Development of genomic reference materials for cystic fibrosis genetic testing

Differentiation between nonobstructive azoospermia and obstructive azoospermia: then and now

Male infertility has seen an increase in prevalence with cases of azoospermia estimated to affect 10%-15% of infertile men. Confirmation of azoospermia subsequently necessitates an early causal differentiation between obstructive azoospermia (OA) and nonobstructive azoospermia (NOA). Although less common when compared to NOA, OA can represent upward 20%-40% of cases of azoospermia. While there are a multitude of etiologies responsible for causing NOA and OA, correctly distinguishing between the two types of azoospermia has profound implications in managing the infertile male. This review represents an amalgamation of the current guidelines and literature which will supply the reproductive physician with a diagnostic armamentarium to properly distinguish between NOA and OA, therefore providing the best possible care to the infertile couple.

Cost-effectiveness of the CFTR gene-sequencing test for asymptomatic carriers in the Colombian population

Introducción.

La fibrosis quística es una enfermedad genética de carácter autosómico recesivo clasificada como enfermedad huérfana de alto costo.

Objetivo.

Determinar la razón de costo-efectividad de la prueba diagnóstica de secuenciación del gen CFTR para los portadores asintomáticos familiares en primer, segundo y tercer grados de consanguinidad.

Materiales y métodos.

Se hizo una búsqueda sistemática sobre la evaluación de las características operativas de la prueba diagnóstica y los modelos de árbol de decisiones en estudios de costo-efectividad. Se elaboró un modelo de árbol de decisiones tomando como unidad de análisis la prevención de futuras concepciones. Los costos de la enfermedad se obtuvieron del reporte de alto costo del Ministerio de Salud de Colombia. Los costos de la prueba se obtuvieron de laboratorios nacionales. Se hizo un análisis de sensibilidad, determinístico y probabilístico, con la perspectiva del tercer pagador y horizonte a un año.

Resultados.

Se obtuvo una razón incremental de costo-efectividad (RICE) de USD$ 5.051,10 por obtener 10,89 % más de probabilidades de evitar el nacimiento de un niño enfermo con fibrosis quística por pareja. Para los familiares de segundo y tercer grados, se encontró una RICE de USD$ 19.380,94 y USD$ 55.913,53, respectivamente, al aplicar el PIB per cápita. Esta tecnología fue costo-efectiva en 39 %, 61,18 % y 74,36 % para 1, 2 y 3 PIB per cápita en familiares de primer grado de consanguinidad.

Conclusiones.

La prueba genética de detección de portadores del gen CFTR resultó costo-efectiva dependiendo del umbral de la disponibilidad de pagar, y de los supuestos y limitaciones establecidas en el modelo.

Assessing the Performance of Dried-Blood-Spot DNA Extraction Methods in Next Generation Sequencing

An increasing number of newborn screening laboratories in the United States and abroad are moving towards incorporating next-generation sequencing technology, or NGS, into routine screening, particularly for cystic fibrosis. As more programs utilize this technology for both cystic fibrosis and beyond, it is critical to identify appropriate DNA extraction methods that can be used with dried blood spots that will result in consistent, high-quality sequencing results. To provide comprehensive quality assurance and technical assistance to newborn screening laboratories wishing to incorporate NGS assays, CDC's Newborn Screening and Molecular Biology Branch designed a study to evaluate the performance of nine commercial or laboratory-developed DNA extraction methods that range from a highly purified column extraction to a crude detergent-based no-wash boil prep. The DNA from these nine methods was used in two NGS library preparations that interrogate the CFTR gene. All DNA extraction methods including the cruder preps performed reasonably well with both library preps. One lower-concentration, older sample was excluded from one of the assay evaluations due to poor performance across all DNA extraction methods. When 84 samples, versus eight, were run on a flow cell, the DNA quality and quantity were more significant variables.

