Restriction endonuclease enhanced polymorphic sequence detection
Provided in part herein is an improved method for the detection of specific polymorphic alleles in a mixed DNA population. The method comprises enriching the relative percentage of a given polymorphic allele that is exponentially amplifiable by PCR. Provided also are methods for selectively enriching target nucleic acid, for example, fetal nucleic acid in a maternal sample. In the case of detecting fetal nucleic acid in a maternal sample, a restriction enzyme is introduced that can discriminate between the alleles of a polymorphic site. In some embodiments, the maternal allele is digested and nucleic acid comprising the paternal allele is relatively enriched.
1. A method for detecting in nucleic acid the presence or absence of one or more target alleles of paternal origin, comprising:
a) cleaving nucleic acid from a sample with a Tsp509I restriction enzyme;
b) exposing the nucleic acid after (a) to amplification conditions that amplify uncleaved nucleic acid but not cleaved nucleic acid, and which amplification conditions are capable of generating amplification products comprising some or all of the single nucleotide polymorphic loci selected from the group consisting of:
rs11835780
rs748773
rs7323716
rs4311632
rs6488494
rs9652080
rs13110085
rs1363267
rs10785736
rs13269702
rs10840805
rs7356482
rs1797700
rs2723307
rs7831906
rs2993531
rs4764597
rs9818611
rs1885121
rs4589569
rs12903747
rs1372688
rs2820107
rs7320201
rs1904161
rs6766358
rs4869315
rs1720839
rs12675087
rs3913810
rs10901705
rs7689368
rs6542638
rs6582294
rs725849
rs12450474
rs7144509
rs7900002
rs1346718
rs10234234
rs910500
rs1503660
rs8016543
rs4489023
rs2007475
rs11221881
rs1916803
rs683262
rs13155942
rs10260483
rs10110766
rs494220
rs4488809
rs1041409
rs3912319
rs4533845
rs11099210
rs9428474
rs3816551
rs10754776
rs9929404
rs6556642
rs4130306
rs7294836
rs7205009
rs2734574
rs4673821
rs12674093
rs1401454
rs614004
rs2322301
rs9285190
rs1444647
rs7741525
rs179596
rs7818415
rs17074340
rs331893
rs12007
rs2462049
rs9787011
rs9356029
rs10806232
rs273172
rs6569474
rs11105611
rs9989393
rs10898954
rs12107918
rs1342995
rs6043856
rs664358
rs263025
rs1593443 and
rs6142841, thereby
generating amplification products; and
c) detecting the presence or absence of one or more target alleles based on the amplification products.
2. The method of claim 1 , wherein part (b) is conducted using amplification primer pairs selected the group consisting of:
5′-ACGTTGGATGGGCTCTAGTTTTCAGCAGAC-3′ and
5′-ACGTTGGATGCTCAAAACCTGGCTACCTTG-3′;
5′-ACGTTGGATGCTTCTTTTCCCTGCATCATC-3′ and
5′-ACGTTGGATGAGGGAAGTGTTGTAGCATGG-3′;
5′-ACGTTGGATGAAGCAGGTACTTACTATGGG-3′ and
5′-ACGTTGGATGGTACTGTTAGTGTGTCACTC-3′;
5′-ACGTTGGATGTTGCCTAGCCTTACATCCTG-3′ and
5′-ACGTTGGATGCTCAAAATAGATGATGGACTG-3′;
5′-ACGTTGGATGCAATCAGCTACTGCTGATCC-3′ and
5′-ACGTTGGATGTGGTTTGGTTTCTCAGCTGG-3′;
5′-ACGTTGGATGGAGAGAGGGAGAAAGTAGAG-3′ and
5′-ACGTTGGATGCCCTTACTCAGTGATTCCTC-3′;
5′-ACGTTGGATGCCTACCTTGCTCTGAGAAAC-3′ and
5′-ACGTTGGATGCTTCCTGCTTTTAAGCAGTC-3′;
5′-ACGTTGGATGAGTGCAACAGAAAAGGCAGG-3′ and
5′-ACGTTGGATGGGTCCTTGGTATGTGTTCTC-3′;
5′-ACGTTGGATGTCTGAAGGTAGACCTGGATG-3′ and
5′-ACGTTGGATGCTCAGGATATCATTACACACC-3′;
5′-ACGTTGGATGGTTACACTGACAATCAAGGG-3′ and
5′-ACGTTGGATGACTCTCATGTACCCTCTCTG-3′;
5′-ACGTTGGATGAGAAGATATGTTGAGAGGGC-3′ and
