Whole Exome Sequencing Identifies Novel Genetic Alterations in Patients with Pheochromocytoma/Paraganglioma

BACKGROUND

Pheochromocytoma and paragangliomas (PPGL) are known as tumors with the highest level of heritability, approximately 30% of all cases. Clinical practice guidelines of PPGL recommend genetic testing for germline variants in all patients. In this study, we used whole exome sequencing to identify novel causative variants associated with PPGL to improve the detection of rare genetic variants in our cohort.

METHODS

Thirty-six tested negative for pathogenic variants in previous Sanger sequencing or targeted gene panel testing for PPGL underwent whole exome sequencing. Whole exome sequencing was performed using DNA samples enriched using TruSeq Custom Enrichment Kit and sequenced with MiSeq (Illumina Inc.). Sequencing alignment and variant calling were performed using SAMtools.

RESULTS

Among previously mutation undetected 36 patients, two likely pathogenic variants and 13 variants of uncertain significance (VUS) were detected in 32 pheochromocytoma-related genes. SDHA c.778G>A (p.Gly260Arg) was detected in a patient with head and neck paraganglioma, and KIF1B c.2787-2A>C in a patient with a bladder paraganglioma. Additionally, a likely pathogenic variant in BRCA2, VUS in TP53, and VUS in NFU1 were detected.

CONCLUSION

Exome sequencing further identified genetic alterations by 5.6% in previously mutation undetected patients in PPGL. Implementation of targeted gene sequencing consisted of extended genes of PPGL in routine clinical screening can support the level of comprehensive patient assessment.

VarWatch-A stand-alone software tool for variant matching

Massively parallel DNA sequencing of clinical samples holds great promise for the gene-based diagnosis of human inherited diseases because it allows rapid detection of putatively causative mutations at genome-wide level. Without additional evidence complementing their initial bioinformatics evaluation, however, the clinical relevance of such candidate genetic variants often remains unclear. In consequence, dedicated 'matching' services have been established in recent years that aim at the discovery of other, comparable case reports to facilitate individual diagnoses. However, legal concerns have been raised about the global sharing of genetic data, particularly in Europe where the recently enacted General Data Protection Regulation EU-2016/679 classifies genetic data as highly sensitive. Hence, unrestricted sharing of genetic data from clinical cases on platforms outside the national jurisdiction increasingly may be perceived as problematic. To allow collaborative data producers, particularly large consortia of diagnostic laboratories, to acknowledge these concerns while still practicing efficient case matching internally, novel tools are required. To this end, we developed VarWatch, an easy-to-deploy and highly scalable case matching software that provides users with comprehensive programmatic tools and a user-friendly interface to fulfil said purpose.

Integrated routine workflow using next-generation sequencing and a fully-automated platform for the detection of KRAS, NRAS and BRAF mutations in formalin-fixed paraffin embedded samples with poor DNA quality in patients with colorectal carcinoma

Background

KRAS and NRAS mutations are identified resistance mutations to anti-epidermal growth factor receptor monoclonal antibodies in patients with metastatic colorectal cancer. BRAF status is also routinely assessed for its poor prognosis value. In our institute, next-generation sequencing (NGS) is routinely used for gene-panel mutations detection including KRAS, NRAS and BRAF, but DNA quality is sometimes not sufficient for sequencing. In our routine practice, Idylla platform is used for the analysis of samples that don’t reach sufficient quality criteria for NGS assay.

Methods

In this study, data from mCRC samples analyzed from May 2017 to 2018 were retrospectively collected. All samples with a poor DNA quality for sequencing have been assessed using Idylla platform. First, KRAS Idylla assay cartridge has been used for the determination of KRAS mutational status. All KRAS wild-type samples have then been analyzed using NRAS-BRAF assay. Among 669 samples, 67 samples failed the DNA quality control and have been assessed on Idylla KRAS mutation test.

Results

Among 67 samples, 50 (75%) samples had a valid result with Idylla KRAS mutation test including 22 carrying a KRAS mutation. For 28 samples, NRAS and BRAF mutational statuses have been assessed using Idylla NRAS-BRAF mutation test. Among 28 samples, 27 (96%) had a valid result including 2 samples bearing a NRAS mutation and 3 samples bearing a BRAF mutation.

Conclusions

Our study shows that an integrated workflow using NGS and Idylla platform allows the determination of KRAS, NRAS and BRAF mutational statuses of 651/669 (97.3%) samples and retrieve 49/67 (73.1%)samples that don’t reach DNA quality requirements for NGS.

Interinstitutional variation in predictive value of the ThyroSeq v2 genomic classifier for cytologically indeterminate thyroid nodules

BACKGROUND

The ThyroSeq v2 next-generation sequencing assay estimates the probability of malignancy in indeterminate thyroid nodules. Its diagnostic accuracy in different practice settings and patient populations is not well understood.

METHODS

We analyzed 273 Bethesda III/IV indeterminate thyroid nodules evaluated with ThyroSeq at 4 institutions: 2 comprehensive cancer centers (n = 98 and 102), a multicenter health care system (n = 60), and an academic medical center (n = 13). The positive and negative predictive values of ThyroSeq and distribution of final pathologic diagnoses were analyzed and compared with values predicted by Bayes theorem.

