C. Mattocks

A standardized framework for the validation and verification of clinical molecular genetic tests

The validation and verification of laboratory methods and procedures before their use in clinical testing is essential for providing a safe and useful service to clinicians and patients. This paper outlines the principles of validation and verification in the context of clinical human molecular genetic testing. We describe implementation processes, types of tests and their key validation components, and suggest some relevant statistical approaches that can be used by individual laboratories to ensure that tests are conducted to defined standards.

Identification of a mutation that perturbs NF1 agene splicing using genomic DNA samples and a minigene assay

Neurofibromatosis type 1 (NF1) is a common autosomal dominant genetic disease. In recent studies on the neurofibromatosis type 1 (NF1) gene neurofibromin, splicing abnormalities were seen in 30-50% of cases when RNA taken from cell lines was analysed.1,2 Unlike mutations that alter critical amino acids or generate premature stop codons, splicing abnormalities can be very hard to predict from sequence analysis alone. Apart from the two base pairs 5′ and 3′ of each exon, few of the nucleotides in regions critical for splicing are absolutely conserved. As a consequence, it can be very difficult to conclude that a sequence variation found in a patient will alter splicing and so represents a pathogenic mutation. ### Key points This difficulty is well illustrated by a family with NF1 in which we recently identified a sequence variation. The three generation family is from the UK and meets NIH diagnostic criteria. The index case, at the age of 82, has classical features of NF1 including multiple cafe au lait macules, neurofibromas, and axillary and inguinal freckling. Her son was similarly affected and died …

Automated comparative sequence analysis identifies mutations in 89% of NF1 patients and confirms a mutation cluster in exons 11–17 distinct from the GAP related domain

Neurofibromatosis type 1 (NF1), formerly known as Von Recklinghausen Neurofibromatosis, is a common genetic disorder affecting approximately 1 in 3000–5000 people. It is a fully penetrant autosomal dominant disorder. Strict diagnostic criteria that include cafe au lait spots, neurofibromas, plexiform neurofibromas, freckling in the axillary or inguinal regions, Lisch nodules (iris haematomas), optic or chiasma glioma, pseudoarthrosis, and sphenoid dysplasia define NF1. Most disease features are present in more than 90% of patients at puberty.1 Further manifestations are known to occur in this disorder, including macrocephaly, short stature, learning difficulties, scoliosis and certain malignancies.2–4 There is, however, great intra and interfamilial phenotypic variability. In addition a number of patients who have a clinical picture suspected to be NF1 do not fulfil the diagnostic criteria particularly in the younger age groups. As a consequence genetic testing would have a major impact on the diagnosis and management of these families. The NF1 gene maps to chromosome 17q11.2 and is thought to be a tumour suppressor gene because loss of heterozygosity is associated with the occurrence of benign and malignant tumours in tissues derived from the neural crest5–7 as well as myeloid malignancies.8 It spans a region of about 350 kb of genomic DNA and contains 60 exons.9–11 It harbours at least three other embedded genes—EV12A, EV12B, and ONGP—transcribed from the opposite strand of NF1 intron 27b. The NF1 gene transcribes several mRNAs in the size range 11–13 kb expressed in neurones, oligodendrocytes and non-myelinating Schwann cells.12 The most common transcript codes for a polypeptide of 2818 amino acids called neurofibromin.13–15 A 360 amino acid region of the predicted protein product shows homology with the GTPase activating (GAP) family of proteins in yeast and mammals.16 The GAP related domain (GRD) is …

Review of massively parallel DNA sequencing technologies

Since the development of technologies that can determine the base-pair sequence of DNA, the ability to sequence genes has contributed much to science and medicine. However, it has remained a relatively costly and laborious process, hindering its use as a routine biomedical tool. Recent times are seeing rapid developments in this field, both in the availability of novel sequencing platforms, as well as supporting technologies involved in processes such as targeting and data analysis. This is leading to significant reductions in the cost of sequencing a human genome and the potential for its use as a routine biomedical tool. This review is a snapshot of this rapidly moving field examining the current state of the art, forthcoming developments and some of the issues still to be resolved prior to the use of new sequencing technologies in routine clinical diagnosis.

A SNP profiling panel for sample tracking in whole-exome sequencing studies

Abstract?This is an Erratum to Genome Medicine 2013, 5:89, highlighting an error in Table 1 of the original article. Please see related article: http://genomemedicine.com/content/5/9/89.