5′-ACGTTGGATGTATTCCCTTTCTGGCTGTGG-3′;
5′-ACGTTGGATGCTGCCTATTCTTCTACGGTC-3′ and
5′-ACGTTGGATGCAGAAACATGCTTGTAGCAG-3′;
5′-ACGTTGGATGAATGAGAGCTTGCTTACTTC-3′ and
5′-ACGTTGGATGAGTGTCGTTCAGACACTAGC-3′;
5′-ACGTTGGATGTTTAATAGGGAAAGTATTGG-3′ and
5′-ACGTTGGATGCACACCCAGAAGCACTGATA-3′;
5′-ACGTTGGATGCCTTCTGCTCAACTACCAAG-3′ and
5′-ACGTTGGATGGCCAAAGACGATGTGGAATG-3′;
5′-ACGTTGGATGTTTCACAGGGTTAGGATGGG-3′ and
5′-ACGTTGGATGCTAGCAAAGGCTGGATTCTG-3′;
5′-ACGTTGGATGAGCCACCAAAACCAAGCTTC-3′ and
5′-ACGTTGGATGCTTGTAAGGCAGGTCTGATG-3′;
5′-ACGTTGGATGGCTTGCAGAGGTTCACTAAC-3′ and
5′-ACGTTGGATGTGAGGCCATTAAAAGCAGGG-3′;
5′-ACGTTGGATGAGCAAGTGTTCCCTTTTTGG-3′ and
5′-ACGTTGGATGCACGCGTAGGCTATGGTTTA-3′;
5′-ACGTTGGATGCGGTTTCTTTTGAGGACTGG-3′ and
5′-ACGTTGGATGGCTCAGTGTCTGACAAAAGC-3′;
5′-ACGTTGGATGAAGAATGGAAAGTGATGAG-3′ and
5′-ACGTTGGATGCTAGGCTTGTTCACTATTTG-3′;
5′-ACGTTGGATGCATTGCTTGGGTCTTCTCAG-3′ and
5′-ACGTTGGATGGGGTTCTGGCAGATATATCC-3′;
5′-ACGTTGGATGTATGGATGCAAGCCTTTCCC-3′ and
5′-ACGTTGGATGAGGCTGAAGAATGCTTTCCC-3′;
5′-ACGTTGGATGTGTGCAGCACTTTTCACAAG-3′ and
5′-ACGTTGGATGCAGGGTCACATCACAGATTG-3′;
5′-ACGTTGGATGGCTTGTTAAATGTGTGTTCC-3′ and
5′-ACGTTGGATGTCCCTCAGTTTAGTTTTGTC-3′;
5′-ACGTTGGATGGATAATATTGTGCTGCATGCT-3′ and
5′-ACGTTGGATGACCTTGTTCTGTGTGTGTGG-3′;
5′-ACGTTGGATGCTCCCATCTATGATTTCCAG-3′ and
5′-ACGTTGGATGATGCATATCTGGAGACACAC-3′;
5′-ACGTTGGATGCCAGTCAAGGAAGCAGTTTC-3′ and
5′-ACGTTGGATGGTCTGATTAGGCCTAAGAGC-3′;
5′-ACGTTGGATGTACCATGCTCATTGAACTCG-3′ and
5′-ACGTTGGATGGGAGATTTGATAGGAAGTGC-3′;
5′-ACGTTGGATGAAATGCTACTCCAACAGAGG-3′ and
5′-ACGTTGGATGCTTCATTATCCCCACTGCTG-3′;
5′-ACGTTGGATGGATGATGAAAGCATAAGTC-3′ and
5′-ACGTTGGATGGAGATGTTGCAAAGATGCAAG-3′;
5′-ACGTTGGATGCTGGATCTTACCTCCATAGC-3′ and
5′-ACGTTGGATGACTAGAATCGTGCAGAGAAC-3′;
5′-ACGTTGGATGAAGTGCTGGGATTACAGGAG-3′ and
5′-ACGTTGGATGGAGACAGGCAAAGATGCAAC-3′;
5′-ACGTTGGATGGAGACGATTCTTCAGGAAAC-3′ and
5′-ACGTTGGATGCCATGACTCTAGTGACCTTC-3′;
5′-ACGTTGGATGTAAGCATCCATGGACCTACC-3′ and
5′-ACGTTGGATGCAGGTGGTAAATGTGCTCAG-3′;
5′-ACGTTGGATGTTGACTCACCCACTTCTGTC-3′ and
5′-ACGTTGGATGTGTTGATGAGGTGAAGAGGG-3′;
5′-ACGTTGGATGAGCTTGGGCTGAATGTTAGG-3′ and
5′-ACGTTGGATGTAAAAGCAAAACAGCTTCCC-3′;
5′-ACGTTGGATGTTTTTCCTCCTGTACCCTGC-3′ and
5′-ACGTTGGATGTACATGTGGTTAGAGTCTGG-3′;
5′-ACGTTGGATGGGGAAGGTGTTTGTCTCATA-3′ and
5′-ACGTTGGATGTGGTACAGTTTGAAAGGAGC-3′;
5′-ACGTTGGATGGCATTATGCTAAAGGCTGTC-3′ and
5′-ACGTTGGATGTCCTCTGATTTAGGCCCTTC-3′;
5′-ACGTTGGATGGGATCAAGAGGAAAAAATGGG-3′ and
5′-ACGTTGGATGTAGTTTCAATCTCTGTGCTG-3′;
5′-ACGTTGGATGCTATGTTTTCCCCCAGCTTG-3′ and
5′-ACGTTGGATGGCAAAAGAACAACCACCCAG-3′;
5′-ACGTTGGATGGACCTTCCTGTTCCTAGATG-3′ and
5′-ACGTTGGATGTGACTGGACTGTGACATAGC-3′;
5′-ACGTTGGATGAGATTGGTCCCTCACAATGG-3′ and
5′-ACGTTGGATGATTTGGCCCTGAGGCTTATC-3′;
5′-ACGTTGGATGCACTGAGAGATACAGGAAAG-3′ and
5′-ACGTTGGATGCTTGTTTCCCCAACATAAGG-3′;
5′-ACGTTGGATGATCCATCTCTGTCAGAGTTC-3′ and
5′-ACGTTGGATGAGAGAACTGACCCTTCACTG-3′;
5′-ACGTTGGATGGGTGGAGATGGGATTCTCTG-3′ and
5′-ACGTTGGATGAACCCAGTCTACACACACAG-3′;
5′-ACGTTGGATGACTGGCCATGCAGATGTAAG-3′ and
5′-ACGTTGGATGCACTGCCCATAGACTCTTTC-3′;
5′-ACGTTGGATGTTACGACCCAATCACCTTGC-3′ and
5′-ACGTTGGATGTGTGTCCCCAACCACATTTC-3′;
5′-ACGTTGGATGAACTGATGGCTCGTACTACC-3′ and
5′-ACGTTGGATGGCTCTTTTCCCTATGATGTG-3′;
5′-ACGTTGGATGGGTTTATTGGAAATGAAGTC-3′ and
5′-ACGTTGGATGGATCCTACTTACTTCCAGTC-3′;
5′-ACGTTGGATGGCAAGCATCTGCTCTTGAGG-3′ and
5′-ACGTTGGATGCTGTGTAAAAGAGTTTGAGG-3′;
5′-ACGTTGGATGGGGCTCTTATTATTGTACTC-3′ and
5′-ACGTTGGATGAACAAGCCCAAGTTCTCCAG-3′;