RESULTS

Across 4 institutions, the positive predictive value was 35% (22%-43%) and negative predictive value was 93% (88%-100%). Predictive values correlated closely with Bayes theorem estimates (r² = 0.84), although positive predictive values were lower than expected. RAS mutations were the most common molecular alteration. Among 84 RAS-mutated nodules, malignancy risk was variable (25%, range 10%-37%) and distribution of benign diagnoses differed across institutions (adenoma/hyperplasia 12%-85%, noninvasive follicular thyroid neoplasm with papillary-like nuclear features 5%-46%).

CONCLUSION

In a multi-institutional analysis, ThyroSeq positive predictive values were variable and lower than expected. This is attributable to differences in the prevalence of malignancy and variability in pathologist interpretations of noninvasive tumors. It is important that clinicians understand ThyroSeq performance in their practice setting when evaluating these results.

[A novel quantitative JAK2V617F detection kit: prospective clinical performance study comparing MPN patients and healthy subjects]

The JAK2V617F mutation is the commonest major genetic mutation of myeloproliferative neoplasms (MPNs) and has been defined in the WHO diagnostic criteria for MPNs. However, there is still no approved in vitro diagnostic test kit available in Japan. We evaluated a JAK2V617F allele quantification kit (test method) in a prospective, multicenter clinical performance study involving patients with MPNs who were diagnosed with polycythemia vera, essential thrombocythemia, and primary myelofibrosis; healthy volunteers were also included in the analysis. Good correlation was observed between the allele burden determined using the test method vs. that determined using next-generation sequencing (NGS) in the patient group (r=0.998, y=1.071x-0.069; n=156). Furthermore, all allele burdens in the healthy group (n=54) were below the lower limit of the measurement range of the test method (0.042%). Our results confirmed that the test method could quantitatively measure the JAK2V617F allele burden in patients with MPN. Thus, the novel JAK2V617F allele quantification kit can be considered useful for the diagnosis of MPNs.

Medical Devices; Exemption From Premarket Notification; Class II Devices; Autosomal Recessive Carrier Screening Gene Mutation Detection System. Final order

The Food and Drug Administration (FDA or Agency) is publishing an order to exempt autosomal recessive carrier screening gene mutation detection systems from the premarket notification requirements, subject to certain limitations. This exemption from 510(k), subject to certain limitations, is immediately in effect for autosomal recessive carrier screening gene mutation detection systems. This exemption will decrease regulatory burdens on the medical device industry and will eliminate private costs and expenditures required to comply with certain Federal regulations. FDA is also amending the codified language for the autosomal recessive carrier screening gene mutation detection system devices classification regulation to reflect this final determination.

Medical Devices; Immunology and Microbiology Devices; Classification of the Genetic Health Risk Assessment System. Final order

The Food and Drug Administration (FDA, the Agency, or we) is classifying the genetic health risk assessment system into class II (special controls). The special controls that apply to the device type are identified in this order and will be part of the codified language for the genetic health risk assessment system's classification. We are taking this action because we have determined that classifying the device into class II (special controls) will provide a reasonable assurance of safety and effectiveness of the device. We believe this action will also enhance patients' access to beneficial innovative devices, in part by reducing regulatory burdens.

Conditions of High Resolution Melting Analysis on the Cobas z480 Instrument for the Genotyping of VKORC1 in the Clinical Routine Laboratory

BACKGROUND

High resolution melting (HRM) of amplicons is a simple method for genotyping of single nucleotide polymorphisms (SNPs). Albeit many applications reported, HRM seems to be rarely used in clinical laboratories. The suitability of HRM-PCR for the clinical laboratory was investigated for genotyping of SNPs of the vitamin K epoxide reductase complex unit 1 gene.

METHODS

About 100 DNA samples were analyzed by two different HRM-PCRs on the Cobas z480 instrument and compared with a PCR with fluorescently labeled probes (HybProbe-PCR) on the LightCycler 2.0 instrument as reference.

RESULTS

Reliable genotyping with 100% matching results was obtained, when the amplicon size was small (63 bp) and DNA input was limited by e.g., sample dilution with salt-free water.

CONCLUSIONS

DNA extracted by differing methods may be used for genotyping by HRM-PCR. Compared with HybProbe-PCR, HRM-PCR on the Cobas z480 instrument allows for higher through-put, however, at the cost of a higher degree of laboratory standardization and a slower turnaround.

Medical Devices; Immunology and Microbiology Devices; Classification of Autosomal Recessive Carrier Screening Gene Mutation Detection System. Final order

The Food and Drug Administration (FDA) has classified an autosomal recessive carrier screening gene mutation detection system into class II (special controls). The special controls that apply to this device are identified in this order and will be part of the codified language for the autosomal recessive carrier screening gene mutation detection system classification. The Agency has classified the device into class II (special controls) in order to provide a reasonable assurance of safety and effectiveness of the device.

Static self-directed sample dispensing into a series of reaction wells on a microfluidic card for parallel genetic detection of microbial pathogens

A microfluidic card is described for simultaneous and rapid genetic detection of multiple microbial pathogens. The hydrophobic surface of native acrylic and a novel microfluidic mechanism termed "airlock" were used to dispense sample into a series of 64 reaction wells without the use of valves, external pumping peripherals, multiple layers, or vacuum assistance. This airlock mechanism was tested with dilutions of whole human blood, saliva, and urine, along with mock samples of varying viscosities and surface tensions. Samples spiked with genomic DNA (gDNA) or crude lysates from clinical bacterial isolates were tested with loop mediated isothermal amplification assays (LAMP) designed to target virulence and antibiotic resistance genes. Reactions were monitored in real time using the Gene-Z, which is a portable smartphone-driven system. Samples loaded correctly into the microfluidic card in 99.3% of instances. Amplification results confirmed no carryover of pre-dispensed primer between wells during sample loading, and no observable diffusion between adjacent wells during the 60 to 90 min isothermal reaction. Sensitivity was comparable between LAMP reactions tested within the microfluidic card and in conventional vials. Tests demonstrate that the airlock card works with various sample types, manufacturing techniques, and can potentially be used in many point-of-care diagnostics applications.

