Utility of PCR for DNA analysis from dried blood spots on filter paper blotters

Detection of transgenes in equine dried blood spots using digital PCR and qPCR for gene doping control

Due to the ease of collection, transport and storage, the use of dried blood spots (DBS) offers an attractive alternative matrix for detection of the abuse of gene therapy, otherwise known as gene doping. This study evaluated the recovery, extraction efficiency and resulting detection capability of DNA from DBS by evaluating different target types, DNA extraction kits, the number of punches and blood tube preservatives. The long-term storage stability of low-copy-number transgene targets in DBS was not assessed in this study but would be noteworthy to investigate further. DNA was quantified using two detection methods: qPCR and digital PCR (dPCR). Using six punches with the Qiagen Investigator kit gave the best overall DNA yield compared with other extraction methods. Including three punches, however, gave better DNA extraction efficiency. Reference material could be detected using qPCR and dPCR in DBS spiked with 5000 copies/mL of blood (approximately 15 copies per 3 mm of punch). The optimal DNA extraction protocol was used on DBS samples from a custom recombinant adeno-associated virus administration study and showed successful detection of vector targets in DBS samples.

Newborn screening system: Safety, technology, advocacy

Newborn screening (NBS) is more than 50 years old and has proven to be a powerful and successful public health system. NBS must be regarded as a system and not simply as a test. We need to work as a community to improve the culture of safety for the NBS system and thereby to reduce the risk of babies being missed by the NBS system. Adding new technologies will not prevent system failures; that will require adherence to the culture of safety. Some have argued that every newborn should have their genome sequenced at birth and this sequencing could be part of NBS. However, NBS has depended on biomarker phenotypes throughout its history and our understanding of the relationships between genotype and phenotype is imperfect. Therefore, we should avoid being seduced by genomic sequencing technology and continue to focus on phenotypic biomarkers in NBS.

Paper microfluidics for nucleic acid amplification testing (NAAT) of infectious diseases

The diagnosis of infectious diseases is entering a new and interesting phase. Technologies based on paper microfluidics, coupled to developments in isothermal amplification of Nucleic Acids (NAs) raise opportunities for bringing the methods of molecular biology in the field, in a low setting environment. A lot of work has been performed in the domain over the last few years and the landscape of contributions is rich and diverse. Most often, the level of sample preparation differs, along with the sample nature, the amplification and detection methods, and the design of the device, among other features. In this review, we attempt to offer a structured description of the state of the art. The domain is not mature and there exist bottlenecks that hamper the realization of Nucleic Acid Amplification Tests (NAATs) complying with the constraints of the field in low and middle income countries. In this domain however, the pace of progress is impressively fast. This review is written for a broad Lab on a Chip audience.

Dosage of Sex Chromosomal Genes in Blood Deposited on Filter Paper for Neonatal Screening of Sex Chromosome Aneuploidy

AIMS

In this study, we examined the doses of the stature homeobox (SHOX), vesicle-associated membrane protein 7 (VAMP7), and SRY genes to establish a protocol for using peripheral blood samples deposited on filter paper for the screening of sex chromosome aneuploidy in neonates. We also measured correlations with karyotypes to assess this method as a neonatal screening strategy.

MATERIALS AND METHODS

This was an observational, descriptive, comparative blind study. Thirty-two healthy young adults (17 women, 15 men; age, ≥18 years), four patients with known sex chromosome aneuploidy (positive control group), and 1000 healthy newborns were included. Gene dosages were determined using quantitative real-time polymerase chain reaction (RT-PCR). Values with standard deviations (SDs) of three or more were considered abnormal.

RESULTS

Men and women differed in the gene dosage of the SRY gene. Cases with Turner syndrome showed values below 3 SDs for SHOX and VAMP7 genes, and cases with Klinefelter syndrome showed values above 3 SDs for SHOX and VAMP7 genes. Two suspected cases of sex chromosome aneuploidy were diagnosed using our neonatal screening strategy; these cases were confirmed as Turner syndrome and 47,XYY syndrome by karyotyping.

CONCLUSIONS

Our data establish a basis for the determination of chromosomal sex and neonatal screening of sex chromosome aneuploidy using RT-PCR.

Evaluation of Amount of Blood in Dry Blood Spots: Ring-Disk Electrode Conductometry

A fixed area punch in dried blood spot (DBS) analysis is assumed to contain a fixed amount of blood, but the amount actually depends on a number of factors. The presently preferred approach is to normalize the measurement with respect to the sodium level, measured by atomic spectrometry. Instead of sodium levels, we propose electrical conductivity of the extract as an equivalent nondestructive measure. A dip-type small diameter ring-disk electrode (RDE) is ideal for very small volumes. However, the conductance (G) measured by an RDE depends on the depth (D) of the liquid below the probe. There is no established way of computing the specific conductance (σ) of the solution from G. Using a COMSOL Multiphysics model, we were able to obtain excellent agreement between the measured and the model predicted conductance as a function of D. Using simulations over a large range of dimensions, we provide a spreadsheet-based calculator where the RDE dimensions are the input parameters and the procedure determines the 99% of the infinite depth conductance (G99) and the depth D99 at which this is reached. For typical small diameter probes (outer electrode diameter ∼ <2 mm), D99 is small enough for dip-type measurements in extract volumes of ∼100 μL. We demonstrate the use of such probes with DBS extracts. In a small group of 12 volunteers (age 20-66), the specific conductance of 100 μL aqueous extracts of 2 μL of spotted blood showed a variance of 17.9%. For a given subject, methanol extracts of DBS spots nominally containing 8 and 4 μL of blood differed by a factor of 1.8-1.9 in the chromatographically determined values of sulfate and chloride (a minor and major constituent, respectively). The values normalized with respect to the conductance of the extracts differed by ∼1%. For serum associated analytes, normalization of the analyte value by the extract conductance can thus greatly reduce errors from variations in the spotted blood volume/unit area.

Single Lysis-Salting Out Method of Genomic DNA Extraction From Dried Blood Spots

BACKGROUND

Dried blood spots (DBS) are an important form of bio-sampling and valuable approach for storing blood samples for genetic studies. This has necessitated in developing an effective protocol to isolate genomic DNA (gDNA) from DBS samples.In this study, we have elucidated a dependable and non-hazardous "single lysis-salting out" (SLSO) protocol of gDNA extraction from DBS and compared against the available commercial kits.

