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The diagnosis of tuberous sclerosis was made according to standard diagnostic criteria (2). Blood samples (obtained after informed consent) were used for DNA preparation, either directly or after creation of immortalized Epstein-Barr virus-transformed lymphoblastoid cell lines. Linkage to the TSC1 region was inferred if a family demonstrated obligate recombination with markers within 2 centimorgans (cM) of TSC2 and had positive lod scores (logarithm of the odds ratio for linkage) in analyses with 9q34 markers (Fig. 1). Families providing critical recombinant events were analyzed with multiple markers from 9q34, and haplotype analysis was performed manually to identify the site of recombination.
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Cosmid, BAC, or PAC DNA was digested with Pst I or Bam HI, and a library of subclones was prepared in pSPL3 [A. J. Buckler et al., Proc. Natl. Acad. Sci. U.S.A. 88, 4005 (1991); E. P. Henske et al., Ann. Hum. Genet. 59, 25 (1995)]. Exons identified in this manner were used to identify cDNA clones (i) by screening cDNA libraries by conventional methods, (ii) by screening GenBank and dbEST databases, and (iii) in reverse transcription PCR experiments. IMAGE clones were obtained from Research Genetics or the UK Human Genome Mapping Project (HGMP) Resource Centre.
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Cosmid, BAC, or PAC DNA was digested with Pst I or Bam HI, and a library of subclones was prepared in pSPL3 [A. J. Buckler et al., Proc. Natl. Acad. Sci. U.S.A. 88, 4005 (1991); E. P. Henske et al., Ann. Hum. Genet. 59, 25 (1995)]. Exons identified in this manner were used to identify cDNA clones (i) by screening cDNA libraries by conventional methods, (ii) by screening GenBank and dbEST databases, and (iii) in reverse transcription PCR experiments. IMAGE clones were obtained from Research Genetics or the UK Human Genome Mapping Project (HGMP) Resource Centre.
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Complementary DNA selection was performed using the end-ligation coincident sequence cloning method [A. J. Brookes et al., Hum. Mol. Genet. 3, 2011 (1994)]. A normalized infant brain cDNA library [M. B. Soares et al., Proc. Natl. Acad. Sci. U.S.A. 91, 9228 (1994)] was screened using whole cosmids as probes. A human fetal brain cDNA library (Clontech) was screened by standard phage plating and filter lift methods.
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Complementary DNA selection was performed using the end-ligation coincident sequence cloning method [A. J. Brookes et al., Hum. Mol. Genet. 3, 2011 (1994)]. A normalized infant brain cDNA library [M. B. Soares et al., Proc. Natl. Acad. Sci. U.S.A. 91, 9228 (1994)] was screened using whole cosmids as probes. A human fetal brain cDNA library (Clontech) was screened by standard phage plating and filter lift methods.
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Soares, M.B.1
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Cosmid (15) DNA was sheared and subcloned into M13mp18. Single clear plaques were picked using an automated picking device (PBA Technologies, Cambridge, UK) and expanded with JM101, and phage supernatant was collected. M13 DNA isolation was performed with the Sequatron robotic system [T. L. Hawkins et al., Science 276, 1887 (1997)] following the solid-phase reversible immobilization protocol [T. L. Hawkins, T. O'Connor, A. Roy, C. Santillan, Nucleic Acids Res. 22, 4543 (1994)]. Dye primer DNA sequencing used energy transfer primers and thermosequenase (Amersham), and electrophoresis was performed on Applied Biosystems 377 DNA sequencers. Gel files were extracted, signal-processed, and bases called with the program Trout (available from genome.wi. mit.edu/distribution/software/trout) and were assembled with Alewife, a sequence assembly package. Typically, 1200 reads from a single cosmid assembled into one to three contigs, which were then finished by directed primer walking and directed selection of reverse reads from existing M13 templates to span sequence gaps. All sequence data and protocols were available during the sequence process from our Web site, http://www-seq.wi.mit.edu.
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Science
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Hawkins, T.L.1
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Cosmid (15) DNA was sheared and subcloned into M13mp18. Single clear plaques were picked using an automated picking device (PBA Technologies, Cambridge, UK) and expanded with JM101, and phage supernatant was collected. M13 DNA isolation was performed with the Sequatron robotic system [T. L. Hawkins et al., Science 276, 1887 (1997)] following the solid-phase reversible immobilization protocol [T. L. Hawkins, T. O'Connor, A. Roy, C. Santillan, Nucleic Acids Res. 22, 4543 (1994)]. Dye primer DNA sequencing used energy transfer primers and thermosequenase (Amersham), and electrophoresis was performed on Applied Biosystems 377 DNA sequencers. Gel files were extracted, signal-processed, and bases called with the program Trout (available from genome.wi. mit.edu/distribution/software/trout) and were assembled with Alewife, a sequence assembly package. Typically, 1200 reads from a single cosmid assembled into one to three contigs, which were then finished by directed primer walking and directed selection of reverse reads from existing M13 templates to span sequence gaps. All sequence data and protocols were available during the sequence process from our Web site, http://www-seq.wi.mit.edu.