The lot-to-lot variability in the mitochondrial genome of controls

Current research in the biomedical field has illustrated how cell lines used as reference standards can change over time and, more importantly, can affect research and diagnostic results obtained from these cell lines. With the use of increasingly sensitive and highly resolving technologies (e.g., massively parallel sequencing), forensic scientists must be aware of and account for potential variability in the cell lines used as controls in their validation studies and day-to-day casework. In this study, multiple lot numbers from four commonly-used control cell line DNAs were sequenced with massively parallel sequencing on the Ion S5. The variability among these different lots was evaluated, and the effect on forensic laboratory work discussed.

MRI findings of obstructive azoospermia: lesions in and out of pelvic cavity

Obstructive azoospermia (OA) is caused by excurrent duct obstruction, which can occur anywhere along the course of the male reproductive tract and is classically characterized by normal spermatogenesis. To be familiar with the imaging anatomy of normal and abnormal male genital ducts is essential to the diagnosis of OA. In some circumstances, OA can also be related to some specific syndromes; thus, making an accurate diagnosis may require an integral view of the whole abdomen and pelvis. MR is a great complementary imaging modality either for the detection of obstructive factors, especially for characterization of those indeterminate features on ultrasound, or for the identification of specific syndromes related to OA. In this article, a series of patients with OA caused by different kinds of lesions in and out of the pelvic cavity (abdomen) shown on MR imaging were included, and some cases of specific syndromes related to OA were also reviewed.

The Journal of Molecular Diagnostics: 20 Years Defining Professional Practice

This editorial highlights 20 years of JMD defining professional practice.

Development and Characterization of Reference Materials for Genetic Testing: Focus on Public Partnerships

Characterized reference materials (RMs) are needed for clinical laboratory test development and validation, quality control procedures, and proficiency testing to assure their quality. In this article, we review the development and characterization of RMs for clinical molecular genetic tests. We describe various types of RMs and how to access and utilize them, especially focusing on the Genetic Testing Reference Materials Coordination Program (Get-RM) and the Genome in a Bottle (GIAB) Consortium. This review also reinforces the need for collaborative efforts in the clinical genetic testing community to develop additional RMs.

Genetic evaluation of male infertility

Men with severe oligospermia (<5 million sperm/mL ejaculate fluid) or azoospermia should receive genetic testing to clarify etiology of male infertility prior to treatment. Categorization by obstructive azoospermia (OA) or non-obstructive azoospermia (NOA) is critical since genetic testing differs for the former with normal testicular function, testicular volume (~20 mL), and follicle-stimulating hormone (FSH) (1-8 IU/mL) when compared to the latter with small, soft testes and increased FSH. History and physician examination along with laboratory testing (following appropriate genetic counseling) is critical to accurate selection of genetic testing appropriate for azoospermia due to primary testicular failure as compared with congenital hypogonadotropic hypogonadism (HH). Genetic testing options include cystic fibrosis transmembrane conductance regulator (CFTR) testing for men with congenital absence of the vas, while karyotype, Y chromosome microdeletions (YCMD), and other specific genetic tests may be warranted depending on the clinical context of severe oligospermia or NOA. The results of genetic testing guide management options. The most recent techniques for genetic analysis, including sperm microRNA (miRNA) and epigenetics, are forming the foundation for future genetic diagnosis and therapeutic targets in male infertility.

Newborn Screening Quality Assurance Program for CFTR Mutation Detection and Gene Sequencing to Identify Cystic Fibrosis

All newborn screening laboratories in the United States and many worldwide screen for cystic fibrosis. Most laboratories use a second-tier genotyping assay to identify a panel of mutations in the CF transmembrane regulator (CFTR) gene. Centers for Disease Control and Prevention’s Newborn Screening Quality Assurance Program houses a dried blood spot repository of samples containing CFTR mutations to assist newborn screening laboratories and ensure high-quality mutation detection in a high-throughput environment. Recently, CFTR mutation detection has increased in complexity with expanded genotyping panels and gene sequencing. To accommodate the growing quality assurance needs, the repository samples were characterized with several multiplex genotyping methods, Sanger sequencing, and 3 next-generation sequencing assays using a high-throughput, low-concentration DNA extraction method. The samples performed well in all of the assays, providing newborn screening laboratories with a resource for complex CFTR mutation detection and next-generation sequencing as they transition to new methods.