METHODS

For the purpose of this study, blood spots were collected on S&S 903 filter cards from 10 healthy volunteers and 30 patients with glutaric aciduria type I (GA-I). The gDNA was extracted from theseDBS samples by SLSO, QIAamp® gDNA Micro kit and innuPREP forensic kit methods. The quantity and quality of gDNA obtained from these methods were determined by measuring the absorbance using a Nanodrop spectrophotometer.

RESULTS

The SLSO method showed four-fold and eight-fold increased yield of gDNA in healthy volunteers and patient samples, respectively, compared to commercial kits (p<0.0001). The protocol was also found to be cost efficient, reducing the per sample cost to almost half. The suitability of this method for genetic studies was confirmed by performing R402W genotyping by RFLP in GA-I patients. The genotyping results showed the presence of R402W mutation in 20% (6/30) of patients.

CONCLUSION

The SLSO method was found to be inexpensive, non-hazardous and a suitable technique for isolating gDNA from DBS samples for genetic studies.

Evaluation of artemether-lumefantrine efficacy in the treatment of uncomplicated malaria and its association with pfmdr1, pfatpase6 and K13-propeller polymorphisms in Luanda, Angola

Background

Drug resistance in Plasmodiumfalciparum has posed an obstacle to effective treatment and challenges many malaria control programmes in endemic areas. In Angola, until 2003, chloroquine (CQ) was used as first-line therapy for uncomplicated malaria. It was replaced initially by amodiaquine and, in 2006, by artemisinin-based combination therapy (ACT) with artemether-lumefantrine (AL, Coartem^®). Efficacy study of ACT, conducted in Angola between 2004 and 2005, showed a baseline efficacy of ≈99 %.

Methods

103 malaria patients were enrolled according to WHO proceedings. Patients were followed up with clinical and parasitological evaluations for 28 days, parasite density and identification was evaluated by microscopy, the pfmsp2 were genotyped by nested-PCR, to distinguish parasite recrudescence from new infections; the polymorphisms at codons 86 and 1246 of pfmdr1 gene, and 769 of pfatp6 gene were assessed by PCR–RFLP and sequencing for pfk13-propeller genotype.

Results

The cure rate was 91.3 %. The obtained results showed that from 103 patients, 12.6 % (n = 13) still had parasitaemia 1 day after the treatment was finished. On day 0, of the 94 evaluated samples, wild-type alleles were identified in 73.4 % (n = 69) for pfmdr1 N86Y position and only one sample carried the mutant allele (Y) for pfmdr1 1246; 14 % of these samples showed increased pfmdr1 copy number; 100 % (n = 21) had wild-type allele of k13 gene in all the studied positions.

Discussion

These results showed changes in parasite profile susceptibility to AL in comparison to the baseline data from 2002 to 2004 and on the genotyping characteristics; the clinical outcome after treatment with AL did not link a particular genotype with treatment failure; observed changes do not provide sufficient evidence for a treatment policy change, but they suggest that a carefully monitoring is needed in this area.

Evaluation of dried blood spot collection paper blotters for avian sexing by direct PCR

Abstract 1. Avian sexing by polymerase chain reaction (PCR) plays an important role in sexual identification of avian species with similar phenotypes. Dried blood spots (DBSs) on paper blotters can help reduce the cost and problem of sample transportation and processing. 2. In the first experiment, several kinds of papers were evaluated for collecting DBS for chicken sexing by direct PCR with different processing methods. The most practical method with cost optimality was the utilisation of Whatman grade 1 filter paper with the combination of methanol fixation and boiling. 3. A second experiment was performed to determine whether cross-contamination could occur among samples cut with the same scissors. No-clean scissors were compared with ones cleaned with bleach-ethanol combination or 0.3N HCl. The PCR results showed that all three methods provided correct amplicon sizes without any false-positives regardless of the utilisation of cleaning intervention. 4. In conclusion, a technique that is suitable for DBS collection for avian sexing by direct PCR with cost efficacy was developed, and it was also shown that the utilisation of the same pair of scissors for several DBS samples did not affect the PCR results.

Superparamagnetic-bead Based Method: An Effective DNA Extraction from Dried Blood Spots (DBS) for Diagnostic PCR

INTRODUCTION

Storing blood as dried spots on filter paper is a trustworthy approach used in genetic screening issues which justifies the necessity for a reliable DNA extraction method. The present work aims to investigate the effectiveness of superparamagnetic-bead based method in extracting DNA from dried blood spots (DBS).

MATERIALS AND METHODS

Sixteen venous blood samples collected in K3-EDTA tubes (400μl of whole blood) were used for the spotting (4 circles each 100μl) on Ahlstrom 226 grad filter papers, for extraction and comparison. To ensure effectiveness, the extracted DNA was checked for quantity using the Quant-iT™ dsDNA Broad-Range Assay Kit and for quality by polymerase chain reaction (PCR) amplification of 344 bp segment of the HBB gene. Hybridization assays based on the dynamic allele specific hybridization (DASH) technique for two hemoglobin beta (HBB) mutations in genomic DNA extracted from DBS of ß-thalassemia patients were also performed to ensure the quality of extraction.

RESULTS

The results revealed a compatible effectiveness of the superparamagnetic-bead based method in extracting DNA from DBS particularly when incubating the DBS with lysis buffers BL+BLM overnight. A mean concentration of 21ng/ μl was obtained with lysis buffers BL+BLM overnight incubation compared to 5.2 ng/μl for 2 h incubation with lysis buffers BL+BLM and 4.7 ng/μl when extraction performed using the lysis buffer BLM alone. Moreover, PCR amplification of 344 bp segment of the HBB showed a good quality of the extracted DNA.

CONCLUSION

It was concluded that the superparamagnetic-bead based method is a reliable and effective method for DNA extraction from DBS and can be adopted for genetic diagnostic purposes.

The use of Taqman genotyping assays for rapid confirmation of β-thalassaemia mutations in the Malays: accurate diagnosis with low DNA concentrations

INTRODUCTION

In Malaysia, β-thalassaemia is a common inherited blood disorder in haemoglobin synthesis with a carrier rate of 4.5%. Currently, PCR-incorporating techniques such as amplification refractory mutation system (ARMS) or reverse dot blot hybridization (RDBH) are used in β-thalassaemia mutation detection. ARMS allows single-mutation identification using two reactions, one for wild type and another for mutant alleles. RDBH requires probe immobilization and optimization of hybridization and washing temperatures which is time consuming. The aim of our study was to investigate whether β-thalassaemia mutations can be identified in samples with low DNA concentrations.

METHODS

Genotype identification of common β-thalassaemia mutations in Malays was carried out using Taqman genotyping assays.

