Background: The aim of this study was to characterize human embryonic stem (ES) cells at the molecular level by performing large-scale complementary DNA (cDNA) analysis using DNA micro-arrays. Methods: The transcription profile of human ES cells was determined by comparing it to 2, 10 and 30-day old embryoid bodies (EBs) using Affymetrix Genechip human micro-arrays (U133). Results: According to this analysis we demonstrate that two human ES cell lines are more close to each other than to their differentiated derivatives. We also show the spectrum of cytokine receptors that they express, and demonstrate the presence of five genes that are highly specific to human ES cells and to germ cells. Moreover, by profiling different stages in the differentiation of human embryoid bodies, we illustrate the clustering of five sets of temporally expressed genes, which could be related to the sequential stages of embryonic development. Among them are known genes that are involved in early pattern formation. Conclusions: The present study provides a molecular basis for the identity of human ES cells and demonstrates that during their in vitro differentiation they express embryonic specific genes in a stage specific manner.

We describe genetic analysis of a large pedigree with an X-linked syndrome of polyendocrinopathy, immune dysfunction, and diarrhea (XPID), which frequently results in death during infancy or childhood. Linkage analysis mapped the XPID gene to a 17-cM interval defined by markers DXS8083 and DXS8107 on the X chromosome, at Xp11. 23-Xq13.3. The maximum LOD score was 3.99 (recombination fraction0) at DXS1235. Because this interval also harbors the gene for Wiskott-Aldrich syndrome (WAS), we investigated mutations in the WASP gene, as the molecular basis of XPID. Northern blot analysis detected the same relative amount and the same-sized WASP message in patients with XPID and in a control. Analysis of the WASP coding sequence, an alternate promoter, and an untranslated upstream first exon was carried out, and no mutations were found in patients with XPID. A C-->T transition within the alternate translation start site cosegregated with the XPID phenotype in this family; however, the same transition site was detected in a normal control male. We conclude that XPID maps to Xp11.23-Xq13.3 and that mutations of WASP are not associated with XPID.

Most mutation detection methods are based on analysis of PCR amplified segments and the application of multiplex PCR is one central approach to improving screening efficiency. Genes like the breast-ovarian cancer susceptibility gene BRCA1 pose a difficult challenge to efficient mutation screening because of large coding regions, numerous exons, and complex mutational spectra. The application to BRCA1 of a general approach to effective multiplex PCR is described here. Fifteen triplex PCRs and a single PCR reaction condition were used for amplification of all BRCA1 coding regions and the BRCA1-specific segments from the duplicated promoter region. SSCP/HDX gel analysis of the multiplex products detected mobility distinctions for 34/34 sets of allelic BRCA1 fragments. A novel polymorphism was found, CTTCT(4)CT(10)CT(12) >CT(4)CT(11), a compound deletion in a region beginning at the +33 position of IVS7 and resulting in a net deletion of 15 bp. This change was shown to be one of the common polymorphisms that define the two major haplotypes of the BRCA1-RNU2 region in a large proportion of the world population. A triplex PCR for SSCP detection of this deletion and two other distantly located common polymorphisms may be used to screen haplotype content and facilitate comparison of samples with similar haplotypes in subsequent mutation screening. The approach for robust multiplex amplification is generally applicable and allows rapid development of efficient testing for a wide variety of mutations in any gene(s) encompassing a large coding region or numerous exons and including as many as 50 different genomic PCR products.

We report the isolation and characterization of a serine/threonine kinase expressed during rat pancreas development. This kinase was cloned as part of a general screen using degenerate oligonucleotides to map expression of kinases and receptors during the course of pancreatic development. Sequence analysis showed it to be a member of the ste20-like serine/threonine kinase family. Northern blotting analysis against both fetal and adult tissues showed two transcripts, one of 2 kb and the other of 4 kb. The ratio of transcript expression varied with the tissue. In situ hybridization analysis showed that this gene is expressed in the early gut and pancreatic epithelium. By embryonic Day 15, the transcript is localized to cells that will eventually become exocrine in nature. In situ hybridization analysis also demonstrated high levels of expression in the choroid plexus, the developing myocardium, kidney, CNS, dorsal root ganglia, and testes. In addition, a search of the EST database revealed a related human kinase not previously described.