5′-ACGTTGGATGGGCAGAACAAGGACAGATAG-3′ and
5′-ACGTTGGATGAGTCTAGTAAAAGTTCTGCC-3′;
5′-ACGTTGGATGTACATTCAGACGATAGTGCC-3′ and
5′-ACGTTGGATGAGACCAAGTAACCCCAAACC-3′;
5′-ACGTTGGATGGTCACTGAACTCTGGAGTAG-3′ and
5′-ACGTTGGATGGCAGTTTTCAAAGGAAACCC-3′;
5′-ACGTTGGATGAGATCCTCCAGCTCATCTTC-3′ and
5′-ACGTTGGATGTAATCCTTGGAGGCTCTCTG-3′;
5′-ACGTTGGATGTAGAGCTCACAGAGCACTTC-3′ and
5′-ACGTTGGATGAGCACTTAACTGAGTCTGGG-3′;
5′-ACGTTGGATGCTTTGCTCACAAGAAAGTTGG-3 and
5′-ACGTTGGATGCCCCCAAGGCAATGATTTTC-3′;
5′-ACGTTGGATGTAATACCCTGAGCAAGGACG-3′ and
5′-ACGTTGGATGGTGCATTTAAAATCCATGTG-3′;
5′-ACGTTGGATGTGTTACAGCAGCTAGTGTTG-3′ and
5′-ACGTTGGATGCCTCTAATAGCACCCAGTTC-3′;
5′-ACGTTGGATGGTCCATTTAACGGTGTGGAG-3′ and
5′-ACGTTGGATGGGTTCATGAAATGTTAGTTCC-3′;
5′-ACGTTGGATGTATCCATCCTTCAGACACCC-3′ and
5′-ACGTTGGATGATGGGACAGTAACTGCAGAC-3′;
5′-ACGTTGGATGCTCAGTTTAAAGTCACTGCC-3′ and
5′-ACGTTGGATGTAACCCTGCAAAGACTAGAG-3′;
5′-ACGTTGGATGGCCAGCTTGTCCATTAAAGG-3′ and
5′-ACGTTGGATGCTGGCTTATAAATAAAAGACC-3′;
5′-ACGTTGGATGCATTGCAGTAACTGGAGGTC-3′ and
5′-ACGTTGGATGGGCACAGTAGTTCAGTTACC-3′;
5′-ACGTTGGATGAGTGAGACTTAACCGTGGAG-3′ and
5′-ACGTTGGATGCACCCCCACATTAGCAAAAG-3′;
5′-ACGTTGGATGATCTTCATGTCCCAAGGAGG-3′ and
5′-ACGTTGGATGCCAAGTTTATGAAACGTAG-3′;
5′-ACGTTGGATGCACATGCTAGAGAAAGAGGG-3′ and
5′-ACGTTGGATGTATGTCCTTCCCTGATTTTC-3′;
5′-ACGTTGGATGAGGATGCCTGTTGGGTTTTC-3′ and
5′-ACGTTGGATGATCAGACTTTTCCCAGGCAG-3′;
5′-ACGTTGGATGAAGCAACTGGCACTCCTAAG-3′ and
5′-ACGTTGGATGGAGTGTTGTGATGCATGCC-3′;
5′-ACGTTGGATGGTATCTCCCACTCTTGTACC-3′ and
5′-ACGTTGGATGCTGGAATACAACATTTCTGG-3′;
5′-ACGTTGGATGTTGTGTGCTATCTTACACTG-3′ and
5′-ACGTTGGATGACTAGTTGGAATGGGCTTGG-3′;
5′-ACGTTGGATGACTCCCTACCTATCTCTTTG-3′ and
5′-ACGTTGGATGTCCACAGCCACTGAATAGTC-3′;
5′-ACGTTGGATGTCATGTAACCAAGCACCACC-3′ and
5′-ACGTTGGATGGCTCATTTATAGAAGCAGTC-3′;
5′-ACGTTGGATGCAGTGGATTTCAAATCCGGC-3′ and
5′-ACGTTGGATGTGTTCAGAGGGTGTTGGATG-3′;
5′-ACGTTGGATGCATCAGCAATATAATGCCGC-3′ and
5′-ACGTTGGATGTGTGGATCACTGTTCACAGG-3′;
5′-ACGTTGGATGCACCAGTGCAAACACACAAC-3′ and
5′-ACGTTGGATGCCTGATTGTTTTGGAAGGAG-3′;
5′-ACGTTGGATGAGTTGCCATGTTTCCACAGG-3′ and
5′-ACGTTGGATGGACTAATACTCAGGTTGAGG-3′;
5′-ACGTTGGATGTGGAAGGCAGAGTGATATAC-3′ and
5′-ACGTTGGATGGCTTTCTTCACTCAGAAGGG-3′;
5′-ACGTTGGATGGAGGAGTTATAAGACCTAGAG-3′ and
5′-ACGTTGGATGACCATATCACAGTTGTTGGG-3′;
5′-ACGTTGGATGCTACGTGACCCAAAGTTCAG-3′ and
5′-ACGTTGGATGTCTCACTCCTGGTTACCTAC-3′;
5′-ACGTTGGATGTTATACAGGTTCCAGCCAGC-3′ and
5′-ACGTTGGATGCAGAGAGAAAAGGGAGTAGG-3′;
5′-ACGTTGGATGACTGATACCCTACAGTGTGC-3′ and
5′-ACGTTGGATGGTGCTCAGAGCACTTAAACG-3′;
5′-ACGTTGGATGAATCTTGGAGCCTTGGAGAC-3′ and
5′-ACGTTGGATGGTGCTTCTCACAAAAGCCTG-3′;
5′-ACGTTGGATGATCCTGGGCTTTCCTTTGTC-3′ and
5′-ACGTTGGATGGAGTCTAGTGGACAAGAGAG-3′;
5′-ACGTTGGATGTGGAGGCCACTGGATTAAAG-3′ and
5′-ACGTTGGATGAGACACAGCTAGCACTTTCC-3′;
5′-ACGTTGGATGGTTTGGTGACTATAGAAACAG-3′ and
5′-ACGTTGGATGCAGTTTAAAGTCATATTCAC-3′;
5′-ACGTTGGATGGAGCACTTATCACAGGTCAG-3′ and
5′-ACGTTGGATGGAAGGTGGGATAAACAAGGG-3′;
5′-ACGTTGGATGGTTCTGGATGTTGGCCATTC-3′ and
5′-ACGTTGGATGCCACATCATATGCATCTGGG-3′;
5′-ACGTTGGATGGAGATGAGTAAGAGCAGGTG-3′ and
5′-ACGTTGGATGCTCATAAGACCCTGAACACC-3′;
5′-ACGTTGGATGACTGAAGCATAACGCCTCTG-3′ and
5′-ACGTTGGATGGGTGCCCAAACATGTTATGC-3′;
5′-ACGTTGGATGAGAAGGAGGTCATTCTAGGC-3′ and
5′-ACGTTGGATGACATGGACTCTAAAGCCACC-3′;
5′-ACGTTGGATGTGAATCCCATGAGCATGAGC-3′ and
5′-ACGTTGGATGATTCCACACAGCATTGCCTC-3′; and
5′-ACGTTGGATGCTGTCAAAAGCCAGGCTAAG-3′ and
5′-ACGTTGGATGGAGGTTCAAAGAGTATAAAG-3′.