RESULTS

Results show that the Taqman assays allow mutation detection with DNA template concentrations as low as 2-100 ng. In addition, consistent reproducibility was observed in the Taqman assays when repeated eight times and at different time intervals.

CONCLUSION

The developed sensitive Taqman assays allow molecular characterization of β-thalassaemia mutations in samples with low DNA concentrations. The Taqman genotyping assays have potential as a diagnostic tool for foetal blood, chorionic villi or pre-implantation genetic diagnosis where DNA is limited and precious.

Isolation of human genomic DNA for genetic analysis from premature neonates: a comparison between newborn dried blood spots, whole blood and umbilical cord tissue

Background

Genotyping requires biological sample collection that must be reliable, convenient and acceptable for patients and clinicians. Finding the most optimal procedure of sample collection for premature neonates who have a very limited blood volume is a particular challenge. The aim of the current study was to evaluate the use of umbilical cord (UC) tissue and newborn dried blood spot (DBS)-extracted genomic DNA (gDNA) as an alternative to venous blood-derived gDNA from premature neonates for molecular genetic analysis.

All samples were obtained from premature newborn infants between 24-32 weeks of gestation. Paired blood and UC samples were collected from 31 study participants. gDNA was extracted from ethylenediaminetetraacetic acid (EDTA) anticoagulant-treated blood samples (~500 μl) and newborn DBSs (n = 723) using QIAamp DNA Micro kit (Qiagen Ltd., Crawley, UK); and from UC using Qiagen DNAeasy Blood and Tissue kit (Qiagen Ltd., Crawley, UK). gDNA was quantified and purity confirmed by measuring the A₂₆₀:A₂₈₀ ratio. PCR amplification and pyrosequencing was carried out to determine suitability of the gDNA for molecular genetic analysis. Minor allele frequency of two unrelated single nucleotide polymorphisms (SNPs) was calculated using the entire cohort.

Results

Both whole blood samples and UC tissue provided good quality and yield of gDNA, which was considerably less from newborn DBS. The gDNA purity was also reduced after 3 years of storage of the newborn DBS. PCR amplification of three unrelated genes resulted in clear products in all whole blood and UC samples and 86%-100% of newborn DBS. Genotyping using pyrosequencing showed 100% concordance in the paired UC and whole blood samples. Minor allele frequencies of the two SNPs indicated that no maternal gDNA contamination occurred in the genotyping of the UC samples.

Conclusions

gDNAs from all three sources are suitable for standard PCR and pyrosequencing assays. Given that UC provide good quality and quantity gDNA with 100% concordance in the genetic analysis with whole blood, it can replace blood sampling from premature infants. This is likely to reduce the stress and potential side effects associated with invasive sample collection and thus, greatly facilitate participant recruitment for genetic studies.

High quality genome-wide genotyping from archived dried blood spots without DNA amplification

Spots of blood are routinely collected from newborn babies onto filter paper called Guthrie cards and used to screen for metabolic and genetic disorders. The archived dried blood spots are an important and precious resource for genomic research. Whole genome amplification of dried blood spot DNA has been used to provide DNA for genome-wide SNP genotyping. Here we describe a 96 well format procedure to extract DNA from a portion of a dried blood spot that provides sufficient unamplified genomic DNA for genome-wide single nucleotide polymorphism (SNP) genotyping. We show that SNP genotyping of the unamplified DNA is more robust than genotyping amplified dried blood spot DNA, is comparable in cost, and can be done with thousands of samples. This procedure can be used for genome-wide association studies and other large-scale genomic analyses that require robust, high-accuracy genotyping of dried blood spot DNA.

Profiling of acylcarnitines and sterols from dried blood or plasma spot by atmospheric pressure thermal desorption chemical ionization (APTDCI) tandem mass spectrometry

Free carnitine and acylcarnitines play an important role in the metabolism of fatty acids. Sterols are structural lipids found in the membranes of many eukaryotic cells, and they also have functional roles such as the regulation of membrane permeability and fluidity, activity of membrane-bound enzymes and signals transduction. Abnormal profiles of these compounds in biological fluids may be useful markers of metabolic changes. In this review, we describe the subset of the lipidome represented by acylcarnitines and sterols, and we summarize how these compounds have been analyzed in the past. Over the last 50years, lipid mass spectrometry (MS) has evolved to become one of the most useful techniques for metabolic analysis. Today, the introduction of new ambient ionization techniques coupled to MS (AMS), which are characterized by the direct desorbing/ionizing of molecules from solid samples, is generating new possibilities for in situ analysis. Recently, we developed an AMS approach called APTDCI to desorb/ionize using a heated gas flow and an electrical discharge to directly analyze sterols and indirectly investigate acylcarnitines in dried blood or plasma spot samples. Here, we also describe the APTDCI method and some of its clinical applications, and we underline the common complications and issues that remain to be resolved.

A powerful couple in the future of clinical biochemistry: in situ analysis of dried blood spots by ambient mass spectrometry

Since the early 1960s, dried blood spots (DBS) on filter paper have been used in clinical applications. The first key milestone in the use of DBS was the screening of phenylketonuria and other inborn errors of metabolism using microbiological and enzymatic analytical methods. 20 years after its introduction, advanced mass spectrometers and new soft ionization techniques have permitted the coupling of liquid chromatography with MS and tandem MS (MS/MS) and since the 1990s, DBS analysis by LC-MS/MS expanded screening to many inborn errors of metabolism simultaneously. Recently, DBS-LC-MS/MS analysis has been used in other fields such as pharmacology, toxicology and forensic sciences. Today, new ambient ionization techniques, coupled to MS, directly desorb/ionize molecules from solid samples. This presents new opportunities for the in situ analysis of DBS. Most likely, ambient MS methods will be used to analyze DBS, increasing the clinical applications of MS within the next 10 years.

Long-term stability of thyroid hormones and DNA in blood spots kept under varying storage conditions

BACKGROUND

Congenital hypothyroidism is screened using blood spotted on filter paper that may be transported from remote areas to central testing facilities. However, storage conditions and transportation may affect sample quality.

METHODS

We examined long-term stability of thyroid-stimulating hormone (TSH) and thyroxin (TT4) in blood spotted on filter paper, which was stored at room temperature (RT), 4°C and -20°C under continuous or intermittent power supply (six hours on and six hours off around the clock.) Hormone levels in the discs were measured periodically for up to ten years. Extraction of DNA from blood spots and polymerase chain reaction were performed.

