DNA techniques for screening of inborn errors of metabolism

Identification of the genomic BCR-ABL1 fusion sequence from blood specimen stored on filter paper

Chronic myeloid leukaemia (CML) is characterized by the Philadelphia chromosome resulting in the BCR-ABL1 gene whose mRNA transcript detection is commonly used for diagnosis and monitoring of therapeutic response. However, in collected blood specimen degradation of mRNA has to be considered during storage and transport thus jeopardizing the analysis. We here describe an alternative DNA-based technique applied after long-term blood storage. DNA was isolated from dried blood stains from CML patients stored on filter paper (Guthrie cards) after a median period from diagnosis of 11 years (range: 5-12 years) and analyzed with a two round long-range multiplex PCR (MLR-PCR) to identify the genomic BCR-ABL1 breakpoint. Patient-specific individual BCR-ABL1 fusion sites were successfully detected in 10 out of 13 patients. Dried blood stains represent a valuable resource for genomic DNA analyses. Long term preservation is easily manageable in paper envelopes with the patient's medical files with a minimum of financial costs and efforts. Such the cooperation between laboratories and hospitals separated by long distances is facilitated rendering possible offering specialized genomic analyses to patients with CML virtually everywhere around the world. This technique may also be a valuable approach for diagnostic procedures on a high molecular level in related haematological malignancies.

Use of tandem mass spectrometry for multianalyte screening of dried blood specimens from newborns

BACKGROUND

Over the past decade laboratories that test for metabolic disorders have introduced tandem mass spectrometry (MS/MS), which is more sensitive, specific, reliable, and comprehensive than traditional assays, into their newborn-screening programs. MS/MS is rapidly replacing these one-analysis, one-metabolite, one-disease classic screening techniques with a one-analysis, many-metabolites, many-diseases approach that also facilitates the ability to add new disorders to existing newborn-screening panels.

METHODS

During the past few years experts have authored many valuable articles describing various approaches to newborn metabolic screening by MS/MS. We attempted to document key developments in the introduction and validation of MS/MS screening for metabolic disorders. Our approach used the perspective of the metabolite and which diseases may be present from its detection rather than a more traditional approach of describing a disease and noting which metabolites are increased when it is present.

CONTENT

This review cites important historical developments in the introduction and validation of MS/MS screening for metabolic disorders. It also offers a basic technical understanding of MS/MS as it is applied to multianalyte metabolic screening and explains why MS/MS is well suited for analysis of amino acids and acylcarnitines in dried filter-paper blood specimens. It also describes amino acids and acylcarnitines as they are detected and measured by MS/MS and their significance to the identification of specific amino acid, fatty acid, and organic acid disorders.

CONCLUSIONS

Multianalyte technologies such as MS/MS are suitable for newborn screening and other mass screening programs because they improve the detection of many diseases in the current screening panel while enabling expansion to disorders that are now recognized as important and need to be identified in pediatric medicine.

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.

Mutation detection by TaqMan-allele specific amplification: application to molecular diagnosis of glycogen storage disease type Ia and medium-chain acyl-CoA dehydrogenase deficiency

We have devised an allele-specific amplification method with a TaqMan fluorogenic probe (TaqMan-ASA) for the detection of point mutations. Pairwise PCR amplification using two sets of allele-specific primers in the presence of a TaqMan probe was monitored in real time with a fluorescence detector. Difference in amplification efficiency between the two PCR reactions was determined by "threshold" cycles to differentiate mutant and normal alleles without post-PCR processing. The method measured the efficiency of amplification rather than the presence or absence of end-point PCR products, therefore allowing greater flexibility in designing allele-specific primers and an ample technical margin for allelic discrimination. We applied the TaqMan-ASA method to detect a prevalent 727G>T mutation in Japanese patients with glycogen storage disease type Ia and a common 985A>G mutation in Caucasian patients with medium-chain acyl-CoA dehydrogenase deficiency. The method can be automated and may be applicable to the DNA diagnosis of various genetic diseases.

A fluorogenic allele-specific amplification method for DNA-based screening for inherited metabolic disorders

Rapidly growing mutation databases for various inherited metabolic diseases raise the possibility of neonatal screening by DNA-based diagnosis. It is therefore important to develop a simple DNA diagnostic method which is suitable for processing a large number of samples. We have devised an allele-specific amplification (ASA) method with a fluorogenic probe (TaqMan probe) to detect point mutations. A pairwise PCR amplification with two sets of allele-specific primers was performed in the presence of the TaqMan probe with real-time fluorescence monitoring on an ABI PRISM 7700 sequence detector. The difference in the amplification efficiency between two PCR reactions was determined by "threshold" cycles to differentiate mutant and normal alleles. The method, TaqMan-ASA, does not require post-PCR processing, thus obviating potential PCR contamination. Since the entire procedure can be carried out in a 96-well microtiter plate format, it is easy to automate. We successfully applied TaqMan-ASA to detect a common g727t mutation in Japanese patients with glycogen storage disease type Ia and a prevalent a985g mutation in Caucasian patients with medium-chain acyl-CoA dehydrogenase deficiency.

Current activities at the Centers for Disease Control and Prevention's National Diabetes Laboratory

In 1997, the Centers for Disease Control and Prevention established the National Diabetes Laboratory in order to help prevent and treat type 1 diabetes. This state-of-the-art laboratory collaborates with research scientists and key national and international organizations throughout the world to identify and study risk factors for type 1 diabetes by developing measurements for glycosylated proteins, developing and evaluating technology for measuring genetic risk factors for the disease, and working to standardize autoantibody measurements. Developing improved technologies for diagnosing and managing diabetes and developing reference materials for properly calibrating and standardizing blood glucose meters are also critical aspects of the laboratory's work. In addition, the laboratory provides quality storage for valuable collections of biologics and other materials and facilitates sharing of specimens, associated epidemiologic data, and test results. Working with our partners in diabetes research, we are improving the diagnosis, treatment, and prevention of type 1 diabetes.

Genomic DNA from mice: a comparison of recovery methods and tissue sources

Our aim is to identify an extraction method and the source of mouse tissue(s) that could allow a high-resolution genomic scan from a living mouse. We compared and optimized two methods for yield, purity of DNA, and their use in the polymerase chain reaction (PCR) of DNA extracted from different mouse tissues. In addition to whole blood, tissue samples from the brain, liver, testis, and tail were included in this study. The Rapid Method (RM) is preferable for the whole blood samples and testis and brain tissue samples because it is quicker, less toxic, and more cost-effective than the proteinase K method (PM). For liver the PM produced higher yields of DNA with less degradation than the RM. For tail tip, the PM produced a higher yield of DNA, but the RM resulted in a higher yield of PCR product. From a living mouse, a tail snip generated a sufficient amount of DNA for several hundred PCRs but not a complete genomic scan. We suggest that the RM can be used to extract genomic DNA for a complete genomic scan which requires either testicular tissues or repeated blood samples from the suborbital sinus over several months without sacrificing the animal.