Fundamental to most genetic analysis is availability of genomic DNA of adequate quality and quantity. Because DNA yield from human samples is frequently limiting, much effort has been invested in developing methods for whole genome amplification (WGA) by random or degenerate oligonucleotide-primed PCR. However, existing WGA methods like degenerate oligonucleotideprimed PCR suffer from incomplete coverage and inadequate average DNA size. We describe a method, termed multiple displacement amplification (MDA), which provides a highly uniform representation across the genome. Amplification bias among eight chromosomal loci was less than 3-fold in contrast to 4 -6 orders of magnitude for PCR-based WGA methods. Average product length was >10 kb. MDA is an isothermal, strand-displacing amplification yielding about 20 -30 g product from as few as 1-10 copies of human genomic DNA. Amplification can be carried out directly from biological samples including crude whole blood and tissue culture cells. MDA-amplified human DNA is useful for several common methods of genetic analysis, including genotyping of single nucleotide polymorphisms, chromosome painting, Southern blotting and restriction fragment length polymorphism analysis, subcloning, and DNA sequencing. MDA-based WGA is a simple and reliable method that could have significant implications for genetic studies, forensics, diagnostics, and long-term sample storage.F or genomic studies, the quality and quantity of DNA samples is critical. High-throughput genetic analysis requires large amounts of template for testing, yet typically the yield of DNA from individual patient samples is limited. Forensic and paleoarcheology work also can be severely limited by DNA sample size. An important goal is to supply a sufficient amount of genomic sequence for a variety of procedures as well as longterm storage for future work and archiving of patient samples. Methods include the time-consuming process of creating of Epstein-Barr virus-transformed cell lines and whole genome amplification (WGA) by random or degenerate oligonucleotideprimed PCR (DOP-PCR) (1-3). However, PCR-based WGA methods may generate nonspecific amplification artifacts (2), give incomplete coverage of loci (4), and generate DNA less than 1 kb long (1-3) that cannot be used in many applications.Recently, a rolling circle amplification (5) method was developed for amplifying large circular DNA templates such as plasmid and bacteriophage DNA (6). Using 29 DNA polymerase and random exonuclease-resistant primers, DNA was amplified in a 30°C reaction not requiring thermal cycling. This is made possible in part by the great processivity of 29 DNA polymerase, which synthesizes DNA strands 70 kb in length (7). Here we extend the use of exonuclease-resistant primers and 29 DNA polymerase to WGA. The amplification is surprisingly uniform across the genomic target, with the relative representation of different loci differing by less than 3-fold. In contrast, PCR-based WGA methods exhibited strong amplification bias ranging fr...

Preparation of genomic DNA from clinical samples is a bottleneck in genotyping and DNA sequencing analysis and is frequently limited by the amount of specimen available. We use Multiple Displacement Amplification (MDA) to amplify the whole genome 10,000-fold directly from small amounts of whole blood, dried blood, buccal cells, cultured cells, and buffy coats specimens, generating large amounts of DNA for genetic testing. Genomic DNA was evenly amplified with complete coverage and consistent representation of all genes. All 47 loci analyzed from 44 individuals were represented in the amplified DNA at between 0.5-and 3.0-fold of the copy number in the starting genomic DNA template. A high-fidelity DNA polymerase ensures accurate representation of the DNA sequence. The amplified DNA was indistinguishable from the original genomic DNA template in 5 SNP and 10 microsatellite DNA assays on three different clinical sample types for 20 individuals. Amplification of genomic DNA directly from cells is highly reproducible, eliminates the need for DNA template purification, and allows genetic testing from small clinical samples. The low amplification bias of MDA represents a dramatic technical improvement in the ability to amplify a whole genome compared with older, PCR-based methods.