RESULTS

Our results showed that TT4 was stable for up to 6.1, 5.34 and 5.16 years when stored at -20°C, 4°C and RT, respectively. TSH was stable for up to 2.7 years at RT, and for up to 6.5 and 4.1 years when stored at -20°C and 4°C, respectively, under continuous power supply. However, under intermittent power supply, TSH was stable for up to 3.8 and 2.5 years when stored at 4°C and -20°C, respectively. Mitochondrial cytochrome oxidase and sex-determining region of Y chromosome genes were successfully amplified from DNA extracted from the blood spots.

CONCLUSION

Our data indicate that TT4 and TSH are most stable in blood spots stored at -20°C under continuous power supply. However, they can be stored at RT or at 4°C and -20°C under interrupted power supply for at least 2.5 years. Moreover, the DNA extracted from the blood spots was intact and suitable for genetic studies.

Meeting report: the use of newborn blood spots in environmental research: opportunities and challenges

INTRODUCTION

Dried blood spots (DBS) are routinely collected from newborns in the United States using a heel stick. The DBS are screened for inborn errors of metabolism and other disorders. More states are keeping residual spots and making them available for research purposes. DNA extraction from the DBS has been widely applied; however, the development of methods to measure a range of environmental toxicants in DBS has been a more recent goal for laboratory scientists and epidemiologists.

OBJECTIVES

The purpose of the meeting was to examine the utility of DBS to measure environmental exposures. Speakers and discussants were invited to present data and discuss approaches to measure a range of analytes using DBS.

RESULTS

This meeting was held on 20 February 2007 at the University of North Carolina at Chapel Hill. The audience consisted of epidemiologists, chemists, and staff from state public health programs, the Centers for Disease Control and Prevention, and the National Institutes of Health. The meeting included presentations on measurement of flame-retarding chemicals and pesticides, metals, perchlorate, infectious agents, markers of immune status, and protein adducts. Analytical methods included mass spectrometry, atomic absorption, molecular methods, and microfluidic techniques. Significant progress was reported, but important challenges remain. Concerns including storage conditions, sample volume, contamination, and normalization require additional systematic evaluation. In addition, DBS storage and access policies require coordination.

CONCLUSIONS

DBS remain a highly valuable resource for clinical, epidemiologic, and toxicologic investigation. The use of DBS to measure environmental exposures shows promise but additional work is necessary before more widespread use is warranted.

Molecular genetic confirmatory testing from newborn screening samples for the common African-American, Asian Indian, Southeast Asian, and Chinese beta-thalassemia mutations

beta-Thalassemia is a serious health problem in the United States, especially in California, due to increased Asian immigration. Neonatal screening by using high-performance liquid chromatography (HPLC) or isoelectric focusing (IEF) may lead to confusion due to interactions of various hemoglobinopathies with beta-thalassemia. Our purpose was to develop single-tube multiplexed PCR assays using original neonatal screening specimens to identify the mutations responsible for beta-thalassemia in order to expedite diagnostic confirmation. Primers were designed for two to six common ethnic-specific mutations using the amplification refractory mutation system (ARMS). This multiplex ARMS approach was standardized using DNA samples with known mutations for beta-thalassemia in those of Asian (Southeast Asian, Chinese, and Asian Indian) and African-American descent. Specimens from African-American neonates were tested for two mutations (-88 and -29); Asian Indians for five mutations (IVSI-1, IVSI-5, codons (Cd) 41/42, Cd 8/9, and 619-bp deletion); Chinese, Taiwanese, and Southeast Asians for seven mutations (Cd 41/42, Cd 17, -28, IVSII-654, Cd 71/72, IVSI-5, and IVSI-1). We identified each of these beta-thalassemia mutations in multiplexed ARMS from positive control samples. We tested 25 anonymized dried blood specimens from neonates who had been diagnosed with beta-thalassemia and who also belonged to these ethnic groups. We detected a mutation specific to the neonate's ethnic group using the ARMS approach in nearly all specimens, and the results were confirmed by sequencing. Multiplexed ARMS for ethnic-specific beta-thalassemia mutations from the original newborn screening dried blood specimens is a rapid and efficient approach for diagnostic confirmation.

Recently available techniques applicable to genetic problems in the Middle East

In this paper, we address the preventive health aspects of genetic problems in the Middle East and provide guidelines to prioritize preventive strategies. Applications of various novel genetic techniques such as comprehensive neonatal screening, high throughput heterozygote detection, preimplantation genetic diagnosis, Affymetrix systems, the NanoChip system and a new way of sensitive karyotyping for single-cell chromosome abnormalities are discussed. In conclusion, from the various genetic techniques available, each country should adopt strategies most suitable to its genetic needs and should prioritize the programs to be used in prevention.

Genetic screening: carriers and affected individuals

Genetic screening utilizes analytical approaches adapted for high throughput to identify carrier and affected individuals in a targeted population. Currently, genetic screening focuses on carrier screening, prenatal screening, and newborn screening. Newborn screening should serve as a model for all genetic screening, with more than forty years of experience and numerous lessons learned. As with all genetic screening, there are policy concerns in newborn screening regarding which disorders and technologies should be selected, and how centralized or decentralized the process to set policy should be. The need to share experiences and develop databases transcends all other policy considerations in genetic screening. The future will see population-based screening for adult-onset disorders. However, there needs to be extensive research to define predictive risk for various ethnocultural groups and to determine effective interventions. Ethical concerns regarding the timing of population screening, as well as the scope of use of information, will need to be resolved if genomic medicine will achieve its promise of a predictive, preventive, and personalized medicine.

Blood acylcarnitine levels in normal newborns and heterozygotes for medium-chain acyl-CoA dehydrogenase deficiency: a relationship between genotype and biochemical phenotype?

Patients with medium-chain acyl-CoA dehydrogenase (MCAD) deficiency are unable to metabolize medium-chain fatty acids. Affected patients display a characteristic acylcarnitine profile when blood spots are collected after birth and analysed by tandem mass spectrometry. To determine the potential risk of metabolic decompensation in newborns with elevations of diagnostic metabolites (octanoylcarnitine>0.3, but <1 micromol/L), we investigated the relationship between octanoylcarnitine (C8) concentration in neonatal blood spots and the 985A>G MCAD genotype. Octanoylcarnitine values from 7140 newborns' blood spots were sorted. The highest C8 was approximately 0.7 micromol/L, which is below the range in classical MCAD deficiency. Samples with C8 levels above 0.25 micromol/L (group C) represented 1.4% of the total. Values between 0.05 and 0.25 micromol/L (group B) made up 87.8% of the total; 10.8% of the samples had C8 values less than 0.05 micromol/L (group A). One hundred samples from each group were selected at random and genomic DNA was amplified by PCR and analysed for the presence of the 985A>G mutation. The analysed samples from groups A and B were all homozygous normal. The 100 samples from group C contained 26 samples that were heterozygous for the 985A>G mutation. These findings indicated that the frequency distribution of heterozygotes is not random within this population. Group C was further divided into C1, the 26 heterozygotes, and C2, the remaining 74 newborns in group C. In group C1 only 2 (8%) were in the 'high-risk' group characterized by either low birth weight or requiring admission to the neonatal intensive care unit. In contrast, 28 (38%) from C2 had low birth weight or were in the neonatal intensive care unit. In our dataset, C8/C2 and C8/C12 ratios were also significantly elevated in both groups C1 and C2 compared to controls (group B). In contrast to what others have reported, the ratio of C8/C10 did not differentiate the group B controls from heterozygotes or other patients in metabolic distress (group C2), but were lower than those seen in classic MCAD or mild MCAD deficiency.

