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Synpolydactyly (SPD, MIM 186000), also known as syndactyly type II, is a dominantly inherited limb malformation with incomplete penetrance and variable expressivity. Polyalanine tract expansion in HOXD13 has been shown to be the disease-causing mutation in SPD. The present study was designed to identify mutation in HOXD13 and to provide prenatal diagnosis, in a large Chinese SPD family consisting of 54 individuals.The proband and 4 other affected individuals in the family were evaluated physically and radiologically to ascertain the SPD phenotype. Genomic DNA was extracted from peripheral blood samples obtained from 18 family members (9 affected and 9 unaffected), and from amniotic fluid and chorionic villus samples obtained from the proband during her two consecutive pregnancies. With the use of a pair of specific primers, a fragment of 161bp was amplified by polymerase chain reaction (PCR) to cover the imperfect GCN triplet repeat sequence in exon 1 of HOXD13 encoding the 15-residue polyalanine tract. The PCR products were detected by agarose gel electrophoresis, and sequenced after cloning into pMD18T vector. To confirm prenatal diagnosis, haplotype analysis was also performed by allele-typing three microsatellite markers, including the intronic CA repeats in HOXD13.Digital and radiographic findings indicated a typical SPD phenotype in the family. These included 3/4 finger syndactyly and 4/5 toe syndactyly with an extra digit in the syndactylous web. Unilateral finger syndactyly in the proband, unilateral toe syndactyly in 2 individuals, bilateral brachydactyly of the fifth toes in 1 individual, and clinodactyly of the fifth fingers in 4 individuals were also observed, indicating variable expressivity. Gel electrophoresis of the PCR products showed an additional longer fragment in all 9 affected individuals but not in the unaffected ones. Sequence analysis of the longer fragment revealed a 9-alanine expansion. The expansion was detectable in DNA from the amniotic fluid and chorionic villus samples. Furthermore, haplotype analysis ruled out potential contamination of the maternal DNA. These suggested that the two fetuses carried the same polyalanine expansion.HOXD13 polyalanine expansion was detected in a large Chinese family with SPD and prenatal diagnosis of two affected fetuses was achieved. This is the first report on prenatal diagnosis of SPD by detecting the HOXD13 polyalanine expansion in the Han population of the Chinese mainland.