3. The method of claim 1 , further comprising contacting the amplification products with one or more extension primers.
4. The method of claim 3 , wherein the extension primers are selected from the group consisting of:
5′-gCCTGGGAGAAAGAAAACAA-3′,
5′-catccGTTTTTCCCTCTTGACTGAAT-3′,
5′-cgggACTTACTATGGGGAATAGAAT-3′,
5′-caccTCCTGAATACTTTCTCATATAGA-3′,
5′-TGATCCACTGGCTCAA-3′,
5′-ggagGGTGGTTAGAGAACTCAATGAAT-3′,
5′-AGCCTGCACTGTGAA-3′,
5′-CAAGTCTTCTATCAAGGGAAT-3′,
5′-aCTGAGAGCAACCACTAA-3′,
5′-cGAGGAGGGCAGAGAAGAAT-3′,
5′-cccctAGAGGGCAGATAAATAGTTAAAT-3′,
5′-gtcgTCTACGGTCTTTTTCTTATCAA-3′,
5′-ctAGCTTGCTTACTTCTAAAAA-3′,
5′-aaatcTAAATAGCCAAGAAAACAGCCAA-3′,
5′-attaTGCTCAACTACCAAGTTAAGA-3′,
5′-acatGGAGTTTCCTGTACTTTAAAAAA-3′,
5′-tgAGCAAGTGCTGAGGG-3′,
5′-gATACAGCTTGGCCAAT-3′,
5′-GGGGCTGGTAGGAAAT-3′,
5′-ctcTCTTTCTCCAGGGATGA-3′,
5′-cGTGATGAGATTTCTATCATACAA-3′,
5′-cccccCCTTCCATGGGACTCATTA-3′,
5′-GACTATCCTCTTCAGACCAA-3′,
5′-cccCAAGTTGAAAACTTATTCCAA-3′,
5′-tttcAAATGTGTGTTCCATCATCTA-3′,
5′-gggtTGCTGCATGCTGTAAAT-3′,
5′-ccacATCATGCCTCTATTGACA-3′,
5′-cCAGTTTCAATAACAGATAGTAAAT-3′,
5′-aaAAAACTCAATATAGTAAAGGTATCAA-3′,
5′-GGAGGTGACATAAGTAAGTA-3′,
5′-ATGATGAAAGCATAAGTCTTTTAAT-3′,
5′-agCTTACCTCCATAGCATCTAA-3′,
5′-TGGCCAGAACTAATCAA-3′,
5′-AAGACAAAGGACACCAA-3′,
5′-caGACCTACCACCCAAAT-3′,
5′-ACTTCTGTCTCAGTATCCA-3′,
5′-ctAGCGTTTCACGTTCAAAA-3′,
5′-aaaTGCAATCTGTCTGGAAA-3′,
5′-ggtcCTTTCTGCAGCTCATATTCTGCAA-3′,
5′-GGCTGTCACAGATTTATAAAA-3′,
5′-cATGGGAAACATGCCTCAATAAAT-3′,
5′-acttTGCTAGGTCTTACATGAA-3′,
5′-acgTTCCTGTTCCTAGATGATCAAAAT-3′,
5′-AGTCTTTCTGAGCCCAA-3′,
5′-agcGAGATACAGGAAAGTGTAAAT-3′,
5′-aggTCTCAAATAAAAATGCAAAGGAAA-3′,
5′-GGGATTCTCTGGTTGTAAA-3′,
5′-gCCAACAGAGAAAGTAACAA-3′,
5′-tCCTCCTCAAACATTAAGGACAAAA-3′,
5′-tGTACTACCCAGTGGAATAAA-3′,
5′-tcTTTAAAGTGCTACATCTATGAA-3′,
5′-cgGCTCTTGAGGCAGTAAA-3′,
5′-cGGCTCTTATTATTGTACTCTATAAA-3′,
5′-atcGGTGGATGTTTCAGGGAAGTAAA-3′,
5′-ggtaAGACGATAGTGCCAGAAAAT-3′,
5′-agCAGATAGCCTCTTGTGAAT-3′,
5′-GCTCATCTTCCTCTGAA-3′,
5′-GCACTTCCCTACAAACAA-3′,
5′-TTGGAACTATCGTTCAAAAAGTATTA-3′,
5′-cccatGACGTCACCCTGTAAAAA-3′,
5′-tcGCTAGTGTTGCACTAATAAAAAAAT-3′,
5′-cccccGTGTGGAGAAGTGCGAGT-3′,
5′-AGACACCCAGGCCAA-3′,
5′-cCACTGCCAGTGACCTAA-3′,
5′-cACTTGAAAAATACTTTAGACTTTCTT-3′,
5′-gATCATTGTATAGGTTCCCAGA-3′,
5′-aaatTGAACTGTAGCAAGAAACAAA-3′,
5′-ggatGGAAAAGCTGAAAAGGAA-3′,
5′-ccctcAATCATTCTATGAAGCCAAT-3′,
5′-gTACTGAGATTGACAAGTCATTAAA-3′,
5′-TGGCACTCCTAAGACCAAA-3′,
5′-cCTCTTGTACCCCAGAAAAA-3′,
5′-cGTAGCTTCCTAGCCAAA-3′,
5′-gtcgCTTTGAAAAGCCTTAACCATTAA-3′,
5′-cccccCCCCAAAAACCTACTGAAAT-3′,
5′-GCCGCACATCAGAAT-3′,
5′-CAATCCTTTATCTCTCTCTAATAC-3′,
5′-gaagtAATGGAGAACCTGGTTAA-3′,
5′-ccCAGGATCCTCTAGATTGTGAAAA-3′,
5′-agagACTGAGACAGGCAGTAGCCTAAT-3′,
5′-tgaagGAGAGCTTAACTAAAATAAACAA-3′,
5′-ggggcCCCAAAGTTCAGGATGGTAA-3′,
5′-ACCTGATACTGAAGCCAAA-3′,
5′-TGGATATGACTTGCCCAA-3′,
5′-gTAGTTTCTTTAGCTCTTGAATAAAAT-3′,
5′-acTTGTCACACCTCTTCAAAT-3′,
5′-ggTTAAAGGAGACAATGTATGTAAAT-3′,
5′-gaagGTGTTGCCAAAAGCTAAT-3′,
5′-gtaatTGCCCCTTCAAGTGAAT-3′,
5′-GTGCTATCTCATTGTTGTTTGAAA-3′,
5′-GAGCAGGTGAAATGTTTCTA-3′,
5′-gaCTCTGGGACTACTAAGAAGA-3′,
5′-gggcGGTCATTCTAGGCCATTAATAA-3′,
5′-GAGCCCACTGCTACA-3′, and
5′-CCAGGCTAAGGCAAAT-3′.
5. The method of claim 1 , wherein the sample is from a pregnant female or a female suspected of being pregnant.
6. The method of claim 5 , wherein the sample is blood.
7. The method of claim 1 , wherein 20 or more of the single nucleotide polymorphic loci are assayed.
8. The method of claim 1 , wherein 60 or more of the single nucleotide polymorphic loci are assayed.
9. The method of claim 1 , wherein 90 or more of the single nucleotide polymorphic loci are assayed.
10. The method of claim 1 , wherein the target allele concentration is 10% or less of total nucleic acid concentration prior to cleaving and amplifying the nucleic acid.
11. The method of claim 1 , wherein four or more of the single nucleotide polymorphic loci are informative of the presence or absence of the one or more target alleles.