Rapid confirmation of Southeast Asian and Filipino alpha-thalassemia genotypes from newborn screening specimens

Alpha(+)-thalassemia (-alpha) is prevalent throughout tropical and subtropical regions of world, whereas alpha(0)-thalassemia (--) occurs at higher frequency in Southeast Asia. Homozygosity for the alpha(0)-thalassemia deletion (--/--) is a serious health problem in Southeast Asia and the Philippines and is responsible for the majority of hydrops fetalis in this region. Asian immigration in United States has impacted the demography of genetic disease in U.S. As Asians comprise of 10% of all California births and represent a population at highest risk for alpha(0)-thalassemia, we developed a rapid and efficient PCR approach to detect the common alpha(0)-thalassemia deletions in Southeast Asians and Filipinos using newborn screening specimen.

High frequency of leukemic clones in newborn screening blood samples of children with B-precursor acute lymphoblastic leukemia

The detection of leukemia cells on newborn genetic screening cards ("Guthrie cards") of a small group of patients and several sets of identical twins developing acute lymphoblastic leukemia (ALL) with identical phenotypic and chromosomal markers has provided evidence that childhood ALL cases may arise in utero. We conducted a retrospective study of a randomly selected group of childhood B-precursor ALL patients to determine the frequency of the presence of "leukemic" clones prenatally in ALL cases by testing newborn screening cards. The 17 ALL patients analyzed had a median age of 46 months (range, 18 months to 13 years) and had median presenting white blood cell (WBC) counts of 10 950/microL (range, 2900-70 300/microL) at diagnosis. A clonal rearrangement of the immunoglobulin heavy chain (IgH) gene was identified in diagnostic lymphoblasts and sequenced and patient-specific primers were used to amplify DNA from blood samples on the patient's newborn screening cards. Twelve of the 17 (71%) analyzed newborn cards had detectable IgH rearrangements amplified by seminested polymerase chain reaction. DNA sequencing confirmed that the IgH rearrangements detected matched the IgH sequences identified from diagnostic leukemia cells, indicating the presence of a "leukemic" clone at birth. There were no differences in age or presenting WBC counts between the cases with or without positive newborn screening cards. All 6 patients with hyperdiploid ALL had detectable "leukemic" clones on their cards. The results of our study support the notion that a high proportion of childhood B-precursor ALL cases arise in utero, although postnatal events are also important factors in leukemogenesis.

Outcome of the first 3-years of a DNA-based neonatal screening program for glutaric acidemia type 1 in Manitoba and northwestern Ontario, Canada

Glutaric acidemia type 1 (GA1) is overrepresented in the aboriginal population of Island Lake, Manitoba, and northwestern Ontario who speak the Ojibway-Cree (Oji-Cree) dialect. The carrier frequency in these communities has been predicted to be as high as 1 in 10 individuals. Prior to beginning newborn screening for GA1 in May 1998, 18 of 20 affected patients diagnosed at this center have been from these high-risk communities. Most have followed an acute encephalopathic course with permanent neurologic sequelae and high mortality. They excrete small amounts of glutaric acid and 3-hydroxyglutaric acid and have significant residual enzyme activity. A single homozygous mutation in glutaryl-CoA-dehydrogenase (GCDH IVS-1 + 5g right arrow t) has been identified in this population. DNA-based newborn screening targeted to our high-risk communities was begun in order to provide presymptomatic detection and treatment of affected patients. Of the first 1176 newborns screened, 4 affected infants were identified and treated with a low-protein diet, carnitine, and riboflavin. All 4 infants have required numerous hospitalizations for treatment of intercurrent illnesses. Eventually, 3 infants presented with acute dystonic encephalopathy and seizures along with permanent neurological sequelae. One of these infants died unexpectedly at home at 18 months of age. The fourth, now 9 months old, has had a gastrostomy tube placed to facilitate fluid replacement in addition to a standard treatment protocol and is doing well. The reasons for our initial disappointing outcomes in the first 3 of 4 affected babies are likely multiple. Based on our early experience and that of other centers screening newborns for GA1, current therapeutic strategies may be insufficient in preventing the occurrence of neurologic sequelae in some children. An incomplete understanding of the neurotoxic mechanisms underlying this devastating disorder hampers effective management.

Population-based screening for rare mutations: high-throughput DNA extraction and molecular amplification from Guthrie cards

To determine the population-based frequency of a rare mutation (the 121ins2 mutation in the surfactant protein B gene), we developed high-throughput techniques to extract reliably and rapidly amplifiable DNA from Guthrie cards. Using a 3-mm punch from each of 10,044 Guthrie cards obtained from the Missouri Department of Health, we extracted DNA with deionized water by heating in the presence of 2% Chelex in a 96-well format. Average yield of DNA from each punch was 52.6 +/- 21 microg. Using 36mer primers and a 10-microL reaction volume, we amplified a 354-bp fragment of the surfactant protein B gene that contained the mutation and identified the mutation by its susceptibility to restriction enzyme digestion with SfuI. The procedure required 5 h per 96 samples but only 2 h of technician time. The amplification rate on the first attempt was 99.2%. Based on detection of eight individuals heterozygous for the mutation (confirmed by direct sequencing), we estimate the allele frequency to be 0.8/1000 individuals, an estimate not significantly different from previous estimates based on independent methods. High-throughput DNA extraction and amplification will permit establishment of DNA banks as well as efficient estimation of population-based genotype frequency for both rare and common genetic disorders.