Population-based breast and ovarian cancer family registries can facilitate studies to evaluate genetic and environmental factors in the etiology of these malignancies. The purpose of this study is to describe what is, as far as we know, the first population-based breast and ovarian cancer family registry and to estimate breast and ovarian cancer risk in relatives of breast and ovarian cancer probands. Population-based consecutive incident cases of breast and ovarian cancer were invited to participate in the University of California, Irvine breast and ovarian family registry. In this study, we report data on 1567 breast cancer and 328 ovarian cancer probands. The operational components of this family registry include enrollment of probands, family history interviewing, confidentiality, pathology, verification and review, biospecimen bank, statistical/genetic analysis, and special studies on positional cloning of known genes. All of the components are tracked through the University of California, Irvine Genetic Research Information System. In non-Hispanic-white breast cancer probands, relative risk (RR) of breast cancer in mothers and sisters is significantly elevated [RR = 1.7 and 95% confidence interval (CI) = 1.4-2.0 and RR = 2.8 and 95% CI = 2.3-3.3, respectively]. In families of ovarian cancer probands, mothers are at increased risk of ovarian cancer (RR = 4.6; 95% CI, 2.1-8.7). RR of breast cancer in mothers of Hispanic breast cancer probands is significantly elevated (RR = 4.9; 95% CI, 2.6-8.5). No elevation of breast or ovarian cancer risk was observed among relatives of Asian probands. In general, there is a decrease in RR among mothers and sisters with increase in age of onset of probands. In second-degree relatives and first cousins, the breast cancer hazards ratios increase with increase in the number of affected first-degree relatives and decrease with increase in age at onset of the proband.

The objective of this study was to provide more accurate frequency estimates of breast cancer susceptibility gene 1 (BRCA1) germline alterations in the ovarian cancer population. To achieve this, we determined the prevalence of BRCA1 alterations in a population-based series of consecutive ovarian cancer cases. This is the first population-based ovarian cancer study reporting BRCA1 alterations derived from a comprehensive screen of the entire coding region. One hundred and seven ovarian cancer cases were analyzed for BRCA1 alterations using the RNase mismatch cleavage assay followed by direct sequencing. Two truncating mutations, 962del4 and 3600del11, were identified. Both patients had a family history of breast or ovarian cancer. Several novel as well as previously reported uncharacterized variants were also identified, some of which were associated with a family history of cancer. The frequency distribution of common polymorphisms was determined in the 91 Caucasian cancer cases in this series and 24 sister controls using allele-specific amplification, The rare form of the Q356R polymorphism was significantly (P = 0.03) associated with a family history of ovarian cancer, suggesting that this polymorphism may influence ovarian cancer risk. In summary, our data suggest a role for some uncharacterized variants and rare forms of polymorphisms in determining ovarian cancer risk, and highlight the necessity to screen for missense alterations as well as truncating mutations in this population.

We have analyzed the transmission of maternal alleles at loci spanning the length of the X chromosome in 47 normal, genetic disease-free families. We found a significant deviation from the expected Mendelian 1:1 ratio of grandpaternal:grandmaternal alleles at loci in Xp11.4-p21.1. The distortion in inheritance ratio was found only among male offspring and was manifested as a strong bias in favor of the inheritance of the alleles of the maternal grandfather. We found no evidence for significant heterogeneity among the families, which implies that the major determinant involved in the generation of the non-Mendelian ratio is epigenetic. Our analysis of recombinant chromosomes inherited by male offspring indicates that an 11.6-cM interval on the short arm of the X chromosome, bounded by DXS538 and DXS7, contains an imprinted gene that affects the survival of male embryos.

