Novel (CA)n marker DXYS241 on the nonrecombinant part of the human Y chromosome.

The origin of modern humans can be traced by comparing polymorphic sites in either mitochondria or genomic sequences between humans and other primates. The human Y chromosome has both a non-recombining region and X-Y homologous pseudo-autosomal regions. In the nonrecombining region events during evolution can be directly detected. At least a part of homology between Xq21 and Yp11 is a result of rather recent translocations from the X chromosome to the Y chromosome. DNA markers residing in the nonrecombining region of the human Y chromosome are potentially useful in tracing male-specific gene flow in human evolution. However, the number of available markers in the region is limited. Here, we report a novel X-Y homologous (CA)n repeat locus in the nonrecombining region of the Y chromosome. This marker, DXYS241, has several interesting features. Y- and X-chromosome alleles are distinguishable because the Y-chromosome alleles are shorter than the X-chromosome alleles most of the time. We developed 2 primer sets for specific examination of Y- and X-chromosome alleles. The marker should be useful in establishing relationships between populations based on patrilineal gene flow. Sequences homologous to DXYS241 are also found on the X chromosome of primates. Four events during primate evolution that led to the modern human Y chromosome were identified.

Polymerase chain reaction analysis of the Y chromosome long arm in azoospermic patients: lack of the Y chromosome recognition motif (YRRM1) gene.

We analyzed DNA from a patient with azoospermia whose Y chromosome was cytogenetically normal. A total of 16 loci on the Y chromosome long arm were examined: 15 loci between DYS7E and DYZ1, and the Y chromosome RNA recognition motif (YRRM1) locus, a candidate gene for the azoospermic factor AZF. We did not detect the YRRM1 gene in this patient. This finding supports the theory that YRRM1 is an essential gene for spermatogenesis.

An ancient retrotransposal insertion causes Fukuyama-type congenital muscular dystrophy.

Fukuyama-type congenital muscular dystrophy (FCMD), one of the most common autosomal recessive disorders in Japan (incidence is 0.7-1.2 per 10,000 births), is characterized by congenital muscular dystrophy associated with brain malformation (micropolygria) due to a defect in the migration of neurons. We previously mapped the FCMD gene to a region of less than 100 kilobases which included the marker locus D9S2107 on chromosome 9q31. We have also described a haplotype that is shared by more than 80% of FCMD chromosomes, indicating that most chromosomes bearing the FCMD mutation could be derived from a single ancestor. Here we report that there is a retrotransposal insertion of tandemly repeated sequences within this candidate-gene interval in all FCMD chromosomes carrying the founder haplotype (87%). The inserted sequence is about 3 kilobases long and is located in the 3' untranslated region of a gene encoding a new 461-amino-acid protein. This gene is expressed in various tissues in normal individuals, but not in FCMD patients who carry the insertion. Two independent point mutations confirm that mutation of this gene is responsible for FCMD. The predicted protein, which we term fukutin, contains an amino-terminal signal sequence, which together with results from transfection experiments suggests that fukutin is a secreted protein. To our knowledge, FCMD is the first human disease to be caused by an ancient retrotransposal integration.

YAC and cosmid contigs encompassing the Fukuyama-type congenital muscular dystrophy (FCMD) candidate region on 9q31.

Fukuyama-type congenital muscular dystrophy (FCMD), the second most common form of childhood muscular dystrophy in Japan, is an autosomal recessive severe muscular dystrophy associated with an anomaly of the brain. We had mapped the FCMD gene to an approximately 5-cM interval between D9S127 and D9S2111 on 9q31-q33 and had also found evidence for linkage disequilibrium between FCMD and D9S306 in this candidate region. Through further analysis, we have defined another marker, D9S172, which showed stronger linkage disequilibrium than D9S306. A yeast artificial chromosome (YAC) contig spanning 3,5 Mb, which includes this D9S306-D9S172 interval on 9q31, has been constructed by a combination of sequence-tagged site, Alu-PCR, and restriction mapping. Also, cosmid clones subcloned from the YAC were assembled into three contigs, one of which contains D9S2107, which showed the strongest linkage disequilibrium with FCMD. These contigs also allowed us to order the markers as follows: cen-D9S127-(approximately 800 kb)-D9S306 (identical to D9S53)-(approximately 700 kb)-A107XF9-(approximately 500 kb)-D9S172-(approximately 30 kb)-D9S299 (identical to D9S774)-(approximately 120 kb)-WI2269-tel. Thus, we have constructed the first high-resolution physical map of the FCMD candidate region. The YAC and cosmid contigs established here will be a crucial resource for identification of the FCMD gene and other genes in this region.