[The current status of genetic testing for leukemia]

The pathogenic chromosome translocations present in various hematological malignancies result in the formation of fusion genes, which are detected by a reverse transcription-polymerase chain reaction method. Furthermore, with this method, it is possible to sensitively detect minimal residual disease (MRD), which is difficult by a morphological testing. It has now been established that the detection of MRD is important for the diagnosis, treatment policy, evaluation of the prognosis, and monitoring of leukemia. In particular, quantitative analysis of MRD is important for evaluation of the curative effect and prediction of recurrence. In addition, mutation analysis is valuable to decide on the therapeutic protocol for imatinib-resistant patients, and the stratification of treatment for acute myeloid leukemia. At present, however, there is no standard laboratory procedure for genetic testing for leukemia. Here, the problems related to external precision management and analytical error are discussed.

IROme, a new high-throughput molecular tool for the diagnosis of inherited retinal dystrophies-a price comparison with Sanger sequencing

The molecular diagnosis of retinal dystrophies (RD) is difficult because of genetic and clinical heterogeneity. Previously, the molecular screening of genes was done one by one, sometimes in a scheme based on the frequency of sequence variants and the number of exons/length of the candidate genes. Payment for these procedures was complicated and the sequential billing of several genes created endless paperwork. We therefore evaluated the costs of generating and sequencing a hybridization-based DNA library enriched for the 64 most frequently mutated genes in RD, called IROme, and compared them to the costs of amplifying and sequencing these genes by the Sanger method. The production cost generated by the high-throughput (HT) sequencing of IROme was established at CHF 2,875.75 per case. Sanger sequencing of the same exons cost CHF 69,399.02. Turnaround time of the analysis was 3 days for IROme. For Sanger sequencing, it could only be estimated, as we never sequenced all 64 genes in one single patient. Sale cost for IROme calculated on the basis of the sale cost of one exon by Sanger sequencing is CHF 8,445.88, which corresponds to the sale price of 40 exons. In conclusion, IROme is cheaper and faster than Sanger sequencing and therefore represents a sound approach for the diagnosis of RD, both scientifically and economically. As a drop in the costs of HT sequencing is anticipated, target resequencing might become the new gold standard in the molecular diagnosis of RD.

Towards clinical molecular diagnosis of inherited cardiac conditions: a comparison of bench-top genome DNA sequencers

BACKGROUND

Molecular genetic testing is recommended for diagnosis of inherited cardiac disease, to guide prognosis and treatment, but access is often limited by cost and availability. Recently introduced high-throughput bench-top DNA sequencing platforms have the potential to overcome these limitations.

METHODOLOGY/PRINCIPAL FINDINGS

We evaluated two next-generation sequencing (NGS) platforms for molecular diagnostics. The protein-coding regions of six genes associated with inherited arrhythmia syndromes were amplified from 15 human samples using parallelised multiplex PCR (Access Array, Fluidigm), and sequenced on the MiSeq (Illumina) and Ion Torrent PGM (Life Technologies). Overall, 97.9% of the target was sequenced adequately for variant calling on the MiSeq, and 96.8% on the Ion Torrent PGM. Regions missed tended to be of high GC-content, and most were problematic for both platforms. Variant calling was assessed using 107 variants detected using Sanger sequencing: within adequately sequenced regions, variant calling on both platforms was highly accurate (Sensitivity: MiSeq 100%, PGM 99.1%. Positive predictive value: MiSeq 95.9%, PGM 95.5%). At the time of the study the Ion Torrent PGM had a lower capital cost and individual runs were cheaper and faster. The MiSeq had a higher capacity (requiring fewer runs), with reduced hands-on time and simpler laboratory workflows. Both provide significant cost and time savings over conventional methods, even allowing for adjunct Sanger sequencing to validate findings and sequence exons missed by NGS.

CONCLUSIONS/SIGNIFICANCE

MiSeq and Ion Torrent PGM both provide accurate variant detection as part of a PCR-based molecular diagnostic workflow, and provide alternative platforms for molecular diagnosis of inherited cardiac conditions. Though there were performance differences at this throughput, platforms differed primarily in terms of cost, scalability, protocol stability and ease of use. Compared with current molecular genetic diagnostic tests for inherited cardiac arrhythmias, these NGS approaches are faster, less expensive, and yet more comprehensive.

Gene-Z: a device for point of care genetic testing using a smartphone

By 2012, point of care (POC) testing will constitute roughly one third of the $59 billion in vitro diagnostics market. The ability to carry out multiplexed genetic testing and wireless connectivity are emerging as key attributes of future POC devices. In this study, an inexpensive, user-friendly and compact device (termed Gene-Z) is presented for rapid quantitative detection of multiple genetic markers with high sensitivity and specificity. Using a disposable valve-less polymer microfluidic chip containing four arrays of 15 reaction wells each with dehydrated primers for isothermal amplification, the Gene-Z enables simultaneous analysis of four samples, each for multiple genetic markers in parallel, requiring only a single pipetting step per sample for dispensing. To drastically reduce the cost and size of the real-time detector necessary for quantification, loop-mediated isothermal amplification (LAMP) was performed with a high concentration of SYTO-81, a non-inhibiting fluorescent DNA binding dye. The Gene-Z is operated using an iPod Touch, which also receives data and carries out automated analysis and reporting via a WiFi interface. This study presents data pertaining to performance of the device including sensitivity and reproducibility using genomic DNA from Escherichia coli and Staphylococcus aureus. Overall, the Gene-Z represents a significant step toward truly inexpensive and compact tools for POC genetic testing.