Second SPIDIA-DNA External Quality Assessment (EQA): Influence of pre-analytical phase of blood samples on genomic DNA quality

BACKGROUND

In order to develop evidence-based quality guidelines for the pre-analytical phase of blood samples used for DNA molecular testing, two pan-European External Quality Assessments (EQAs) were implemented within the European Commission funded project SPIDIA. Here we report the results of the 2nd SPIDIA EQA that has been implemented on the basis of the 1st DNA EQA with the inclusion of some stringent conditions related to blood storage temperature and time.

METHODS

SPIDIA facility sent to all the participants the same blood sample to be processed by their own procedure following SPIDIA suggestion for time and temperature storage. Evaluated genomic DNA (gDNA) quality parameters were: purity and yield by UV spectrophotometric analysis, PCR interferences by Kineret software and integrity by a dedicated algorithm.

RESULTS/CONCLUSIONS

188 applications have been collected from 26 European countries. A high variability of gDNA integrity was observed whereas purity, yield and PCR interferences had a narrow distribution within laboratories. A dedicated analysis on pre-analytical variables and the evaluated gDNA quality parameters showed that blood storage and DNA extraction procedures influence gDNA integrity. The performances of the participants were improved in comparison with the 1st SPIDIA-DNA EQA, probably due to adopted more stringent pre-analytical conditions.

Cystic Fibrosis: A Review of Associated Phenotypes, Use of Molecular Diagnostic Approaches, Genetic Characteristics, Progress, and Dilemmas

Cystic fibrosis (CF) is an autosomal recessive disease with significant associated morbidity and mortality. It is now appreciated that the broad phenotypic CF spectrum is not explained by obvious genotype-phenotype correlations, suggesting that CF transmembrane conductance regulator (CFTR)-related disease may occur because of multiple additive effects. These contributing effects include complex CFTR alleles, modifier genes, mutations in alternative genes that produce CF-like phenotypes, epigenetic factors, and environmental influences. Most patients in the United States are now diagnosed through newborn screening and use of molecular testing methods. We review the molecular testing approaches and laboratory guidelines for carrier screening, prenatal testing, newborn screening, and clinical diagnostic testing, as well as recent developments in CF treatment, and reasons for the lack of a molecular diagnosis in some patients.

Review of Azoospermia

Azoospermia is classified as obstructive azoospermia (OA) or non-obstructive azoospermia (NOA), each having very different etiologies and treatments. The etiology, diagnosis, and management of azoospermia were reviewed and relevant literature summarized. Differentiation between these two etiologies is of paramount importance and is contingent upon thorough history and physical examination and indicated laboratory/genetic testing. OA occurs secondary to obstruction of the male reproductive tract, and is diagnosed through a combination of history/physical examination, laboratory testing, genetics (CFTR for congenital OA), and imaging studies. NOA (which includes primary testicular failure and secondary testicular failure) is differentiated from OA by clinical assessment (testis consistency/volume), laboratory testing (FSH), and genetic testing (karyotype, Y chromosome microdeletion, or specific genetic testing for hypogonadotropic hypogonadism). For obstructive azoospermia, management includes microsurgical reconstruction when feasible using microsurgical vasovasostomy or vasoepididymostomy. Microsurgical epididymal sperm aspiration with in vitro fertilization/intracytoplasmic sperm injection (IVF/ICSI) is utilized for those cases not amenable to reconstruction. NOA management includes medical management for congenital hypogonadotropic hypogonadism and microdissection testicular sperm extraction with IVF/ICSI for appropriate candidates based on laboratory/genetic testing. Overall, this important review provides an updated summary of the most recent available literature describing etiology, diagnosis, and management of azoospermia.

