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

Experience of a 2-year spinal muscular atrophy NBS pilot study in Italy: towards specific guidelines and standard operating procedures for the molecular diagnosis

BACKGROUND

Spinal muscular atrophy (SMA) is due to the homozygous absence of SMN1 in around 97% of patients, independent of the severity (classically ranked into types I-III). The high genetic homogeneity, coupled with the excellent results of presymptomatic treatments of patients with each of the three disease-modifying therapies available, makes SMA one of the golden candidates to genetic newborn screening (NBS) (SMA-NBS). The implementation of SMA in NBS national programmes occurring in some countries is an arising new issue that the scientific community has to address. We report here the results of the first Italian SMA-NBS project and provide some proposals for updating the current molecular diagnostic scenario.

METHODS

The screening test was performed by an in-house-developed qPCR assay, amplifying SMN1 and SMN2. Molecular prognosis was assessed on fresh blood samples.

RESULTS

We found 15 patients/90885 newborns (incidence 1:6059) having the following SMN2 genotypes: 1 (one patient), 2 (eight patients), 2+c.859G>C variant (one patient), 3 (three patients), 4 (one patient) or 6 copies (one patient). Six patients (40%) showed signs suggestive of SMA at birth. We also discuss some unusual cases we found.

CONCLUSION

The molecular diagnosis of SMA needs to adapt to the new era of the disease with specific guidelines and standard operating procedures. In detail, SMA diagnosis should be felt as a true medical urgency due to therapeutic implications; SMN2 copy assessment needs to be standardised; commercially available tests need to be improved for higher SMN2 copies determination; and the SMN2 splicing-modifier variants should be routinely tested in SMA-NBS.

Extraction, quantitation, and evaluation of function DNA from various sample types

Two vital pre-requisites for genetic epidemiology have been fullfiled during the past decade and have led to a virtual explosion of knowledge concerning disease risks. Reliable databases over genetic variation derived from, e.g. the HUGO and HapMap projects, coupled with technological advances make large-scale genetic analyses and downstream bioinformatics suddenly affordable. Although recent prospective population-based biobanks have included DNA collection and purification in their planning, it is the older projects that currently are of greatest value due to the numbers of accumulated disease endpoints. In this chapter, methods to purify and use DNA derived from a variety of archival materials, including whole blood, formalin-fixed paraffin-embedded (FFPE) tissues, sera, dried blood spots (DBS), cervical cell suspensions, and mouthwash are presented and evaluated in a context of quality control guidelines to provide objective measure of the usefulness of various sample types for genetic epidemiology.

Detection of toxoplasmosis in experimentally infected goats by PCR

PCR was used to diagnose toxoplasmosis in two pairs of Barbari goats infected by oral administration of doses of either 10(4) or 10(5) oocysts of Toxoplasma gondii. Blood and lymph node aspirates were collected from the infected goats and control goat at intervals, and tissues were also collected from a fetus that was aborted and a doe that died during the trial. Both processed and unprocessed samples were used for the PCR, using primers directed to the multicopy B1 gene. None of the blood samples was positive, but a specific signal was obtained from the lymph node aspirates after partial DNA extraction. Direct PCR of the lung, muscle and mesenteric lymph node of the doe and lung tissue of the aborted fetus yielded the target fragment. The simplified PCR protocols, including partial DNA extraction and direct assay of lung tissue, were effective for the diagnosis of toxoplasmosis.

Polymerase chain reaction amplification of DNA from aged blood stains: quantitative evaluation of the "suitability for purpose" of four filter papers as archival media

In collaboration with the Armed Forces Institute of Pathology's Department of Defense DNA Registry, the National Institute of Standards and Technology recently evaluated the performance of a short tandem repeat multiplex with dried whole blood stains on four different commercially available identification card matrixes. DNA from 70 stains that had been stored for 19 months at ambient temperature was extracted or directly amplified and then processed using routine methods. All four storage media provided fully typeable (qualitatively identical) samples. After standardization, the average among-locus fluorescence intensity (electropherographic peak height or area) provided a suitable metric for quantitative analysis of the relative amounts of amplifiable DNA in an archived sample. The amounts of DNA in Chelex extracts from stains on two untreated high-purity cotton linter pulp papers and a paper treated with a DNA-binding coating were essentially identical. Average intensities for the aqueous extracts from a paper treated with a DNA-releasing coating were somewhat lower but also somewhat less variable than for the Chelex extracts. Average intensities of directly amplified punches of the DNA-binding paper were much larger but somewhat more variable than the Chelex extracts. Approximately 25% of the observed variation among the intensity measurements is shared among the four media and thus can be attributed to intrinsic variation in white blood count among the donors. All of the evaluated media adequately "bank" forensically useful DNA in well-dried whole blood stains for at least 19 months at ambient temperature.