A molecular monopoly? HPV testing, the Pap smear and the molecularisation of cervical cancer screening in the USA

DNA-based molecular testing for human papillomavirus has emerged as a novel approach to cervical cancer screening in the context of well-entrenched existing technology, the Pap smear. This article seeks to elucidate the process of molecularisation in the context of screening programmes. We illustrate how, although Pap has long been problematised and could be seen as a competing technological option, the existing networks and regime for Pap were important in supporting the entrenchment process for the artefacts, techniques and new diagnostics industry entrant, Digene, associated with the new test. The article provides insights into how the molecularisation of screening unfolds in a mainstream market. We reveal an incremental and accretive, rather than revolutionary, process led by new commercial interests in an era when diagnostic innovation is increasingly privatised. We show Digene's reliance on patents, an international scientific network and their position as an obligatory point of passage in the clinical research field with regard to the new technology's role, as well as on controversial new marketing practices. The article is based on a mixed method approach, drawing on a wide range of contemporary sources (including patents, statutory filings by companies, scientific literature and news sources) as well as interviews.

[Multiplex Ligation - dependent Probe Amplification (MLPA) as a screening test in children with developmental defects and intellectual disability of unknown etiology]

Developmental delay and intellectual disability are significant medical and social problems which concern 1-3% of population. The etiology remains unknown in over half of the cases.

THE AIM

To evaluate the efficiency of MLPA (Multiplex Ligation-dependent Probe Amplification) as a screening test in diagnosis of patients with developmental delay and/or intellectual disability.

MATERIAL AND METHODS

313 MLPA tests were performed in 256 patients with developmental delay and/ or intellectual disability with unknown etiology. MLPA test was made after exclusion of genetic disorders possible to diagnose by dysmorphological examination or using specifi c genetic tests. Positive results were confirmed by FISH analysis with appropriate probes.

RESULTS

Chromosomal microaberrations were identifi ed in 15 patients (4,8%): deletions of 1p36 in 4 cases, in one case deletion of 22q11.21, 22q13.33, SNRPN1, 4ptel, 6qtel, 7q11.23, 16ptel, 18qtel as well as one ca se of deletion 3ptel/duplication 15qtel; deletion 18qtel/duplication Xqtel, and also duplication 7q11.23. Detail clinical analysis was performed in patients with diagnosed microaberrations in MLPA test.

CONCLUSIONS

The molecular MLPA test, screening for chromosomal microaberration syndromes, should be performed in each patient with developmental delay and/or intellectual disability of unknown etiology and normal cytogenetic analysis, even if congenital defects and positive familial history do not exist.

Determining sequence length or content in zero, one, and two dimensions

High-throughput assays are essential for the practical application of mutation detection in medicine and research. Moreover, such assays should produce informative data of high quality that have a low-error rate and a low cost. Unfortunately, this is not currently the case. Instead, we typically witness legions of people reviewing imperfect data at astronomical expense yielding uncertain results. To address this problem, for the past decade we have been developing methods that exploit the inherent quantitative nature of DNA experiments. By generating high-quality data, careful DNA-signal quantification permits robust analysis for determining true alleles and certainty measures. We will explore several assays and methods. In a one-dimensional readout, short tandem repeat (STR) data display interesting artifacts. Even with high-quality data, PCR artifacts such as stutter and relative amplification can confound correct or automated scoring. However, by appropriate mathematical analysis, these artifacts can be essentially removed from the data. The result is fully automated data scoring, quality assessment, and new types of DNA analysis. These approaches enable the accurate analysis of pooled DNA samples, for both genetic and forensic applications. On a two-dimensional surface (comprised of zero-dimensional spots) one can perform assays of extremely high-throughput at low cost. The question is how to determine DNA sequence length or content from nonelectrophoretic intensity data. Here again, mathematical analysis of highly quantitative data provides a solution. We will discuss new lab assays that can produce data containing such information; mathematical transformation then determines DNA length or content.

Analysis of SNPs and other genomic variations using gel-based chips

Application of microarrays for the analysis of point mutations and SNPs in genomic DNAs is currently under intensive development. Various technologies are being investigated, employing enzymatic, chemical, and physical tools [for review, see Tillib and Mirzabekov, 2001]. Our current approach is based on the use of IMAGE chips (immobilized microarrays of gel elements) consisting of an array of gel pads attached to a hydrophobic glass surface. The gel pads range in size from picoliters to nanoliters and are used for immobilization of oligonucleotide probes, as well as miniature test tubes for chemical or enzymatic reactions with tethered compounds. Nucleic acids are hybridized, fractionated, modified, and subjected to enzymatic reactions inside the pads. All steps of sequence analysis (PCR-amplification, activation or release of primers and products, DNA extension, hybridization, and reading of the results) can be performed within the same pad. A flexible and inexpensive technology platform enables one to monitor processes in the arrays in both real time and steady-state. Identification of SNPs, microsequencing, and other specific tasks are easily performed. In particular, stacking interactions with short oligonucleotides enhance the capability of high-throughput screening. The IMAGE chips can be analyzed using a variety of equipment, from a dedicated multi-color fluorescent microscope or MALDI-spectrometer to an inexpensive portable analyzer suitable for field conditions. Customized gel-based chips were successfully used for screening of SNPs in a broad range of biologically meaningful genes.

