Journal of Human Genetics

Kawano, Toshio; Wang, Chunxia; Hotta, Yoshihiro; Sato, Miho; Iwata-Amano, Emi; Hikoya, Akiko; Fujita, Naoya; Koyama, Norihisa; Shirai, Shoichiro; Azuma, Noriyuki; Ohtsubo, Masafumi; Shimizu, Nobuyoshi; Minoshima, Shinsei

doi: 10.1007/s10038-007-0153-2pmid: 17568989

Mutations in the PAX6 gene of Japanese aniridia patients were analyzed. Four types of mutations including one known (474delC) and three novel (786_787ins10, 678_688del11 and 572_575delAATCins14) were found in six patients from four families. A patient with the mutation 572_575delAATCins14 also manifested VATER association. This is the first case of aniridia accompanied by VATER association. All of mutations found in this study are frameshift type, resulting in premature termination of translation. The database for PAX6 gene mutation has been made using a graphical data display system MutationView ( http://mutview.dmb.med.keio.ac.jp/ ).

Yamazaki, Keiko; Onouchi, Yoshihiro; Takazoe, Masakazu; Kubo, Michiaki; Nakamura, Yusuke; Hata, Akira

doi: 10.1007/s10038-007-0156-zpmid: 17534574

Inflammatory bowel diseases, Crohn’s disease (CD) and ulcerative colitis are characterised by chronic transmural, segmental and typically granulomatous inflammation of the gut. Each has a peak age of onset in the second to fourth decades of life and prevalence has been increasing significantly in both Western countries and Japan over the last decade, while their pathogenesis remains largely unknown. Recently, positive association of CD with the variants in interleukin 23 receptor (IL23R), autophagy-related 16-like 1 (ATG16L1) genes and chromosome 5p13.1 locus was reported through genome-wide association studies which are now recognised as a robust tool for the identification of susceptibility genes for complex diseases. To examine an association of reported susceptible variants in the three loci with Japanese CD patients, a total of 484 CD patients and 439 controls were genotyped. No evidence of positive association for any of these loci with CD was found in the Japanese population, even after clinically stratified subgroups of CD were used. Our result revealed a distinct ethnic difference of genetic background of CD that we reported previously in other genes between Japanese and Caucasian populations. Further genetic studies are required to confirm our findings with ethnically divergent populations.

Zhou, Ruixia; An, Lizhe; Wang, Xunling; Shao, Wei; Lin, Gonghua; Yu, Weiping; Yi, Lin; Xu, Shijian; Xu, Jiujin; Xie, Xiaodong

doi: 10.1007/s10038-007-0155-0pmid: 17579807

The Liqian people in north China are well known because of the controversial hypothesis of an ancient Roman mercenary origin. To test this hypothesis, 227 male individuals representing four Chinese populations were analyzed at 12 short tandem repeat (STR) loci and 12 single nucleotide polymorphisms (SNP). At the haplogroup levels, 77% Liqian Y chromosomes were restricted to East Asia. Principal component (PC) and multidimensional scaling (MDS) analysis suggests that the Liqians are closely related to Chinese populations, especially Han Chinese populations, whereas they greatly deviate from Central Asian and Western Eurasian populations. Further phylogenetic and admixture analysis confirmed that the Han Chinese contributed greatly to the Liqian gene pool. The Liqian and the Yugur people, regarded as kindred populations with common origins, present an underlying genetic difference in a median-joining network. Overall, a Roman mercenary origin could not be accepted as true according to paternal genetic variation, and the current Liqian population is more likely to be a subgroup of the Chinese majority Han.