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.

An effective strategy of using molecular testing to screen mentally retarded individuals for fragile X syndrome

Fragile X syndrome (FXS) is the most common form of familial mental retardation (MR). It is caused by the expansion of the CGG repeat in the FMR1 gene on the X chromosome. To date, FXS is not treatable, but can be prevented by prenatal genetic examination. Identifying women who carry a full mutation or premutation FMR1 gene is thus very important, and can be done by tracing family members of FXS subjects. However, most of the FXS subjects in Taiwan as well as those in many other countries have not been identified. In this study the authors attempt to develop reliable and inexpensive tests suitable for a large-scale screen of subjects with MR for FXS. Together with their previous study, a total of 311 male and 160 female subjects with MR were screened with nonradioactive Southern blot assay using mixed deoxyribonucleic acid from three subjects of the same sex. From these subjects, nine male subjects and one female FXS subject were diagnosed. All male subjects were also screened with nonradioactive polymerase chain reaction (PCR). These nine male FXS subjects were also detected on the basis of PCR amplification failure. No false-negative results were discerned. The PCR procedure was simplified further by combining it with an analysis of a blood spot on filter paper, which is a much simpler and cheaper method for sample collection and DNA preparation. This method was then used to screen 104 boys with MR. Two of them were suspected, and later confirmed with Southern blot assay, as subjects with FXS. This study suggests that simple PCR combined with blood spot analysis could be a reliable, inexpensive test that is feasible for a large-scale screening of male subjects with MR for FXS. However, Southern blot assay with mixed deoxyribonucleic acid is appropriate for screening female subjects. Based on this strategy, most FXS subjects could be identified easily for further management.

Techniques for the evaluation of nucleic acid amplification technology performance with specimens containing interfering substances: efficacy of boom methodology for extraction of HIV-1 RNA

Accurate HIV-1 RNA quantitation with nucleic acid amplification assays (NAAA) is partly dependent on overall assay design to ensure proper and reproducible functioning in the presence of endogenous interfering substances present in a clinical specimen, or exogenous interfering substances introduced as a result of specimen collection or handling. This study tested various methods of evaluating interfering substances that could potentially affect the outcome of HIV-1 RNA amplification in a NAAA. Clinical specimens from HIV-1 seronegative subjects containing various endogenous interferents were evaluated with and without an HIV-1 RNA spike to assess recovery and specificity, respectively, with a non-PCR NAAA (NASBA HIV-1 RNA QT, Organon Teknika) that incorporates Boom methodology for nucleic acid extraction. Additional specimens were prepared to simulate various circumstances that might occur during specimen preparation to result in the introduction of exogenous interferents. A retrovirus reverse transcriptase inhibitor, zidovudine (AZT), was added to plasma specimens prior to testing. NAAA results obtained with 127 total clinical specimens, 10 bacterially contaminated specimens, 5 platelet enriched specimens, 5 AZT specimens, and 30 anticoagulated specimens were consistent with the expected outcomes in the presence and absence of the HIV-1 RNA spike, giving an assay specificity of 100%. The spiked HIV-1 RNA copies in the clinical specimens reported by the assay were 99% of the copies reported for a positive index control (normal plasma plus HIV-1 RNA spike). Compared to the amplification levels of the three internal assay calibrators obtained for normal plasma controls, no differences in the amplification levels of the calibrators for each type of specimen were observed. This result indicated that the interferents examined did not affect adversely assay function. Addition of known PCR interferents (hemoglobin and heparin) and AZT to isolated HIV-1 RNA resulted in a substantial reduction of amplification and invalid results, whereas no inhibition was observed when these interferents were added to the test system prior to isolation; these results directly demonstrate the efficient removal of such interferents during the NASBA HIV-1 RNA QT isolation procedure. The several approaches to investigate interference described in this study may be utilized for the evaluation of other assays using nucleic acid amplification technology.