Bridging the gap: moving predictive and prognostic assays from research to clinical use

The development of clinically useful molecular diagnostics requires validation of clinical assay performance and achievement of clinical qualification in clinical trials. As discussed elsewhere in this Focus section on molecular diagnostics, validation of assay performance must be rigorous, especially when the assay will be used to guide treatment decisions. Here we review some of the problems associated with assay development, especially for academic investigators. These include lack of expertise and resources for analytical validation, lack of experience in designing projects for a specific clinical use, lack of specimens from appropriate patient groups, and lack of access to Clinical Laboratory Improvement Amendments-certified laboratories. In addition, financial support for assay validation has lagged behind financial support for marker discovery or drug development, even though the molecular diagnostic may be considered necessary for the successful use of the companion therapeutic. The National Cancer Institute supports a large number of clinical trials and a significant effort in drug development. In order to address some of these barriers for predictive and prognostic assays that will be used in clinical trials to select patients for a particular treatment, stratify patients into molecularly defined subgroups, or choose between treatments for molecularly defined tumors, the National Cancer Institute has begun a pilot program designed to lessen barriers to the development of validated prognostic and predictive assays.

CFTR mutation analysis and haplotype associations in CF patients

Most newborn screening (NBS) laboratories use second-tier molecular tests for cystic fibrosis (CF) using dried blood spots (DBS). The Centers for Disease Control and Prevention's NBS Quality Assurance Program offers proficiency testing (PT) in DBS for CF transmembrane conductance regulator (CFTR) gene mutation detection. Extensive molecular characterization on 76 CF patients, family members or screen positive newborns was performed for quality assurance. The coding, regulatory regions and portions of all introns were sequenced and large insertions/deletions were characterized as well as two intronic di-nucleotide microsatellites. For CF patient samples, at least two mutations were identified/verified and four specimens contained three likely CF-associated mutations. Thirty-four sequence variations in 152 chromosomes were identified, five of which were not previously reported. Twenty-seven of these variants were used to predict haplotypes from the major haplotype block defined by HapMap data that spans the promoter through intron 19. Chromosomes containing the F508del (p.Phe508del), G542X (p.Gly542X) and N1303K (p.Asn1303Lys) mutations shared a common haplotype subgroup, consistent with a common ancient European founder. Understanding the haplotype background of CF-associated mutations in the U.S. population provides a framework for future phenotype/genotype studies and will assist in determining a likely cis/trans phase of the mutations without need for parent studies.

Molecular diagnostics: harmonization through reference materials, documentary standards and proficiency testing

There is a great need for harmonization in nucleic acid testing for infectious disease and clinical genetics. The proliferation of assay methods, the number of targets for molecular diagnostics and the absence of standard reference materials contribute to variability in test results among laboratories. This article provides a comprehensive overview of reference materials, related documentary standards and proficiency testing programs. The article explores the relationships among these resources and provides necessary information for people practicing in this area that is not taught in formal courses and frequently is obtained on an ad hoc basis. The aim of this article is to provide helpful tools for molecular diagnostic laboratories.

Mutation analysis of SLC26A4 for Pendred syndrome and nonsyndromic hearing loss by high-resolution melting

Pendred syndrome and DFNB4 (autosomal recessive nonsyndromic congenital deafness, locus 4) are associated with autosomal recessive congenital sensorineural hearing loss and mutations in the SLC26A4 gene. Extensive allelic heterogeneity, however, necessitates analysis of all exons and splice sites to identify mutations for individual patients. Although Sanger sequencing is the gold standard for mutation detection, screening methods supplemented with targeted sequencing can provide a cost-effective alternative. One such method, denaturing high-performance liquid chromatography, was developed for clinical mutation detection in SLC26A4. However, this method inherently cannot distinguish homozygous changes from wild-type sequences. High-resolution melting (HRM), on the other hand, can detect heterozygous and homozygous changes cost-effectively, without any post-PCR modifications. We developed a closed-tube HRM mutation detection method specific for SLC26A4 that can be used in the clinical diagnostic setting. Twenty-eight primer pairs were designed to cover all 21 SLC26A4 exons and splice junction sequences. Using the resulting amplicons, initial HRM analysis detected all 45 variants previously identified by sequencing. Subsequently, a 384-well plate format was designed for up to three patient samples per run. Blinded HRM testing on these plates of patient samples collected over 1 year in a clinical diagnostic laboratory accurately detected all variants identified by sequencing. In conclusion, HRM with targeted sequencing is a reliable, simple, and cost-effective method for SLC26A4 mutation screening and detection.