Approximately 85% of patients with Alport syndrome (hereditary nephritis) have been estimated to have mutations in the X chromosomal COL4A5 collagen gene; the remaining cases are autosomal with mutations in the COL4A3 or COL4A4 genes located on chromosome 2. In the present work, the promoter sequence and previously unknown intron sequences flanking exons 2 and 37 of COL4A5 were determined. Furthermore, intron sequences flanking the other 49 exons were expanded from 35 to 190 to facilitate mutation analysis of the gene. Using this information, all 51 exons and the promoter region were PCR-amplified and sequenced from DNA of 50 randomly chosen patients with suspected Alport syndrome. Mutations were found in 41 patients, giving a mutation detection rate of 82%. Retrospective analysis of clinical data revealed that two of the cases might be autosomal. Although it could not be determined whether the remaining seven cases (14%) were autosomal or X chromosome-linked, it is likely that some of them were autosomal. It is concluded that PCR amplification and direct DNA sequencing of the promoter and exons is currently the best procedure to detect mutations in COL4A5 in Alport syndrome.

Mutations in the COL4A5 gene, located at Xq22, cause Alport syndrome (AS), a nephritis characterized by progressive deterioration of the glomerular basement membrane and usually associated with progressive hearing loss. We have identified a novel mutation, L1649R, present in 9 of 121 independently ascertained families. Affected males shared the same haplotype of eight polymorphic markers tightly linked to COL4A5, indicating common ancestry. Genealogical studies place the birth of this ancestor >200 years ago. The L1649R mutation is a relatively common cause of Alport syndrome in the western United States, in part because of the rapid growth and migratory expansion of mid-nineteenth-century pioneer populations carrying the gene. L1649R affects a highly conserved residue in the NC1 domain, which is involved in key inter- and intramolecular interactions, but results in a relatively mild disease phenotype. Renal failure in an L1649R male typically occurs in the 4th or 5th decade and precedes the onset of significant hearing loss by approximately 10 years.

Conditions for polymerase chain-reaction amplification of ten exon regions (Exons 3, 7, 11 through 13, and 15 through 19) of the collagen COL4A5 gene and four exon regions (Exons 2, and 12 through 14) of the COL4A6 gene were sequenced and established in this study. These Type IV collagen genes contain 51 and 48 exons, respectively. The sequences of these exons were determined in the two genes in 250 male patients with hematuria and suspected Alport syndrome. Seventeen mutations were found in nine of the ten exons studied in the COL4A5 gene in 17 patients, whereas no mutations were identified in COL4A6. One mutation was identical in two patients known to be unrelated. The results indicate that mutations in COL4A5 that leading to renal failure are more frequent than those involved in classic Alport syndrome, and also that mutations in COL4A6 are not likely to cause this disease. Furthermore, mutations in COL4A5 are distributed quite randomly and no "hot spots" were found.

X-linked hereditary spastic paraplegias (HSP) present with two distinct phenotypes, pure and complicated. The pure form is characterized by spasticity and gait difficulties but lacks the additional features (nystagmus, dysarthria, mental retardation) present in the complicated form. The complicated form is heterogeneous, caused by mutations of the L1CAM gene at Xq28 (SPG1) or the PLP gene at Xq22 (SPG2) that is allelic to Pelizaeus-Merzbacher disease (PMD). Since in one kindred (K313) the pure form of HSP was also mapped to Xq22, this raises the issue as to whether a pure form of HSP exists that is allelic to X-linked complicated HSP (SPG2) and PMD. To answer this question, we carried out linkage analysis in a new pedigree with pure HSP (K101) and refined linkage in pedigree K313. The PLP gene was also screened for mutation by direct sequencing and reverse-transcriptase polymerase chain reaction (RT-PCR). In both families, the disease locus mapped to Xq22 with Lod scores at zero recombination of 5.3 for COL4A5 2B6 in K313 and 2.4 for DXS101 in K101. A T to C transition in exon 5 of the PLP gene was identified from affected individuals of K313. This transition causes a Ser to Pro mutation in the major extracellular loop of PLP/DM20. This finding demonstrates that a form of X-linked pure spastic paraplegia, X-Linked complicated HSP (SPG2) and PMD are allelic disorders. There was no evidence of mutations in either coding sequences or the intron/exon junctions of PLP in pedigree K101, suggesting that the disease-producing mutation may be in the noncoding portions of PLP or in a nearby gene.