates the individual is a full mutation carrier.

2. A method according to claim 1, wherein said assaying nucleic acids to determine gender comprises nucleic acid amplification.

3. A method according to claim 2, wherein said nucleic acid amplification comprises

amplifying a region of the amelogenin gene which produces different sizes of amplification products from the amelogenin gene on the X chromosome and the amelogenin gene on the Y chromosome,

determining the size of the amplification product or products, wherein the presence of one product of a single size indicates the gender is female and the presence of two products of different sizes indicates the gender is male.

4. A method according to claim 3, wherein said amplifying of a region of the amelogenin gene is performed in multiplex with the amplifying of the tandem repeat region of the FMR1 gene.

5. A method according to claim 4, wherein said multiplex amplification further comprises amplifying one or more control sequences.

6. The method according to claim 1 wherein said step of cleaving all or a portion of the tandem repeat segment from said marker sequence in fragments which contain said tandem repeat segment and said marker sequence precedes identifying those fraction(s) containing the segment by detecting the marker sequence.