-
4
-
-
2642714753
-
-
L. Piassa et al., Arch. Ophthalmol. 1041, 1336 (1986); T. Rosenberg, et al., Clin. Genet. 5, 314 (1997).
-
(1986)
Arch. Ophthalmol.
, vol.1041
, pp. 1336
-
-
Piassa, L.1
-
5
-
-
0030922189
-
-
L. Piassa et al., Arch. Ophthalmol. 1041, 1336 (1986); T. Rosenberg, et al., Clin. Genet. 5, 314 (1997).
-
(1997)
Clin. Genet.
, vol.5
, pp. 314
-
-
Rosenberg, T.1
-
6
-
-
0027058632
-
-
J. Kaplan et al., Genomics 14, 979 (1992); W. J. Kimberling et al., ibid., p. 988; R. J. Smith et al., ibid., p. 995; S. Wayne et al., Hum. Mol. Genet. 5, 1689 (1996); H. Chaib et al., ibid., 6, 27 (1997); W. J. Kimberling et al., Genomics 7, 245 (1990); S. Pieke Dahl et al., J. Med. Genet. 30, 843 (1993); E. M. Sankila et al., Hum. Mol. Genet. 4, 93 (1995).
-
(1992)
Genomics
, vol.14
, pp. 979
-
-
Kaplan, J.1
-
7
-
-
0027058632
-
-
J. Kaplan et al., Genomics 14, 979 (1992); W. J. Kimberling et al., ibid., p. 988; R. J. Smith et al., ibid., p. 995; S. Wayne et al., Hum. Mol. Genet. 5, 1689 (1996); H. Chaib et al., ibid., 6, 27 (1997); W. J. Kimberling et al., Genomics 7, 245 (1990); S. Pieke Dahl et al., J. Med. Genet. 30, 843 (1993); E. M. Sankila et al., Hum. Mol. Genet. 4, 93 (1995).
-
Genomics
, pp. 988
-
-
Kimberling, W.J.1
-
8
-
-
0027058632
-
-
J. Kaplan et al., Genomics 14, 979 (1992); W. J. Kimberling et al., ibid., p. 988; R. J. Smith et al., ibid., p. 995; S. Wayne et al., Hum. Mol. Genet. 5, 1689 (1996); H. Chaib et al., ibid., 6, 27 (1997); W. J. Kimberling et al., Genomics 7, 245 (1990); S. Pieke Dahl et al., J. Med. Genet. 30, 843 (1993); E. M. Sankila et al., Hum. Mol. Genet. 4, 93 (1995).
-
Genomics
, pp. 995
-
-
Smith, R.J.1
-
9
-
-
0029798669
-
-
J. Kaplan et al., Genomics 14, 979 (1992); W. J. Kimberling et al., ibid., p. 988; R. J. Smith et al., ibid., p. 995; S. Wayne et al., Hum. Mol. Genet. 5, 1689 (1996); H. Chaib et al., ibid., 6, 27 (1997); W. J. Kimberling et al., Genomics 7, 245 (1990); S. Pieke Dahl et al., J. Med. Genet. 30, 843 (1993); E. M. Sankila et al., Hum. Mol. Genet. 4, 93 (1995).
-
(1996)
Hum. Mol. Genet.
, vol.5
, pp. 1689
-
-
Wayne, S.1
-
10
-
-
0031032971
-
-
J. Kaplan et al., Genomics 14, 979 (1992); W. J. Kimberling et al., ibid., p. 988; R. J. Smith et al., ibid., p. 995; S. Wayne et al., Hum. Mol. Genet. 5, 1689 (1996); H. Chaib et al., ibid., 6, 27 (1997); W. J. Kimberling et al., Genomics 7, 245 (1990); S. Pieke Dahl et al., J. Med. Genet. 30, 843 (1993); E. M. Sankila et al., Hum. Mol. Genet. 4, 93 (1995).
-
(1997)
Hum. Mol. Genet.
