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

By Ryan E. Mills, Christopher T. Luttig, Christine E. Larkins, Adam D. Beauchamp, Circe W. Tsui, William Stephen Pittard, S. Devine. Genome Research, 2006

678 citations recorded by the source corpus.

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.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/23f95b8cef210b516185f0d3fa64ae9a13de4296

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Citations in the corpus

Computational methods for discovering structural variation with next-generation sequencing (2009, background): “Whereas this signature is detectable with longer read”
The Diploid Genome Sequence of an Individual Human (2007, methodology): “NCBI human genome reference assembly [55].”
FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads (2012, background): “More importantly, the accuracy of paired reads alignment might be affected both by genomic variations that are widely distributed among individuals such as large scale structural variations [21], copy number variations [22], small insertion/deletion variations [23], and single-nucleotide polymorphis”
From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline (2013, background): “Current Protocols in Bioinformatics Supplement 43 Known and true sites training resource: Mills indel dataset (Mills et al., 2006) This resource is an indel call set that has been validated to a high degree of conﬁdence.”
Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing (2013, background): “Indeed, initial indel mapping efforts revealed upwards of 800,000 indels in a diverse population that map to known human genes, some of which can be associated with genetic disease [42,43], while recent estimates from the 1000 Genomes Project [44] suggest a 10:1 ratio of SNVs to indels in individual”
Natural genetic variation caused by small insertions and deletions in the human genome. (2011, methodology): “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).”
INDELible: A Flexible Simulator of Biological Sequence Evolution (2009, background): “Estimates also suggest that deletions occur more often than insertions, with kD/kI ranging from 1.3 to 4 (Gu and Li 1995; Zhang and Gerstein 2003; Arndt and Hwa 2004), although Mills et al. (2006) estimated kD/kI 1 in a comparison of human and chimpanzee genomes.”