Bhaskar, L.; Thangaraj, K.; Shah, Anish; Pardhasaradhi, G.; Praveen Kumar, K.; Reddy, A.; Papa Rao, A.; Mulligan, C.; Singh, Lalji; Rao, V.

doi: 10.1007/s10038-007-0158-xpmid: 17554476

NPY is a 36-aminoacid peptide expressed in several areas of the nervous system. Neuropeptide Y (NPY) receptors represent a widely diffused system that is involved in the regulation of multiple biological functions. The human NPY gene is located in chromosome 7. The functional significance of coding Leu7Pro polymorphism in the signal peptide of preproNPY is known. Six hundred and fifty four individuals of 14 ethnic Indian populations were screened for three mutations in the NPY gene, including Leu7Pro. We found that the Pro7 frequencies among the studied populations were much higher than in previous studies from other parts of the world. The highest allele frequency of Pro7 was detected in the Kota population in the Nilgiri Hill region of south India, and this may reflect a founder event in the past or genetic drift. All populations followed the Hardy–Weinberg equilibrium for the assayed markers. A total of five haplotypes were observed, only two of which were found to occur with a high frequency in all populations. No linkage disequilibrium (LD) was observed across the tested alleles in any population with the exception of Leu7Pro and Ser50Ser in the Badaga population (χ 2 = 13.969; p = 0.0001).

Zeharia, Avraham; Ebberink, Merel; Wanders, Ronald; Waterham, Hans; Gutman, Alisa; Nissenkorn, Andreea; Korman, Stanley

doi: 10.1007/s10038-007-0157-ypmid: 17534573

Mutations in 12 different PEX genes can cause a generalized peroxisomal biogenesis disorder with clinical phenotypes ranging from Zellweger syndrome to infantile Refsum disease. To identify the specific PEX gene to be sequenced, complementation analysis is first performed in fibroblasts using catalase immunofluorescence. A patient with a relatively mild phenotype of infantile cholestasis, hypotonia and motor delay had elevated plasma very long-chain fatty acids and bile acid precursors, but fibroblast studies revealed normal or only mildly abnormal peroxisomal parameters and mosaic catalase immunofluorescence. This mosaicism persisted even when the incubation temperature was increased from 37 °C to 40 °C, a maneuver previously shown to abolish mosaicism by exacerbating peroxisomal dysfunction. As mosaicism precludes complementation analysis, a candidate gene approach was employed. After PEX1 sequencing was unrewarding, PEX12 sequencing revealed homozygosity for a novel c.102A>T (p.R34S) missense mutation affecting a partially conserved residue in the N-terminal region important for localization to peroxisomes. Transfection of patient fibroblasts with wild-type PEX12 cDNA confirmed that a PEX12 defect was the basis for the PBD. Homozygosity for c.102A>T was identified in a second patient of similar ethnic origin also presenting with a mild phenotype. PEX12 is a highly probable candidate gene for direct sequencing in the context of a mild clinical phenotype with mosaicism and minimally abnormal peroxisomal parameters in fibroblasts.

Zhang, Zhujun; Habara, Yasuaki; Nishiyama, Atsushi; Oyazato, Yoshinobu; Yagi, Mariko; Takeshima, Yasuhiro; Matsuo, Masafumi

doi: 10.1007/s10038-007-0163-0pmid: 17579806

The dystrophin gene, which is mutated in Duchenne and Becker muscular dystrophy, is characterized by its extremely large introns. Seven cryptic exons from the intronic sequences of the dystrophin gene have been shown to be inserted into the processed mRNA. In this study, we have cloned seven novel cryptic exons embedded in dystrophin introns that were amplified from dystrophin mRNA isolated from lymphocytes. All of these sequences, which ranged in size from 27 to 151 bp, were found to be cryptic exons because they were completely homologous to intronic sequences (introns 1, 18, 29, 63, 67, and 77), and possessed consensus sequences for branch points, splice acceptor sites, and splice donor sites. Compared with the 77 authentic dystrophin exons, the 14 cryptic exons were characterized by (1) lower Shapiro’s splicing probability scores for the splice donor and acceptor sites; (2) smaller and larger densities of splicing enhancer and silencer motifs, respectively; (3) a longer distance between the putative branch site and the splice acceptor site; and (4) with one exception, the introduction of premature stop codons into their respective transcripts. These characteristics indicated that the cryptic exons were weaker than the authentic exons. Our results suggested that a mutation deep within an intron that changed these parameters could cause dystrophinopathy. The cryptic exons identified provide areas that should be examined for the detection of mutations in the dystrophin gene, and they may help us to understand the roles of large dystrophin introns.