Rapid detection of the prion protein M129V polymorphism with the LightCycler

The common single nucleotide polymorphism at codon 129 of the prion protein gene is a key determinant of the genetic susceptibility to Creutzfeldt-Jakob disease (CJD). Recently, a molecular classification of sporadic CJD based on the M129V genotype in conjunction with other determinants was proposed. In the present study, we describe the development and evaluation of a rapid fluorescent-based assay to detect this polymorphism using the LightCycler system. The two polymorphic alleles could be clearly distinguished by their melting points at 52.1 and 60.4 degrees C, representing the 129V and 129M alleles, respectively. These results were confirmed by DNA sequencing. We evaluated our test in 400 patient samples and found no deviations from the expected melting patterns. The calculated allele frequency for the M-allele was 0.66. Thus, we have established a rapid, reliable fluorescent assay for high-throughput detection of the prion protein M129V polymorphism.

High-speed plasmid isolation using 96-well, size-exclusion filter plates

The accelerating pace of genomics analysis has necessitated the abbreviation of DNA sample preparation protocols. We have developed a size-exclusion-based system for the rapid isolation ofplasmid DNA in a 96-well microplate format. This high-speed protocol employs a modified alkaline lysis methodfor the preparation of the bacterial lysate, followed by three short vacuum filtration steps. Unlike traditional bind/wash/elute methods, there is no need to use chaotropic salts or ethanol. The samples are recovered from the top side of the MultiScreen96 PLASMID plates. Starting with bacterial cell pellets, the entire prycedure for purifying the plasmid DNA can be performed in 30 min with a multichannel pipettor. The high yields, reproducibility, and quality of the plasmids make this system a good choice for any cloning or DNA sequencing operation.

Laser microdissection as a new approach to prefertilization genetic diagnosis

The genetic status of oocytes can be determined by polar body (PB) analysis. Following PB extraction, a genetic evaluation is performed. As each PB contains the complementary genetic material of the oocyte, PB analysis reveals information about its genetic status. Genetically altered oocytes may then be excluded from in vitro fertilization. The aim of our study was to evaluate laser microdissection as a tool for PB extraction purposes. Compared to the PB extraction with a sharp-ending pipette only, we could show that laser microdissection of the zona pellucida (laser zona drilling) with a UV-A laser and subsequent extraction with a blunt-ending pipette decreases the degeneration rate of oocytes. It is shown that laser pressure catapulting of extracted PB enables their contact-free transfer into tubes, thus decreasing the risk of contamination for further analysis.

[Genetic testing for cystic fibrosis: evaluation of the Elucigene CF20 kit in blood and buccal cells]

Routine determination of mutations in cystic fibrosis requires accurate, rapid, reliable and low-cost methods, permitting the simultaneous detection of multiple mutations. The Elucigene CF20 kit developped by Cellmark Diagnostics, uses multiplex ARMS, which allows the screening for 20 CFTR gene mutations (deltaF508, G542X, N1303K, 1717-1G>A, G551D, W1282X, R553X, deltaI507, 1078delT, 2183AA>G, 3849+10kbC>T, R1162X, 621+1G>T, R334W, R347P, 3659delC, R117H, S1251N, E60X, A455E ) in a work day without specific instrumentation. The kit distinguishes between homozygotes and heterozygotes for deltaF508, but not for rare mutations. The kit detects from 68 to 92% of defective alleles in Caucasians. We evaluate the kit in a blind study in two independent laboratories. Thirty blood samples and thirty mouthwash samples from CF patients, carriers and unaffected individuals were analysed by the Elucigene CF20 kit. All the samples were previously analysed by denaturing gradient gel electrophoresis and sequencing. The Elucigene CF20 kit consists of three multiplexes. Each mutiplex contains ARMS specific primers for six to eight mutations and two control reactions. The absence of the upper control fragment indicates that a repeat test is required. We demonstrated a first time amplification rate of 98.3%: of the 60 samples tested, one required a reamplification. Results compared with the reference method demonstrated that in all cases where one or more of the 20 mutations detected by the kit were present in the test set, the kit accurately identified them. Reproducibility was assessed by repeating the analysis of a blood and mouthwash sample five times. Cross reactivity between R117C and R117H, R117P and R117H, R347P and R347H, deltaI507 and deltaF508, G551D and R553X were evaluated. Only a cross reactivity between R347P and R347H was observed. The kit is specially useful for first line study of patients and carrier identification.

