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Method Detail
Submitter Method Handle: TSC-CSHL
Submitter Method ID: TSC-SANGER-19-26
Submitted method description:
The following method definition consists of one or more
protocols used in The SNP Consortium project by the
participating laboratory SANGER.
See the TSC website (http://snp.cshl.org/cgi-bin/protocol)
for a complete list of TSC protocols.
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SNP production protocol TSCM0019 (
http://snp.cshl.org/cgi-bin/protocol?id=TSCM0019)
Title: Library preparation and sequencing for PvuII enzyme
Lab: Sanger Center, Cambridge
Contact: snp@sanger.ac.uk
Description:
A panel of 24 DNAs was digested with PvuII, size
fractionated on an agarose gel, and cloned into puc18-based vectors.
Size fractions were taken at 1.0-1.1kb, 1.1-1.2kb, 1.2-1.4kb, 1.4-1.6kb,
1.6-1.8kb, 1.8-2.1kb, 2.1-2.5kb, 2.5-3.0kb, 3.0-3.5kb and 3.5-4.0kb,
from which libraries were constructed. Samples from these libraries were
named such that the size insert can be identified. The sample names
start with p1_0, p1_1, p1_3, p1_5, p1_7, p1_9, p2_3, p2_7, p3_2 and
p3_7, with respect to the size fractions listed above. Sequences were
obtained primarily from ABI 3700 capillilary sequencers. Base-calling
was performed with Phrap, which provides the quality values upon which
the SNP detection is based.
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SNP detection protocol TSCM0026 (
http://snp.cshl.org/cgi-bin/protocol?id=TSCM0026)
Title: SNPs from reads detected using SsahaSNP from public human genomic sequence
Lab: Sanger Center, Cambridge
Contact: snp@sanger.ac.uk
Description:
All reads were clipped of sequencing vector and low quality ends,
which set a usable read length for each read. The clipped reads
were screened for repetitive sequence with RepeatMasker, using
the default human settings. Only reads with >=80 non-repetitive
bases and >= 100 Phred quality (Q) >=30 bases were used in this
analysis. The reads were aligned using SsahaSNP to available
finished and unfinished (with quality values) public human
genomic sequence which is available via anonymous ftp at
snp.cshl.org in the files pub/SNP/gbfinished* and pub/SNP/nr*.
All reads which aligned to genomic sequence within 50bp of the
start and 60bp of the end of their usable read length, were as-
sembled with the matching region of genomic sequence (Q was set
to 40 for finished genomic sequence). High quality base
discrepancies (Q>=23) were identified as candidate SNPs. Further
restrictions on the candidate SNPs were that its neighbouring 5
bases all had Phred quality values of >=15 and at least 9 of the
10 neighbours match. If the number of detected SNPs in one clique
was greater than 4 then all SNPs were discarded for that
clique.

This method was used in the following submission:

Submitter Handle Batch Type Submitter batch id Release build id
TSC-CSHL Assay TSC-SANGER-19-26-000905-RESUBMISSION 85
TSC-CSHL Assay 001018_3.dat 89
TSC-CSHL Assay 001018_14 89
TSC-CSHL Assay 001018_17 89
TSC-CSHL Assay 001018_20 89
TSC-CSHL Assay 001018_25 89
TSC-CSHL Assay 001018_22 89
TSC-CSHL Assay 001018_24 89
TSC-CSHL Assay 001018_13 89
TSC-CSHL Assay 001219_2 92
TSC-CSHL Assay 001219_2b 92
TSC-CSHL Assay TSC-SANGER-19-26_101012214 92
TSC-CSHL Assay TSC-SANGER-19-26_101052517 96
TSC-CSHL Assay TSC-SANGER-19-26_101060714 96
TSC-CSHL Assay TSC-SANGER-Sep-19-2002-SNP_SUBMISSION-19-26 107

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