System and method for detection of HIV tropism variants

Details System and method for detection of HIV tropism variants System and method for detection of HIV tropism variants

2011-02-15

2011-02-15

Chunduru, Suryaprabha (Department: 1637)

Chemistry: molecular biology and microbiology

Measuring or testing process involving enzymes or...

Involving nucleic acid

C435S091200, C536S024330

Reexamination Certificate

active

07888034

ABSTRACT:
An embodiment of a method for detecting low frequency occurrence of one or more HIV sequence variants associated with drug resistance is described that comprises the steps of: generating cDNA species from each RNA molecule in an HIV sample population; amplifying at least one first amplicon from the cDNA species, wherein each first amplicon comprises a plurality of amplified copies and is amplified with a pair of nucleic acid primers that define a locus of the first amplicon; clonally amplifying the amplified copies of the first amplicons to produce a plurality of second amplicons wherein a plurality of the second amplicons comprise an immobilized population of substantially identical copies from one of the amplified copies of first amplicons; determining a nucleic acid sequence composition of the substantially identical copies from at least 100 of the immobilized populations in parallel on a single substrate; and detecting one or more sequence variants that occur at a frequency of 5% or less in the nucleic acid sequence composition of the at least 100 immobilized populations; and correlating the detected sequence variants with variation associated with HIV tropism.

REFERENCES:
patent: 6210891 (2001-04-01), Nyren et al.
patent: 6258568 (2001-07-01), Nyren
patent: 6274320 (2001-08-01), Rothberg et al.
patent: 6727060 (2004-04-01), Philpott et al.
patent: 6828100 (2004-12-01), Ronaghi
patent: 7206699 (2007-04-01), Larder et al.
patent: 7211390 (2007-05-01), Rothberg et al.
patent: 7323305 (2008-01-01), Leamon et al.
patent: 7575865 (2009-08-01), Leamon et al.
patent: 7601499 (2009-10-01), Berka et al.
patent: 2004/0185484 (2004-09-01), Costa et al.
patent: 2004/0191269 (2004-09-01), Lu et al.
patent: 2005/0042648 (2005-02-01), Griffiths et al.
patent: 2005/0064460 (2005-03-01), Holliger et al.
patent: 2005/0079510 (2005-04-01), Berka et al.
patent: 2005/0227264 (2005-10-01), Nobile et al.
patent: 2006/0228721 (2006-10-01), Leamon et al.
patent: 2006/0228722 (2006-10-01), Kim et al.
patent: 2009/0053724 (2009-02-01), Roth et al.
patent: 2009/0105959 (2009-04-01), Braverman et al.
patent: 2009/0203086 (2009-08-01), Chen et al.
patent: 2009/0233291 (2009-09-01), Chen et al.
patent: WO 2007/088201 (2007-08-01), None
patent: WO 2007088201 (2007-08-01), None
patent: WO 2008/062385 (2008-05-01), None
patent: WO 2008/115427 (2008-09-01), None
patent: WO 2010/000427 (2010-01-01), None
Lowe et al., A computer program for selection of oligonucleotide primers for polymerase chain reactions. Nucleic Acids Research, vol. 18, No. 7, pp. 1757-1761, 1990.
U.S. Appl. No. 12/380,139, filed Feb. 23, 2009, Simons et al.
U.S. Appl. No. 61/118,815, filed Dec. 1, 2008, Simen et al.
Ahmadian et al. (2000), Analytical Biochemistry, 280:103-110.
Altschul et al. (1990), Journal Molecular Biology, 215:403-410.
Archer et al. (2009), AIDS, 23:1209-1218.
Jensen et al. (2003), AIDS, 5:104-112.
Jensen et al. (2003), Journal of Virology, 77:13376-13388.
Jensen et al. (2006), Journal of Virology, 80:4698-4704.
Lewis, et al. (2007), 14thConference on Retroviruses and Opportunistic Infections, Abstract 680.
Merrifield (1964), Biochemistry, 3:1385-1390.
Nelson et al. (1997), Journal of Virology, 71:8750-8758.
Poveda et al. (2006), AIDS, 20:1359-1367.
Rickert et al. (2002), BioTechniques, 32:592-603.
Smith et al. (1981), Journal Molecular Biology, 147:195-197.
Thompson et al. (1997), Nucleic Acids Research, 25:4876-4882.
Wang et al. (2007), Genome Research, 17:1195-1201.
Westby et al. (2006), Journal of Virology, 80:4909-4920.
International Search Report for PCT/EP2009/004672, mailed Oct. 8, 2009.

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