An SNP map of human chromosome 22

Mullikin, James C.; Hunt, Sarah; Cole, Charlotte G.; Mortimore, Beverley; Rice, Catherine M.; Burton, John H.; Matthews, Lucy; Pavitt, R.; Plumb, Robert; Sims, Sarah; Ainscough, R.; Attwood, J.; Bailey, J.; Barlow, K. F.; Bruskiewich, Richard; Butcher, P. N.; Carter, Emma; Chen, Y.; Clee, Chris; Coggill, Penny; Davies, Joy; Davies, Robert M.; Dawson, Elisabeth; Francis, Matthew D.; Joy, A. A.; Lamble, R. G.; Langford, Cordelia; Macarthy, J.; Mall, V.; Moreland, A.; Overton-Larty, E. K.; Ross, Mark T.; Smith, Lauren; Steward, Charles A.; Sulston, John; Tinsley, Emma; Turney, K. J.; Willey, David L.; Wilson, Greer; McMurray, Amanda; Dunham, Ian; Rogers, Jane; Bentley, David

doi:10.1038/35035089

Cited by 135 publications

(71 citation statements)

References 25 publications

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“…SNPs have been identified in specific genes (Nickerson et al 1998;Rieder et al 1999;Taillon-Miller et al 1999;TaillonMiller and Kwok 2000), on whole chromosomes (Mullikin et al 2000;Dawson et al 2001), and throughout the human genome (Altshuler 2000;The International SNP Map Working Group 2001). Most recently, the International HapMap project has completed an extensive SNP discovery effort to further increase the density of SNPs across the human genome (The International HapMap Consortium 2003).…”

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confidence: 99%

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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confidence: 99%

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

et al. 2006

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“…To date, the number of publicly available single-nucleotide polymorphisms (SNPs) well exceeds two million (dbSNP build 105). The main data sources for computational SNP discovery have been expressed sequence tags (ESTs) (1,2), genomic restriction fragments (3), sequences aligned to genome both from the ends of bacterial artificial chromosomes (BACs) and from random shotgun sequences of clone sequence, and overlapping regions of genomic clone sequences themselves (4,5). Generally, SNPs from these data were detected in surveys of a few chromosomes, an ascertainment strategy that biases allele frequency patterns toward common variations (6), and thus these data are expected to fall into a range that is unlikely to contain the majority of clinically important mutations (7,8).…”

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confidence: 99%

Sequence variations in the public human genome data reflect a bottlenecked population history

Marth

Schuler

Yeh

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

108

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Single-nucleotide polymorphisms (SNPs) constitute the great majority of variations in the human genome, and as heritable variable landmarks they are useful markers for disease mapping and resolving population structure. Redundant coverage in overlaps of large-insert genomic clones, sequenced as part of the Human Genome Project, comprises a quarter of the genome, and it is representative in terms of base compositional and functional sequence features. We mined these regions to produce 500,000 high-confidence SNP candidates as a uniform resource for describing nucleotide diversity and its regional variation within the genome. Distributions of marker density observed at different overlap length scales under a model of recombination and population size change show that the history of the population represented by the public genome sequence is one of collapse followed by a recent phase of mild size recovery. The inferred times of collapse and recovery are Upper Paleolithic, in agreement with archaeological evidence of the initial modern human colonization of Europe.

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“…III). In human SNP screening studies, the SNP density reported is much lower, and one SNP is reported to occur in every 1000-2000 bases when two human chromosomes are compared [2,23,28]. Another study analysing SNP incidence in 106 human genes, provided a higher density of one SNP per 348 bp, and their θ values of synonymous and non-synonymous SNP in coding regions were 1.0 × 10 −3 and 1.96 × 10 −4 when corrected for sample size.…”

Section: Discussionmentioning

confidence: 99%

“…In humans, several high resolution SNP maps have been created for several chromosomes or even the whole genome, providing useful resources for studies on haplotypes associated with human diseases [2,23,28]. Furthermore, an SNP map of porcine chromosome 2 has been reported [18], however such studies have not been performed in the chicken yet.…”

Section: Introductionmentioning

confidence: 99%

Identification and characterization of single nucleotide polymorphisms in 12 chicken growth-correlated genes by denaturing high performance liquid chromatography

Nie¹,

Lei²,

Ouyang³

et al. 2005

Genet. Sel. Evol.

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-The genes that are part of the somatotropic axis play a crucial role in the regulation of growth and development of chickens. The identification of genetic polymorphisms in these genes will enable the scientist to evaluate the biological relevance of such polymorphisms and to gain a better understanding of quantitative traits like growth. In the present study, 75 pairs of primers were designed and four chicken breeds, significantly differing in growth and reproduction characteristics, were used to identify single nucleotide polymorphisms (SNP) using the denaturing high performance liquid chromatography (DHPLC) technology. A total of 283 SNP were discovered in 31 897 base pairs (bp) from 12 genes of the growth hormone (GH), growth hormone receptor (GHR), ghrelin, growth hormone secretagogue receptor (GHSR), insulin-like growth factor I and II (IGF-I and -II), insulin-like growth factor binding protein 2 (IGFBP-2), insulin, leptin receptor (LEPR), pituitary-specific transcription factor-1 (PIT-1), somatostatin (SS), thyroid-stimulating hormone beta subunit (TSH-β). The observed average distances in bp between the SNP in the 5'UTR, coding regions (non-and synonymous), introns and 3'UTR were 172, 151 (473 and 222), 89 and 141 respectively. Fifteen non-synonymous SNP altered the translated precursors or mature proteins of GH, GHR, ghrelin, IGFBP-2, PIT-1 and SS. Fifteen indels of no less than 2 bps and 2 poly (A) polymorphisms were also observed in 9 genes. Fifty-nine PCR-RFLP markers were found in 11 genes. The SNP discovered in this study provided suitable markers for association studies of candidate genes for growth related traits in chickens.chickens / genes / SNP / DHPLC * Corresponding author: xqzhang@scau.edu.cn 340 Q. Nie et al.

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An SNP map of human chromosome 22

Cited by 135 publications

References 25 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

Sequence variations in the public human genome data reflect a bottlenecked population history

Identification and characterization of single nucleotide polymorphisms in 12 chicken growth-correlated genes by denaturing high performance liquid chromatography

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