Comparison of yield and genotyping performance of multiple displacement amplification and OmniPlex™ whole genome amplified DNA generated from multiple DNA sources

New Perspectives for Whole Genome Amplification in Forensic STR Analysis

Modern PCR-based analytical techniques have reached sensitivity levels that allow for obtaining complete forensic DNA profiles from even tiny traces containing genomic DNA amounts as small as 125 pg. Yet these techniques have reached their limits when it comes to the analysis of traces such as fingerprints or single cells. One suggestion to overcome these limits has been the usage of whole genome amplification (WGA) methods. These methods aim at increasing the copy number of genomic DNA and by this means generate more template DNA for subsequent analyses. Their application in forensic contexts has so far remained mostly an academic exercise, and results have not shown significant improvements and even have raised additional analytical problems. Until very recently, based on these disappointments, the forensic application of WGA seems to have largely been abandoned. In the meantime, however, novel improved methods are pointing towards a perspective for WGA in specific forensic applications. This review article tries to summarize current knowledge about WGA in forensics and suggests the forensic analysis of single-donor bioparticles and of single cells as promising applications.

Effectiveness of whole genome amplification prior to short tandem repeat analysis for degraded DNA

Short tandem repeat (STR) analysis is prone to failure as DNA is frequently damaged by various environmental factors; hence, increasing the number of starting templates may constitute a feasible approach to improve STR profiling success. Whole genome amplification (WGA) is often applied to bolster starting template quantity. Moreover, WGA can reportedly be used on degraded DNA samples in forensics. Therefore, we utilized a PCR-based WGA method, termed "modified improved primer extension preamplification" (mIPEP), prior to STR analysis of degraded DNA, as this method is less affected by DNA quantity and quality than most others. Saliva from four volunteers was dried on glass fiber filter papers (paper) and glass slides (glass) and irradiated with UVA light (365 nm). The mIPEP method was initiated using 5, 0.5, and 0.05 ng of DNA following DNA extraction. The DNA degradation index (DI) was calculated based on the ratio of 129 to 41 bp DNA fragments; lower numbers indicate higher degradation. Following mIPEP, STR analysis was performed using the AmpFlSTR Identifiler PCR amplification kit. The number of detectable STR loci, with and without mIPEP, decreased according to reduced DI in a different manner for the various DNA concentrations extracted from paper and glass. Specifically, for the 5 ng DNA sample on paper, at a DI < 0.2, the number of detectable STR loci was greater with mIPEP than without it, owing to fewer locus drop-outs. Similarly, the 0.05 ng DNA sample deposited on paper, at DI ≥ 0.7, exhibited higher numbers of detectable STR loci when prepared using mIPEP owing to fewer allele drop-outs. Moreover, among samples deposited on glass, the 0.05 ng DNA sample at DI ≥ 0.4 afforded a larger number of detectable STR loci when prepared using mIPEP than those without mIPEP, owing to fewer locus drop-outs. These findings suggest that performing mIPEP in accordance with sample DNA condition (e.g., quantity and quality) may lead to increased success of STR analysis. Notably, the conditions identified as most responsive to mIPEP were consistent across both UVA-irradiated and environmentally-damaged sample states. Taken together, our results suggest that applying mIPEP would be beneficial to obtain improved STR profiles under conditions involving severely degraded samples with large quantities of DNA, or with small quantities of DNA albeit with slight degradation.

Inflammatory Gene Polymorphisms in Lung Cancer Susceptibility

INTRODUCTION

Chronic inflammation has been implicated in carcinogenesis, with increasing evidence of its role in lung cancer. We aimed to evaluate the role of genetic polymorphisms in inflammation-related genes in the risk for development of lung cancer.

METHODS

A nested case-control study design was used, and 625 cases and 625 well-matched controls were selected from participants in the β-Carotene and Retinol Efficacy Trial, which is a large, prospective lung cancer chemoprevention trial. The association between lung cancer incidence and survival and 23 polymorphisms descriptive of 11 inflammation-related genes (interferon gamma gene [IFNG], interleukin 10 gene [IL10], interleukin 1 alpha gene [IL1A], interleukin 1 beta gene [IL1B], interleukin 2 gene [IL2], interleukin 4 receptor gene [IL4R], interleukin 4 gene [IL4], interleukin 6 gene [IL6], prostaglandin-endoperoxide synthase 2 gene [PTGS2] (also known as COX2), transforming growth factor beta 1 gene [TGFB1], and tumor necrosis factor alpha gene [TNFA]) was evaluated.

RESULTS

Of the 23 polymorphisms, two were associated with risk for lung cancer. Compared with individuals with the wild-type (CC) variant, individuals carrying the minor allele variants of the IL-1β-511C>T promoter polymorphism (rs16944) (CT and TT) had decreased odds of lung cancer (OR = 0.74, [95% confidence interval (CI): 0.58-0.94] and OR = 0.71 [95% CI: 0.50-1.01], respectively, p = 0.03). Similar results were observed for the IL-1β-1464 C>G promoter polymorphism (rs1143623), with presence of the minor variants CG and CC having decreased odds of lung cancer (OR = 0.75 [95% CI: 0.59-0.95] and OR = 0.69 [95% CI: 0.46-1.03], respectively, p = 0.03). Survival was not influenced by genotype.

CONCLUSIONS

This study provides further evidence that IL1B promoter polymorphisms may modulate the risk for development of lung cancer.

Comparison of whole genome amplification techniques for human single cell exome sequencing

BACKGROUND

Whole genome amplification (WGA) is currently a prerequisite for single cell whole genome or exome sequencing. Depending on the method used the rate of artifact formation, allelic dropout and sequence coverage over the genome may differ significantly.

RESULTS

The largest difference between the evaluated protocols was observed when analyzing the target coverage and read depth distribution. These differences also had impact on the downstream variant calling. Conclusively, the products from the AMPLI1 and MALBAC kits were shown to be most similar to the bulk samples and are therefore recommended for WGA of single cells.

DISCUSSION

In this study four commercial kits for WGA (AMPLI1, MALBAC, Repli-G and PicoPlex) were used to amplify human single cells. The WGA products were exome sequenced together with non-amplified bulk samples from the same source. The resulting data was evaluated in terms of genomic coverage, allelic dropout and SNP calling.

