Human Diallelic Insertion/Deletion Polymorphisms

Weber, James L.; David, Donna E.; Heil, Jeremy; Fan, Ying; Zhao, Chengfeng; Marth, Gábor

doi:10.1086/342727

Cited by 315 publications

(233 citation statements)

References 25 publications

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“…Our initial validation efforts with single-base pair INDELs yielded relatively low validation rates (only about half of these INDELs were validated in our initial attempts). A previous study also reported relatively low validation rates for single-base pair INDELs (Weber et al 2002). These results collectively indicate that singlebase pair INDELs are particularly difficult to identify accurately from trace data, even when quality scores are used to guide INDEL discovery.…”

Section: Validation Studiesmentioning

confidence: 78%

“…Since the majority of INDELs examined in our validation studies (147/ 185 or 80%) had minor allelic frequencies that were greater than 5%, a large fraction of our INDELs also could serve as genetic markers for the HapMap. Previous studies have indicated that small INDELs resembling those detected by our pipeline can be used effectively as genetic markers in humans (Weber et al 2002;Bhangale et al 2005). …”

Section: Utility Of Our Indel Mapmentioning

confidence: 91%

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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 Studiesmentioning

confidence: 78%

Section: Utility Of Our Indel Mapmentioning

confidence: 91%

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

et al. 2006

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“…The extreme bias affecting this set of indels-which are a subset of over 2000 indels described by Weber et al (2002)-came as a surprise. It is doubtful this bias can be fully ascribed to standard ascertainment bias (that is bias for markers which are more polymorphic than average in the sample used for marker discovery).…”

Section: Strong Bias On Indelsmentioning

confidence: 99%

How accurate is the current picture of human genetic variation?

et al. 2008

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Our understanding of the distribution of worldwide human genomic diversity has greatly increased over recent years thanks to the availability of large data sets derived from short tandem repeats (STRs), insertion deletion polymorphisms (indels) and single nucleotide polymorphisms (SNPs). A concern, however, is that the current picture of worldwide human genomic diversity may be inaccurate because of biases in the selection process of genetic markers (so-called 'ascertainment bias'). To evaluate this problem, we first compared the distribution of genomic diversity between these three types of genetic markers in the populations from the HGDP-CEPH panel for evidence of bias or incongruities. In a second step, using a very relaxed set of criteria to prevent the intrusion of bias, we developed a new set of unbiased STR markers and compared the results against those from available panels. Contrarily to recent claims, our results show that the STR markers suffer from no discernible bias, and can thus be used as a baseline reference for human genetic diversity and population differentiation. The bias on SNPs is moderate compared to that on the set of indels analysed, which we recommend should be avoided for work describing the distribution of human genetic diversity or making inference on human settlement history.

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“…10 In this study, we tested a method of quantitative PCR of insertions-deletions (indels) diallelic polymorphisms. [11][12][13] RQ-PCRs were performed with TaqMan technology at an ABI Prism 7500 apparatus (Applied Biosystems, Foster City, CA, USA). The TaqMan reaction is based on the 5′ nuclease activity of Taq DNA polymerase to cleave an oligonucleotide probe during PCR, thereby generating a detectable signal that is analyzed in a dedicated thermocycler.…”

mentioning

confidence: 99%