DHPLC-based germline mutation screening in the analysis of the VHL tumor suppressor gene: usefulness and limitations

In order to evaluate the sensitivity and specificity of the recently introduced high-throughput method DHPLC (denaturing high performance liquid chromatography) for mutation screening in the VHL tumor suppressor gene, we subjected DNA from 43 unrelated VHL patients with previously sequenced VHL germline mutations to this method. In addition, 36 genomic DNAs of unrelated individuals suspected of being VHL carriers but with unknown germline status were analyzed by DHPLC and sequencing. The aims of the present study were to compare mutation results obtained by direct sequencing and DHPLC, and a comparison of two different DHPLC systems. The sensitivity of DHPLC was tested with two commercial devices and protocols, i.e., the Varian-Helix system and the Wave Nucleic Acid Fragment Analysis system. Both resolved all but one mutation in exons 2 and 3 of the VHL gene. In contrast, the GC-rich exon 1 showed discrepancies in the rate of mutation detection. Whereas the Varian-Helix system detected 10/15 (67%) of the known mutations, the Wave Nucleic Acid Fragment Analysis system detected 13/14 (93%). All three mutations in samples with unknown mutation status were revealed by both systems raising the mutation detection rate to 72% and 94%, respectively. Cases with different substitutions at the same nucleotide showed different elution profiles, but similar elution profiles could be obtained from different mutations. The Wave Nucleic Acid Fragment Analysis system detected most VHL mutations; however, when a 100% detection rate is needed, sequencing is still required and must therefore be the standard VHL mutation detection procedure. Once a family-specific mutation has been established, DHPLC may be suitable for the rapid and cost-effective determination of VHL carrier status in family members.

A semi-automated system for analysis and storage of SNPs

The discovery of single nucleotide polymorphisms ( SNPs) is currently pursued with a tremendous effort. SNPs represent a rich source for molecular markers, since estimations predict six to seven million of these DNA variations in the human genome. A subset of these genetic variants is thought to have a pervasive impact on modern medicine, be it for the elucidation of differential pharmacological response or for the facilitated identification of genes involved in monogenetic and complex human diseases. Here we describe the overall process that leads to the set up of a SNP database. We describe a high-throughput sequencing assay for SNP discovery, automation of the dataflow from the DNA sequencer to the SNP analysis, and the tools to facilitate it. At the end of the process, a web-accessible interface collects the SNP information, which is processed in order to be written into the SNP database and to be available for end users who would like to select appropriate SNPs for their special screening needs.

High throughput screening of gene expression signatures

This paper focuses on microarray image analysis and discusses a completely automated approach to image processing, which eliminates human intervention. A system for automated image processing is described, which is capable of processing image files in a batch-mode thus allowing high-throughput of microarray image analysis. Grid-placement and spot finding are achieved without operator's help. The software eliminates noise signals from the data analysis process and minimizes operator's involvement in the procedure.

A reliable screening test to identify adult carriers of the (--SEA) alpha zero-thalassemia deletion. Detection of embryonic zeta-globin chains by enzyme-linked immunosorbent assay

Homozygous (--SEA) alpha zero-thalassemia deletion, the cause of up to 80% of fetal hydrops in Southeast Asia, is encountered in many other countries. Heterozygous carrier rates of the deletion in Southeast Asian populations range from 4% to 14%. The laboratory screening for adult carriers of (--SEA) and other alpha zero-thalassemia deletions currently rests primarily with microscopic detection of hemoglobin H inclusion bodies within erythrocytes (Hb H screen). This test is laborious and observer dependent and has poor sensitivity. We assessed a colorimetric enzyme-linked immunosorbent assay (ELISA) to detect embryonic zeta-globin chains in adult hemolysates as an alternative to detect (--SEA) alpha zero-thalassemia deletion carriers. Blood samples from 221 adults with a mean corpuscular volume less than 80 micron 3 (80 fL) were studied prospectively by currently accepted hemoglobin screening tests and ELISA. Suspected cases of alpha-thalassemia were confirmed by DNA-based diagnostics. ELISA was highly sensitive (1.0) and specific (0.94) for the detection of adult carriers of (--SEA) alpha zero-thalassemia deletion. The hemoglobin H screen had a sensitivity of 0.47 and specificity of 0.99. The zeta-globin ELISA proved simple to perform, rapid, and applicable to high volume or population-based screening programs.

Arrayed primer extension: solid-phase four-color DNA resequencing and mutation detection technology

The technology and application of arrayed primer extension (APEX) is presented. We describe an integrated system with DNA chip and template preparation, multiplex primer extension on the array, fluorescence imaging, and data analysis. The method is based upon an array of oligonucleotides, immobilized via the 5' end on a glass surface. A patient DNA is amplified by PCR, digested enzymatically, and annealed to the immobilized primers, which promote sites for template-dependent DNA polymerase extension reactions using four unique fluorescently labeled dideoxy nucleotides. A mutation is detected by a change in the color code of the primer sites. The technology was applied to the analysis of 10 common beta-thalassemia mutations. Nine patient DNA samples, each of which carries a different mutation, and four wild-type DNA samples were correctly identified. The signal-to-noise ratio of this technology is, on the average, 40:1, which enables the identification of heterozygous mutations with a high confidence level. The APEX method can be applied to any DNA target for efficient analysis of mutations and polymorphisms.

Development of a high-throughput process for detection and screening of genetic polymorphisms

A method is described that uses the ABI PRISM 310 genetic analyzer in conjunction with custom-designed software to identify and classify RAPD products. This methodology will also work well with AFLPs and microsatellite analyses. The methodology uses the ABI PRISM 310's high-throughput (> 500 samples per week) capabilities and in-lane molecular weight standards to efficiently separate and size DNA products. Peak detection, locus classification and export of the data in a form accessible by several genetic analysis programs were accomplished through a custom-written software program (Peaks). Various criteria used by the program to identify and classify loci are described, and their effect on population analyses is examined. Criteria providing an effective, robust determination of population structure are presented.

