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Volumn 280, Issue 5370, 1998, Pages 1753-1757

Mutation of a gene encoding a protein with extracellular matrix motifs in Usher syndrome type IIa

(20)  Eudy, James D a   Weston, Michael D b   Yao, SuFang a   Hoover, Denise M b   Rehm, Heidi L c   Ma Edmonds, Manling a   Yan, Denise d   Ahmad, Iqbal e   Cheng, Jason J a   Ayuso, Carmen f   Cremers, Cor g   Davenport, Sandra h   Moller, Claes i   Talmadge, Catherine B a   Beisel, Kirk W b   Tamayo, Marta j   Morton, Cynthia C k   Swaroop, Anand d   Kimberling, William J b   Sumegi, Janos a  


Author keywords

[No Author keywords available]

Indexed keywords

CELL ADHESION MOLECULE; COLLAGEN; COMPLEMENTARY DNA; CONTIG; DNA; EPIDERMAL GROWTH FACTOR; FIBRONECTIN; MYOSIN; PROTEIN; RNA; SCLEROPROTEIN;

EID: 0032511101     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.280.5370.1753     Document Type: Article
Times cited : (331)

References (36)
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    • Fluorescent (6-carboxyfluorescein, tetrachlorofluorescein, or hexachlorofluorescein) oligonucleotide primers were used to amplify polymorphic markers around the USH2A locus, as described earlier (8). PCR products were pooled, denatured, and separated on 4.25% polyacrylamide gels with an ABI 377 automated sequencer running GENESCAN2.1 software. Genotyping data were collected and analyzed with GENEOTYPER 2.0. The order of the markers was obtained from the Genome Database at Johns Hopkins University and the database at the Whitehead Institute for Biomedical Research/Massachusetts Institute of Technology (MIT) Center for Genome Research (www.genome.wi.mit.edu)
    • Fluorescent (6-carboxyfluorescein, tetrachlorofluorescein, or hexachlorofluorescein) oligonucleotide primers were used to amplify polymorphic markers around the USH2A locus, as described earlier (8). PCR products were pooled, denatured, and separated on 4.25% polyacrylamide gels with an ABI 377 automated sequencer running GENESCAN2.1 software. Genotyping data were collected and analyzed with GENEOTYPER 2.0. The order of the markers was obtained from the Genome Database at Johns Hopkins University (gdbwww.gdb.org/gdb/ regionSearcn.html) and the database at the Whitehead Institute for Biomedical Research/Massachusetts Institute of Technology (MIT) Center for Genome Research (www.genome.wi.mit.edu).
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    • Screening of BAC libraries from Research Genetics and Genome Systems (St. Louis, MO) was performed with PCR primer pairs from the STSs (AFM248NC1, AFM143XF10, AFM268ZD1, AFM144XF2, WI-3484, WI-3128, WI-6236, and WI-9496) listed at Whitehead Institute for Biomedical Research/MIT Center for Genome Research. BACs were propagated and DNA extracted according to the manufacturer's recommendation. Rescue of the BAG insert end was performed by digestion of 1 μg of BAC DNA with Nhe I, followed by phenol-chloroform extraction and precipitation. DNA was religated and used to transform Escherichia coli DH5alpha. Colonies were propagated, the DNA was extracted and sequenced with IRD700-labeled T 7 and SP6 primers, and the SequiTherm EXCEL II Long-Read Premix DNA Sequencing Kit (Epicentre Technologies) was optimized for use with the LI-COR 4000LS automated sequencer. We used the following PCR primer pairs, designed by the Oligo 5.0 primer analysis software program (NBI): 1STS4277: 5′-GTCCCTTCAGGAATGGATCTCC-3′/5′-TGCCTGTGACAAAGTCTGAGAACTG- 3′ (product size 292 bp), 1STS1336: 5′-GGTCTTTGCATTGGTCACAACG-3′/5′-TCATGCCATACAACTGGTGCAG- 3′ (product size 109 bp), 1STS526: 5′-CAATGAATTGCCTTCTTGTGCC-3′/5′-CTCTTTGGAGAACAGGACTGATCC- 3′ (product size 267 bp), 1STS1337: 5′-TGGACTGGACGTTGTCTCAGCTTC-3′/5′-AGTTTCTGTCATTTCTGTCCTCGC- 3′ (product size 164 bp), 1STS527: 5′-ATGGACCCTTAGTGCAGCCTTAGG-3′/5′-TGATTCTCTTTCGGTAGGAGTCTGC- 3′ (product size 137 bp), 1STS1976: 5′-GGAACTGGATTTATTCTGCTCCTG-3′/5′-AATTGGGGGAATTTCGGGG- 3′, (product size 100 bp), 1STS1977: 5′-CTCATCAAGAGCTGTCAGGGATTAG-3′/5′-GCACATGGGACAATCTTCAGATCAC- 3′ (product size 288 bp). All PCR reactions were carried out in the same standard buffer condition at 55°C annealing temperature. BACs were sized by digestion of 1 μg of DNA with Not I followed by field inversion electrophoresis (FIGE).
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    • Single-letter abbreviations for the amino acid residues are as follows: A, Ala; C, Cys; D, Asp; E, Glu; F, Phe; G, Gly; H, His; I, Ile; K, Lys; L, Leu; M, Met; N, Asn; P, Pro; Q, Gln; R, Arg; S, Ser; T, Thr; V, Val; W, Trp; and Y, Tyr.
    • Single-letter abbreviations for the amino acid residues are as follows: A, Ala; C, Cys; D, Asp; E, Glu; F, Phe; G, Gly; H, His; I, Ile; K, Lys; L, Leu; M, Met; N, Asn; P, Pro; Q, Gln; R, Arg; S, Ser; T, Thr; V, Val; W, Trp; and Y, Tyr.
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    • note
    • This work was supported by a grant from NIH-NIDCD 5PO1 DC01813-05, by the Nebraska Research nitiative Fund, and by a grant from the Foundation Fighting Blindness. We extend our sincere gratitude to the patients and their families involved in the study for their assistance and cooperation. We thank M. Gillett for assistance. A.S. is a recipient of a Research to Prevent Blindness Lew R. Wasserman Merit Award and supported by EY07003 (CORE). C.C.M. is supported by the John Alden Trust and NIH-NIDCD DC03402. The retina EST was provided by the IMAGE Consortium. We thank J. Edwards for artwork and V. Wrobleski for preparation of the manuscript.


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