dbSNP: a database of single nucleotide polymorphisms

Abstract

In response to a need for a general catalog of genome variation to address the large-scale sampling designs required by association studies, gene mapping and evolutionary biology, the National Cancer for Biotechnology Information (NCBI) has established the dbSNP database. Submissions to dbSNP will be integrated with other sources of information at NCBI such as GenBank, PubMed, LocusLink and the Human Genome Project data. The complete contents of dbSNP are available to the public at website: http://www.ncbi.nlm.nih.gov/SNP. Submitted SNPs can also be downloaded via anonymous FTP at ftp://ncbi.nlm.nih.gov/snp/

Quantitative analysis of mitochondrial DNA 4977-bp deletion in sporadic breast cancer and benign breast diseases

“…The following primers were used to amplify DNA fragments representing the normal mtDNA (mtDNA normal ) or the mtDNA 4977 mutation respectively: mtDNA normal forward primer 5 -acgccataaaactcttcaccaa -3 , reverse primer 5 -ggttcggttggtctcgtcta -3 ; mtDNA 4977 mutation forward primer 5 -accactttcaccgctacacg -3 , reverse primer 5 -agggaggtagcgatgagagt -3 . The putative amplicon sequences for both the wild-type and mutated targets had been previously screened by BLASTn to eliminate any redundancies in human genome DNA and screened against both the NCBI SNP database and the Japanese Mitochondrial SNP Database (13,14). The PCR products of mtDNA normal and the mtDNA 4977 mutation yield 437 bp and 484 bp amplicons, respectively.…”

“…The primers and probes for the mtDNA normal or the mtDNA 4977 mutation were designed by and obtained from Applied Biosystems (Foster, CA) ( Table 1). Submitted sequences for both the wild-type and mutated targets had been previously screened by BLASTn to eliminate any redundancies in human genome DNA and were screened against both the NCBI SNP database and the Japanese Mitochondrial SNP Database (13,14). Quantitative real-time PCR was performed in a 96-well optical plate on an ABI PRISM® 7900HT Sequence Detection System (Applied Biosystems), and the data were analyzed using SDS (Ver.…”

Targeted next generation sequencing of clinically significant gene mutations and translocations in leukemia

“…29 SNVs were then called from the aligned sequence data using the UnifiedGenotyper in the GATK package. 30 The list of SNVs was then referenced against dbSNP (build 130) to flag known variants. The SNVs were further filtered by removing all SNVs occurring within non-coding regions.…”

Two Distinct De novo Pathogenic Sequence Variants in the SCN2A Gene in Children with Early Infantile Epileptic Encephalopathy/Ohtahara Syndrome

“…Duplicates clean bam files were indel realigned using Genome Analysis TK (v3.6) [16]. Base Quality Score Recalibration (BQSR) was performed in two steps using Genome AnalysisTK and dbSNP (v147) [17] variants were used as a set of known variants. Coverage of targeted regions was explored using bed tools (v2.23.0) [18].…”