(B) Comparison of unconditional association test P-values (y axis, as in panel (A)), and after additionally conditioning on genotypes at DUP4 (x axis). 1B, and protein-coding genes are shown below. Black triangles represent SNPs where the association signal was previously reported and replicated in further samples. Directly typed SNPs are denoted with black plusses, and CNVs with diamonds. Points are colored by LD with DUP4 in east African reference panel populations. P-values are computed under an additive model of association using meta-analysis across the three African populations included in our study. (A) The evidence for association at SNPs, short indels, and CNVs across the glycophorin region. The recombination rate from LD-based recombination maps (52, 53) and locations of DSB hotspots (24) are annotated below.
(C) Positions of breakpoints, colored as the variant names in (B) and shaded by whether the variant has a single pair of homologous breakpoints, a single pair of non-homologous breakpoints, or is a multi-segment CNV. A horizontal gray line indicates the expected coverage without copy number variation and blue vertical lines mark the locations of the three genes. The inferred CNVs are indicated with deletion in yellow, duplication in light blue, and triplication in dark blue. Black dashes show the mean normalized sequence coverage across heterozygous individuals not carrying another CNV.
S.t.a.l.k.e.r. 2 2017 windows#
(B) Sequence coverage in 1600 bp windows and copy number for non-singleton CNVs.
The locations of protein-coding genes and the segmentally duplicated units are indicated below, with sequences of at least 100 bp that are unique to one or two out of the three segmentally duplicated units marked in black and gray, respectively. Pairwise identity is inferred from a multiple sequence alignment, with mean of 0.96 indicated with a red dashed line. The number of mappable sites and the maximum pairwise identity between homologous locations in the segmental duplication are shown in 1600 bp windows. 21 Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.20 International Blood Group Reference Laboratory, National Health Service (NHS) Blood and Transplant, 500 North Bristol Park, Filton, Bristol BS34 7QH, UK.19 College of Osteopathic Medicine, Michigan State University, East Lansing, MI 48824, USA.18 Blantyre Malaria Project, Queen Elizabeth Central Hospital, College of Medicine, Post Office Box 30096, Chichiri, Blantyre 3, Malawi.17 Liverpool School of Tropical Medicine, Pembroke Place, Liverpool 元 5QA, UK.16 Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, College of Medicine, Post Office Box 30096, Chichiri, Blantyre 3, Malawi.15 National Institute for Medical Research, Mwanza Research Centre, Mwanza City, Tanzania.14 Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK.13 Joint Malaria Programme, Kilimanjaro Christian Medical Centre, Post Office Box 2228, Moshi, Tanzania.12 Faculty of Medicine, Department of Medicine, Imperial College, Exhibition Road, London SW7 2AZ, UK.11 Nuffield Department of Medicine, NDM Research Building, Roosevelt Drive, Headington, Oxford OX3 7FZ, UK.10 Kenyan Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Post Office Box 230-80108, Kilifi, Kenya.9 Department of Biochemistry and Molecular Biology, University of Buea, Post Office Box 63, Buea, South West Region, Cameroon.8 Department of Medical Laboratory Sciences, University of Buea, Post Office Box 63, Buea, South West Region, Cameroon.7 University of Rome La Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy.6 Centre National de Recherche et de Formation sur le Paludisme (CNRFP), 01 BP 2208 Ouagadougou 01, Burkina Faso.5 Royal Victoria Teaching Hospital, Independence Drive, Post Office Box 1515, Banjul, The Gambia.4 Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK.
3 Medical Research Council Unit, Atlantic Boulevard, Fajara, Post Office Box 273, The Gambia.2 Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.1 Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
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