Calibration, specificity and trueness of a postheparin plasma lipoprotein lipase assay

Measurement of lipoprotein lipase activity in postheparin plasma is generally accompanied by moderate within-run variation CV(W-R) (<10%) and higher between-run variation CV(B-R) (5-25%). A calibration system was introduced in order to improve the reproducibility of measurements and to compare lipoprotein lipase activities from different days. Every day a calibration curve for lipoprotein lipase activity was constructed. Fifteen calibration curves designed over 2 years, show linearity over the whole biological spectrum and a considerable reduction of between-run variation in lipoprotein lipase activity, from 42% to 5.3% as estimated from two control postheparin plasma samples. The lipoprotein lipase calibration system is an easy and very cheap arrangement, which makes it possible to compare lipoprotein lipase activities achieved over years. When the lipoprotein lipase control values are compared with reference lipoprotein lipase samples determined in other lipase laboratories, the calibration-control system becomes an important tool for reducing analytical bias. The article reviews the original analytical criteria of catalytic measurement of lipoprotein lipase activity and describes the implementation of the calibration-control system. We describe a model for reduction of the analytical variability in the measurement of lipoprotein lipase activity. Other standardization efforts need to be made in the future, especially to define the reference material for calibration.

Genetic disorders of neonatal respiratory function

Genetic risk for respiratory distress in infancy has been recognized with increasing frequency in neonatal intensive care units. Reports of family clusters of affected infants and of ethnic- and gender-based respiratory phenotypes point to the contribution of inheritance. Similarly, different outcomes among gestationally matched infants with comparable exposures to oxygen, mechanical ventilation, or nutritional deficiency also suggest a genetic risk for respiratory distress. Examples of inherited deficiency of surfactant protein B in both humans and genetically engineered murine lineages illustrate the importance of identifying markers of genetic risk. In contrast to developmental, inflammatory, or nutritional causes of respiratory distress that may resolve as infants mature, genetic causes result in both acute and chronic (and potentially irreversible) respiratory failure. The availability of clinically useful genetic markers of risk for respiratory distress in infancy will permit development of rational strategies for treatment of genetic lung disorders of infancy and more accurate counseling of families whose infants are at genetic risk for development of respiratory distress at birth or during early childhood. We review examples of genetic variations known to be associated with or cause respiratory distress in infancy.

Use of filter paper for the collection and analysis of human whole blood specimens

The Centers for Disease Control and Prevention and its partners have been operating the Newborn Screening Quality Assurance Program for >20 y. The program helps participating laboratories to evaluate and improve the quality of their newborn-screening testing efforts by providing quality control dried blood spot materials and proficiency-testing materials for the external evaluation of screening programs. The Newborn Screening Quality Assurance Program provides an independent evaluation of filter papers approved by the Food and Drug Administration for the collection of blood for clinical tests. These activities have created a mechanism for the validation of the filter paper blood collection device and the standardization of materials and methods for the analysis of dried blood spots.

Hepatic carnitine palmitoyl transferase 1 (CPT1 A) deficiency in North American Hutterites (Canadian and American): evidence for a founder effect and results of a pilot study on a DNA-based newborn screening program

We describe six patients with hepatic carnitine palmitoyl transferase (CPT1 A) deficiency who are members of a large extended Hutterite kindred living in widely scattered communities in the United States and Canadian Prairies. Two patients have significant neurological impairment due to severe recurrent hypoglycemic crises. The remaining four patients with earlier detection and treatment have near normal outcomes. The Canadian and American Hutterite families share two common ancestors who married in 1812, about 60 years before the Hutterites arrived in North America and prior to their subdivision into the three groups (Schmiedeleut, Dariusleut, and the Lehrerleut). These patients share a common haplotype on chromosome 11q13 and are all homozygous for a common CPT1 A G710E mutation, suggesting a founder effect. The clustering of such a rare disorder of fatty acid oxidation prompted us to initiate a pilot DNA-based neonatal screening program to determine the carrier frequency of this mutation in Hutterite newborns with the participation and support of the community. To date our carrier frequency is 1/16, close to the predicted frequency based on diagnosed patients and number of births. We believe our newborn screening program for CPT1 A deficiency in the Hutterite community will serve as a prototype model for delivery of targeted genetic services to other similar unique genetic isolates.

Platelet PlA2 polymorphism enhances risk of neurocognitive decline after cardiopulmonary bypass. Multicenter Study of Perioperative Ischemia (McSPI) Research Group

BACKGROUND

Neurocognitive decline, often produced by atherosclerotic plaque embolization, remains a frequent complication of cardiopulmonary bypass. Plaque fragments may initiate local thrombosis, which, in turn, aggravates the embolic insult. Prothrombotic genetic factors may exacerbate this process. We investigated whether the PlA2 polymorphism of platelet GPIIIa, a prothrombotic risk factor in other cardiovascular settings, is associated with early neurocognitive decline after cardiopulmonary bypass.

METHODS

Neurocognitive changes were evaluated by the Mini-Mental State Examination administered preoperatively and on postoperative day 4 and the PlA genotype determined in 70 patients undergoing cardiopulmonary bypass.

RESULTS

Forty-nine patients were PlA1/A1, and 21 were PlA1/A2 or PlA2/A2. Fifty-two patients (74%) demonstrated post-cardiopulmonary bypass neurocognitive decline, of which 34 were PlA1/A1 and 18 were PlA1/A2 or PlA2/A2 Multivariate analysis revealed that the PlA2 genotype and baseline Mini-Mental State Examination were significantly associated with greater neurocognitive decline (decreased Mini-Mental State Examination scores, p = 0.036 and 0.024, respectively).

CONCLUSIONS

This study demonstrates a link between the PlA2 allele of platelet GPIIIa and more severe neurocognitive decline after cardiopulmonary bypass. Although the mechanism is unknown, it could represent exacerbation of platelet-dependent thrombotic processes associated with plaque embolism.

Antifreeze solution improves DNA recovery by preserving the integrity of pathogen-infected blood and other tissues

Preserving blood samples for shipping and later DNA extraction has been performed by cooling, freezing, drying, freeze-drying, and protease treatment, among other methods. Most methods to preserve field samples for further DNA extraction do not prevent cellular and DNA damage or are useful only in preserving them for short periods. This report introduces a novel method for blood and tissue that allows preservation in freezing temperatures for a prolonged period of time. The solution reported here (20% ethylene glycol-propylene glycol) preserves cells and tissues integrity, as judged by microscopic analysis, and improves DNA yield and quality.

