Sharper tools and simpler methods

In this issue of The Chipping Forecast, we are witnesses to the adolescence of a class of technologies that are enabling us to monitor globally aspects of gene expression. Chip-based technologies are specific examples of a more general trend toward the implementation of systematic and comprehensive methods in biological research. We need to recognize, however, that these technologies, while seductive, can sometimes be corruptive. In other words, we must guard against committing the mortal sin of genomics by confusing throughput with output, which too often blurs the distinction between data and knowledge. Instead, we must maintain the necessary focus to achieve an ever-more operational understanding of all the molecular components and the interactions that define a cell or an organism.

SNP genotyping on pooled DNAs: comparison of genotyping technologies and a semi automated method for data storage and analysis

We have compared the accuracy, efficiency and robustness of three methods of genotyping single nucleotide polymorphisms on pooled DNAs. We conclude that (i) the frequencies of the two alleles in pools should be corrected with a factor for unequal allelic amplification, which should be estimated from the mean ratio of a set of heterozygotes (k); (ii) the repeatability of an assay is more important than pinpoint accuracy when estimating allele frequencies, and assays should therefore be optimised to increase the repeatability; and (iii) the size of a pool has a relatively small effect on the accuracy of allele frequency estimation. We therefore recommend that large pools are genotyped and replicated a minimum of four times. In addition, we describe statistical approaches to allow rigorous comparison of DNA pool results. Finally, we describe an extension to our ACeDB database that facilitates management and analysis of the data generated by association studies.

Service provision of complex mutation analysis: a technical and economic appraisal using dystrophin point mutation analysis as an example

Duchenne muscular dystrophy (DMD) results from mutations in the dystrophin gene. One-third of cases arise from point mutations, which are heterogeneous and difficult to detect. The aims of this study of dystrophin point mutation analysis were to assess its technical feasibility in a routine diagnostic laboratory, and to estimate its costs and clinical benefits. The methods used were a laboratory based study using reverse transcription-polymerase chain reaction (RT-PCR) and a protein truncation test, and a mathematical model to estimate costs and clinical benefits. None of the cases analyzed had an identifiable dystrophin deletion or duplication. They were 12 males affected with DMD and two obligate female carriers; two female carriers of known dystrophin point mutations were also analyzed. Point mutations were detected in six out of 12 males, but in none of the female carriers. Assuming a sensitivity of 50% the model predicts significant clinical benefits of point mutation analysis over linkage analysis, including a reduction in the number of prenatal diagnoses (by 0.77 per family), terminations of pregnancy (by 0.18 per family), and terminations of unaffected fetuses (by 0.16 per family). The mean cost of point mutation analysis to prevent the termination of an unaffected fetus is 6220 US dollars.

An efficient strategy for large-scale high-throughput transposon-mediated sequencing of cDNA clones

We describe an efficient high-throughput method for accurate DNA sequencing of entire cDNA clones. Developed as part of our involvement in the Mammalian Gene Collection full-length cDNA sequencing initiative, the method has been used and refined in our laboratory since September 2000. Amenable to large scale projects, we have used the method to generate >7 Mb of accurate sequence from 3695 candidate full-length cDNAs. Sequencing is accomplished through the insertion of Mu transposon into cDNAs, followed by sequencing reactions primed with Mu-specific sequencing primers. Transposon insertion reactions are not performed with individual cDNAs but rather on pools of up to 96 clones. This pooling strategy reduces the number of transposon insertion sequencing libraries that would otherwise be required, reducing the costs and enhancing the efficiency of the transposon library construction procedure. Sequences generated using transposon-specific sequencing primers are assembled to yield the full-length cDNA sequence, with sequence editing and other sequence finishing activities performed as required to resolve sequence ambiguities. Although analysis of the many thousands (22 785) of sequenced Mu transposon insertion events revealed a weak sequence preference for Mu insertion, we observed insertion of the Mu transposon into 1015 of the possible 1024 5mer candidate insertion sites.

Multiplex minisequencing of the 21-hydroxylase gene as a rapid strategy to confirm congenital adrenal hyperplasia

BACKGROUND

Congenital adrenal hyperplasia (CAH) is a frequent autosomal recessive disease, with a wide range of clinical manifestations, most commonly attributable to mutations in the 21-hydroxylase gene (CYP21). Large gene deletions, large gene conversions, a small 8-basepair deletion, and eight point mutations in CYP21 account for approximately 95% of all enzyme deficiencies. We developed a new strategy for a rapid CYP21 analysis.

METHODS

DNA samples from 40 CAH patients previously genotyped by direct DNA sequencing were reanalyzed by allele-specific amplification of the functional CYP21 gene followed by a multiplex minisequencing reaction using 13 primers. In addition, a second PCR that amplified a part of exon 3 was used to demonstrate the presence or absence of at least one functional gene.