Sato, Takehiro; Amano, Tetsuya; Ono, Hiroko; Ishida, Hajime; Kodera, Haruto; Matsumura, Hirofumi; Yoneda, Minoru; Masuda, Ryuichi

doi: 10.1007/s10038-007-0164-zpmid: 17568987

In order to investigate the phylogenetic status of the Okhotsk people that were distributed in northern and eastern Hokkaido as well as southern Sakhalin during the fifth to the thirteenth centuries, DNA was carefully extracted from human bone and tooth remains excavated from archaeological sites. The hypervariable region 1 sequences of the mitochondrial DNA (mtDNA) control region were successfully amplified and 16 mtDNA haplotypes were identified from 37 individuals of the Okhotsk people. Of the 16 haplotypes found, 6 were unique to the Okhotsk people, whereas the other 10 were shared by northeastern Asian people that are currently distributed around Sakhalin and downstream of the Amur River. The phylogenetic relationships inferred from mtDNA sequences showed that the Okhotsk people were more closely related to the Nivkhi and Ulchi people among populations of northeastern Asia. In addition, the Okhotsk people had a relatively closer genetic affinity with the Ainu people of Hokkaido, and were likely intermediates of gene flow from the northeastern Asian people to the Ainu people. These findings support the hypothesis that the Okhotsk culture joined the Satsumon culture (direct descendants of the Jomon people) resulting in the Ainu culture, as suggested by previous archaeological and anthropological studies.

Koga, Akihiko; Shimada, Atsuko; Kuroki, Toshiya; Hori, Hiroshi; Kusumi, Junko; Kyono-Hamaguchi, Yoriko; Hamaguchi, Satoshi

doi: 10.1007/s10038-007-0161-2pmid: 17554475

DNA-based transposable elements can be used as tools for gene engineering and gene therapy. A great advantage over RNA-mediated elements and retroviruses is the simplicity and safety of usage. The Tol1 element of the medaka fish Oryzias latipes has structural features of DNA-based elements. Although its excision has already been demonstrated, de novo insertion has not been observed, and a transposase has not been hitherto identified. We first cloned, through in silico search alignments and genomic library screenings, a 4.4-kb Tol1 copy carrying open reading frames and then identified, by mRNA analysis, a 2.9-kb transcript coding for 851 amino acids. The protein product of this transcript catalyzed transposition of a nonautonomous Tol1 copy in human and mouse culture cells. This identification of a fully functional Tol1 transposase could lead to the development of new tools for basic and translational molecular biology applications in mammals.

Mori, Keisuke; Horie-Inoue, Kuniko; Kohda, Masakazu; Kawasaki, Izumi; Gehlbach, Peter; Awata, Takuya; Yoneya, Shin; Okazaki, Yasushi; Inoue, Satoshi

doi: 10.1007/s10038-007-0162-1pmid: 17568988

The purpose of this investigation was to determine whether the high-temperature requirement A-1 (HTRA1) gene polymorphism is associated with age-related macular degeneration (AMD) in native, unrelated Japanese patients. A total of 123 patients with AMD and 133 control subjects without AMD were recruited for this study. The single-nucleotide polymorphism (SNP) rs11200638 in the HTRA1 gene was assessed using a TaqMan assay. The risk A allele frequencies in the AMD cases and control patients were 0.577 and 0.380, respectively, and were associated with a significant risk of developing AMD (p=7.75×10−6). The results were more significant in subtype analyses with wet AMD (p=5.96×10−7). We conclude that the rs11200638 variant in the HTRA1 gene is strongly associated with AMD in the Japanese population. This result supports the hypothesis that the HTRA1 gene may increase susceptibility to AMD development and can participate in a potential new molecular pathway for AMD pathogenesis by extending this association across diverse ethnicities.