Evaluation of single nucleotide polymorphism typing with invader on PCR amplicons and its automation

Large-scale pharmacogenetics and complex disease association studies will require typing of thousands of single-nucleotide polymorphisms (SNPs) in thousands of individuals. Such projects would benefit from a genotyping system with accuracy >99% and a failure rate <5% on a simple, reliable, and flexible platform. However, such a system is not yet available for routine laboratory use. We have evaluated a modification of the previously reported Invader SNP-typing chemistry for use in a genotyping laboratory and tested its automation. The Invader technology uses a Flap Endonuclease for allele discrimination and a universal fluorescence resonance energy transfer (FRET) reporter system. Three hundred and eighty-four individuals were genotyped across a panel of 36 SNPs and one insertion/deletion polymorphism with Invader assays using PCR product as template, a total of 14,208 genotypes. An average failure rate of 2.3% was recorded, mostly associated with PCR failure, and the typing was 99.2% accurate when compared with genotypes generated with established techniques. An average signal-to-noise ratio (9:1) was obtained. The high degree of discrimination for single base changes, coupled with homogeneous format, has allowed us to deploy liquid handling robots in a 384-well microtitre plate format and an automated end-point capture of fluorescent signal. Simple semiautomated data interpretation allows the generation of approximately 25,000 genotypes per person per week, which is 10-fold greater than gel-based SNP typing and microsatellite typing in our laboratory. Savings on labor costs are considerable. We conclude that Invader chemistry using PCR products as template represents a useful technology for typing large numbers of SNPs rapidly and efficiently.

Fast and efficient mutation detection method using multiplex PCR and cycle sequencing--application to haemophilia B

A method using multiplex PCR followed by cycle-sequencing has been developed to detect mutations in the FIX gene. The procedure was evaluated in 45 severe or mild haemophilia B patients from 45 unrelated families. At least one deleterious mutation was identified in every haemophiliac demonstrating the efficiency of the method. Furthermore the described procedure offers many advantages compared to other screening detection methods: it is fast (less than 48 h), simple (partly automated) and of relatively low cost (it requires only one PCR).

Tissue microarrays for gene amplification surveys in many different tumor types

Gene amplifications are common in many different tumor types and may confer diagnostic, prognostic, or therapeutic information for patient management. Tedious experiments are often required to determine which tumor types have amplifications of a specific oncogene. To facilitate rapid screening for molecular alterations in many different malignancies, a tissue microarray consisting of samples from 17 different tumor types was generated. Altogether, 397 individual tumors were arrayed in a single paraffin block. To determine whether results from the literature can be reproduced on minute tissue samples (diameter, 0.6 mm), amplification of three extensively studied oncogenes (CCND1, CMYC, and ERBB2) was analyzed in three fluorescence in situ hybridization experiments from consecutive sections cut from the tissue microarray. Amplification of CCND1 was found in breast, lung, head and neck, and bladder cancer, as well as in melanoma. ERBB2 was amplified in bladder, breast, colon, stomach, testis, and lung cancer. CMYC was amplified in breast, colon, kidney, lung, ovary, bladder, head and neck, and endometrial cancer. These results confirm and even extend existing data in the literature on such amplifications. In summary, we applied three fluorescence in situ hybridization experiments to analyze amplifications of three oncogenes in three x 397 tumors within a week. This demonstrates the power of using minute arrayed tissue specimens for tumor screening.

High-throughput tissue microarray analysis to evaluate genes uncovered by cDNA microarray screening in renal cell carcinoma

Many genes and signaling pathways are involved in renal cell carcinoma (RCC) development. However, genetic tumor markers have not gained use in RCC diagnostics and prognosis prediction. Identification and evaluation of new molecular parameters are of utmost importance in cancer research and cancer treatment. Here we present a novel approach to rapidly identify clinically relevant molecular changes in cancer. To identify genes with relevance to RCC, a cDNA array analysis was first performed on 5184 cDNA clones on a filter to screen for genes with differential expression between the renal cancer cell line CRL-1933 and normal kidney tissue. There were 89 differentially expressed genes in the cancer cell line, one of them coding for vimentin, a cytoplasmic intermediate filament. In a second step, a renal cancer tissue microarray containing 532 RCC specimen was used to determine vimentin expression by immunohistochemistry. Vimentin expression was seen frequently in clear cell (51%) and papillary RCC (61%), but rarely in chromophobe RCC (4%) and oncocytomas (12%). Furthermore, vimentin expression was significantly associated with poor patient prognosis (P < 0.007) independent of grade and stage. These results obtained from minute arrayed tumor samples match well with previous findings on vimentin expression in renal tumors. It is concluded that the combination of tumor arrays and cDNA arrays is a powerful approach to rapidly identify and further evaluate genes that play a role in tumor biology.

Facial measurements in clinical genetics: How important are the instruments we use?

Prompted by our finding that a popular compendium of clinical measurements often suggests a transparent ruler as a suitable substitute for anthropometric calipers (which were typically used by the original researchers to collect the normative data), we compared facial measurements taken with a ruler and calipers. Our objectives were to compare facial measurement data taken with these instruments by two classes of observer: expert and inexperienced. Ten facial measurements were repeated on four medically normal women by one expert and one inexperienced observer. Both observers' data showed that the caliper-derived means were usually the larger, but, whereas the expert observer's caliper-derived data typically were the least variable, the novice observer had smaller standard deviations and ranges for the ruler-derived data. Statistically significant differences were found between the ruler- and caliper-derived data from both observers on all four subjects, except for subnasale-pogonion and stomion-pogonion. For the novice observer only, endocanthion-endocanthion, left exocanthion-endocanthion, and alare-alare were also nonsignificant. The calibrations of the sliding caliper and ruler were compared to determine if differences between them could explain the statistical results, but were the same. We concluded that the differences between the caliper- and ruler-derived measurements resulted because the ruler often could not be placed directly on the landmarks, as could the arms of the calipers. We recommend that clinicians interested in taking facial measurements to assess their patients consult the original publications for information on the techniques and instruments used so that reliable comparisons with the normative data can be made.