Next-Generation Sequencing Workflow for NSCLC Critical Samples Using a Targeted Sequencing Approach by Ion Torrent PGM™ Platform

Next-generation sequencing (NGS) is a cost-effective technology capable of screening several genes simultaneously; however, its application in a clinical context requires an established workflow to acquire reliable sequencing results. Here, we report an optimized NGS workflow analyzing 22 lung cancer-related genes to sequence critical samples such as DNA from formalin-fixed paraffin-embedded (FFPE) blocks and circulating free DNA (cfDNA). Snap frozen and matched FFPE gDNA from 12 non-small cell lung cancer (NSCLC) patients, whose gDNA fragmentation status was previously evaluated using a multiplex PCR-based quality control, were successfully sequenced with Ion Torrent PGM™. The robust bioinformatic pipeline allowed us to correctly call both Single Nucleotide Variants (SNVs) and indels with a detection limit of 5%, achieving 100% specificity and 96% sensitivity. This workflow was also validated in 13 FFPE NSCLC biopsies. Furthermore, a specific protocol for low input gDNA capable of producing good sequencing data with high coverage, high uniformity, and a low error rate was also optimized. In conclusion, we demonstrate the feasibility of obtaining gDNA from FFPE samples suitable for NGS by performing appropriate quality controls. The optimized workflow, capable of screening low input gDNA, highlights NGS as a potential tool in the detection, disease monitoring, and treatment of NSCLC.

Assessing the utility of whole genome amplified DNA for next-generation molecular ecology

DNA quantity can be a hindrance in ecological and evolutionary research programmes due to a range of factors including endangered status of target organisms, available tissue type, and the impact of field conditions on preservation methods. A potential solution to low-quantity DNA lies in whole genome amplification (WGA) techniques that can substantially increase DNA yield. To date, few studies have rigorously examined sequence bias that might result from WGA and next-generation sequencing of nonmodel taxa. To address this knowledge deficit, we use multiple displacement amplification (MDA) and double-digest RAD sequencing on the grey mouse lemur (Microcebus murinus) to quantify bias in genome coverage and SNP calls when compared to raw genomic DNA (gDNA). We focus our efforts in providing baseline estimates of potential bias by following manufacturer's recommendations for starting DNA quantities (>100 ng). Our results are strongly suggestive that MDA enrichment does not introduce systematic bias to genome characterization. SNP calling between samples when genotyping both de-novo and with a reference genome are highly congruent (>98%) when specifying a minimum threshold of 20X stack depth to call genotypes. Relative genome coverage is also similar between MDA and gDNA, and allelic dropout is not observed. SNP concordance varies based on coverage threshold, with 95% concordance reached at ~12X coverage genotyping de-novo and ~7X coverage genotyping with the reference genome. These results suggest that MDA may be a suitable solution for next-generation molecular ecological studies when DNA quantity would otherwise be a limiting factor.

Multiple displacement amplification of whole genomic DNA from urediospores of Puccinia striiformis f. sp. tritici

Biotrophic fungi, such as Puccinia striiformis f. sp. tritici, because they cannot be cultured on nutrient media, to obtain adequate quantity of DNA for molecular genetic analysis, are usually propagated on living hosts, wheat plants in case of P. striiformis f. sp. tritici. The propagation process is time-, space- and labor-consuming and has been a bottleneck to molecular genetic analysis of this pathogen. In this study we evaluated multiple displacement amplification (MDA) of pathogen genomic DNA from urediospores as an alternative approach to traditional propagation of urediospores followed by DNA extraction. The quantities of pathogen genomic DNA in the products were further determined via real-time PCR with a pair of primers specific for the β-tubulin gene of P. striiformis f. sp. tritici. The amplified fragment length polymorphism (AFLP) fingerprints were also compared between the DNA products. The results demonstrated that adequate genomic DNA at fragment size larger than 23 Kb could be amplified from 20 to 30 urediospores via MDA method. The real-time PCR results suggested that although fresh urediospores collected from diseased leaves were the best, spores picked from diseased leaves stored for a prolonged period could also be used for amplification. AFLP fingerprints exhibited no significant differences between amplified DNA and DNA extracted with CTAB method, suggesting amplified DNA can represent the pathogen's genomic DNA very well. Therefore, MDA could be used to obtain genomic DNA from small precious samples (dozens of spores) for molecular genetic analysis of wheat stripe rust pathogen, and other fungi that are difficult to propagate.

Bias in Whole Genome Amplification: Causes and Considerations

Whole genome amplification (WGA) is a widely used molecular technique that is becoming increasingly necessary in genetic research on a range of sample types including individual cells, fossilized remains and entire ecosystems. Multiple methods of WGA have been developed, each with specific strengths and weaknesses, but with a common defect in that each method distorts the initial template DNA during the course of amplification. The type, extent, and circumstance of the bias vary with the WGA method and particulars of the template DNA. In this review, we endeavor to discuss the types of bias introduced, the susceptibility of common WGA techniques to these bias types, and the interdependence between bias and characteristics of the template DNA. Finally, we attempt to illustrate some of the criteria specific to the analytical platform and research application that should be considered to enable combination of the appropriate WGA method, template DNA, sequencing platform, and intended use for optimal results.

Human Nail Clippings as a Source of DNA for Genetic Studies

Blood samples have traditionally been used as the main source of DNA for genetic analysis. However, this source can be difficult in terms of collection, transportation, and long-term storage. In this study, we investigated whether human nail clippings could be used as a source of DNA for SNP genotyping, null-allele detection, and whole-genome amplification. From extracted nail DNA, we achieved amplicons up to a length of ~400 bp and >96% concordance for SNP genotyping and 100% concordance for null-allele detection compared to DNA derived from matched blood samples. For whole-genome amplification, OmniPlex performed better than Multiple Displacement Amplification with a success rate of 89.3% and 76.8% for SNP genotyping and null-allele detection, respectively. Concordance was ~98% for both methods. When combined with OmniPlex whole-genome amplification, human nail clippings could potentially be used as an alternative to whole blood as a less invasive and more convenient source of DNA for genotyping studies.

Principles of Whole-Genome Amplification

Modern molecular biology relies on large amounts of high-quality genomic DNA. However, in a number of clinical or biological applications this requirement cannot be met, as starting material is either limited (e.g., preimplantation genetic diagnosis (PGD) or analysis of minimal residual cancer) or of insufficient quality (e.g., formalin-fixed paraffin-embedded tissue samples or forensics). As a consequence, in order to obtain sufficient amounts of material to analyze these demanding samples by state-of-the-art modern molecular assays, genomic DNA has to be amplified. This chapter summarizes available technologies for whole-genome amplification (WGA), bridging the last 25 years from the first developments to currently applied methods. We will especially elaborate on research application, as well as inherent advantages and limitations of various WGA technologies.