12. The method of claim 1 , further comprising determining whether fetal nucleic acid is present in the sample.
13. A method for detecting in nucleic acid the presence or absence of one or more target alleles of paternal origin, comprising:
a) cleaving nucleic acid from a sample with a Tsp509I restriction enzyme;
b) exposing the nucleic acid after (a) to amplification conditions that amplify uncleaved nucleic acid but not cleaved nucleic acid, and which amplification conditions are capable of generating amplification products comprising the following single nucleotide polymorphic loci:
rs748773
rs7323716
rs4311632
rs6488494
rs9652080
rs7356482
rs13110085
rs1363267
rs10785736
rs13269702
rs10840805
rs7320201
rs1797700
rs2723307
rs2993531
rs4764597
rs9818611
rs3913810
rs1885121
rs4589569
rs12903747
rs1372688
rs2820107
rs12450474
rs1904161
rs6766358
rs4869315
rs1720839
rs12675087
rs1503660
rs10901705
rs7689368
rs6542638
rs6582294
rs725849
rs683262
rs7144509
rs7900002
rs1346718
rs10234234
rs910500
rs10754776
rs8016543
rs4489023
rs2007475
rs11221881
rs1916803
rs2734574
rs13155942
rs10110766
rs494220
rs4488809
rs1041409
rs9285190
rs3912319
rs4533845
rs11099210
rs9428474
rs3816551
rs331893
rs9929404
rs6556642
rs4130306
rs7294836
rs7205009
rs273172
rs4673821
rs12674093
rs1401454
rs614004
rs2322301
rs1342995
rs1444647
rs7741525
rs179596
rs7818415
rs17074340
rs6142841
rs12007
rs2462049
rs9787011
rs9356029
rs10806232
rs1593443
rs6569474
rs11105611
rs9989393
rs10898954
rs263025
rs664358
rs6043856 and
rs12107918,
thereby generating amplification products; and
c) detecting the presence or absence of one or more target alleles based on the amplification products.
14. The method of claim 13 , wherein part (b) is conducted using amplification primer pairs:
5′-ACGTTGGATGGGCTCTAGTTTTCAGCAGAC-3′ and
5′-ACGTTGGATGCTCAAAACCTGGCTACCTTG-3′;
5′-ACGTTGGATGCTTCTTTTCCCTGCATCATC-3′ and
5′-ACGTTGGATGAGGGAAGTGTTGTAGCATGG-3′;
5′-ACGTTGGATGAAGCAGGTACTTACTATGGG-3′ and
5′-ACGTTGGATGGTACTGTTAGTGTGTCACTC-3′;
5′-ACGTTGGATGTTGCCTAGCCTTACATCCTG-3′ and
5′-ACGTTGGATGCTCAAAATAGATGATGGACTG-3′;
5′-ACGTTGGATGCAATCAGCTACTGCTGATCC-3′ and
5′-ACGTTGGATGTGGTTTGGTTTCTCAGCTGG-3′;
5′-ACGTTGGATGGAGAGAGGGAGAAAGTAGAG-3′ and
5′-ACGTTGGATGCCCTTACTCAGTGATTCCTC-3′;
5′-ACGTTGGATGCCTACCTTGCTCTGAGAAAC-3′ and
5′-ACGTTGGATGCTTCCTGCTTTTAAGCAGTC-3′;
5′-ACGTTGGATGAGTGCAACAGAAAAGGCAGG-3′ and
5′-ACGTTGGATGGGTCCTTGGTATGTGTTCTC-3′;
5′-ACGTTGGATGTCTGAAGGTAGACCTGGATG-3′ and
5′-ACGTTGGATGCTCAGGATATCATTACACACC-3′;
5′-ACGTTGGATGGTTACACTGACAATCAAGGG-3′ and
5′-ACGTTGGATGACTCTCATGTACCCTCTCTG-3′;
5′-ACGTTGGATGAGAAGATATGTTGAGAGGGC-3′ and
5′-ACGTTGGATGTATTCCCTTTCTGGCTGTGG-3′;
5′-ACGTTGGATGCTGCCTATTCTTCTACGGTC-3′ and
5′-ACGTTGGATGCAGAAACATGCTTGTAGCAG-3′;
5′-ACGTTGGATGAATGAGAGCTTGCTTACTTC-3′ and
5′-ACGTTGGATGAGTGTCGTTCAGACACTAGC-3′;
5′-ACGTTGGATGTTTAATAGGGAAAGTATTGG-3′ and
5′-ACGTTGGATGCACACCCAGAAGCACTGATA-3′;
5′-ACGTTGGATGCCTTCTGCTCAACTACCAAG-3′ and
5′-ACGTTGGATGGCCAAAGACGATGTGGAATG-3′;
5′-ACGTTGGATGTTTCACAGGGTTAGGATGGG-3′ and
5′-ACGTTGGATGCTAGCAAAGGCTGGATTCTG-3′;
5′-ACGTTGGATGAGCCACCAAAACCAAGCTTC-3′ and
5′-ACGTTGGATGCTTGTAAGGCAGGTCTGATG-3′;
5′-ACGTTGGATGGCTTGCAGAGGTTCACTAAC-3′ and
5′-ACGTTGGATGTGAGGCCATTAAAAGCAGGG-3′;
5′-ACGTTGGATGAGCAAGTGTTCCCTTTTTGG-3′ and
5′-ACGTTGGATGCACGCGTAGGCTATGGTTTA-3′;
5′-ACGTTGGATGCGGTTTCTTTTGAGGACTGG-3′ and
5′-ACGTTGGATGGCTCAGTGTCTGACAAAAGC-3′;
5′-ACGTTGGATGAAGAATGGAAAGTGATGAG-3′ and
5′-ACGTTGGATGCTAGGCTTGTTCACTATTTG-3′;
5′-ACGTTGGATGCATTGCTTGGGTCTTCTCAG-3′ and
5′-ACGTTGGATGGGGTTCTGGCAGATATATCC-3′;
5′-ACGTTGGATGTATGGATGCAAGCCTTTCCC-3′ and
5′-ACGTTGGATGAGGCTGAAGAATGCTTTCCC-3′;
5′-ACGTTGGATGTGTGCAGCACTTTTCACAAG-3′ and
5′-ACGTTGGATGCAGGGTCACATCACAGATTG-3′;
5′-ACGTTGGATGGCTTGTTAAATGTGTGTTCC-3′ and
5′-ACGTTGGATGTCCCTCAGTTTAGTTTTGTC-3′;
5′-ACGTTGGATGGATAATATTGTGCTGCATGCT-3′ and
5′-ACGTTGGATGACCTTGTTCTGTGTGTGTGG-3′;
5′-ACGTTGGATGCTCCCATCTATGATTTCCAG-3′ and
5′-ACGTTGGATGATGCATATCTGGAGACACAC-3′;