Rapid, efficient method for multiplex amplification from filter paper

Guthrie cards derived from the New York State Newborn Screening Program were utilized to develop a rapid, economical method for amplifying multiple genes to detect mutations that impact public health. These specimens are untraceable to the donor because identifiers are removed and discarded; therefore, these pilot studies were carried out anonymously. The sample preparation requires minimal manipulation, is amenable to automation, and is useful in laboratories which routinely process large numbers of samples, such as those in typical newborn screening laboratories. Multiple gene fragments may be amplified from a 1 mm punch which contains less than 1 microl of whole blood. The blood spots used in these studies contain sufficient material for up to 25 amplification reactions which multiplex at least four different gene fragments each. Since sufficient material remains on the card after the routine testing is complete, this simple assay can greatly expand the efficacy of current newborn screening programs by permitting DNA diagnosis of some disorders when indicated, particularly those in which genotype-phenotype correlations are useful. In addition to newborn screening specimens, this method is also applicable to whole blood from adults after phlebotomy and from lymphoblastoid cell lines. Use of filter paper for DNA analysis is particularly useful for shipped specimens or for population studies whose subjects are refractory to phlebotomy.

AluY insertion (IVS4-52ins316alu) in the glycerol kinase gene from an individual with benign glycerol kinase deficiency

Glycerol kinase deficiency has three distinct forms: an isolated form which may be benign or symptomatic, and a complex form which is symptomatic and part of an Xp21 contiguous gene syndrome. Here we report the case of a male with benign isolated glycerol kinase deficiency who was incidentally identified after observation of pseudohypertriglyceridemia. DNA sequencing of this subject's glycerol kinase gene showed the insertion of an AluY sequence in intron 4 of the glycerol kinase gene. Although Alu insertions have been implicated in other diseases, and a closely related AluY element is found as an insert in the C1 inhibitor gene in patients with hereditary angioedema, this is the first case of glycerol kinase deficiency caused by an Alu insertion.

Optimization of an automated DNA purification protocol for neonatal screening

CONTEXT

Collection of blood from newborns is a standard clinical procedure used for genetic screening. Typically, blood from a heel prick is absorbed onto standard collection paper and dried before analysis of metabolites, proteins, hormones, and more recently DNA.

OBJECTIVE

To evaluate strategies to purify DNA for use with automated workstations.

DESIGN

Two factors were used to evaluate several DNA purification protocols: residual heme contamination and amplification yield. The protocol that produced DNA with the lowest heme content and the highest amplification yield was selected. In combination with those two performance factors, the protocol with the fewest number of steps was chosen to reduce reagent use and processing time.

SETTING

Industrial research and development laboratory.

RESULTS

Robust amplification of DNA isolated from dried blood spots was demonstrated using both fluorescence and agarose gel-based detection methods. In addition, the samples had consistent DNA volumes and had no detectable cross-contamination. Suggested instrument settings, equipment, and supplies were included for automated processing of DNA from dried blood spots.

CONCLUSION

A 4-step DNA processing protocol was developed for dried blood spots. The protocol could be performed in either a manual or automated format, making it possible to process hundreds of samples in 1 day.

Biological specimen banks in neonatal screening

The Danish neonatal screening program analyses dried blood spot samples (DBSS) from close to 70,000 newborns annually from Denmark, Greenland and the Faroe Islands. Since 1982, all DBSS have been stored in a biological specimen bank at -20 degrees C as a routine procedure after analysis. Before sampling, parents are given written information about the screening tests, the biobank and its use, and can choose to opt out. Since 1993 the biobank has been regulated by specific legislation, and thus assumes a unique position among biological specimen banks. Its purposes are: (i) diagnosis and treatment of diseases screened for, including repeat testing, quality assurance and group statistics; (ii) other diagnostic uses during infancy; and (iii) research projects. The stored samples have been used successfully to diagnose a range of genetic diseases using biochemical and molecular genetic assays, and to diagnose congenital CMV and toxoplasmosis infections using assays for specific IgM antibodies and pathogen nucleic acids. The unbiased nature and comprehensive coverage of the samples in the biobank make them attractive for research purposes. Our studies have focused on the epidemiology of genetic disease alleles and other molecular disease markers and on retrospective screening projects, which have allowed rapid appraisal of the performance of novel screening modalities, saving years of prospective screening trials. Storage of neonatal screening samples is thus beneficial not only to the individual testees, but also to future generations of newborns.

Bacterial species identification after DNA amplification with a universal primer pair

The diagnosis of bacterial infections can be difficult and time consuming. Rapid and reliable molecular triage of potentially infected patients, particularly the young and the elderly, would prevent unnecessary hospitalizations, reduce associated medical costs, and improve the quality of care. Polymerase chain reaction (PCR) amplification utilizing a universal bacterial primer pair, followed by hybridization with species-specific probes, would allow rapid identification of the presence or absence of bacterial DNA, along with an identification of the bacterial species present. Molecular microbiological analyses will require access to bacterial strain standards that can be catalogued and distributed to clinical laboratories. We amplified template DNA in filter paper spots containing boiled bacteria from 14 clinical isolates using a universal primer pair for the 16S ribosomal RNA (rDNA) coding sequence. Species-specific probes were hybridized to the amplification products for bacterial species identification. We conclude that template DNA can be identified with species-specific probes after universal bacterial amplification with a single primer pair. We also demonstrate a rapid and efficient method for the long-term storage and cataloguing of bacterial DNA for use in quality control at clinical laboratories adopting molecular diagnostic methodologies. We speculate that PCR amplification combined with species-specific probe hybridization not only will represent an improvement over culture-based methods in terms of speed, sensitivity, and cost, but will also allow for the identification of unculturable bacteria and emerging or reemerging pathogenic organisms.

Amplification of Guthrie card DNA: effect of guanidine thiocyanate on binding of natural whole blood PCR inhibitors

Amplification of DNA from whole blood collected on Guthrie card filter paper presents considerable technical obstacles due to the presence of natural PCR inhibitors (protein, heavy metals, heme, and heme degradation products) and low copy number of genomic material. For this purpose we evaluated guanidine thiocyanate-impregnated filter paper (GT-903), a DNA collection device designed specifically to bind PCR inhibitors and preserve DNA in an aqueous extractable form. Compared to standard 903, which retains DNA and elutes inhibitors during aqueous extraction, we found GT-903 retained 90% of protein, hemoglobin, and iron. SDS-PAGE analysis indicated that the majority of the protein released from standard 903 corresponded to albumin (70-) and globin (15-kDa); negligible levels of these proteins were eluted from GT-903. To evaluate PCR efficiency, we amplified the 491 bp region encoding the cystic fibrosis delta F508 mutation. Using comparable template, we found GT-903 amplification more efficient than standard 903 following qualitative (TBE-PAGE) and quantitative (anti-dsDNA EIA) determination. We conclude that GT-903 provides a good DNA collection device and addresses the complications associated with natural PCR inhibitors.