Despite the extensive molecular information on serum-derived human hepatitis B viruses (HBV), liver-derived replicative HBV genomes have remained largely uninvestigated. We have examined the sequences of the entire core antigen (nucleocapsid) of liver-derived HBVs in 15 different hepatoma patients. Bona fide mutations, rather than subtype polymorphism, have been identified based on the high-frequency occurrence of structural differences from wild type at the highly evolutionarily conserved positions, instead of at the positions known to contain genetic heterogeneity among different isolates from different geographic locations. The distribution of these naturally occurring mutations of HBV core gene appears to be nonrandom and is found predominantly within three major (I, IV, and V) and four minor domains (II, III, VI, and VII). In general, domain IV mutations correlate with domain V mutations. The replicative HBV DNAs tend to accumulate a higher number of mutated core domains than the integrated HBV DNAs. At the domain level, there is no significant difference in HBV core mutation frequencies between the liver tumors and the adjacent nontumorous livers. Strikingly, domains I, III, and V coincide with three major known T cell epitopes within the core protein in acute and chronic hepatitis B patients. Furthermore, these domains coincide with HLA class II-restricted T cell epitopes, rather than with the conventional HLA class I-restricted epitopes of cytotoxic T lymphocytes. Our results support the hypothesis that HBV core antigen variants can accomplish immunoevasion via accumulated escape mutations. In addition, they also provide a potential molecular explanation for the maintenance of persistent infection of human hepatitis B virus in chronic carriers.

The WT1 tumor suppressor gene encodes a transcription factor that can activate and repress gene expression. Transcriptional targets relevant for the growth suppression functions of WT1 are poorly understood. We found that mesenchymal NIH 3T3 fibroblasts stably expressing WT1 exhibit growth suppression and features of epithelial differentiation including up-regulation of E-cadherin mRNA. Acute expression of WT1 in NIH 3T3 fibroblasts after retroviral infection induced murine Ecadherin expression. In transient transfection experiments, the human and murine E-cadherin promoters were activated by co-expression of WT1. E-cadherin promoter activity was increased in cells overexpressing WT1 and was blocked by a dominant negative form of WT1. WT1 activated the murine E-cadherin promoter through a conserved GC-rich sequence similar to an EGR-1 binding site as well as through a CAAT box sequence. WT1 produced in vitro or derived from nuclear extracts bound to the WT1-response element within the murine E-cadherin promoter, but not the CAAT box. E-cadherin, a gene important in epithelial differentiation and neoplastic transformation, represents a downstream target gene that links the roles of the WT1 in differentiation and growth control.The WT1 tumor suppressor gene is associated with Wilms' tumor, which can be considered a disease of disordered development, since the tumors exhibit the three elements of primordial kidney development including blastemal, stromal, and epithelial elements (1). The WT1 gene is predominantly expressed in the developing kidney, but WT1 expression is also detected in the fetal gonad, spleen, mesothelium, breast, and other tissues (reviewed in Ref. 2). During early nephrogenesis, WT1 expression is first detected in the metanephric mesenchyme. At the onset of epithelial differentiation, WT1 expression increases as the mesenchyme surrounding the ureteric bud condenses to form primary vesicles. These cells further differentiate into comma-and S-shaped bodies, and subsequently mature into glomeruli and proximal tubules. This phenomenon and the finding that mice null for WT1 fail to develop kidneys (3) suggest an essential role for WT1 in controlling the mesenchymal-epithelial transition of renal development. WT1 differs from other tumor suppressor genes such as Rb and p53 in that Rb and p53 are widely expressed in a variety of developing and adult tissues, while WT1 expression is restricted. The restricted pattern of WT1 expression suggests that its growthsuppressive properties may be linked to its role in organogenesis.WT1 gene encodes a Cys-His zinc finger transcription factor, which functions as both a transcriptional repressor and activator (2, 4 -6). The DNA binding activity of WT1 was demonstrated on several different sequences including 5Ј-GCGGGG-GCG-3Ј, which is also recognized by EGR-1, EGR-2, and EGR-3 (4, 7-10). Alternative splicing of the WT1 gene yields four major isoforms of the WT1 protein. Isoforms C and D include a 3-amino acid (KTS) segment between zinc fingers three and four of the...