PMC:2812425 / 3013-5820 JSONTXT

{"project":"MyTest","denotations":[{"id":"19633868-16195711-29215964","span":{"begin":2205,"end":2207},"obj":"16195711"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"text":"Materials and methods\nWe ascertained a German four-generation family with autosomal dominant transmission of HGF without evidence for parental imprinting through a proband. Fifteen family members were examined and nine (five male and four female) were classified as affected (Fig. 1, individuals 12170, 3, 11284, 13230, 11602, 12163, 13232, 11603, and 11606) based on the following criteria: enlarged gingiva covering at least one third of clinical dental crowns of five or more teeth and lack of exposure of affected members to any inducible drugs; individuals were otherwise healthy. The deceased male founder of this family (Fig. 1, individual 1) was reported as having been affected by HGF. Five spouses of family members were also examined, and samples were taken for molecular investigation (individuals 12021, 11378, 13231, 11253, and 11760 in Fig. 1). No samples were available from individuals 1–6 shown in Fig. 1, and their genotypes were inferred and haplotypes were re-constructed (see below).\nFig. 1 Pedigree and haplotypes of the HGF family under study. The proband, indicated by an arrow, has two affected and two unaffected children with four different partners. Haplotype analysis excluded the SOS1 gene at the GINGF1 locus as the disease gene in this family and narrowed the original 11.42-cM, 13.04-Mb GINGF3 locus, flanked by marker loci D2S2221 and D2S1788, down to the region between markers D2S220 and D2S352\nInformed consent was obtained from all participants following genetic counseling. DNA was extracted from peripheral blood samples, from paraffin-embedded tissue sections, and from buccal smears, and RNA was extracted from cultured fibroblasts using an automated extractor according to the manufacturer's protocols (GenoM 48, Qiagen, Vienna, Austria). For linkage analysis, highly polymorphic microsatellite markers were selected from 2p21–p23.3 and from 5q13–q22 (http://www.gdb.org/). Locus order and sex-averaged inter-marker distances were taken from the Marshfield map (http://research.marshfieldclinic.org/genetics/). Marker alleles were detected by electrophoresing the PCR products on 6% polyacrylamide gels followed by silver staining. We used the Allegro program [10] to compute haplotypes as well as two-point and multipoint logarithm of the odds (LOD) scores, under the assumption of autosomal dominant inheritance with 100% penetrance, and with the disease-allele frequency set at.0001, and equal marker allele frequencies. A whole-genome analysis of copy number variation was conducted in one patient (12170, Fig. 1) using the Affymetrix Genome-Wide Human SNP 6.0 array according to the specifications of the manufacturer. Oligonucleotide primer sequences and conditions to sequence the ALK and C2orf18 genes in complementary DNA (cDNA) are available on request."}

{"project":"2_test","denotations":[{"id":"19633868-16195711-29215964","span":{"begin":2205,"end":2207},"obj":"16195711"}],"text":"Materials and methods\nWe ascertained a German four-generation family with autosomal dominant transmission of HGF without evidence for parental imprinting through a proband. Fifteen family members were examined and nine (five male and four female) were classified as affected (Fig. 1, individuals 12170, 3, 11284, 13230, 11602, 12163, 13232, 11603, and 11606) based on the following criteria: enlarged gingiva covering at least one third of clinical dental crowns of five or more teeth and lack of exposure of affected members to any inducible drugs; individuals were otherwise healthy. The deceased male founder of this family (Fig. 1, individual 1) was reported as having been affected by HGF. Five spouses of family members were also examined, and samples were taken for molecular investigation (individuals 12021, 11378, 13231, 11253, and 11760 in Fig. 1). No samples were available from individuals 1–6 shown in Fig. 1, and their genotypes were inferred and haplotypes were re-constructed (see below).\nFig. 1 Pedigree and haplotypes of the HGF family under study. The proband, indicated by an arrow, has two affected and two unaffected children with four different partners. Haplotype analysis excluded the SOS1 gene at the GINGF1 locus as the disease gene in this family and narrowed the original 11.42-cM, 13.04-Mb GINGF3 locus, flanked by marker loci D2S2221 and D2S1788, down to the region between markers D2S220 and D2S352\nInformed consent was obtained from all participants following genetic counseling. DNA was extracted from peripheral blood samples, from paraffin-embedded tissue sections, and from buccal smears, and RNA was extracted from cultured fibroblasts using an automated extractor according to the manufacturer's protocols (GenoM 48, Qiagen, Vienna, Austria). For linkage analysis, highly polymorphic microsatellite markers were selected from 2p21–p23.3 and from 5q13–q22 (http://www.gdb.org/). Locus order and sex-averaged inter-marker distances were taken from the Marshfield map (http://research.marshfieldclinic.org/genetics/). Marker alleles were detected by electrophoresing the PCR products on 6% polyacrylamide gels followed by silver staining. We used the Allegro program [10] to compute haplotypes as well as two-point and multipoint logarithm of the odds (LOD) scores, under the assumption of autosomal dominant inheritance with 100% penetrance, and with the disease-allele frequency set at.0001, and equal marker allele frequencies. A whole-genome analysis of copy number variation was conducted in one patient (12170, Fig. 1) using the Affymetrix Genome-Wide Human SNP 6.0 array according to the specifications of the manufacturer. Oligonucleotide primer sequences and conditions to sequence the ALK and C2orf18 genes in complementary DNA (cDNA) are available on request."}