5′-ACGTTGGATGCCAGTCAAGGAAGCAGTTTC-3′ and
5′-ACGTTGGATGGTCTGATTAGGCCTAAGAGC-3′;
5′-ACGTTGGATGTACCATGCTCATTGAACTCG-3′ and
5′-ACGTTGGATGGGAGATTTGATAGGAAGTGC-3′;
5′-ACGTTGGATGAAATGCTACTCCAACAGAGG-3′ and
5′-ACGTTGGATGCTTCATTATCCCCACTGCTG-3′;
5′-ACGTTGGATGGATGATGAAAGCATAAGTC-3′ and
5′-ACGTTGGATGGAGATGTTGCAAAGATGCAAG-3′;
5′-ACGTTGGATGCTGGATCTTACCTCCATAGC-3′ and
5′-ACGTTGGATGACTAGAATCGTGCAGAGAAC-3′;
5′-ACGTTGGATGAAGTGCTGGGATTACAGGAG-3′ and
5′-ACGTTGGATGGAGACAGGCAAAGATGCAAC-3′;
5′-ACGTTGGATGGAGACGATTCTTCAGGAAAC-3′ and
5′-ACGTTGGATGCCATGACTCTAGTGACCTTC-3′;
5′-ACGTTGGATGTAAGCATCCATGGACCTACC-3′ and
5′-ACGTTGGATGCAGGTGGTAAATGTGCTCAG-3′;
5′-ACGTTGGATGTTGACTCACCCACTTCTGTC-3′ and
5′-ACGTTGGATGTGTTGATGAGGTGAAGAGGG-3′;
5′-ACGTTGGATGAGCTTGGGCTGAATGTTAGG-3′ and
5′-ACGTTGGATGTAAAAGCAAAACAGCTTCCC-3′;
5′-ACGTTGGATGTTTTTCCTCCTGTACCCTGC-3′ and
5′-ACGTTGGATGTACATGTGGTTAGAGTCTGG-3′;
5′-ACGTTGGATGGGGAAGGTGTTTGTCTCATA-3′ and
5′-ACGTTGGATGTGGTACAGTTTGAAAGGAGC-3′;
5′-ACGTTGGATGGCATTATGCTAAAGGCTGTC-3′ and
5′-ACGTTGGATGTCCTCTGATTTAGGCCCTTC-3′;
5′-ACGTTGGATGGGATCAAGAGGAAAAAATGGG-3′ and
5′-ACGTTGGATGTAGTTTCAATCTCTGTGCTG-3′;
5′-ACGTTGGATGCTATGTTTTCCCCCAGCTTG-3′ and
5′-ACGTTGGATGGCAAAAGAACAACCACCCAG-3′;
5′-ACGTTGGATGGACCTTCCTGTTCCTAGATG-3′ and
5′-ACGTTGGATGTGACTGGACTGTGACATAGC-3′;
5′-ACGTTGGATGAGATTGGTCCCTCACAATGG-3′ and
5′-ACGTTGGATGATTTGGCCCTGAGGCTTATC-3′;
5′-ACGTTGGATGCACTGAGAGATACAGGAAAG-3′ and
5′-ACGTTGGATGCTTGTTTCCCCAACATAAGG-3′;
5′-ACGTTGGATGATCCATCTCTGTCAGAGTTC-3′ and
5′-ACGTTGGATGAGAGAACTGACCCTTCACTG-3′;
5′-ACGTTGGATGGGTGGAGATGGGATTCTCTG-3′ and
5′-ACGTTGGATGAACCCAGTCTACACACACAG-3′;
5′-ACGTTGGATGACTGGCCATGCAGATGTAAG-3′ and
5′-ACGTTGGATGCACTGCCCATAGACTCTTTC-3′;
5′-ACGTTGGATGTTACGACCCAATCACCTTGC-3′ and
5′-ACGTTGGATGTGTGTCCCCAACCACATTTC-3′;
5′-ACGTTGGATGAACTGATGGCTCGTACTACC-3′ and
5′-ACGTTGGATGGCTCTTTTCCCTATGATGTG-3′;
5′-ACGTTGGATGGGTTTATTGGAAATGAAGTC-3′ and
5′-ACGTTGGATGGATCCTACTTACTTCCAGTC-3′;
5′-ACGTTGGATGGCAAGCATCTGCTCTTGAGG-3′ and
5′-ACGTTGGATGCTGTGTAAAAGAGTTTGAGG-3′;
5′-ACGTTGGATGGGGCTCTTATTATTGTACTC-3′ and
5′-ACGTTGGATGAACAAGCCCAAGTTCTCCAG-3′;
5′-ACGTTGGATGGGCAGAACAAGGACAGATAG-3′ and
5′-ACGTTGGATGAGTCTAGTAAAAGTTCTGCC-3′;
5′-ACGTTGGATGTACATTCAGACGATAGTGCC-3′ and
5′-ACGTTGGATGAGACCAAGTAACCCCAAACC-3′;
5′-ACGTTGGATGGTCACTGAACTCTGGAGTAG-3′ and
5′-ACGTTGGATGGCAGTTTTCAAAGGAAACCC-3′;
5′-ACGTTGGATGAGATCCTCCAGCTCATCTTC-3′ and
5′-ACGTTGGATGTAATCCTTGGAGGCTCTCTG-3′;
5′-ACGTTGGATGTAGAGCTCACAGAGCACTTC-3′ and
5′-ACGTTGGATGAGCACTTAACTGAGTCTGGG-3′;
5′-ACGTTGGATGCTTTGCTCACAAGAAAGTTGG-3 and
5′-ACGTTGGATGCCCCCAAGGCAATGATTTTC-3′;
5′-ACGTTGGATGTAATACCCTGAGCAAGGACG-3′ and
5′-ACGTTGGATGGTGCATTTAAAATCCATGTG-3′;
5′-ACGTTGGATGTGTTACAGCAGCTAGTGTTG-3′ and
5′-ACGTTGGATGCCTCTAATAGCACCCAGTTC-3′;
5′-ACGTTGGATGGTCCATTTAACGGTGTGGAG-3′ and
5′-ACGTTGGATGGGTTCATGAAATGTTAGTTCC-3′;
5′-ACGTTGGATGTATCCATCCTTCAGACACCC-3′ and
5′-ACGTTGGATGATGGGACAGTAACTGCAGAC-3′;
5′-ACGTTGGATGCTCAGTTTAAAGTCACTGCC-3′ and
5′-ACGTTGGATGTAACCCTGCAAAGACTAGAG-3′;
5′-ACGTTGGATGGCCAGCTTGTCCATTAAAGG-3′ and
5′-ACGTTGGATGCTGGCTTATAAATAAAAGACC-3′;
5′-ACGTTGGATGCATTGCAGTAACTGGAGGTC-3′ and
5′-ACGTTGGATGGGCACAGTAGTTCAGTTACC-3′;
5′-ACGTTGGATGAGTGAGACTTAACCGTGGAG-3′ and
5′-ACGTTGGATGCACCCCCACATTAGCAAAAG-3′;
5′-ACGTTGGATGATCTTCATGTCCCAAGGAGG-3′ and
5′-ACGTTGGATGCCAAGTTTATGAAACGTAG-3′;
5′-ACGTTGGATGCACATGCTAGAGAAAGAGGG-3′ and
5′-ACGTTGGATGTATGTCCTTCCCTGATTTTC-3′;
5′-ACGTTGGATGAGGATGCCTGTTGGGTTTTC-3′ and
5′-ACGTTGGATGATCAGACTTTTCCCAGGCAG-3′;
5′-ACGTTGGATGAAGCAACTGGCACTCCTAAG-3′ and
5′-ACGTTGGATGGAGTGTTGTGATGCATGCC-3′;
5′-ACGTTGGATGGTATCTCCCACTCTTGTACC-3′ and
5′-ACGTTGGATGCTGGAATACAACATTTCTGG-3′;
5′-ACGTTGGATGTTGTGTGCTATCTTACACTG-3′ and
5′-ACGTTGGATGACTAGTTGGAATGGGCTTGG-3′;
5′-ACGTTGGATGACTCCCTACCTATCTCTTTG-3′ and
5′-ACGTTGGATGTCCACAGCCACTGAATAGTC-3′;
5′-ACGTTGGATGTCATGTAACCAAGCACCACC-3′ and
5′-ACGTTGGATGGCTCATTTATAGAAGCAGTC-3′;
5′-ACGTTGGATGCAGTGGATTTCAAATCCGGC-3′ and
5′-ACGTTGGATGTGTTCAGAGGGTGTTGGATG-3′;
5′-ACGTTGGATGCATCAGCAATATAATGCCGC-3′ and