Comparison of phi29-based whole genome amplification and whole transcriptome amplification in dengue virus

Dengue virus is responsible for 50-100 million new infections annually worldwide. The virus uses error-prone RNA polymerase during genome replication in a host, resulting in the formation of closely related viruses known as quasispecies. The availability of next-generation sequencing technology provides opportunities to analyze viral quasispecies. Before analysis, it is crucial to increase the amount of DNA because of the limited amounts of viral genomic material that can be isolated from a patient. However, using specific primers may overlook the occurrence of possible variations at primer binding sites. To address this problem, the performance of two sequence-independent amplification methods was compared for whole genome amplification (WGA): phi29 DNA polymerase-based WGA and whole transcriptome amplification (WTA). Both methods have the ability to provide complete coverage of the dengue genome from template amounts as low as 1 ng. However, WTA showed greater efficiency in terms of yield (WTA: ~10 μg; phi29-based WGA: ~500 ng) and lower amplification bias. In conclusion, the WTA amplification kit was shown to perform substantially better than phi29 DNA polymerase-based WGA in terms of both final concentration and amplification bias in amplifying small genomes, such as that of the dengue virus.

Development of a multiplex polymerase chain reaction-sequence-specific primer method for NKG2D and NKG2F single-nucleotide polymorphism typing using isothermal multiple displacement amplification products

Natural killer group 2 member D (NKG2D) on immune effector cells recognizes multiple stress-inducible ligands. NKG2D single-nucleotide polymorphism (SNP) haplotypes were related to the levels of cytotoxic activity of peripheral blood mononuclear cells. Indeed, these polymorphisms were also located in NKG2F. Isothermal multiple displacement amplification (IMDA) is used for whole genome amplification (WGA) that can amplify very small genomic DNA templates into microgram with whole genome coverage. This is particularly useful in the cases of limited amount of valuable DNA samples requiring multi-locus genotyping. In this study, we evaluated the quality and applicability of IMDA to genetic studies in terms of sensitivity, efficiency of IMDA re-amplification and stability of IMDA products. The smallest amount of DNA to be effectively amplified by IMDA was 200 pg yielding final DNA of approximately 16 µg within 1.5 h. IMDA could be re-amplified only once (second round of amplification), and could be kept for 5 months at 4°C and more than a year at -20°C without loosing genome coverage. The amplified products were used successfully to setup a multiplex polymerase chain reaction-sequence-specific primer for SNP typing of the NKG2D/F genes. The NKG2D/F multiplex polymerase chain reaction (PCR) contained six PCR mixtures for detecting 10 selected SNPs, including 8 NKG2D/F SNP haplotypes and 2 additional NKG2D coding SNPs. This typing procedure will be applicable in both clinical and research laboratories. Thus, our data provide useful information and limitations for utilization of genome-wide amplification using IMDA and its application for multiplex NKG2D/F typing.

Identification of evidence-based biospecimen quality-control tools: a report of the International Society for Biological and Environmental Repositories (ISBER) Biospecimen Science Working Group

Control of biospecimen quality that is linked to processing is one of the goals of biospecimen science. Consensus is lacking, however, regarding optimal sample quality-control (QC) tools (ie, markers and assays). The aim of this review was to identify QC tools, both for fluid and solid-tissue samples, based on a comprehensive and critical literature review. The most readily applicable tools are those with a known threshold for the preanalytical variation and a known reference range for the QC analyte. Only a few meaningful markers were identified that meet these criteria, such as CD40L for assessing serum exposure at high temperatures and VEGF for assessing serum freeze-thawing. To fully assess biospecimen quality, multiple QC markers are needed. Here we present the most promising biospecimen QC tools that were identified.

Preimplantation genetic diagnosis: recent triumphs and remaining challenges

Over the last 20 years, preimplantation genetic diagnosis (PGD) has changed from being an experimental procedure to one that is carried out in specialized diagnostic centers worldwide. Genetic awareness and the rapid identification of germline mutations or chromosomal abnormalities enable individuals to know their risk of transmitting a genetic disease before they have children. This has created a demand for PGD from couples who wish to avoid terminations of affected pregnancies. Although PGD is expensive because it requires couples to go through IVF, there is a trend for diagnosis to move towards automation, which will reduce cost and the need for specialized expertise. This will allow diagnosis to be carried out in routine molecular diagnostic laboratories.

DNA amplification techniques in pharmacogenomics

The variable predisposition of patients, both to disease susceptibility and drug response, is well established. It is largely attributed to genetic, as well as epigenetic variations between individuals, which may be inherited or acquired. The most common variation in the human genome is the SNP, which occurs throughout the genome, both within coding and noncoding regions. Characterization of SNPs in the context of both inherited and acquired conditions, such as cancer, are a main focus of many genotyping procedures. The demand for identifying (diagnosing) targeted SNPs or other variations, as well as the application of genome-wide screens, is continuously directing the development of new technologies. In general, most methods require a DNA amplification step to provide the amounts of DNA needed for the SNP detection step. In addition, DNA amplification is an important step when investigating other types of genomic information, for instance when addressing repeat, deletion, copy number variation or epigenetic regulation by DNA methylation. Besides the widely used PCR technique, there are several alternative approaches for genomic DNA amplification suitable for supporting the detection of genomic variation. In this article, we describe and evaluate a number of techniques, and discuss possible future prospects of DNA amplification in the fields of pharmacogenetics and pharmacogenomics.

Genotyping performance assessment of whole genome amplified DNA with respect to multiplexing level of assay and its period of storage

Whole genome amplification can faithfully amplify genomic DNA (gDNA) with minimal bias and substantial genome coverage. Whole genome amplified DNA (wgaDNA) has been tested to be workable for high-throughput genotyping arrays. However, issues about whether wgaDNA would decrease genotyping performance at increasing multiplexing levels and whether the storage period of wgaDNA would reduce genotyping performance have not been examined. Using the Sequenom MassARRAY iPLEX Gold assays, we investigated 174 single nucleotide polymorphisms for 3 groups of matched samples: group 1 of 20 gDNA samples, group 2 of 20 freshly prepared wgaDNA samples, and group 3 of 20 stored wgaDNA samples that had been kept frozen at −70°C for 18 months. MassARRAY is a medium-throughput genotyping platform with reaction chemistry different from those of high-throughput genotyping arrays. The results showed that genotyping performance (efficiency and accuracy) of freshly prepared wgaDNA was similar to that of gDNA at various multiplexing levels (17-plex, 21-plex, 28-plex and 36-plex) of the MassARRAY assays. However, compared with gDNA or freshly prepared wgaDNA, stored wgaDNA was found to give diminished genotyping performance (efficiency and accuracy) due to potentially inferior quality. Consequently, no matter whether gDNA or wgaDNA was used, better genotyping efficiency would tend to have better genotyping accuracy.