High-throughput screening for known mutations by automated analysis of single sequencing reactions

This work shows that single sequencing reactions analyzed on an automated DNA sequencer can be an efficient way of screening PCR products for known mutations. We have analyzed a mutation in exon 10 of the human aromatase gene and show that an unambiguous genotype could be elucidated in more than 90% of the analyzed samples. Compared to analysis by full sequencing, 4 times more samples can be analyzed per gel, so that the sample capacity of the gel is approaching that of alternative gel-based methods for genotype analysis. Unlike many of these, the method offers direct identification of the variant sequence position and on-line analysis without the need of post-electrophoretic processing of the gel.

High throughput parallel analysis of hundreds of patient samples for more than 100 mutations in multiple disease genes

As more mutations are identified in genes of known sequence, there is a crucial need in the areas of medical genetics and genome analysis for rapid, accurate and cost-effective methods of mutation detection. We have developed a multiplex allele-specific diagnostic assay (MASDA) for analysis of large numbers of samples (> 500) simultaneously for a large number of known mutations (> 100) in a single assay. MASDA utilizes oligonucleotide hybridization to interrogate DNA sequences. Multiplex DNA samples are immobilized on a solid support and a single hybridization is performed with a pool of allele-specific oligonucleotide (ASO) probes. Any probes complementary to specific mutations present in a given sample are in effect affinity purified from the pool by the target DNA. Sequence-specific band patterns (fingerprints), generated by chemical or enzymatic sequencing of the bound ASO(s), easily identify the specific mutation(s). Using this design, in a single diagnostic assay, we tested samples for 66 cystic fibrosis (CF) mutations, 14 beta-thalassemia mutations, two sickle cell anemia (SCA) mutations, three Tay-Sachs mutations, eight Gaucher mutations, four mutations in Canavan disease, four mutations in Fanconi anemia, and five mutations in BRCA1. Each mutation was correctly identified. Finally, in a blinded study of 106 of these mutations in > 500 patients, all mutations were properly identified. There were no false positives or false negatives. The MASDA assay is capable of detecting point mutations as well as small insertion or deletion mutations. This technology is amenable to automation and is suitable for immediate utilization for high-throughput genetic diagnostics in clinical and research laboratories.

Prenatal diagnosis in the 1990s

Prenatal diagnosis has become widely available and detects an increasing variety of birth defects and potentially harmful medical conditions. Many of the studies are complex and must be performed within a specific time period. Most prenatal diagnostic sampling techniques have some degree of risk for the mother or the fetus, and all produce at least transient anxiety. Nurses are involved in identifying families at risk, preparing women for the procedures, providing support, and counseling patients after the results are known; because of this role, nurses need updated information. This review describes current methods for early identification of a potential problem, discusses a variety of prenatal diagnostic procedures, reviews the most common types of laboratory studies, and introduces future trends in the field of prenatal diagnosis.

Micromanipulation of gametes and embryos in preimplantation genetic diagnosis and assisted fertilization

Recent advances in micromanipulation and biopsy of gametes and embryos have made it possible to develop new approaches for early genetic diagnosis and prevention of genetic disease and for treatment of severe male-factor infertility. Preimplantation diagnosis of a number of X-linked and autosomal recessive disorders has been performed, using polar body sampling and blastomere biopsy, coupled with polymerase chain reaction. Blastocyst biopsy has also been performed in human embryos; however, there has been no clinical application so far. Existing data have not shown any detrimental effect of micromanipulation and biopsy involved in the preimplantation development of the human embryo. The existing experience on micromanipulation of gametes (zona-opening procedures, subzonal sperm insertion, and sperm microinjection into the ooplasm) has also demonstrated the clinical usefulness in assisted fertilization, suggesting a possible selective application of various micromanipulation techniques and their combinations in male infertility.

[Dermatoglyphic diagnosis in patients with atopic eczema]

The purpose of this investigation was to find out whether the new Dermalog system could be used in conjunction with dermatoglyphics in patients with atopic dermatitis. For this purpose, 92 patients with atopic eczema (58 women and 34 men) were examined and were compared with two different control groups. The first control group, representing the normal population, consisted of 100 female and 100 male randomly selected subjects. The second control group (55 women and 24 men) excluded any persons with a history of atopic syndrome. First of all, hand and fingerprints were taken. The data were stored in a computer and were statistically analysed with the aid of significance and discrimination tests. Evaluation of the patients' data showed no significant difference from the first control group. Results in the second, selected, control group were better. For example, in this group, in which the probability was 93.1%, 76.4% of the women examined were found to have atopic dermatitis. The probability among the male patients examined was 99.9% and the corresponding sensitivity, 77.0%.

Screening for genetic traits and diseases

Genetic screening should greatly improve the quality of life. A thorough family and medical history is the basis for identifying families at high risk for genetic traits and diseases. Recognition is enhanced by awareness of diseases associated with certain racial, ethnic or geographic groups. Effective genetic screening requires close collaboration between physicians, public health officers and medical investigators.