, vol.6
, pp. 27
-
-
Chaib, H.1
-
11
-
-
0025308736
-
-
J. Kaplan et al., Genomics 14, 979 (1992); W. J. Kimberling et al., ibid., p. 988; R. J. Smith et al., ibid., p. 995; S. Wayne et al., Hum. Mol. Genet. 5, 1689 (1996); H. Chaib et al., ibid., 6, 27 (1997); W. J. Kimberling et al., Genomics 7, 245 (1990); S. Pieke Dahl et al., J. Med. Genet. 30, 843 (1993); E. M. Sankila et al., Hum. Mol. Genet. 4, 93 (1995).
-
(1990)
Genomics
, vol.7
, pp. 245
-
-
Kimberling, W.J.1
-
12
-
-
0027422082
-
-
J. Kaplan et al., Genomics 14, 979 (1992); W. J. Kimberling et al., ibid., p. 988; R. J. Smith et al., ibid., p. 995; S. Wayne et al., Hum. Mol. Genet. 5, 1689 (1996); H. Chaib et al., ibid., 6, 27 (1997); W. J. Kimberling et al., Genomics 7, 245 (1990); S. Pieke Dahl et al., J. Med. Genet. 30, 843 (1993); E. M. Sankila et al., Hum. Mol. Genet. 4, 93 (1995).
-
(1993)
J. Med. Genet.
, vol.30
, pp. 843
-
-
Pieke Dahl, S.1
-
13
-
-
0028836898
-
-
J. Kaplan et al., Genomics 14, 979 (1992); W. J. Kimberling et al., ibid., p. 988; R. J. Smith et al., ibid., p. 995; S. Wayne et al., Hum. Mol. Genet. 5, 1689 (1996); H. Chaib et al., ibid., 6, 27 (1997); W. J. Kimberling et al., Genomics 7, 245 (1990); S. Pieke Dahl et al., J. Med. Genet. 30, 843 (1993); E. M. Sankila et al., Hum. Mol. Genet. 4, 93 (1995).
-
(1995)
Hum. Mol. Genet.
, vol.4
, pp. 93
-
-
Sankila, E.M.1
-
14
-
-
0028815440
-
-
D. Weil et al., Nature 374, 60 (1995).
-
(1995)
Nature
, vol.374
, pp. 60
-
-
Weil, D.1
-
16
-
-
0030201074
-
-
J. Sumegi et al., Genomics 35, 79 (1996).
-
(1996)
Genomics
, vol.35
, pp. 79
-
-
Sumegi, J.1
-
17
-
-
2642675080
-
-
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).
-
-
-
-
18
-
-
2642674245
-
-
note
-
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).
-
-
-
-
21
-
-
2642614340
-
-
note
-
+ plasmid (Stratagene) and sequenced. 5′ RACE was performed with the 133hm B primer and human retinal RACE-ready cDNA from Clontech, following the manufacturer's suggestions. Products were subcloned into pCR2.1 (Invitrogen) and sequenced. cDNA clones and 5′ RACE products were mapped back to the BAC contig by Southern hybridization to ensure their authenticity. The cDNA sequence has been submitted to GenBank (accession number AF055580).
-
-
-
-
22
-
-
2642646023
-
-
note
-
The following primer pairs were used to amplify products for mutation detection: 2186F 5′-TTAGGTGTGATCATTGCAATTTTGG-3′ and 2569B 5′-TCTTATCACAGTTGCAAGGCAGACA-3′ (product size 384 bp), 2869F 5′-TCATGCCATACAACTGGCGCAG-3′ AND 2977R 5′-GGTCTTTGCATTGGTCACAACGTTG-3′ (product size 109 bp), and 4266F 5′-GCTGTTGCACACTGCTAAATCCC-3′ and 4379R 5′-CTGGTCACACAACCAACTGAATTG-3′ (product size 114 bp). Thirty-seven cycles of 95°C for 30 s, 52°C for 30 s, and 72°C for 40 s were used to amplify genomic DNA from patients and controls under standard PCR buffer conditions. Products were subjected to heteroduplex analysis by means of previously established protocols and loaded onto vertical Mutation Detection Enhancement gels (FMC). Gels were stained with ethidium bromide and visualized under ultraviolet light. DNA fragments with altered mobility were sequenced directly by standard cycle sequencing reactions with ABI dye terminators and were analyzed with an ABI 377 sequencer.