Evaluation of quality of DNA extracted from buccal swabs for microarray based genotyping

Buccal cell usage has been shown by many to be a cost effective and safe method to isolate DNA for various biological experiments especially large epidemiological studies (Garcia-Closas et al. Cancer Epidemiol Biomarkers Prev 10:687-696, 2001). Non-invasive DNA collection methods are preferred over phlebotomy in order to increase study participation and compliance in research centers and for sick patients in hospital settings. There have been conflicting reports about the methodology and results obtained from using buccal DNA. It is not very clear if phlebotomy can be confidently replaced by buccal cell DNA. It is often left for the user to take an intelligent decision. To address this issue, we compared the performance of buccal and blood DNA from same subjects in a genotyping experiment and this paper reports the results. Cotton swab derived buccal cells were scraped from the inner side of cheeks from 16 subjects, and blood was also drawn from the same 16 subjects participating in a genotypic association study of a lipid disease. The DNA quality was assessed by resolving on agarose gels, checking purity (A260/A280) and finally by microarray hybridization. This study showed that DNA degradation affects the total yield and performance of the buccal DNA when compared to the blood DNA in microarray based genotyping. Genotyping results can be seriously compromised if care is not taken to check the quality and yields of such specimens.

Evaluation of mailed pediatric buccal cytobrushes for use in a case-control study of birth defects

BACKGROUND

Buccal cell collection is a convenient DNA collection method; however, little attention has been given to the quality of DNA obtained from pediatric populations. The purpose of this study was to determine the effect of a modified cytobrush collection method on the yield and quality of infant buccal DNA collected as part of a population-based case-control study of birth defects. METHODS Cytobrushes were collected from infants, mothers, and fathers using a standard collection method in 1997 to 2003 and a modified protocol that allows air-drying of the cytobrushes after collection from 2003 to the present. Yield and quality of DNA from 1057 cytobrushes was assessed by quantitative PCR and short tandem repeat (STR) genotyping, respectively. RESULTS Air-dried cytobrushes from infants had higher median DNA yields (1300 ng) and STR completion rates (99.5%) than standard collection method cytobrushes (60 ng and 59.5%, respectively). A subset of DNA aliquots was genotyped for six single nucleotide polymorphisms (SNPs). Aliquots from both collection methods that passed the quality protocol (DNA concentration >1 ng/μl, and successful amplification of ≥1 STR) had high genotype completion rates (99-100%). The median DNA yield following whole genome amplification was more than twofold higher for air-dried than standard collection specimens (p < 0.001). CONCLUSION Yield and quality of buccal DNA collected from infants are improved by using a method that incorporates air-drying; however, DNA collected by both methods is suitable for genotyping if stringent quality control procedures are instituted. These findings may be helpful for future epidemiologic studies of birth defects and other adverse pediatric outcomes.

Amplification of viral RNA from drinking water using TransPlex™ whole-transcriptome amplification

Aims:  Viral pathogens in environmental media are generally highly diffuse, yet small quantities of pathogens may pose a health risk. This study evaluates the ability of TransPlex™ whole transcriptome amplification (WTA) to amplify small quantities of RNA viruses from complex environmental matrices containing background nucleic acids.

Methods and Results:  DNA extracts from mock drinking water samples containing mixed microbial populations were spiked with small quantities of echovirus type 13 (EV) RNA. Samples were amplified using a Transplex™ WTA kit, and EV‐specific quantitative reverse transcription polymerase chain reaction (qRT‐PCR) was used to quantify target pathogens before and after application of WTA. Samples amplified by WTA demonstrated a decreased limit of detection. The log‐linear relationship between serial dilutions was maintained following amplification by WTA.

Conclusions:  WTA is able to increase the quantity of target organism RNA in mixed populations, while maintaining log linearity of amplification across different target concentrations.

Significance and Impact of the Study:  WTA may serve as an effective preamplification step to increase the levels of RNA prior to detection by other molecular methods such as PCR, microarrays and sequencing.

Whole genome amplification in preimplantation genetic diagnosis

Preimplantation genetic diagnosis (PGD) refers to a procedure for genetically analyzing embryos prior to implantation, improving the chance of conception for patients at high risk of transmitting specific inherited disorders. This method has been widely used for a large number of genetic disorders since the first successful application in the early 1990s. Polymerase chain reaction (PCR) and fluorescent in situ hybridization (FISH) are the two main methods in PGD, but there are some inevitable shortcomings limiting the scope of genetic diagnosis. Fortunately, different whole genome amplification (WGA) techniques have been developed to overcome these problems. Sufficient DNA can be amplified and multiple tasks which need abundant DNA can be performed. Moreover, WGA products can be analyzed as a template for multi-loci and multi-gene during the subsequent DNA analysis. In this review, we will focus on the currently available WGA techniques and their applications, as well as the new technical trends from WGA products.

Collection of human genomic DNA from neonates: a comparison between umbilical cord blood and buccal swabs

OBJECTIVE

To compare DNA yield from neonatal umbilical cord blood and buccal swab specimens.

STUDY DESIGN

Umbilical cord blood was obtained at birth in a cohort of women enrolled in a preterm labor study. If cord blood was not obtained, neonatal buccal samples were obtained using the Oragene saliva kits. DNA was extracted from all samples using the QIAamp extraction kits. DNA concentration and yield were compared between umbilical cord blood and buccal swabs.

RESULTS

DNA concentrations from umbilical cord blood (n = 35) was greater than that obtained from buccal swabs (n = 20) (total sample: 209.0 ± 110.7 ng/μL vs 6.9 ± 6.7 ng/μL respectively, P < .001; partial sample: n = 30 cord blood vs n = 11 buccal, 70.0 ± 51.4 ng/μL vs 11.3 ± 6.7 ng/μL, respectively, P < .001) and produced more total DNA (total sample: 116.5 ± 70.8 μg vs 4.2 ± 4.0 μg, P < .001; partial:14.0 ± 10.3 μg vs 1.1 ± 0.7 μg, respectively, P < .001).

CONCLUSION

Buccal swabs yield less neonatal DNA than umbilical cord blood specimens.

DNA amplification using phi29 DNA polymerase validates gene polymorphism analysis from buccal mucosa samples

Venous blood is currently the most common source of DNA for gene polymorphism screening; however, blood sampling is invasive and difficult to perform in general dental treatment. Buccal mucosa samples provide an alternative source of DNA, but it is frequently difficult to effectively amplify the DNA owing to the small amounts of sample material obtained. This study was performed to establish a method for performing total genomic DNA amplification from buccal mucosa samples using phi29 DNA polymerase. Total genomic DNA was isolated from buccal mucosa samples obtained from healthy subjects and was amplified using phi29 DNA polymerase. To determine the suitability of the extracted DNA for genotyping, polymerase chain reaction and restriction fragment length polymorphism analyses were performed for the IL-1 gene polymorphism. Genotyping of the IL-1 polymorphism was successful using the amplified DNA from a buccal mucosa, but genotyping was unsuccessful using the unamplified control because of low DNA purity. The method of extracting DNA from a buccal mucosa is painless, simple, minimally invasive, and rapid. Genomic DNA from a buccal mucosa can be amplified by phi29 DNA polymerase in sufficient quantity and quality to conduct gene polymorphism analyses.