5′-ACGTTGGATGTGTGGATCACTGTTCACAGG-3′;
5′-ACGTTGGATGCACCAGTGCAAACACACAAC-3′ and
5′-ACGTTGGATGCCTGATTGTTTTGGAAGGAG-3′;
5′-ACGTTGGATGAGTTGCCATGTTTCCACAGG-3′ and
5′-ACGTTGGATGGACTAATACTCAGGTTGAGG-3′;
5′-ACGTTGGATGTGGAAGGCAGAGTGATATAC-3′ and
5′-ACGTTGGATGGCTTTCTTCACTCAGAAGGG-3′;
5′-ACGTTGGATGGAGGAGTTATAAGACCTAGAG-3′ and
5′-ACGTTGGATGACCATATCACAGTTGTTGGG-3′;
5′-ACGTTGGATGCTACGTGACCCAAAGTTCAG-3′ and
5′-ACGTTGGATGTCTCACTCCTGGTTACCTAC-3′;
5′-ACGTTGGATGTTATACAGGTTCCAGCCAGC-3′ and
5′-ACGTTGGATGCAGAGAGAAAAGGGAGTAGG-3′;
5′-ACGTTGGATGACTGATACCCTACAGTGTGC-3′ and
5′-ACGTTGGATGGTGCTCAGAGCACTTAAACG-3′;
5′-ACGTTGGATGAATCTTGGAGCCTTGGAGAC-3′ and
5′-ACGTTGGATGGTGCTTCTCACAAAAGCCTG-3′;
5′-ACGTTGGATGATCCTGGGCTTTCCTTTGTC-3′ and
5′-ACGTTGGATGGAGTCTAGTGGACAAGAGAG-3′;
5′-ACGTTGGATGTGGAGGCCACTGGATTAAAG-3′ and
5′-ACGTTGGATGAGACACAGCTAGCACTTTCC-3′;
5′-ACGTTGGATGGTTTGGTGACTATAGAAACAG-3′ and
5′-ACGTTGGATGCAGTTTAAAGTCATATTCAC-3′;
5′-ACGTTGGATGGAGCACTTATCACAGGTCAG-3′ and
5′-ACGTTGGATGGAAGGTGGGATAAACAAGGG-3′;
5′-ACGTTGGATGGTTCTGGATGTTGGCCATTC-3′ and
5′-ACGTTGGATGCCACATCATATGCATCTGGG-3′;
5′-ACGTTGGATGGAGATGAGTAAGAGCAGGTG-3′ and
5′-ACGTTGGATGCTCATAAGACCCTGAACACC-3′; and
5′-ACGTTGGATGACTGAAGCATAACGCCTCTG-3′ and
5′-ACGTTGGATGGGTGCCCAAACATGTTATGC-3′.
15. The method of claim 13 , further comprising contacting the amplification products with extension primers.
16. The method of claim 15 , wherein the extension primers are:
5′-gCCTGGGAGAAAGAAAACAA-3′,
5′-catccGTTTTTCCCTCTTGACTGAAT-3′,
5′-cgggACTTACTATGGGGAATAGAAT-3′,
5′-caccTCCTGAATACTTTCTCATATAGA-3′,
5′-TGATCCACTGGCTCAA-3′,
5′-ggagGGTGGTTAGAGAACTCAATGAAT-3′,
5′-AGCCTGCACTGTGAA-3′,
5′-CAAGTCTTCTATCAAGGGAAT-3′,
5′-aCTGAGAGCAACCACTAA-3′,
5′-cGAGGAGGGCAGAGAAGAAT-3′,
5′-cccctAGAGGGCAGATAAATAGTTAAAT-3′,
5′-gtcgTCTACGGTCTTTTTCTTATCAA-3′,
5′-ctAGCTTGCTTACTTCTAAAAA-3′,
5′-aaatcTAAATAGCCAAGAAAACAGCCAA-3′,
5′-attaTGCTCAACTACCAAGTTAAGA-3′,
5′-acatGGAGTTTCCTGTACTTTAAAAAA-3′,
5′-tgAGCAAGTGCTGAGGG-3′,
5′-gATACAGCTTGGCCAAT-3′,
5′-GGGGCTGGTAGGAAAT-3′,
5′-ctcTCTTTCTCCAGGGATGA-3′,
5′-cGTGATGAGATTTCTATCATACAA-3′,
5′-cccccCCTTCCATGGGACTCATTA-3′,
5′-GACTATCCTCTTCAGACCAA-3′,
5′-cccCAAGTTGAAAACTTATTCCAA-3′,
5′-tttcAAATGTGTGTTCCATCATCTA-3′,
5′-gggtTGCTGCATGCTGTAAAT-3′,
5′-ccacATCATGCCTCTATTGACA-3′,
5′-cCAGTTTCAATAACAGATAGTAAAT-3′,
5′-aaAAAACTCAATATAGTAAAGGTATCAA-3′,
5′-GGAGGTGACATAAGTAAGTA-3′,
5′-ATGATGAAAGCATAAGTCTTTTAAT-3′,
5′-agCTTACCTCCATAGCATCTAA-3′,
5′-TGGCCAGAACTAATCAA-3′,
5′-AAGACAAAGGACACCAA-3′,
5′-caGACCTACCACCCAAAT-3′,
5′-ACTTCTGTCTCAGTATCCA-3′,
5′-ctAGCGTTTCACGTTCAAAA-3′,
5′-aaaTGCAATCTGTCTGGAAA-3′,
5′-ggtcCTTTCTGCAGCTCATATTCTGCAA-3′,
5′-GGCTGTCACAGATTTATAAAA-3′,
5′-cATGGGAAACATGCCTCAATAAAT-3′,
5′-acttTGCTAGGTCTTACATGAA-3′,
5′-acgTTCCTGTTCCTAGATGATCAAAAT-3′,
5′-AGTCTTTCTGAGCCCAA-3′,
5′-agcGAGATACAGGAAAGTGTAAAT-3′,
5′-aggTCTCAAATAAAAATGCAAAGGAAA-3′,
5′-GGGATTCTCTGGTTGTAAA-3′,
5′-gCCAACAGAGAAAGTAACAA-3′,
5′-tCCTCCTCAAACATTAAGGACAAAA-3′,
5′-tGTACTACCCAGTGGAATAAA-3′,
5′-tcTTTAAAGTGCTACATCTATGAA-3′,
5′-cgGCTCTTGAGGCAGTAAA-3′,
5′-cGGCTCTTATTATTGTACTCTATAAA-3′,
5′-atcGGTGGATGTTTCAGGGAAGTAAA-3′,
5′-ggtaAGACGATAGTGCCAGAAAAT-3′,
5′-agCAGATAGCCTCTTGTGAAT-3′,
5′-GCTCATCTTCCTCTGAA-3′,
5′-GCACTTCCCTACAAACAA-3′,
5′-TTGGAACTATCGTTCAAAAAGTATTA-3′,
5′-cccatGACGTCACCCTGTAAAAA-3′,
5′-tcGCTAGTGTTGCACTAATAAAAAAAT-3′,
5′-cccccGTGTGGAGAAGTGCGAGT-3′,
5′-AGACACCCAGGCCAA-3′,
5′-cCACTGCCAGTGACCTAA-3′,
5′-cACTTGAAAAATACTTTAGACTTTCTT-3′,
5′-gATCATTGTATAGGTTCCCAGA-3′,
5′-aaatTGAACTGTAGCAAGAAACAAA-3′,
5′-ggatGGAAAAGCTGAAAAGGAA-3′,
5′-ccctcAATCATTCTATGAAGCCAAT-3′,
5′-gTACTGAGATTGACAAGTCATTAAA-3′,
5′-TGGCACTCCTAAGACCAAA-3′,
5′-cCTCTTGTACCCCAGAAAAA-3′,
5′-cGTAGCTTCCTAGCCAAA-3′,
5′-gtcgCTTTGAAAAGCCTTAACCATTAA-3′,
5′-cccccCCCCAAAAACCTACTGAAAT-3′,
5′-GCCGCACATCAGAAT-3′,
5′-CAATCCTTTATCTCTCTCTAATAC-3′,
5′-gaagtAATGGAGAACCTGGTTAA-3′,
5′-ccCAGGATCCTCTAGATTGTGAAAA-3′,
5′-agagACTGAGACAGGCAGTAGCCTAAT-3′,
5′-tgaagGAGAGCTTAACTAAAATAAACAA-3′,
5′-ggggcCCCAAAGTTCAGGATGGTAA-3′,
5′-ACCTGATACTGAAGCCAAA-3′,