-
-
-
-
23
-
-
0018639079
-
-
32P-labeled CRT-1 cDNA probe, generated by Rediprime DNA-labeling kit (Amersham), in Express HYB solution (Clontech) according to standard procedures and the manufacturers' instructions. Total RNA from human fetal cochlea, eye, brain, and kidney and from adult retina, monkey retina, and Y79 retinoblastoma cells was extracted by the guanidine isothiocyanate method (J. M. Chirgwin, A. E. Przybyla, R. J. MacDonald, W. Rutter, Biochemistry 18, 5294 (1979). Some (3 μg) of the total RNA was reverse transcribed with the SuperScript II kit according to the manufacturer's recommendations (GIBCO-BRL). To evaluate genomic contamination, we performed parallel PCR reactions with and without RT. Portions from the +/-RT reactions were used as the templates for PCR. The following PCR primers were used: F11B11 5′-GGGATTTAGCAGTGTGCAACAGC-3′/5′-GGAAAAGTTGTGGGGTATGACATC- 3′ (product size 100 bp) 1STS 1336 5′-GGTCTTTGCATTGGTCACAAGG-3′/5′-TCATGCCATACAACTGGTGCAG- 3′ (product size 109 bp).
-
(1979)
Biochemistry
, vol.18
, pp. 5294
-
-
Chirgwin, J.M.1
Przybyla, A.E.2
MacDonald, R.J.3
Rutter, W.4
-
24
-
-
2642610910
-
-
J. D. Eudy et al., unpublished data
-
J. D. Eudy et al., unpublished data.
-
-
-
-
25
-
-
2642646898
-
-
The Paircoil program (MIT) and TMpred (ISREC, Lausanne, Switzerland) were accessed through the Baylor College of Medicine Search Launcher
-
The Paircoil program (MIT) and TMpred (ISREC, Lausanne, Switzerland) were accessed through the Baylor College of Medicine Search Launcher (http://gc.bcm.tmc.edu:8088/search-launcher/ launcher.html).
-
-
-
-
26
-
-
0031149451
-
-
J. Vielmetter et al., Genomics 41, 414 (1997); M. Streuli, N. X. Krueger, A. Y. Tsai, H. Saito, Proc. Natl. Acad. Sci. U.S.A. 86, 8698 (1989).
-
(1997)
Genomics
, vol.41
, pp. 414
-
-
Vielmetter, J.1
-
27
-
-
0024378995
-
-
J. Vielmetter et al., Genomics 41, 414 (1997); M. Streuli, N. X. Krueger, A. Y. Tsai, H. Saito, Proc. Natl. Acad. Sci. U.S.A. 86, 8698 (1989).
-
(1989)
Proc. Natl. Acad. Sci. U.S.A.
, vol.86
, pp. 8698
-
-
Streuli, M.1
Krueger, N.X.2
Tsai, A.Y.3
Saito, H.4
-
28
-
-
2642704854
-
-
Mosby, St. Louis, MO, ed. 2
-
T. E. Ogden, Retina (Mosby, St. Louis, MO, ed. 2, 1994), pp. 58-71.
-
(1994)
Retina
, pp. 58-71
-
-
Ogden, T.E.1
-
31
-
-
0025292712
-
-
D. F. Barker et al., Science 248, 1224 (1990); T. Mochizuki et al., Nature Genet. 8, 77 (1994).
-
(1990)
Science
, vol.248
, pp. 1224
-
-
Barker, D.F.1
-
32
-
-
0028168648
-
-
D. F. Barker et al., Science 248, 1224 (1990); T. Mochizuki et al., Nature Genet. 8, 77 (1994).
-
(1994)
Nature Genet.
, vol.8
, pp. 77
-
-
Mochizuki, T.1
-
33
-
-
0025940669
-
-
R. Legouis et al., Cell 67, 423 (1991).
-
(1991)
Cell
, vol.67
, pp. 423
-
-
Legouis, R.1
-
35
-
-
2642646022
-
-
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.
-
-
-
-
36
-
-
2642670955
-
-
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.
-
-
-
|