Whole-genome amplification using Φ29 DNA polymerase

The cornerstones of any genetic analysis study are the quality and quantity of the DNA samples. DNA is a precious limited resource, and in human disease studies the accessibility of sample DNA is often governed by the isolation method and the human source. Additionally, forensic analysis and archaeological research are generally infeasible without intact sample DNA. Therefore, mechanisms to preserve or enhance the quantity of the DNA stock are crucial to the success of these studies. Historically, to preserve and maintain DNA stocks, costly and labor-intensive Epstein-Barr-virus-transformed cell lines were produced. The creation of cell lines can be valuable for a number of reasons in addition to creating a renewable resource of DNA, but the cost and effort to create them, as well as the requirement of intact cells to begin with, limit the utility of this approach. More recently, whole-genome amplification (WGA), utilizing the unique property of the enzyme Φ29 DNA polymerase, has been used to generate robust high-fidelity copies of the genome. As described in this protocol, WGA using Φ29 DNA polymerase allows unbiased representation of the genome via multiple-strand displacement, followed by rolling-circle amplification on random primers.

Assessing the efficiency and significance of Methylated DNA Immunoprecipitation (MeDIP) assays in using in vitro methylated genomic DNA

BACKGROUND

DNA methylation contributes to the regulation of gene expression during development and cellular differentiation. The recently developed Methylated DNA ImmunoPrecipitation (MeDIP) assay allows a comprehensive analysis of this epigenetic mark at the genomic level in normal and disease-derived cells. However, estimating the efficiency of the MeDIP technique is difficult without previous knowledge of the methylation status of a given cell population. Attempts to circumvent this problem have involved the use of in vitro methylated DNA in parallel to the investigated samples. Taking advantage of this stratagem, we sought to improve the sensitivity of the approach and to assess potential biases resulting from DNA amplification and hybridization procedures using MeDIP samples.

FINDINGS

We performed MeDIP assays using in vitro methylated DNA, with or without previous DNA amplification, and hybridization to a human promoter array. We observed that CpG content at gene promoters indeed correlates strongly with the MeDIP signal obtained using in vitro methylated DNA, even when lowering significantly the amount of starting material. In analyzing MeDIP products that were subjected to whole genome amplification (WGA), we also revealed a strong bias against CpG-rich promoters during this amplification procedure, which may potentially affect the significance of the resulting data.

CONCLUSION

We illustrate the use of in vitro methylated DNA to assess the efficiency and accuracy of MeDIP procedures. We report that efficient and reproducible genome-wide data can be obtained via MeDIP experiments using relatively low amount of starting genomic DNA; and emphasize for the precaution that must be taken in data analysis when an additional DNA amplification step is required.

Single cell analytics: an overview

The research field of single cell analysis is rapidly expanding, driven by developments in flow cytometry, microscopy, lab-on-a-chip devices, and many other fields. The promises of these developments include deciphering cellular mechanisms and the quantification of cell-to-cell differences, ideally with spatio-temporal resolution. However, these promises are challenging as the analytical techniques have to cope with minute analyte amounts and concentrations. We formulate first these challenges and then present state-of-the-art analytical techniques available to investigate the different cellular hierarchies--from the genome to the phenome, i.e., the sum of all phenotypes.

Whole genome amplification (WGA) for archiving and genotyping of clinical isolates of Cryptosporidium species

Clinical and environmental isolates of pathogens are often unique and may be unculturable, yielding a very limited amount of DNA for genetic studies. Cryptosporidium in particular are difficult to propagate. Whole genome amplification (WGA) is a valuable technique for amplifying genomic material. In this study, we tested 5 WGA commercial kits using Cryptosporidium clinical isolates. DNA of 5 C. hominis and 5 C. parvum clinical isolates and C. parvum IOWA reference strain were used. The majority of the samples were amplified by all of the kits tested. The integrity and fidelity of the amplified genomic DNA were assessed by sequence analysis of several PCR products of varying length. We found evidence that one kit in particular may be more error prone while another seemed the more suitable kit for Cryptosporidium clinical samples, generating high molecular weight DNA from all the samples with high fidelity. Thus WGA was found to be a useful technique for producing amplified DNA suitable for downstream genotyping techniques and archiving of Cryptosporidium clinical isolates.

Quality of DNA extracted from mouthwashes

BACKGROUND

A cost effective, safe and efficient method of obtaining DNA samples is essential in large scale genetic analyses. Buccal cells are an attractive source of DNA, as their collection is non-invasive and can be carried out by mail. However, little attention has been given to the quality of DNA extracted from mouthwashes.

METHODOLOGY

Mouthwash-derived DNA was extracted from 500 subjects participating in a genetic study of high myopia. DNA quality was investigated using two standard techniques: agarose gel electrophoresis and quantitative polymerase chain reaction (qPCR).

PRINCIPAL FINDINGS

Whereas the majority of mouthwash-derived DNA samples showed a single band of high molecular weight DNA by gel electrophoresis, 8.9% (95% CI: 7.1-10.7%) of samples contained only a smear of low-to-medium molecular weight, degraded DNA. The odds of DNA degradation in a subject's second mouthwash sample, given degradation of the first, was significantly greater than one (OR = 3.13; 95% CI: 1.22-7.39; Fisher's test P = 0.009), suggesting that DNA degradation was at least partially a subject-specific phenomenon. Approximately 12.4% (95% CI: 10.4-14.4%) of mouthwash-derived DNA failed to PCR amplify efficiently (using an approximately 200 bp microsatellite marker). However, we found there was no significant difference in amplification success rate between DNA samples judged to be degraded or non-degraded by gel electrophoresis (Fisher's test P = 0.5).

CONCLUSIONS

This study demonstrated that DNA degradation affects a significant minority of saline mouthwashes, and that the phenomenon is partially subject-specific. Whilst the level of degradation did not significantly prevent successful amplification of short PCR fragments, previous studies suggest that such DNA degradation would compromise more demanding applications.

PGD for monogenic disorders: aspects of molecular biology

Preimplantation genetic diagnosis (PGD) for monogenic diseases has known a considerable evolution since its first application in the early 1990s. Especially the technical aspects of the genetic diagnosis itself, the single-cell genetic analysis, has constantly evolved to reach levels of accuracy and efficiency nearing those of genetic diagnosis on regular DNA samples. In this review, we will focus on the molecular biological techniques that are currently in use in the most advanced centers for PGD for monogenic disorders, including multiplex polymerase chain reaction (PCR) and post-PCR diagnostic methods, whole genome amplification (WGA) and multiple displacement amplification (MDA). As it becomes more and more clear that when it comes to ethically difficult indications, PGD goes further than prenatal diagnosis (PND), we will also briefly discuss ethical issues.

