Single nucleotide polymorphisms (SNPs) that map to gaps in the human SNP map

Tsui, Circe; Coleman, Laura E.; Griffith, Jacqulyn L; Bennett, E. Andrew; Goodson, Summer G.; Scott, Jason D.; Pittard, W. Stephen; Devine, Scott E.

doi:10.1093/nar/gkg664

Cited by 21 publications

(17 citation statements)

References 19 publications

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“…another previous study, we observed a validation rate of 29/30 (97%) for SNPs discovered with our pipeline (Table 4; Tsui et al 2003). Therefore, with the exception of the single-base pair INDELs discussed above, our computational pipeline yields accurate predictions for the major polymorphism classes identified in our study.…”

Section: Validation Studiessupporting

confidence: 71%

“…This pipeline has been used previously to identify SNPs (Tsui et al 2003) and transposon insertions (Bennett et al 2004). Traces obtained from TSC or NCBI first were trimmed to remove vector sequences using the VecScreen system from NCBI.…”

Section: Indel Discovery Pipelinementioning

confidence: 99%

“…Validation studies were carried out as described previously (Tsui et al 2003;Bennett et al 2004). In each case, a set of oligonucleotide primers was designed to amplify genomic segments of ∼0.2-1.5 kb that contained the region carrying the polymorphism (Supplemental Table 1).…”

Section: Pcr Validation Studiesmentioning

confidence: 99%

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An initial map of insertion and deletion (INDEL) variation in the human genome

et al. 2006

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Although many studies have been conducted to identify single nucleotide polymorphisms (SNPs) in humans, few studies have been conducted to identify alternative forms of natural genetic variation, such as insertion and deletion (INDEL) polymorphisms. In this report, we describe an initial map of human INDEL variation that contains 415,436 unique INDEL polymorphisms. These INDELs were identified with a computational approach using DNA re-sequencing traces that originally were generated for SNP discovery projects. They range from 1 bp to 9989 bp in length and are split almost equally between insertions and deletions, relative to the chimpanzee genome sequence. Five major classes of INDELs were identified, including (1) insertions and deletions of single-base pairs, (2) monomeric base pair expansions, (3) multi-base pair expansions of 2-15 bp repeat units, (4) transposon insertions, and (5) INDELs containing random DNA sequences. Our INDELs are distributed throughout the human genome with an average density of one INDEL per 7.2 kb of DNA. Variation hotspots were identified with up to 48-fold regional increases in INDEL and/or SNP variation compared with the chromosomal averages for the same chromosomes. Over 148,000 INDELs (35.7%) were identified within known genes, and 5542 of these INDELs were located in the promoters and exons of genes, where gene function would be expected to be influenced the greatest. All INDELs in this study have been deposited into dbSNP and have been integrated into maps of human genetic variation that are available to the research community.

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Section: Validation Studiessupporting

confidence: 71%

Section: Indel Discovery Pipelinementioning

confidence: 99%

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An initial map of insertion and deletion (INDEL) variation in the human genome

et al. 2006

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“…Our computational pipeline simultaneously detects both INDELs and SNPs from ABI trace data, and has high levels of accuracy with both classes of variation (Tsui et al 2003;Mills et al 2006; please see Methods). We determined that the genome-wide ratio of INDELs to SNPs was 0.19 (i.e., 1 INDEL for every 5.3 SNPs) (Supplemental Table 7).…”

Section: Evidence For Strong Purifying Selection On Coding Indelsmentioning

confidence: 99%

“…Traces were processed and compared to the hg18 build of the human genome using quality scores to guide the analysis, as described previously (Mills et al 2006). INDELs were defined as insertions or deletions in the 1-bp to 10,000-bp size range that could be detected by comparing ABI traces to the reference genome as outlined previously (Tsui et al 2003;Bennett et al 2004;Mills et al 2006). All variants were entered into a Perl dbfile hash module to identify redundancies, and then into a MySQL database, which was used to store and analyze the data.…”

Section: Identification and Analysis Of Indels From Ncbi Trace Datamentioning

confidence: 99%

Natural genetic variation caused by small insertions and deletions in the human genome

et al. 2011

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Human genetic variation is expected to play a central role in personalized medicine. Yet only a fraction of the natural genetic variation that is harbored by humans has been discovered to date. Here we report almost 2 million small insertions and deletions (INDELs) that range from 1 bp to 10,000 bp in length in the genomes of 79 diverse humans. These variants include 819,363 small INDELs that map to human genes. Small INDELs frequently were found in the coding exons of these genes, and several lines of evidence indicate that such variation is a major determinant of human biological diversity. Microarray-based genotyping experiments revealed several interesting observations regarding the population genetics of small INDEL variation. For example, we found that many of our INDELs had high levels of linkage disequilibrium (LD) with both HapMap SNPs and with high-scoring SNPs from genome-wide association studies. Overall, our study indicates that small INDEL variation is likely to be a key factor underlying inherited traits and diseases in humans.

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InSNP: A tool for automated detection and visualization of SNPs and InDels

Manaster¹,

Wu²,

Teuber

et al. 2005

Hum. Mutat.

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Availability of high quality SNP data is a rate-limiting factor in understanding the impact of genetic variability on gene function and phenotype. Although global projects like HAPMAP generate large numbers of SNPs in an even spacing throughout the human genome, many variation studies have a more focused approach: in the follow-up of positional association findings, candidate gene studies, and functional genomics experiments, knowledge of all variations in a limited amount of sequence (e.g., a gene) is needed. This leads to a large number of resequencing experiments, for which there is a surprising lack of analysis software. We have thus developed specialized software (InSNP) for targeted mutation detection and compared its performance to Polyphred and Mutation Surveyor using 28 amplicons. Out of a total of 579 (InSNP), 644 (Polyphred), and 526 (Mutation Surveyor) SNP predictions, 39 SNPs were confirmed by human expert inspection, with five SNPs missed by Polyphred and one missed by InSNP using the default settings. For InDel detection, out of 70 (InSNP), 28 (Polyphred), and 693 (Mutation Surveyor) InDel predictions, two InDels were confirmed by human expert inspection, with one InDel missed by Polyphred. InSNP provides a user-friendly interface with better functionality for mutation detection than general-purpose sequence handling software. It provides similar SNP detection sensitivity and specificity as the public domain and commercial alternatives in the investigated dataset. We hope that InSNP lowers the barriers to the use of automated mutation detection software and aids in the improvement of the efficiency of such experiments. The Windows installer (setup) program and sample datasets are available at www.mucosa.de/insnp/.

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Single nucleotide polymorphisms (SNPs) that map to gaps in the human SNP map

Cited by 21 publications

References 19 publications

An initial map of insertion and deletion (INDEL) variation in the human genome

An initial map of insertion and deletion (INDEL) variation in the human genome

Natural genetic variation caused by small insertions and deletions in the human genome

InSNP: A tool for automated detection and visualization of SNPs and InDels

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