Comparison of human genetic and sequence-based physical maps

Yu, Adong; Zhao, Chengfeng; Fan, Ying; Jang, Wonhee; Mungall, Andrew J.; Deloukas, Panos; Olsen, Anne S.; Doggett, Norman A.; Ghebranious, Nader; Broman, Karl W.; Weber, James L.

doi:10.1038/35057185

Cited by 254 publications

(199 citation statements)

References 28 publications

Supporting

Mentioning

182

Contrasting

Unclassified

Order By: Relevance

“…These patterns are due to recombination rate variation as discussed above. We also confirmed previously described relationships between LD and GþC content 78,81,82 , sequence polymorphism 83 and repeat composition 78,82 .…”

Section: Insights Into Recombination and Natural Selectionsupporting

confidence: 77%

See 1 more Smart Citation

A haplotype map of the human genome

Belmont¹,

Boudreau²,

Leal³

et al. 2005

Nature

5,206

1,633

View full text Add to dashboard Cite

A haplotype map of the human genomeThe International HapMap Consortium* Inherited genetic variation has a critical but as yet largely uncharacterized role in human disease. Here we report a public database of common variation in the human genome: more than one million single nucleotide polymorphisms (SNPs) for which accurate and complete genotypes have been obtained in 269 DNA samples from four populations, including ten 500-kilobase regions in which essentially all information about common DNA variation has been extracted. These data document the generality of recombination hotspots, a block-like structure of linkage disequilibrium and low haplotype diversity, leading to substantial correlations of SNPs with many of their neighbours. We show how the HapMap resource can guide the design and analysis of genetic association studies, shed light on structural variation and recombination, and identify loci that may have been subject to natural selection during human evolution.

show abstract

Section: Insights Into Recombination and Natural Selectionsupporting

confidence: 77%

“…15; see also Supplementary Figs 8b and 14) 48,[78][79][80] . These patterns are due to recombination rate variation as discussed above.…”

Section: Insights Into Recombination and Natural Selectionmentioning

confidence: 99%

A haplotype map of the human genome

Belmont¹,

Boudreau²,

Leal³

et al. 2005

Nature

5,206

1,633

View full text Add to dashboard Cite

show abstract

“…29 The increasing use of highly structured distributions of Y chromosome types to investigate the ethnic/geographic Frequencies of E1b1b1b, E1b1b1a-b and J1 chromosomes with 0-1-steps neighbour chromosome within the NW African dataset; the first column refers to the geographic location in Figure 1. 33 2.5% of a typical present day southern European genome would consist on average of 2 Mb regions of African DNA. We therefore believe that signatures of this event would be correctly identified using modern dense genotype data.…”

Section: Resultsmentioning

confidence: 99%

Moors and Saracens in Europe: estimating the medieval North African male legacy in southern Europe

et al. 2009

View full text Add to dashboard Cite

To investigate the male genetic legacy of the Arab rule in southern Europe during medieval times, we focused on specific Northwest African haplogroups and identified evolutionary close STR-defined haplotypes in Iberia, Sicily and the Italian peninsula. Our results point to a higher recent Northwest African contribution in Iberia and Sicily in agreement with historical data. southern Italian regions known to have experienced long-term Arab presence also show an enrichment of Northwest African types. The forensic and genomic implications of these findings are discussed.

show abstract

“…This deviation from the average 1 cM/Mb appears to be due to reduced male recombination rate. 31 Given the established correlation between the local recombination rate and the extent of linkage disequilibrium, 34,35 the former may be directly related to extensive disease haplotype sharing, observed over large physical distances (based on 0.58 cM/Mb, 4.6 Mb for haplotypes V and VI, 7.3 Mb for haplotypes III and IV, and 16.5 Mb for haplotype I; Figure 1). …”

Section: European Journal Of Human Geneticsmentioning

confidence: 99%

Fine mapping of the locus for Shwachman-Diamond syndrome at 7q11, identification of shared disease haplotypes, and exclusion of TPST1 as a candidate gene

et al. 2002

View full text Add to dashboard Cite

Shwachman-Diamond syndrome (SDS) is an autosomal recessive disorder characterised by exocrine pancreatic dysfunction, haematological and skeletal abnormalities. We have previously defined the SDS locus as a 2.7 cM interval spanning the centromere of chromosome 7. To facilitate additional analysis of this complex and poorly characterised region, a framework of ordered genetic markers at 7p11-q11, including six newly identified, has been constructed using somatic cell, radiation hybrid and STS-content mapping. We have identified shared disease haplotypes, that recur in unrelated families of common ethnic origin, and extend across the SDS locus. Detection of ancestral and intrafamilial recombination events in patients refined the SDS locus to a 1.9 cM interval at 7q11, which contains the tyrosylprotein sulfotransferase 1 (TPST1) gene. Patients with SDS were screened for mutations in TPST1 by sequencing of exons and intron ± exon junctions. Two single nucleotide polymorphisms, but no disease-causing mutations, were identified. In addition, Southern blot analysis yielded no evidence of large-scale mutations, and RT ± PCR analysis failed to detect alterations in expression. These results exclude TPST1 as the causative gene for SDS. The established map of the refined SDS locus will assist in the identification and characterisation of other candidate genes for SDS.

show abstract

Comparison of human genetic and sequence-based physical maps

Cited by 254 publications

References 28 publications

A haplotype map of the human genome

A haplotype map of the human genome

Moors and Saracens in Europe: estimating the medieval North African male legacy in southern Europe

Fine mapping of the locus for Shwachman-Diamond syndrome at 7q11, identification of shared disease haplotypes, and exclusion of TPST1 as a candidate gene

Contact Info

Product

Resources

About