Performance of amplified DNA in an Illumina GoldenGate BeadArray assay

Whole genome amplification (WGA) offers a means to enrich DNA quantities for epidemiologic studies. We used an ovarian cancer study of 1,536 single nucleotide polymorphisms (SNPs) and 2,368 samples to assess performance of multiple displacement amplification (MDA) WGA using an Illumina GoldenGate BeadArray. Initial screening revealed successful genotyping for 93.4% of WGA samples and 99.3% of genomic samples, and 93.2% of SNPs for WGA samples and 96.3% of SNPs for genomic samples. SNP failure was predicted by Illumina-provided designability rank, %GC (P < or = 0.002), and for WGA only, distance to telomere and Illumina-provided SNP score (P < or = 0.002). Distance to telomere and %GC were highly correlated; adjustment for %GC removed the association between distance to telomere and SNP failure. Although universally high, per-SNP call rates were related to designability rank, SNP score, %GC, minor allele frequency, distance to telomere (P < or = 0.01), and, for WGA only, Illumina-provided validation class (P < 0.001). We found excellent concordance generally (>99.0%) among 124 WGA:genomic replicates, 15 WGA replicates, 88 replicate aliquots of the same WGA preparation, and 25 genomic replicates. Where there was discordance, it was across WGA:genomic replicates but limited to only a few samples among other replicates suggesting the introduction of error. Designability rank and SNP score correlated with WGA:genomic concordance (P < 0.001). In summary, use of MDA WGA DNA is feasible; however, caution is warranted regarding SNP selection and analysis. We recommend that biological SNP characteristics, notably distance to telomere and GC content (<50% GC recommended), as well as Illumina-provided metrics be considered in the creation of GoldenGate assays using MDA WGA DNA.

Improved multiple displacement amplification with phi29 DNA polymerase for genotyping of single human cells

The ability to genotype multiple loci of single cells would be of significant benefit to investigations of cellular processes such as oncogenesis, meiosis, fertilization, and embryogenesis. We report a simple two-step, single-tube protocol for whole-genome amplification (WGA) from single human cells using components of the GenomiPhi V2 DNA Amplification kit. For the first time, we demonstrate reliable generation of 4-7 microg amplified DNA from a single human cell within 4 h with a minimum amount of artifactual DNA synthesis. DNA amplified from single cells was genotyped for 13 heterozygous short tandem repeats (STRs) and 7 heterozygous single nucleotide polymorphisms (SNPs), and the genotyping results were compared with purified genomic DNA. Accuracy of genotyping (percent of single-cell amplifications genotyped accurately for any particular STR or SNP) varied from 37% to 100% (with an average of 80%) for STRs and from 89% to 100% (averaging 94%) for SNPs. We suggest that the method described in this report is suitable for WGA from single cells, the product of which can be subsequently used for many applications, such as preimplantation genetic analysis (PGD).

Performance of whole-genome amplified DNA isolated from serum and plasma on high-density single nucleotide polymorphism arrays

Defining genetic variation associated with complex human diseases requires standards based on high-quality DNA from well-characterized patients. With the development of robust technologies for whole-genome amplification, sample repositories such as serum banks now represent a potentially valuable source of DNA for both genomic studies and clinical diagnostics. We assessed the performance of whole-genome amplified DNA (wgaDNA) derived from stored serum/plasma on high-density single nucleotide polymorphism arrays. Neither storage time nor usage history affected either DNA extraction or whole-genome amplification yields; however, samples that were thawed and refrozen showed significantly lower call rates (73.9 +/- 7.8%) than samples that were never thawed (92.0 +/- 3.3%) (P < 0.001). Genotype call rates did not differ significantly (P = 0.13) between wgaDNA from never-thawed serum/plasma (92.9 +/- 2.6%) and genomic DNA (97.5 +/- 0.3%) isolated from whole blood. Approximately 400,000 genotypes were consistent between wgaDNA and genomic DNA, but the overall discordance rate of 4.4 +/- 3.8% reflected an average of 11,110 +/- 9502 genotyping errors per sample. No distinct patterns of chromosomal clustering were observed for single nucleotide polymorphisms showing discordant genotypes or homozygote conversion. Because the effects of genotyping errors on whole-genome studies are not well defined, we recommend caution when applying wgaDNA from serum/plasma to high-density single nucleotide polymorphism arrays in addition to the use of stringent quality control requirements for the resulting genotype data.

Multiple strand displacement amplification of mitochondrial DNA from clinical samples

Background

Whole genome amplification (WGA) methods allow diagnostic laboratories to overcome the common problem of insufficient DNA in patient specimens. Further, body fluid samples useful for cancer early detection are often difficult to amplify with traditional PCR methods. In this first application of WGA on the entire human mitochondrial genome, we compared the accuracy of mitochondrial DNA (mtDNA) sequence analysis after WGA to that performed without genome amplification. We applied the method to a small group of cancer cases and controls and demonstrated that WGA is capable of increasing the yield of starting DNA material with identical genetic sequence.

Methods

DNA was isolated from clinical samples and sent to NIST. Samples were amplified by PCR and those with no visible amplification were re-amplified using the Multiple Displacement Amplificaiton technique of whole genome amplification. All samples were analyzed by mitochip for mitochondrial DNA sequence to compare sequence concordance of the WGA samples with respect to native DNA. Real-Time PCR analysis was conducted to determine the level of WGA amplification for both nuclear and mtDNA.

Results

In total, 19 samples were compared and the concordance rate between WGA and native mtDNA sequences was 99.995%. All of the cancer associated mutations in the native mtDNA were detected in the WGA amplified material and heteroplasmies in the native mtDNA were detected with high fidelity in the WGA material. In addition to the native mtDNA sequence present in the sample, 13 new heteroplasmies were detected in the WGA material.

Conclusion

Genetic screening of mtDNA amplified by WGA is applicable for the detection of cancer associated mutations. Our results show the feasibility of this method for: 1) increasing the amount of DNA available for analysis, 2) recovering the identical mtDNA sequence, 3) accurately detecting mtDNA point mutations associated with cancer.

Successful genome-wide scan in paired blood and buccal samples

Interest in genome-wide association studies to identify susceptibility alleles for cancer is growing, and several are currently planned or under way. Although the feasibility of collecting buccal cell samples as an alternative to venous blood samples as a source of genomic DNA has been shown, the validity of using DNA from buccal cells for genome-wide scans has not been assessed. We used 46 paired buffy coat and buccal cell samples to test the feasibility of using DNA from buccal cells for genotyping with the HumanHap300 Bead Chip (v.1.0.0) on the Illumina Infinium II platform. Genotyping was successful in every sample, regardless of DNA yield or sample type. Of the 317,502 genotypes attempted, 315,314 (99.3%) were successfully called. Completion rates were similar for buffy coat and buccal cell samples (99.63% and 99.44%, respectively; P = 0.15). Completion rates <99% were observed in only four samples and did not differ by specimen type. The paired samples showed exceptionally high concordance (99.96%). These results show that buccal cell samples collected and processed under optimal conditions can be used for genome-wide association studies with results comparable to those obtained from DNA extracted from buffy coat.