RESULTS

The assay detected the P453S mutation and nine of the most common mutations (P30L, intron 2 splice, Delta 8bp, I172N, exon 6 cluster, V281L, F306+t, Q318X, and R356W) caused by microconversions from the CYP21P pseudogene. The concordance was 100% for detecting these mutations, including gene deletions and large gene conversions. The 40 patient DNA samples were analyzed in 1.5 working days by one technician (actual hands-on time, 3.5 h). The material cost for analyzing one sample was approximately 10.00 Euros (US $9.00).

CONCLUSIONS

This novel mutation screening strategy rapidly detects 90-95% of all mutations associated with CAH and appears applicable as a tool for confirmation of increased 17-hydroxyprogesterone found in neonatal CAH screening.

Large-scale genotyping by mass spectrometry: experience, advances and obstacles

Single nucleotide polymorphism (SNP) genotyping has become a key technology for genetic studies. In recent years, matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry has emerged as a very powerful method for SNP genotyping. Here, we discuss our experience in implementing a high-throughput SNP genotyping facility based on MALDI, and the issues encountered in adapting this to large-scale genetic studies. Most of these issues are not specific to using MALDI approaches, and they will also serve as valuable pointers for establishing high-throughput genotyping with other methods.

A new approach to genome mapping and sequencing: slalom libraries

We describe here an efficient strategy for simultaneous genome mapping and sequencing. The approach is based on physically oriented, overlapping restriction fragment libraries called slalom libraries. Slalom libraries combine features of general genomic, jumping and linking libraries. Slalom libraries can be adapted to different applications and two main types of slalom libraries are described in detail. This approach was used to map and sequence (with approximately 46% coverage) two human P1-derived artificial chromosome (PAC) clones, each of approximately 100 kb. This model experiment demonstrates the feasibility of the approach and shows that the efficiency (cost-effectiveness and speed) of existing mapping/sequencing methods could be improved at least 5-10-fold. Furthermore, since the efficiency of contig assembly in the slalom approach is virtually independent of length of sequence reads, even short sequences produced by rapid, high throughput sequencing techniques would suffice to complete a physical map and a sequence scan of a small genome.

MEMS-based sample preparation for molecular diagnostics

Completion of the Human Genome Project is driving the rapid development of molecular diagnostics in the laboratory. To accelerate the penetration of genetic tests and other nucleic acid-based tests into clinical markets, simple, compact, automatic sample-preparation systems for molecular diagnostics must be developed. Microelectromechanical systems (MEMS) is a promising approach for the development of automated sample preparation for the clinical laboratory or point-of-care setting. This review discusses MEMS-based components that could be applied to the different stages of the sample-preparation process such as cell separation, nucleic acid purification, and nucleic acid amplification. Examples of functional component integration are given. Issues discussed include partitioning of functions between the instrument and disposable unit, methods of propulsion of fluids and particles, vapor and liquid barriers, and sample size. Although further evaluation and development are needed to provide practical solutions to some of these issues, we conclude that MEMS-based components might contribute to some components in a sample-preparation system consisting of modular instruments and disposable units, but will not provide a generic or a totally integrated solution.

Octamer-primed sequencing technology: effects of dNTP supplementation

Octamer-primed sequencing is a directed DNA sequencing strategy that employs the use of a presynthesized octamer primer library. Together with electronic octamer sequencing technology (eOST) it provides a faster, less expensive way to obtain DNA sequence information and can be used as a valuable tool for gap closure in large-scale genomic sequencing. In this paper we discuss the effect of dGTP/TTP supplementation on octamer sequencing. We show that addition of 75 microM dGTP and 5 microM TTP can improve the sequencing success rate by increasing the length and accuracy of generated sequence information. We also discuss the effect of template base composition immediately downstream of the octamer primer on the outcome of octamer sequencing.

A method for parallel, automated, thermal cycling of submicroliter samples

A large fraction of the cost of DNA sequencing and other DNA-analysis processes results from the reagent costs incurred during cycle sequencing or PCR. In particular, the high cost of the enzymes and dyes used in these processes often results in thermal cycling costs exceeding $0.50 per sample. In the case of high-throughput DNA sequencing, this is a significant and unnecessary expense. Improved detection efficiency of new sequencing instrumentation allows the reaction volumes for cycle sequencing to be scaled down to one-tenth of presently used volumes, resulting in at least a 10-fold decrease in the cost of this process. However, commercially available thermal cyclers and automated reaction setup devices have inherent design limitations which make handling volumes of <1 microL extremely difficult. In this paper, we describe a method for thermal cycling aimed at reliable, automated cycling of submicroliter reaction volumes.

