Haplotype and LOD score analyses excluded GINGF1 (Figs. 1 and 4 and Table 1) and GINGF2 (data not shown) in this adHGF family. Linkage of the disease to GINGF3 was demonstrated with a maximal two-point LOD score of 3.45 with marker D2S171 (θ = 0; Table 1) and a maximal multipoint LOD score of 3.91 with marker D2S390 (θ = 0; Fig. 4). Recombinations defined markers D2S220 and D2S352 as boundaries of the linked interval (Fig. 1). The candidate region defined in the presented family overlaps with the 11.42-cM, 13.04-Mb GINGF3 interval flanked by marker loci D2S2221 and D2S1788, originally defined in one Chinese family [6]. According to the current NCBI draft sequence of the human genome, build 36.3, the original and the refined GINGF3 candidate region contain 131 and 112 known and hypothetical genes. Prioritarization of candidate genes for mutation analysis considers expression in gingival or connective tissue and a putative function of the gene product in cell cycle control or extracellular matrix composition. Three interactive, web-based implementations, SUSPECTS (http://www.genetics.med.ed.ac.uk/suspects/), GeneWanderer (http://compbio.charite.de/genewanderer/GeneWanderer), and GeneDistiller (http://www.genedisteller.org) [11] were queried in addition to a manual approach to identify the disease gene based on expression and functional data contained in the NCBI database (http://www.ncbi.nlm.nih.gov/sites/gene). However, sequencing two candidate genes, ALK, encoding a receptor protein–tyrosine kinase and C2orf18 encoding an adenine nucleotide translocase 2 binding protein in cDNA from fibroblasts did not reveal a mutation in a patient from the presented family. A whole-genome analysis of copy number variation in the same patient detected neither aberrations at the GINGF3 locus nor elsewhere.
Fig. 4 Multipoint LOD score. The order of analyzed markers on chromosome 2p is shown on the X-axis, and distances are given in centiMorgan. The Y-axis refers to the LOD score
Table 1 Two-point linkage analysis between the HGF locus and chromosome 2p markers
Marker Genetic LOD score at θ  Z max  θ max
Distance (cM) 0.00 0.01 0.05 0.10 0.20 0.30 0.40
D2S320 38.33 −∞ 1.04 1.53 1.58 1.44 1.22 1.01 1.58 0.09
D2S2233 39.93 −∞ 0.78 1.29 1.36 1.24 1.06 0.87 1.36 0.10
D2S2342 40.47 0.95 0.93 0.84 0.74 0.56 0.41 0.29 0.95 0
D2S220 42.65 −0.69 1.26 1.76 1.82 1.67 1.44 1.22 1.82 0.09
D2S2201a 41.57 1.83 1.79 1.64 1.45 1.13 0.87 0.66 1.83 0
D2S2221 44.09 2.19 2.15 1.99 1.80 1.46 1.16 0.92 2.19 0
D2S171 45.30 3.45 3.39 3.16 2.89 2.40 1.97 1.60 3.45 0
D2S144 45.30 3.42 3.36 3.13 2.86 2.37 1.95 1.59 3.42 0
D2S365 47.97 0.95 0.93 0.85 0.75 0.58 0.44 0.33 0.95 0
D2S390 48.50 3.31 3.25 3.03 2.77 2.30 1.89 1.54 3.31 0
D2S352 50.65 −∞ −1.51 −0.29 0.11 0.33 0.35 0.32 0.36 0.27
D2S2347 50.65 −∞ −0.34 0.24 0.40 0.45 0.42 0.37 0.45 0.19
D2S367 54.96 0.95 0.93 0.88 0.82 0.69 0.59 0.49 0.95 0
D2S1788 55.51 −∞ −0.92 0.27 0.62 0.76 0.71 0.61 0.76 0.20
D2S2163 59.36 −∞ −0.61 −0.02 0.15 0.23 0.22 0.19 0.23 0.23
D2S177 59.36 −∞ −4.01 −2.05 −1.32 −0.71 −0.43 −0.28 −0.28 0.40
D2S2238 60.45 −∞ −2.49 −1.20 −0.73 −0.36 −0.21 −0.13 −0.13 0.40
aThe physical map of chromosome 2 (NCBI draft sequence of the human genome, build 36.3) indicates that D2S2201 localizes centromeric to D2S220, contrasting with the Marshfield genetic map of chromosome 2.