A novel (CA)n polymorphism on 6p21.1-21.2.

A novel highly polymorphic CA repeat locus D6S2213 was identified on human chromosome 6p21.1-21.2. It should be a useful marker for linkage studies on chromosome 6 and also in forensic use.

Linkage-disequilibrium mapping narrows the Fukuyama-type congenital muscular dystrophy (FCMD) candidate region to <100 kb.

Fukuyama-type congenital muscular dystrophy (FCMD), the second most common form of muscular dystrophy in Japan, is an autosomal recessive severe muscular dystrophy associated with brain anomalies. After our initial mapping of the FCMD locus to chromosome 9q31-33, we have further defined the locus within a approximately 5-cM region between D9S127 and D9S2111 and have found linkage disequilibrium between FCMD and D9S306 in this candidate region on 9q31. The high prevalence of FCMD among the Japanese, who are a relatively isolated population, provides an opportunity to utilize linkage-disequilibrium mapping. We developed three new microsatellites, near D9S306, from the FCMD YAC contig, determined their positions on YACs, and performed linkage-disequilibrium mapping with these markers and other newly published loci. The maximum value of p(excess), which represents the strength of linkage disequilibrium, was obtained at D9S2107; and this value showed a relatively steady rise and fall across the region that is likely to contain FCMD. Distances between FCMD and each marker were presumed to be approximately 1 Mb, approximately 350 kb, approximately 140 kb, approximately 20 kb, approximately 280 kb, approximately 450 kb, and approximately 740 kb for D9S306, A107XF9, D9S2105, D9S2107, D9S172, D9S299, and D9S2109, respectively. Haplotype analysis using the three closest markers D9S2105, D9S2107, and D9S172 indicated that most FCMD-bearing chromosomes are derived from a single ancestral founder and suggested that these markers can be used for the diagnosis of sporadic FCMD. Thus, the FCMD gene is most likely to lie within a region of <100 kb containing D9S2107.

Long Y-associated (GATA)n alleles were observed in a few ethnic groups in Asia.

A Y-associated polymorphic locus, DYS19, was analyzed in a few ethnic groups in Asia and compared with that in Caucasians and Negroes. The locus contains 4-nucleotide repeats, (GATA)n, and the length of the repeated segments can be determined by the polymerase chain reaction (PCR). The predominant allele was 202 bp followed by 198 bp in all the 3 Asian populations examined. Long repeats that were rare in other populations were found more frequently in these Asian populations.

Sex reversal in a child with duplication of sex reversing locus on the short arm of the X chromosome (Xp).

We report a child with a female phenotype possessing a karyotype of 46,XY,13p+. The child had female external genitalia, and manifested severe mental retardation, pulmonary atresia and multiple congenital abnormalities. Laparoscopy revealed the presence of streak gonads and Müllerian structures. Histological examination of the gonads showed ovarian-like stroma with immature seminiferous tubules. Chromosome and gene analyses demonstrated Xp11.23 (or 11.3)-pter duplication and an intact sex determinating factor of Y (SRY). The findings of this case suggest that duplication of Xp causes sex reversal in the presence of SRY.

A unique origin and multistep process for the generation of expanded DRPLA triplet repeats.

Dentatorubral and pallidoluysian atrophy (DRPLA) is an autosomal dominant neurodegenerative disorder associated with the expansion of a CAG repeat at chromosome band 12p13. Epidemiological studies have demonstrated an increased prevalence of DRPLA in Japan, although several DRPLA kindreds of non-Japanese ancestry have been identified. To define the molecular basis for this geographic variation in prevalence, we have analyzed haplotypes around the repeat in several different ethnic groups. Two intragenic biallelic polymorphisms distinguished three haplotypes, each of which formed a predominant haplotype found in the three major racial populations. All the expanded repeats of Japanese and Caucasian patients studied were associated with a particular haplotype, which otherwise was associated with longer repeats commonly found in Asians. Our results support a multi-step model for repeat expansion, and suggest that expanded DRPLA repeats may have evolved from an ancient chromosomal haplotype of Asian origin. We also propose that a combination of a highly polymorphic microsatellite marker with relatively stable biallelic markers in a range of PCR amplification is a powerful tool for studies on human genome diversity, which may reveal the ancient human migration and the formation of ethnic groups.