Characterization of equine microsatellites and microsatellite-linked repetitive elements (eMLREs) by efficient cloning and genotyping methods

We performed efficient cloning and genotyping methods for isolation of a large number of polymorphic microsatellites. The methods contain the time-efficient cloning method of constructing microsatellite-enriched libraries and the economic genotyping method of fluorescent labeling of PCR products. Eighty novel equine microsatellites cloned were efficiently isolated from the enrichment library and analyzed for genotype polymorphism. Of these, 72 microsatellites were analyzed with a good resolution. The average heterozygosity of all loci was 0.52, and the number of alleles ranged from one to 9 with an average of 4.5 alleles. The other eight loci showed multiple bands of PCR products, suggesting the occurrence of microsatellites in a repetitive element, in which the number of microsatellite repeats varies among different members of the repetitive element. We found five homologous groups at flanking regions in comparison with the flanking regions of microsatellites from DNA databases. One of them showed homology to equine repetitive element-2. In the other four homologous groups, the two groups were named equine microsatellite-linked repetitive element-1 (eMLRE-1) and equine microsatellite-linked repetitive element-2 (eMLRE-2) as novel equine repetitive elements identified from equine genome. These data should help the analysis of equine DNA sequences and the design of equine genome markers.

The case for caution--being protective of human dignity in the face of corporate forces taking title to our DNA

Thirteen years ago, commenting on the treatment of the human body and its cell lines as patentable commodities, Mary Taylor Danforth wrote:

In his insightful article, David Resnik would have us travel further down the path of allowing the patenting of DNA in order to advance scientific research and the welfare of humankind. Dr. Resnik suggests that that the acquisition of such proprietary rights in DNA research must proceed cautiously

DNA patents and human dignity

Those objecting to human DNA patenting frequently do so on the grounds that the practice violates or threatens human dignity. For example, from 1993 to 1994, more than thirty organizations representing indigenous peoples approved formal declarations objecting to the National Institutes of Health's (NIH) bid to patent viral DNA taken from subjects in Papua New Guinea and the Solomon Islands. Although these were not patents on human DNA, the organizations argued that the patents could harm and exploit indigenous peoples and violate their cultural values. NIH eventually dropped one of its patent applications.

On May 18, 1995, 180 religious leaders, led by biotechnology critic Jeremy Rifkin, held a press conference objecting to DNA patenting in Washington, D.C. In their “Joint Appeal against Human and Animal Patenting,” these leaders decried any attempt to patent nature. Some of the more outspoken members of the Joint Appeal likened DNA patenting to slavery, while others objected to treating human beings as marketable commodities. In his recent book,The Biotech Century,Rifkin rehashed the objections to DNA patenting voiced by members of the Joint Appeal.

RIKEN integrated sequence analysis (RISA) system--384-format sequencing pipeline with 384 multicapillary sequencer

The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto sequencer (RISA sequencer), a 384-multicapillary array assembler (CAS), and a 384-multicapillary casting device. The RISA sequencer can simultaneously analyze 384 independent sequencing products. The optical system is a scanning system chosen after careful comparison with an image detection system for the simultaneous detection of the 384-capillary array. This scanning system can be used with any fluorescent-labeled sequencing reaction (chain termination reaction), including transcriptional sequencing based on RNA polymerase, which was originally developed by us, and cycle sequencing based on thermostable DNA polymerase. For long-read sequencing, 380 out of 384 sequences (99.2%) were successfully analyzed and the average read length, with more than 99% accuracy, was 654.4 bp. A single RISA sequencer can analyze 216 kb with >99% accuracy in 2.7 h (90 kb/h). For short-read sequencing to cluster the 3' end and 5' end sequencing by reading 350 bp, 384 samples can be analyzed in 1.5 h. We have also developed a RISA inoculator, RISA filtrator and densitometer, RISA plasmid preparator which can handle throughput of 40,000 samples in 17.5 h, and a high-throughput RISA thermal cycler which has four 384-well sites. The combination of these technologies allowed us to construct the RISA system consisting of 16 RISA sequencers, which can process 50,000 DNA samples per day. One haploid genome shotgun sequence of a higher organism, such as human, mouse, rat, domestic animals, and plants, can be revealed by seven RISA systems within one month.

Rapid determination of short DNA sequences by the use of MALDI-MS

We have developed a protocol for rapid sequencing of short DNA stretches (15-20 nt) using MALDI-TOF-MS. The protocol is based on the Sanger concept with the modification that double-stranded template DNA is used and all four sequencing reactions are performed in one reaction vial. The sequencing products are separated and detected by MALDI-TOF-MS and the sequence is determined by comparing measured molecular mass differences to expected values. The protocol is optimized for low costs and broad applicability. One reaction typically includes 300 fmol template, 10 pmol primer and 200 pmol each nucleotide monomer. Neither the primer nor any of the nucleotide monomers are labeled. Solid phase purification, concentration and mass spectrometric sample preparation of the sequencing products are accomplished in a few minutes and parallel processing of 96 samples is possible. The mass spectrometric analyses and subsequent sequence read-out require only a few seconds per template.