Reliability of high-throughput genotyping of whole genome amplified DNA in SNP genotyping studies

Whole genome amplification (wga) of DNA is being widely implemented in many laboratories to extend the life of samples only available in limited quantities for genetic analysis. We determined the reliability of wgaDNA genotypes in three sets of replicates from the same individuals: (i) 23 pairs of genomic DNA (gDNA), (ii) 43 pairs gDNA versus wgaDNA, and (iii) 29 pairs of independently amplified wgaDNA. Amplification was performed using multiple displacement amplification (MDA). Genotyping was successful for both DNA types for 1268 out of 1534 SNPs from 164 cardiovascular candidate genes assayed in a single Illumina panel. Amplified DNA failed for 77 SNPs (6%) that were genotyped successfully with genomic material. Percent of successful SNP calls, and concordance between pairs and kappa statistics (kappa) were determined. A total of 54 110 genotypes from gDNA-wgaDNA pairs were available for concordance analysis. Mean kappa for gDNA-wgaDNA pairs was 0.99. Concordance between gDNA-wgaDNA pairs was higher than amongst wgaDNA pairs (mean kappa for the 29 independently amplified pairs of wgaDNA was 0.95; interquartile range: 0.93-1.00). A statistical analysis of those SNPs which failed to genotype from amplified DNA only revealed that those loci were more likely to be closer to the telomeres and in locally GC-rich sequences. In summary, the MDA method produces wgaDNA samples that can be genotyped using high-throughput technology with a very high reproducibility to the original DNA but with slightly lower call rates. DNA amplification methodologies provide a useful solution for current and future large-scale genetic analyses especially with limited quantities of samples and DNA.

Whole-genome amplification of oral rinse self-collected DNA in a population-based case-control study of breast cancer

The availability of large amounts of genomic DNA (gDNA) is the limiting factor for many of the molecular biology assays in genetic epidemiologic studies. Whole-genome amplification using multiple displacement amplification is used to amplify a representative sample of gDNA from small amounts of gDNA to optimize gDNA yield. We collected oral rinse DNA samples through the mail from 3,377 women enrolled in a population-based U.S. breast cancer case-control study and did whole-genome amplification by multiple displacement amplification. Genotyping was done for 66 single nucleotide polymorphisms (SNP) in 18 candidate susceptibility genes using amplified DNA with genomic replicates included for quality control. The concordance rates (percentages of agreement) in 95 quality control replicates of gDNA and amplified DNA for 66 SNPs ranged from 88% to 100% (median, 97%). The average allelic error rate was 0.9%. However, in further analyses based on the full control series (n = 1,492), >60% of the SNPs failed tests for Hardy-Weinberg equilibrium (P < 0.05), with evidence of heterozygote loss in the great majority. Even eliminating the 9% of samples with lower quality or input DNA, tests for Hardy-Weinberg equilibrium indicated persistent allele bias in nearly a third of the SNPs. Whole-genome amplification may introduce substantial allele amplification bias in gDNA collected using a common protocol in population-based epidemiologic studies.

DNA Quantification of Whole Genome Amplified Samples for Genotyping on a Multiplexed Bead Array Platform

Whole genome amplification (WGA) permits genotyping DNA samples of limited quantity, expanding the number of samples available for genetic epidemiology studies. WGA, however, produces various nucleic acid side products that may interfere with accurate DNA quantification and further analysis. Although quality control of whole genome amplified DNA (wgaDNA) before genotyping is essential to prevent failed or poor genotyping results, little information is available to choose the best method for wgaDNA quantification. Therefore, we quantified wgaDNA from 54 buccal or poor quality blood samples by four methods: UV absorbance, PicoGreen fluorescence calibrated with lambda bacteriophage or calf thymus DNA, and absolute quantification by real-time PCR amplification of human-specific Alu Yd6. We then genotyped these wgaDNA samples and paired high-quality genomic DNA samples on a custom 384-plex Illumina Golden Gate Panel. Of the 54 paired samples, 39 gave high concordance (>99%), whereas 7 had moderate concordance (>90-99%) and 8 had poor concordance (</=90%) of wgaDNA and genomic DNA genotyping results. Quantitative PCR of Alu was the only wgaDNA quantification method to distinguish wgaDNA samples that gave high, moderate, or low concordance results (i.e., wgaDNA quantities in the high, moderate, and poor concordance groups ranged at 4.14-118.32, 0.29-2.19, and 0.01-0.27 ng/microL, respectively). Human-specific quantitative PCR is a highly useful guide for determining the suitability of wgaDNA before high-throughput single-nucleotide polymorphism analysis.

Whole genome amplification of buccal cytobrush DNA collected for molecular epidemiology studies

When cytobrush buccal cell samples have been collected as a genomic DNA (gDNA) source for an epidemiological study, whole genome amplification (WGA) can be critical to maintain sufficient DNA for genotyping. We evaluated REPLI-g WGA using gDNA from two paired cytobrushes (cytobush 'A' kept in a cell lysis buffer, and 'B' dried and kept at room temperature for 3 days, and frozen until DNA extraction) in a pilot study (n=21), and from 144 samples collected by mail in a breast cancer study. WGA success was assessed as the per cent completion/concordance of STR/SNP genotypes. Locus amplification bias was assessed using quantitative PCR of 23 human loci. The pilot study showed > 98% completion but low genotype concordance between cytobrush wgaDNA and paired blood gDNA (82% and 84% for cytobrushes A and B, respectively). Substantial amplification bias was observed with significantly lower human gDNA amplification from cytobrush B than A. Using cytobrush gDNA samples from the breast cancer study (n =20), an independent laboratory demonstrated that increasing template gDNA to the REPLI-g reaction improved genotype performance for 49 SNPs; however, average completion and concordance remained below 90%. To reduce genotype misclassification when cytobrush wgaDNA is used, inclusion of paired gDNA/wgaDNA and/or duplicate wgaDNA samples is critical to monitor data quality.

Single molecule transcription profiling with AFM

Established techniques for global gene expression profiling, such as microarrays, face fundamental sensitivity constraints. Due to greatly increasing interest in examining minute samples from micro-dissected tissues, including single cells, unorthodox approaches, including molecular nanotechnologies, are being explored in this application. Here, we examine the use of single molecule, ordered restriction mapping, combined with AFM, to measure gene transcription levels from very low abundance samples. We frame the problem mathematically, using coding theory, and present an analysis of the critical error sources that may serve as a guide to designing future studies. We follow with experiments detailing the construction of high density, single molecule, ordered restriction maps from plasmids and from cDNA molecules, using two different enzymes, a result not previously reported. We discuss these results in the context of our calculations.