Multiallelic synthetic quality control material: lessons learned from the cystic fibrosis external quality assessment scheme

AIM

With the arrival of increasingly complex molecular tests, we are obliged to create new ways to monitor and troubleshoot the underperformance of these multiplex assays. A synthetic multiallelic quality control material has been designed to augment genomic DNA controls. We aimed to evaluate the control on a large scale, testing it on a wide variety of oligonucleotide ligation assays, test protocols, and analysis software. In addition, we investigated how laboratories treat untried and complex materials.

METHODS

The synthetic control monitored 32 cystic fibrosis transmembrane conductance regulator mutations and polymorphisms simultaneously. Participants of a cystic fibrosis external quality assessment scheme were invited to analyze the quality control.

RESULTS

In total, 58 laboratories participated in this study. Twenty-seven (47%) laboratories detected 32 variants; another 27 laboratories (47%) detected from 31 to 4 variants and 4 participants reported no variants (6%). The main observations included administrative errors when indicating variants on a checklist, errors caused by misreading the instructions for use of the control or assay, and technical problems related to the assay used.

CONCLUSION

Synthetic quality control materials proved to be valuable in troubleshooting underperforming assays and complement existing genomic controls. The study also revealed a strong need for increased quality control in the postanalytical phase of testing.

Development of genomic DNA reference materials for genetic testing of disorders common in people of ashkenazi jewish descent

Many recessive genetic disorders are found at a higher incidence in people of Ashkenazi Jewish (AJ) descent than in the general population. The American College of Medical Genetics and the American College of Obstetricians and Gynecologists have recommended that individuals of AJ descent undergo carrier screening for Tay Sachs disease, Canavan disease, familial dysautonomia, mucolipidosis IV, Niemann-Pick disease type A, Fanconi anemia type C, Bloom syndrome, and Gaucher disease. Although these recommendations have led to increased test volumes and number of laboratories offering AJ screening, well-characterized genomic reference materials are not publicly available. The Centers for Disease Control and Prevention-based Genetic Testing Reference Materials Coordination Program, in collaboration with members of the genetic testing community and Coriell Cell Repositories, have developed a panel of characterized genomic reference materials for AJ genetic testing. DNA from 31 cell lines, representing many of the common alleles for Tay Sachs disease, Canavan disease, familial dysautonomia, mucolipidosis IV, Niemann-Pick disease type A, Fanconi anemia type C, Bloom syndrome, Gaucher disease, and glycogen storage disease, was prepared by the Repository and tested in six clinical laboratories using three different PCR-based assay platforms. A total of 33 disease alleles was assayed and 25 different alleles were identified. These characterized materials are publicly available from Coriell and may be used for quality control, proficiency testing, test development, and research.

Development and characterization of reference materials for MTHFR, SERPINA1, RET, BRCA1, and BRCA2 genetic testing

Well-characterized reference materials (RMs) are integral in maintaining clinical laboratory quality assurance for genetic testing. These RMs can be used for quality control, monitoring of test performance, test validation, and proficiency testing of DNA-based genetic tests. To address the need for such materials, the Centers for Disease Control and Prevention established the Genetic Testing Reference Material Coordination Program (GeT-RM), which works with the genetics community to improve public availability of characterized RMs for genetic testing. To date, the GeT-RM program has coordinated the characterization of publicly available genomic DNA RMs for a number of disorders, including cystic fibrosis, Huntington disease, fragile X, and several genetic conditions with relatively high prevalence in the Ashkenazi Jewish population. Genotypic information about a number of other cell lines has been collected and is also available. The present study includes the development and commutability/genotype characterization of 10 DNA samples for clinically relevant mutations or sequence variants in the following genes: MTHFR; SERPINA1; RET; BRCA1; and BRCA2. DNA samples were analyzed by 19 clinical genetic laboratories using a variety of assays and technology platforms. Concordance was 100% for all samples, with no differences observed between laboratories using different methods. All DNA samples are available from Coriell Cell Repositories and characterization information can be found on the GeT-RM website.