Higher resolution microplate array diagonal gel electrophoresis: application to a multiallelic minisatellite

The 5' polymorphic region of the insulin (INS, MIM# 176730) gene contains a variable tandem repetition of 14-15 bp (a variable number of tandem repeats (VNTR) locus). After PCR amplification, we achieved precise sizing of class I alleles (range 641 to 843 bp) on 96-well open-face polyacrylamide microplate array diagonal gel electrophoresis (MADGE) gels, obtaining resolution of the 2% mobility difference which represents one tandem repeat. PCR products were run double-stranded, but no additional bands were generated except in the case of differences of three, two, and one repeat between alleles; none compromised allele identification, and in the latter case the heteroduplex was a useful confirmation signal. No end labelling of primers was required, as the sensitive Vistra Green intercalating dye for double strands was used for visualization of bands from diluted samples. Duracryl, a high mechanical-strength polyacrylamide derivative, proved to have good resolution properties for electrophoresis. A co-run ladder ensured precise binning without inter-lane variability. Simultaneous electrophoresis of gels in a thermostatically controlled tank allowed up to 1,000 samples to be run in 90 min. Gels were analyzed using a FluorImager 595 fluorescent scanning system, and alleles identified using a combination of Phoretix software for band migration measurement and Microsoft Excel to compute allele sizes. Unlike other systems for minisatellite allele sizing, throughput was not limited (in time or cost) by electrophoresis.

Automated one-step DNA sequencing based on nanoliter reaction volumes and capillary electrophoresis

An integrated system with a nano-reactor for cycle-sequencing reaction coupled to on-line purification and capillary gel electrophoresis has been demonstrated. Fifty nanoliters of reagent solution, which includes dye-labeled terminators, polymerase, BSA and template, was aspirated and mixed with the template inside the nano-reactor followed by cycle-sequencing reaction. The reaction products were then purified by a size-exclusion chromatographic column operated at 50 degrees C followed by room temperature on-line injection of the DNA fragments into a capillary for gel electrophoresis. Over 450 bases of DNA can be separated and identified. As little as 25 nl reagent solution can be used for the cycle-sequencing reaction with a slightly shorter read length. Significant savings on reagent cost is achieved because the remaining stock solution can be reused without contamination. The steps of cycle sequencing, on-line purification, injection, DNA separation, capillary regeneration, gel-filling and fluidic manipulation were performed with complete automation. This system can be readily multiplexed for high-throughput DNA sequencing or PCR analysis directly from templates or even biological materials.

Parking strategies for genome sequencing

The parking strategy is an iterative approach to DNA sequencing. Each iteration consists of sequencing a novel portion of target DNA that does not overlap any previously sequenced region. Subject to the constraint of no overlap, each new region is chosen randomly. A parking strategy is often ideal in the early stages of a project for rapidly generating unique data. As a project progresses, parking becomes progressively more expensive and eventually prohibitive. We present a mathematical model with a generalization to allow for overlaps. This model predicts multiple parameters, including progress, costs, and the distribution of gap sizes left by a parking strategy. The highly fragmented nature of the gaps left after an initial parking strategy may make it difficult to finish a project efficiently. Therefore, in addition to our parking model, we model gap closing by walking. Our gap-closing model is generalizable to many other strategies. Our discussion includes modified parking strategies and hybrids with other strategies. A hybrid parking strategy has been employed for portions of the Human Genome Project.

Human genome. Rival genome sequencers celebrate a milestone together

At a White House ceremony on 26 June, two scientific groups, one funded by the government and the other privately funded, announced that they have generated a nearly complete readout of the 3.1 or so billion nucleotides in the human genome. The White House ceremony was more than a celebration; it was also designed to heal a split in the research community. The ceremony brought together leaders of the rival groups in a kind of truce, cooling off a competition that had grown intense in recent months.

High-throughput DNA sequencing: a genomic data manufacturing process

The progress trends in automated DNA sequencing operation are reviewed. Technological development in sequencing instruments, enzymatic chemistry and robotic stations has resulted in ever-increasing capacity of sequence data production. This progress leads to a higher demand on laboratory information management and data quality assessment. High-throughput laboratories face the challenge of organizational management, as well as technology management. Engineering principles of process control should be adopted in this biological data manufacturing procedure. While various systems attempt to provide solutions to automate different parts of, or even the entire process, new technical advances will continue to change the paradigm and provide new challenges.