Scanning the horizon: What is the future of genome-wide association studies in accelerating discoveries in cancer etiology and prevention?

Genome-wide association studies using recently developed large scale single nucleotide polymorphism platforms are beginning to be performed, and results reported. Initial indications are that these studies are capable of discovering loci associated with relative risks too modest to have been detectable through family-based linkage studies. However, as these studies initially test 500,000 or more polymorphisms in a first series of cases and controls, the need for robust replication in one, or preferably, several independent studies is paramount to winnow out the true positive results from the large number of expected false positives. We discuss the need for the formation of consortia to conduct these multi-stage studies, and stress the importance of full disclosure of allele frequencies in cases and controls from these studies in order to facilitate joint analyses across datasets to speed discovery of reproducible associations, and to explore more complex associations such as gene-gene interactions. Desirable characteristics of studies in which genome-wide association studies will be most informative are discussed. The validation of genetic variants that alter risk of specific cancers may be relevant to screening, the identification of high risk persons for risk-reducing interventions, and the discovery of new biological mechanisms that may provide insight into cancer causes and preventive strategies.

Accuracy of multiplexed Illumina platform-based single-nucleotide polymorphism genotyping compared between genomic and whole genome amplified DNA collected from multiple sources

Association studies designed to identify the genetic determinants underlying complex disease increasingly require sustainable high-quality DNA resources for large-scale single-nucleotide polymorphism (SNP) genotyping. Recent studies have shown that genomic DNA (gDNA) suitable for SNP genotyping can be obtained from buccal cells and from dried blood spots on Guthrie cards. Further, successful SNP genotyping has been done using the reaction product of multiple displacement amplification of gDNA. We evaluated genotype consistency on the Illumina genotyping platform for 717 to 1,744 SNP loci between replicate samples of gDNA and whole genome amplified DNA (wgaDNA) from a variety of sources. Nine healthy adults provided peripheral blood via venipuncture and buccal cells by mouth rinse. DNA was also obtained from urothelial cells in urine samples from five of the nine subjects. gDNA was extracted from all samples, wgaDNA was generated from each gDNA, and all samples were genotyped. To assess SNP genotyping accuracy of DNA obtained from dried blood spots, gDNA was extracted, amplified, and genotyped from peripheral blood samples and paired Guthrie card samples were obtained from eight childhood leukemia patients. Call rates and replicate concordances for all sample types, regardless of amplification, were >97%, with most sample types having call rates and replicate concordances >99%. Using the gDNA from blood samples as the reference for concordances calculated for all other sample types, we observed concordances >98% regardless of sample type or amplification. We conclude that highly multiplexed Illumina genotyping may be done on gDNA and wgaDNA obtained from whole blood, buccal samples, dried blood spots on Guthrie cards, and possibly even urine samples, with minimal misclassification.

Whole Genome Amplification on DNA from Filter Paper Blood Spot Samples: An Evaluation of Selected Systems

As the number of single-nucleotide polymorphism (SNP) screening and other mutation scanning studies have increased explosively, following the development of high-throughput instrumentation, it becomes even more important to have sufficient template DNA. The source of DNA is often limited, especially in epidemiological studies, which require many samples as well as enough DNA to perform numerous SNP screenings or mutation scannings. Therefore, the aim is to solve the problem of stock DNA limitation. This need has been an important reason for the development of whole genome amplification (WGA) methods. Several systems are based on Phi29 polymerase multiple displacement amplification (MDA) or on DNA fragmentation (OmniPlex). Using TaqMan SNP genotyping assays, we have tested four WGA systems -- AmpliQ Genomic Amplifier Kit, GenomiPhi, Repli-g, and GenomePlex -- on DNA extracted from Guthrie cards to evaluate the amplification bias, concordance- and call rates, cost efficiency, and flexibility. All systems successfully amplified picograms of DNA from Guthrie cards to micrograms of product without loss of heterozygosity and with minimal allelic bias. A modified AmpliQ set up was chosen for further evaluation. In all, 2,000 SNP genotyping results from amplified and nonamplified samples were compared and the concordance rates between the samples were 99.7%. The call rate using the TaqMan system was 99.8%. DNA extracted from Guthrie cards and amplified with one of the four evaluated WGA systems is applicable in epidemiological genetic screenings. System choice should be based on requirements for system flexibility, product yield, and use in subsequent analysis.

Optimized amplification and fluorescent labeling of small cell samples for genomic array-CGH

BACKGROUND

Whole genome amplification (WGA) is usually needed in the genetic analysis of samples containing a low number of cells. In genome-wide analysis of DNA copy numbers by array comparative genomic hybridization (array-CGH) it is very important that the genome is evenly represented throughout the amplified product. All currently available WGA techniques are generating some degree of bias.

METHODS

A way to compensate for this is using a reference sample which is similarly amplified, as the introduced amplification bias will be leveled out. Additionally, direct labeling of the amplified DNA is performed to bypass the currently widely applied random primed labeling, which involves an additional amplification of the product and is introducing extra bias.

RESULTS

In this article it is shown that equal processing of the test and reference sample is indeed crucial to generate an optimal array-CGH profile of amplified DNA samples. Also presented here is that the labeling method may significantly effect the array-CGH result, it is shown that with direct chemical labeling using platinum derivates (ULS labeling) optimal array-CGH results are obtained.

CONCLUSIONS

We show that an optimized WGA strategy for both test and reference sample in combination with direct chemical labeling results in a reliable array-CGH profile of samples as low as a 30 cell equivalent.

Technical note: Whole-genome amplification of DNA extracted from cattle semen samples

The bovine genome sequence project and the discovery of many thousands of bovine single nucleotide polymorphisms has opened the door for large-scale genotyping studies to identify genes that contribute to economically important traits with relevance to the beef and dairy industries. Large amounts of DNA will be required for these research projects. This study reports the use of the whole-genome amplification (WGA) method to create an unlimited supply of DNA for use in genotyping studies and long-term storage for future gene discovery projects. Two commercial WGA kits (GenomiPhi, Amersham Biosciences, Sydney, Australia, and REPLI-g, Qiagen, Doncaster, Australia) were used to amplify DNA from straws of bull semen, resulting in an average of 7.2 and 67 microg of DNA per reaction, respectively. The comparison of 3.5 kb of sequences from the amplified and unamplified DNA indicated no detectable DNA differences. Similarly, gene marker analysis conducted on genomic DNA and DNA after WGA indicated no difference in marker amplification or clarity and accuracy of scoring for approximately 10,000 single nucleotide polymorphism markers when compared with WGA samples genotyped in duplicate. These results illustrate that WGA is a suitable method for the amplification and recovery of DNA from bull semen samples for routine genomic investigations.