5′-TGGATATGACTTGCCCAA-3′,
5′-gTAGTTTCTTTAGCTCTTGAATAAAAT-3′,
5′-acTTGTCACACCTCTTCAAAT-3′,
5′-ggTTAAAGGAGACAATGTATGTAAAT-3′,
5′-gaagGTGTTGCCAAAAGCTAAT-3′,
5′-gtaatTGCCCCTTCAAGTGAAT-3′,
5′-GTGCTATCTCATTGTTGTTTGAAA-3′,
5′-GAGCAGGTGAAATGTTTCTA-3′, and
5′-gaCTCTGGGACTACTAAGAAGA-3′.
17. The method of claim 13 , wherein the sample is from a pregnant female or a female suspected of being pregnant.
18. The method of claim 17 , wherein the sample is blood.
19. The method of claim 13 , wherein the target allele concentration is 10% or less of total nucleic acid concentration prior to cleaving and amplifying the nucleic acid.
20. The method of claim 13 , wherein four or more of the single nucleotide polymorphic loci are informative of the presence or absence of the one or more target alleles.
21. The method of claim 13 , further comprising determining whether fetal nucleic acid is present in the sample.
22. A method for detecting in nucleic acid the presence or absence of one or more target alleles of paternal origin, comprising:
a) cleaving nucleic acid from a sample with a Tsp509I restriction enzyme;
b) exposing the nucleic acid after (a) to amplification conditions that amplify uncleaved nucleic acid but not cleaved nucleic acid, and which amplification conditions are capable of generating amplification products comprising some or all of the single nucleotide polymorphic loci selected from the group consisting of:
rs11835780
rs748773
rs13110085
rs1363267
rs1797700
rs2723307
rs1885121
rs4589569
rs1904161
rs6766358
rs10901705
rs7689368
rs7144509
rs7900002
rs8016543
rs4489023
rs13155942
rs10260483
rs3912319
rs4533845
rs9929404
rs6556642
rs4673821
rs12674093
rs1444647
rs7741525
rs12007
rs2462049
rs6569474
rs11105611
rs6043856 and
rs6142841,
thereby generating amplification products; and
c) detecting the presence or absence of one or more target alleles based on the amplification products.
23. A method for detecting in nucleic acid the presence or absence of one or more target alleles of paternal origin, comprising:
a) cleaving nucleic acid from a sample with a Tsp509I restriction enzyme;
b) exposing the nucleic acid after (a) to amplification conditions that amplify uncleaved nucleic acid but not cleaved nucleic acid, and which amplification conditions are capable of generating amplification products comprising some or all of the single nucleotide polymorphic loci selected from the group consisting of:
rs7323716
rs4311632
rs10785736
rs13269702
rs7831906
rs2993531
rs12903747
rs1372688
rs4869315
rs1720839
rs6542638
rs6582294
rs1346718
rs10234234
rs2007475
rs11221881
rs10110766
rs494220
rs11099210
rs9428474
rs4130306
rs7294836
rs1401454
rs614004
rs179596
rs7818415
rs9787011
rs9989393
rs664358
and rs1342995,
thereby generating amplification products; and
c) detecting the presence or absence of one or more target alleles based on the amplification products.
24. A method for detecting in nucleic acid the presence or absence of one or more target alleles of paternal origin, comprising:
a) cleaving nucleic acid from a sample with a Tsp509I restriction enzyme;
b) exposing the nucleic acid after (a) to amplification conditions that amplify uncleaved nucleic acid but not cleaved nucleic acid, and which amplification conditions are capable of generating amplification products comprising some or all of the single nucleotide polymorphic loci selected from the group consisting of:
rs6488494
rs9652080
rs10840805
rs7356482
rs4764597
rs9818611
rs2820107
rs7320201
rs12675087
rs3913810
rs725849
rs12450474
rs910500
rs1503660
rs1916803
rs683262
rs4488809
rs1041409
rs3816551
rs10754776
rs7205009
rs2734574
rs2322301
rs9285190
rs17074340
rs331893
rs9356029
rs10806232
rs10898954
rs12107918
rs263025
rs1593443
and rs273172,
thereby generating amplification products; and
c) detecting the presence or absence of one or more target alleles based on the amplification products.