Pericentric inversion with a minute deletion of the Y chromosome in a severely oligozoospermic man.

An apparent pericentric inversion of the Y chromosome in a severely oligozoospermic infertile patient is described. The karyotype was 46,X,inv (Y) (p11.2 q11.23). DNA analysis, however, revealed a deletion involving nine loci within the most distal part of the euchromatic region of the long arm.

Chromosomal localisation of a Y specific growth gene(s).

Although a Y specific growth gene(s) has been postulated in the Yq11 region, the precise location has not been determined. To localise the growth gene(s), we correlated genotype with stature in 13 Japanese and four European non-mosaic adult male patients with a partial Yq deletion. Fourteen patients preserving the region between DYS11 and DYS246 did not have short stature (11 Japanese, 165-180 cm; three Europeans, 165-173 cm) whereas the remaining three patients with the region deleted had short stature (two Japanese, both 159 cm; one European, 157 cm). The results suggest that the region defined by DYS11 at interval 5C and by DYS246 at interval 5D may be the critical region for the Y specific growth gene(s).

Evaluation of long-term results of Caroli's disease: 21 years' observation of a family with autosomal "dominant" inheritance, and review of the literature.

A 5-year-old girl underwent laparotomy in 1972 because of hepatomegaly and mottled radiopacities shown by cholangiography. Polycystic segmental dilatation of the intrahepatic bile ducts, typical of Caroli's disease, was found. Thereafter she remained in good health for over 21 years with careful medical management. In 1972 mottled radiopacities of the hepatic parenchyma were also demonstrated by cholangiography in her 9-year-old brother, who, however, remained asymptomatic until hematemesis due to esophageal varices suddenly occurred in 1993. At the time of the pre-operative evaluation for esophageal transection, his condition was definitively diagnosed as Caroli's disease. Their father was in good health, but in 1993 was shown by CT to have the same disease. The mode of inheritance is likely to be autosomal dominant, although Caroli's disease or congenital hepatic fibrosis is generally considered autosomal recessive (McKusick number 263200) (1). If we had not examined the father, this particular family would have been accepted as an example of autosomal recessive inheritance. We suggest that further family studies are needed to exclude the autosomal dominant mode of inheritance, and that at least some of the recessive cases in the literature are, in fact, autosomal dominant. Well-documented cases of "classical" Caroli's disease in the literature were reviewed with special reference to the long-term results. In addition, an international questionnaire aimed at establishing the further clinical course of the patient was sent to authors who reported cases after 1968.(ABSTRACT TRUNCATED AT 250 WORDS)

Genetic identity of Fukuyama-type congenital muscular dystrophy and Walker-Warburg syndrome.

Both Fukuyama-type congenital muscular dystrophy (FCMD) and Walker-Warburg syndrome (WWS) are unusual genetic syndromes consisting of congenital muscular dystrophy and complex malformations of the brain and eye. It has been intensively discussed whether FCMD and WWS belong to the same disease entity or not. We analyzed a family in which 3 siblings were affected with either FCMD or WWS by using polymorphic microsatellites flanking the FCMD locus on chromosome 9q31-33. The results suggested that both FCMD and WWS siblings shared the identical combination of mutations on either allele of the FCMD locus. FCMD and WWS could be "genetically" identical.

Monozygotic twins of different apparent sex.

We report on twins of unlike sex who shared a 45,X/46,X,+mar karyotype. The mar chromosome was found to be Yq- by DNA analysis. Marker studies, including 8 VNTR loci, yielded a probability of monozygosity of 0.99999996.

The CpG island of the FMR-1 gene is methylated differently among embryonic tissues: implication for prenatal diagnosis.

We studied the methylation status of the CpG island of the FMR-1 (fragile X syndrome) gene to recognize the possibility of its prenatal diagnosis with early pregnant subjects. Southern hybridization using EcoRI/BssHII restriction enzymes double digestion was performed in the brain and chorionic villi of 8th week embryos, and the placenta and cord blood of newborns. No methylation of the FMR-1 gene occurred in both of the tissues examined in males, while 50% of the cells in females were methylated in both the brain and the cord blood, indicating that methylation occurs with inactivation of the X-chromosome in accordance with the literature. However, there was no methylation in either the chorionic villi or placenta in female as well as in males. Some extra-embryonic tissues such as the chorionic villi and the placenta escape X-chromosome FMR-1 gene inactivation and it can be the exception in the lyonization. To assess the methylation status in prenatal diagnosis, precautions are needed and they are not suitable for prenatal diagnosis.