PKLR-GBA region shows almost complete linkage disequilibrium over 70 kb in a set of worldwide populations

Mateu, Eva; Pérez-Lezaun, Anna; Martínez-Arias, Rosa; Andrés, Aida; Vallés, Mónica; Bertranpetit, Jaume; Calafell, Francesc
June 2002
Human Genetics;Jun2002, Vol. 110 Issue 6, p532
Academic Journal
Haplotype diversity in a genomic region of ~70 kb in 1q21 between genes PKLR and GBA was characterized by typing one single nucleotide polymorphism (SNP) in PKLR, two SNPs in GBA and one short tandem repeat polymorphism (STRP) in PKLR in 1792 chromosomes from 17 worldwide populations. Two other SNPs in GBA were typed in three African populations. Most chromosomes carried one of either two phylogenetically distinct haplotypes with different alleles at each site. Allele diversity at the STRP was tightly linked to haplotype background. Linkage disequilibrium (LD) was highly significant for all SNP pairs in all populations, although it was, on average, slightly higher in non-African populations than in sub-Saharan Africans. Variation at PKLR-GBA was also tightly linked to that at the GBA pseudogene, 16 kb downstream from GBA. Thus, a 90 kb-long LD block was observed, which points to a low recombination rate in this region. Detailed haplotype phylogeny suggests that the chimpanzee GBA haplotype is not one of the two most frequent haplotypes. Based on variability at the PKLR STRP and on the geographical distribution of LD, the expansion of the two main haplotypes may have predated the "Out of Africa" expansion of anatomically modern humans. LD and STRP variability in non-Africans are ∼87% of those in Africans, in contrast with other loci; this implies that the "out of Africa" bottleneck may have had a broad distribution of effects across loci.


Related Articles

  • Human Inter-Individual DNA Sequence Variation in Candidate Genes, Drug Targets, the Importance of Haplotypes and Pharmacogenomics. Hoehe, Margret R.; Timmermann, Bernd; Lehrach, Hans // Current Pharmaceutical Biotechnology;Dec2003, Vol. 4 Issue 6, p351 

    The identification of genes predisposing to human diseases is of paramount importance for understanding the molecular basis of the disease and individually different drug response, and will establish new routes to diagnosis and therapeutic advances of immense medical benefit. A key step common...

  • Maternal donors of polyploids in Pseudoroegneria (Poaceae: Triticeae) and related genera inferred from chloroplast trnL-F sequences.  // Turkish Journal of Biology;2010, Vol. 34 Issue 4, p335 

    No abstract available.

  • AZFc region of the Y chromosome shows singular structural organization. Premi, Sanjay; Srivastava, Jyoti; Epplen, Jörg Thomas; Ali, Sher // Chromosome Research;Jun2010, Vol. 18 Issue 4, p419 

    Owing to clonal inheritance, haploid status and lack of recombination, structural polymorphism in the human Y chromosome is more prevalent than that in the remaining parts of the genome. We studied structural organization of the AZFc region, assessed microdeletions therein and studied copy...

  • Protecting Haploid Polymorphisms in Temporally Variable Environments. Dean, Antony M. // Genetics;Feb2005, Vol. 169 Issue 2, p1147 

    Analysis of a continuous-time model shows that a protected polymorphism can arise in a haploid pop- ulation subject to temporal fluctuations in selection. The requirements are that population size is regulated in a density-dependent manner and that an allele's arithmetic mean relative growth...

  • ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data. Margarido, Gabriel R. A.; Heckerman, David // PLoS Computational Biology;Apr2015, Vol. 11 Issue 4, p1 

    As a result of improvements in genome assembly algorithms and the ever decreasing costs of high-throughput sequencing technologies, new high quality draft genome sequences are published at a striking pace. With well-established methodologies, larger and more complex genomes are being tackled,...

  • Polyploids, genome halving and phylogeny. David Sankoff; Chunfang Zheng; Qian Zhu // Bioinformatics;Jul2007, Vol. 23 Issue 13, pi433 

    Motivation: Autopolyploidization and allopolyploidization events multiply the number of chromosomes and genomic content. Genome rearrangement phylogenetics requires that all genomes analyzed have the same set of orthologs, so that it is not possible to include diploid and polyploid genomes in...

  • Outline of a Genome Navigation System Based on the Properties of GA-Sequences and Their Flanks. Albrecht-Buehler, Guenter // PLoS ONE;2009, Vol. 4 Issue 3, p1 

    Introducing a new method to visualize large stretches of genomic DNA (see Appendix S1) the article reports that most GAsequences [1] shared chains of tetra-GA-motifs and contained upstream poly(A)-segments. Although not integral parts of them, Alu-elements were found immediately upstream of all...

  • Characteristics of 454 pyrosequencing data—enabling realistic simulation with flowsim. Balzer, Susanne; Malde, Ketil; Lanzén, Anders; Sharma, Animesh; Jonassen, Inge // Bioinformatics;Sep2010, Vol. 26 Issue 18, pi420 

    Motivation: The commercial launch of 454 pyrosequencing in 2005 was a milestone in genome sequencing in terms of performance and cost. Throughout the three available releases, average read lengths have increased to ∼500 base pairs and are thus approaching read lengths obtained from...

  • More Science Than Art. BILLINGS, PAUL // GeneWatch;Oct/Nov2012, Vol. 25 Issue 5, p6 

    The article offers insights about next-generation genome sequencing. Prior to the 1990s, methods developed by Fred Sanger and Walter Gilbert were used in the field of DNA sequencing. The estimated size of a haploid human genome is three billion individual DNA bases. As part of the DNA synthesis,...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics