A high-resolution recombination map of the human genome

Abstract

Determination of recombination rates across the human genome has been constrained by the limited resolution and accuracy of existing genetic maps and the draft genome sequence. We have genotyped 5,136 microsatellite markers for 146 families, with a total of 1,257 meiotic events, to build a high-resolution genetic map meant to: (i) improve the genetic order of polymorphic markers; (ii) improve the precision of estimates of genetic distances; (iii) correct portions of the sequence assembly and SNP map of the human genome; and (iv) build a map of recombination rates. Recombination rates are significantly correlated with both cytogenetic structures (staining intensity of G bands) and sequence (GC content, CpG motifs and poly(A)/poly(T) stretches). Maternal and paternal chromosomes show many differences in locations of recombination maxima. We detected systematic differences in recombination rates between mothers and between gametes from the same mother, suggesting that there is some underlying component determined by both genetic and environmental factors that affects maternal recombination rates.

Haplotype tagging efficiency in worldwide populations in CTLA4 gene

“…40 This points to high LD over the region, which has already been reported by Ueda et al 7 Our results not only show this high LD but also that it persists across populations worldwide. Previous studies in other genes, such as PAH 41 or the PKLR-GBA gene region, 42 have shown a general pattern of moderate geographical structure of LD with higher values out of Africa and low values in sub-Saharan Africa.…”

Proximal hip geometry is linked to several chromosomal regions: Genome-wide linkage results from the Framingham Osteoporosis Study

“…We thus computed IBD for 342 'derivative' pedigrees (including 251 intact pedigrees, 51 reduced pedigree, and 40 newly derived pedigrees) for chromosome X multipoint analysis. For the autosomal markers, map distances were obtained from the Center for Medical Genetics (http://research.marshfieldclinic.org/genetics/) whenever available or estimated otherwise; map distances for the X chromosomes were obtained from DeCODE [40]. Marker allele frequencies were estimated from the genotypes of the study participants by simple allele counting; this method yielded allele frequency estimates very similar to those obtained by maximum likelihood estimation.…”

A genome scan in multigenerational families with dyslexia: Identification of a novel locus on chromosome 2q that contributes to phonological decoding efficiency

“…In general, we used the Marshfield map (http:// research.marshfieldclinic.org/genetics) with two exceptions: (1) If there was considerable disagreement between the Marshfield and deCODE maps, 54 we used our data set to resolve the marker order and distances; (2) If there was a large disagreement between the Marshfield map and our data set that could not be resolved, we used the distances provided in the deCODE map if possible, or if not we used our data set to estimate distances. On chromosome 2, the distance between D2S1326 and D2S2241 was almost twice as large, and the distances between markers D2S2241, D2S142 and D2S1353 were considerably smaller, in the deCODE map than in the Marshfield map.…”