title: Classification and regression tree and spatial analyses reveal geographic heterogeneity in genome wide linkage study of Indian visceral leishmaniasis.
abstract: BACKGROUND
  Genome wide linkage studies (GWLS) have provided evidence for loci controlling visceral leishmaniasis on Chromosomes 1p22, 6q27, 22q12 in Sudan and 6q27, 9p21, 17q11-q21 in Brazil. Genome wide studies from the major focus of disease in India have not previously been reported.
  
  
  RESULTS
  We undertook a GWLS in India in which a primary ∼10 cM (515 microsatellites) scan was carried out in 58 multicase pedigrees (74 nuclear families; 176 affected, 353 total individuals) and replication sought in 79 pedigrees (102 nuclear families; 218 affected, 473 total individuals). The primary scan provided evidence (≥2 adjacent markers allele-sharing LOD≥0.59; nominal P≤0.05) for linkage on Chromosomes 2, 5, 6, 7, 8, 10, 11, 20 and X, with peaks at 6p25.3-p24.3 and 8p23.1-p21.3 contributed to largely by 31 Hindu families and at Xq21.1-q26.1 by 27 Muslim families. Refined mapping confirmed linkage across all primary scan families at 2q12.2-q14.1 and 11q13.2-q23.3, but only 11q13.2-q23.3 replicated (combined LOD = 1.59; P = 0.0034). Linkage at 6p25.3-p24.3 and 8p23.1-p21.3, and at Xq21.1-q26.1, was confirmed by refined mapping for primary Hindu and Muslim families, respectively, but only Xq21.1-q26.1 replicated across all Muslim families (combined LOD 1.49; P = 0.0045). STRUCTURE and SMARTPCA did not identify population genetic substructure related to religious group. Classification and regression tree, and spatial interpolation, analyses confirm geographical heterogeneity for linkages at 6p25.3-p24.3, 8p23.1-p21.3 and Xq21.1-q26.1, with specific clusters of families contributing LOD scores of 2.13 (P = 0.0009), 1.75 (P = 0.002) and 1.84 (P = 0.001), respectively.
  
  
  CONCLUSIONS
  GWLS has identified novel loci that show geographical heterogeneity in their influence on susceptibility to VL in India.
authors.affiliation: Cambridge Institute for Medical Research and Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom.
authors.forename: Michaela
authors.initials: M
authors.lastname: Fakiola
authors.forename: Anshuman
authors.initials: A
authors.lastname: Mishra
authors.forename: Madhukar
authors.initials: M
authors.lastname: Rai
authors.forename: Shri Prakash
authors.initials: SP
authors.lastname: Singh
authors.forename: Rebecca A
authors.initials: RA
authors.lastname: O'Leary
authors.forename: Stephen
authors.initials: S
authors.lastname: Ball
authors.forename: Richard W
authors.initials: RW
authors.lastname: Francis
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Firth
authors.forename: Ben T
authors.initials: BT
authors.lastname: Radford
authors.forename: E Nancy
authors.initials: EN
authors.lastname: Miller
authors.forename: Shyam
authors.initials: S
authors.lastname: Sundar
authors.forename: Jenefer M
authors.initials: JM
authors.lastname: Blackwell
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D002648:Child; D002675:Child, Preschool; D002874:Chromosome Mapping; D005260:Female; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study; D006801:Humans; D007194:India; D007223:Infant; D007898:Leishmaniasis, Visceral / Q000235:genetics*; D008126:Lod Score; D008297:Male; D018895:Microsatellite Repeats; D008875:Middle Aged; D010375:Pedigree; D012044:Regression Analysis