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45
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Cosmid (15) DNA was sheared and subcloned into M13mp18. Single clear plaques were picked using an automated picking device (PBA Technologies, Cambridge, UK) and expanded with JM101, and phage supernatant was collected. M13 DNA isolation was performed with the Sequatron robotic system [T. L. Hawkins et al., Science 276, 1887 (1997)] following the solid-phase reversible immobilization protocol [T. L. Hawkins, T. O'Connor, A. Roy, C. Santillan, Nucleic Acids Res. 22, 4543 (1994)]. Dye primer DNA sequencing used energy transfer primers and thermosequenase (Amersham), and electrophoresis was performed on Applied Biosystems 377 DNA sequencers. Gel files were extracted, signal-processed, and bases called with the program Trout (available from genome.wi. mit.edu/distribution/software/trout) and were assembled with Alewife, a sequence assembly package. Typically, 1200 reads from a single cosmid assembled into one to three contigs, which were then finished by directed primer walking and directed selection of reverse reads from existing M13 templates to span sequence gaps. All sequence data and protocols were available during the sequence process from our Web site, http://www-seq.wi.mit.edu.
-
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46
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Genomic sequence was analyzed with the program GRAIL2 to identify possible exons and gene models [Y. Xu, R. Mural, M. Shah, E. Uberbacher, Gene. Eng. Principles Methods 16, 241 (1994)]. Putative transcriptional units were also identified by BLAST searches of public databases and comparison with our own collection of cDNA clones and exon trapping products.
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47
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Oligonucleotide primers were designed to be external to exons by 40 to 60 bp where possible. DNA products with mobility shifts on heteroduplex analysis [F. J. Couch et al., Nature Genet. 13, 123 (1996); A. Ganguly, M. J. Rock, D. J. Prockop, Proc. Natl. Acad. Sci. U.S.A. 90, 10325 (1993)] were subjected to sequence analysis of both strands.
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Couch, F.J.1
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Oligonucleotide primers were designed to be external to exons by 40 to 60 bp where possible. DNA products with mobility shifts on heteroduplex analysis [F. J. Couch et al., Nature Genet. 13, 123 (1996); A. Ganguly, M. J. Rock, D. J. Prockop, Proc. Natl. Acad. Sci. U.S.A. 90, 10325 (1993)] were subjected to sequence analysis of both strands.
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Ganguly, A.1
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A transcriptional unit denoted B2 was identified from a brain cDNA library by hybridization with a cosmid near D9S1830 (22). A 4.5-kb cDNA clone was sequenced and contained no ORF. Database searches showed that this clone was the 3′ portion of a 6.8-kb cDNA clone (KIAA0243) [T. Nagase et al., DNA Res. 3, 321 (1996)], which contained a 2.0-kb ORF. After the discovery of mutations in exon 15 of B2, 5′ RACE was performed with the Marathon cDNA kit (Clontech), using oligonucleotides derived from TSC1 cDNA clones or inferred by analysis of genomic sequence information (24). RACE and other cDNA clones were sequenced fully on both strands by means of Taq cycle sequencing methodology.
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Allele-specific amplification was performed on the renal cell carcinoma DNA using a primer specific for the normal allele, not bearing the 2105delAAAG mutation. Sequence analysis of this product indicated that it contained the 1957delG mutation.
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note
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We thank the hundreds of TSC patients and their families for blood samples and financial support (particularly V. Whittemore and W. Watts), and numerous clinicians (particularly A. Oranje, H. Stroink, M. Wildervanck de Blecourt, H. Kros, B. Prahl-Andersen, and H. L. J. Tanghe) for assistance; H. Galjaard and P. Harper for support; R. Bakker, S. Ramlakhan, D. Humphrey, Q. Wang, M. Maheshwar, A. L. W. Hesseling-Janssen, N. Thomas, and R. Slomski for technical support; and the UK HGMP Resource Centre and the European Collection of Animal Cell Cultures. Supported by the NIH, National Tuberous Sclerosis Association, Tuberous Sclerosis Association of Great Britain, Dutch Organization for Scientific Research (NWO), Dutch Tuberous Sclerosis Association (STSN), Dutch Kidney Foundation, Westminster Medical School Research Trust (Royds Fund), Bath Unit for Research into Paediatrics, and New Zealand Health Resources Council.
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