Increased hepatic iron concentration in nonalcoholic steatohepatitis is associated with increased fibrosis

BACKGROUND & AIMS

Nonalcoholic steatohepatitis (NASH) is a chronic liver disease that occasionally progresses to cirrhosis but usually has a benign course. The aim of this study was to investigate the role of the hemochromatosis mutation Cys282Tyr in development of the mild hepatic iron overload found in some patients with NASH and its association with hepatic damage in these patients.

METHODS

Fifty-one patients with NASH were studied. The presence of the Cys282Tyr mutation was tested in all patients, and the data were analyzed with respect to the histological grade of steatosis, inflammation, Perls' staining, hepatic iron concentration (HIC), and serum iron indices.

RESULTS

Thirty-one percent of patients with NASH were either homozygous or heterozygous for the Cys282Tyr mutation. This mutation was significantly associated with Perls' stain grade (P < 0.005), HIC (P < 0.005), and transferrin saturation percentage (P < 0.005) but not with serum ferritin levels. Linear regression analysis showed that increased hepatic iron (Perls' stain or HIC) had the greatest association with the severity of fibrosis (P < 0.0001).

CONCLUSIONS

The Cys282Tyr mutation is responsible for most of the mild iron overload found in NASH and thus has a significant association with hepatic damage in these patients. Heterozygosity for the hemochromatosis gene mutation therefore cannot always be considered benign.

The clinical and molecular genetic approach to Duchenne and Becker muscular dystrophy: an updated protocol

Detection of large rearrangements in the dystrophin gene in Duchenne and Becker muscular dystrophy is possible in about 65-70% of patients by Southern blotting or multiplex PCR. Subsequently, carrier detection is possible by assessing the intensity of relevant bands, but preferably by a non-quantitative test method. Detection of microlesions in Duchenne and Becker muscular dystrophy is currently under way. Single strand conformational analysis, heteroduplex analysis, and the protein truncation test are mostly used for this purpose. In this paper we review the available methods for detection of large and small mutations in patients and in carriers and propose a systematic approach for genetic analysis and genetic counselling of DMD and BMD families, including prenatal and preimplantation diagnosis.

Use of stored newborn blood spots in research on birth defects: variation in retrieval rates by type of defect and infant characteristics

Stored blood spots from state newborn screening programs represent a potential source of DNA for molecular genetics research on birth defects. The stored blood spots of cases and controls from an epidemiologic database on congenital heart defects were sought in the present study, which aimed to establish the feasibility of linking the data sources and to examine blood spot retrieval rates for selected cardiac defects. Blood spots were located on 341 of 522 infants (65%) with congenital heart defects and for 1,484 of 1,645 infants without birth defects (84%) born in Maryland during 1981-1989. Retrieval rates were low among infants with clinically severe lesions such as truncus arteriosus (26%) but were considerably higher in infants with coarctation of the aorta (62%), pulmonic valve stenosis (71%), and atrial septal defect (76%). Retrieval rates were significantly lower for premature and low-birth-weight infants than among full-term, normal-birth-weight infants. Retrieval rates did not vary significantly by gender, race, county of residence, or parental socioeconomic characteristics. These results demonstrate the feasibility of linking epidemiologic databases with stored newborn blood specimens, especially for normal infants and even for infants with certain congenital heart defects, but raise concerns about the adequacy of such methods to obtain stored specimens from premature infants and from those with severe heart defects.

Beta-globin haplotypes from blood spots for follow-up of newborn hemoglobinopathy screening

The inheritance of sickle-cell anemia upon the background of the major beta-globin gene cluster haplotypes has been associated with differing risks for major organ failure, and more recently with response to hydroxyurea treatment. Early identification of beta-globin haplotypes in individuals with sickle-cell anemia may be a clinically useful prognostic factor for severity of disease expression. This report describes the use of whole-blood spots on filter papers from newborn hemoglobinopathy screening for beta-globin gene cluster haplotyping by the polymerase chain reaction.

Degradation of macromolecules during preservation of lyophilized pathological tissues

Methods of preserving biological specimens are becoming more important due to recent advances in molecular biological analysis. Storing samples in a freezer, however, is still the most commonly used method of preserving pathological specimens. We investigated the feasibility of using freeze-dried tissues stored at room temperature as an alternative method of preserving tissue samples for molecular analysis at the DNA, RNA, and protein levels. The freeze-dried tissues were transferred to a sealed vial filled with nitrogen gas and kept for months at room temperature. DNA and protein were stably preserved for at least 24 weeks. RNA, however, showed slight degradation after 10 weeks of storage. Controlling moisture and temperature during long-term storage was found to be important, as it significantly affected the stability of these cellular molecules in tissues. Shelf-stable preservation eliminates the need for storage in a freezer and allows convenient shipping of samples to distant places. These findings should provide practical basis for the development of a convenient and economical way of preserving pathological specimens for a variety of analyses in the field of molecular biology.

Susceptibility to hepatocellular carcinoma is associated with genetic variation in the enzymatic detoxification of aflatoxin B1

Aflatoxin B1 (AFB1) has been postulated to be a hepatocarcinogen in humans, possibly by causing p53 mutations at codon 249. AFB1 is metabolized via the phase I and II detoxification pathways; hence, genetic variation at those loci may predict susceptibility to the effects of AFB1. To test this hypothesis, genetic variation in two AFB1 detoxification genes, epoxide hydrolase (EPHX) and glutathione S-transferase M1 (GSTM1), was contrasted with the presence of serum AFB1-albumin adducts, the presence of hepatocellular carcinoma (HCC), and with p53 codon 249 mutations. Mutant alleles at both loci were significantly overrepresented in individuals with serum AFB1-albumin adducts in a cross-sectional study. Mutant alleles of EPHX were significantly overrepresented in persons with HCC, also in a case-control study. The relationship of EPHX to HCC varied by hepatitis B surface antigen status and indicated that a synergistic effect may exist. p53 codon 249 mutations were observed only among HCC patients with one or both high-risk genotypes. These results indicate that individuals with mutant genotypes at EPHX and GSTM1 may be at greater risk of developing AFB1 adducts, p53 mutations, and HCC when exposed to AFB1. Hepatitis B carriers with the high-risk genotypes may be an even greater risk than carriers with low-risk genotypes. These findings support the existence of genetic susceptibility in humans to the environmental carcinogen AFB1 and indicate that there is a synergistic increase in risk of HCC with the combination of hepatitis B virus infection and susceptible genotype.