Interlaboratory Diagnostic Validation of Conformation-Sensitive Capillary Electrophoresis for Mutation Scanning

BACKGROUND Indirect alternatives to sequencing as a method for mutation scanning are of interest to diagnostic laboratories because they have the potential for considerable savings in both time and costs. Ideally, such methods should be simple, rapid, and highly sensitive, and they should be validated formally to a very high standard. Currently, most reported methods lack one or more of these characteristics. We describe the optimization and validation of conformation-sensitive capillary electrophoresis (CSCE) for diagnostic mutation scanning. METHODS We initially optimized the performance of CSCE with a systematic panel of plasmid-based controls. We then compared manual analysis by visual inspection with automated analysis by BioNumerics software (Applied Maths) in a blinded interlaboratory validation with 402 BRCA1 (breast cancer 1, early onset) and BRCA2 (breast cancer 1, early onset) variants previously characterized by Sanger sequencing. RESULTS With automated analysis, we demonstrated a sensitivity of >99% (95% CI), which is indistinguishable from the sensitivity for conventional sequencing by capillary electrophoresis. The 95% CI for specificity was 90%-93%; thus, CSCE greatly reduces the number of fragments that need to be sequenced to fully characterize variants. By manual analysis, the 95% CIs for sensitivity and specificity were 98.3%-99.4% and 93.1%-95.5%, respectively. CONCLUSIONS CSCE is amenable to a high degree of automation, and analyses can be multiplexed to increase both capacity and throughput. We conclude that once it is optimized, CSCE combined with analysis with BioNumerics software is a highly sensitive and cost-effective mutation-scanning technique suitable for routine genetic diagnostic analysis of heterozygous nucleotide substitutions, small insertions, and deletions.

Application of Molecular Diagnostics to Hereditary Nonpolyposis Colorectal Cancer

Hereditary nonpolyposis colorectal cancer is a tumor predis– position syndrome characterised by a propensity to develop, typically, but by no means exclusively, young‐onset colorectal and other cancers (1). The condition was first described in 1913 by the US pathologist Warthin in a comprehensive survey of familial cancer (2). He was stimulated to make this study because his seamstress was depressed at the thought of dying prematurely from bowel or womb cancer, as had many of her relatives. She was a member of Family “ G” in his original arti–cle, which incidentally contains examples of most of the cancer genetic conditions recognized today (2). Family “G” was redis– covered in the 1960s by Lynch, although it was not at first real-ized that it was one of Warthins original families (3,4). Lynch later made a distinction between families with only bowel can– cer (Lynch syndrome type 1: site‐specific colorectal cancer) and families with several types of cancer, including bowel (Lynch syndrome type 2: family cancer syndrome). Given the propensity to bowel cancer, but without the polyposis charac– teristic of familial adenomatous polyposis (FAP), the all embracing term “hereditary nonpolyposis colorectal cancer” (HNPCC) is now used (1). However, having to explain all this in the clinic makes the idea of going back to calling it Lynch or family cancer syndrome rather attractive.

Identification of a functionally significant tri-allelic genotype in the Tyrosinase gene ( TYR ) causing hypomorphic oculocutaneous albinism (OCA1B)

Oculocutaneous albinism (OCA) and ocular albinism (OA) are inherited disorders of melanin biosynthesis, resulting in loss of pigment and severe visual deficits. OCA encompasses a range of subtypes with overlapping, often hypomorphic phenotypes. OCA1 is the most common cause of albinism in European populations and is inherited through autosomal recessive mutations in the Tyrosinase (TYR) gene. However, there is a high level of reported missing heritability, where only a single heterozygous mutation is found in TYR. This is also the case for other OCA subtypes including OCA2 caused by mutations in the OCA2 gene. Here we have interrogated the genetic cause of albinism in a well phenotyped, hypomorphic albinism population by sequencing a broad gene panel and performing segregation studies on phenotyped family members. Of eighteen probands we can confidently diagnose three with OA and OCA2, and one with a PAX6 mutation. Of six probands with only a single heterozygous mutation in TYR, all were found to have the two common variants S192Y and R402Q. Our results suggest that a combination of R402Q and S192Y with a deleterious mutation in a ‘tri-allelic genotype’ can account for missing heritability in some hypomorphic OCA1 albinism phenotypes.

Autoimmunity|[sol]|inflammation in a monogenic primary immunodeficiency cohort

Primary immunodeficiencies (PIDs) are rare inborn errors of immunity that have a heterogeneous phenotype that can include severe susceptibility to life‐threatening infections from multiple pathogens, unique sensitivity to a single pathogen, autoimmune/inflammatory (AI/I) disease, allergies and/or malignancy. We present a diverse cohort of monogenic PID patients with and without AI/I diseases who underwent clinical, genetic and immunological phenotyping. Novel pathogenic variants were identified in IKBKG, CTLA4, NFKB1, GATA2, CD40LG and TAZ as well as previously reported pathogenic variants in STAT3, PIK3CD, STAT1, NFKB2 and STXBP2. AI/I manifestations were frequently encountered in PIDs, including at presentation. Autoimmunity/inflammation was multisystem in those effected, and regulatory T cell (Treg) percentages were significantly decreased compared with those without AI/I manifestations. Prednisolone was used as the first‐line immunosuppressive agent in all cases, however steroid monotherapy failed long‐term control of autoimmunity/inflammation in the majority of cases and additional immunosuppression was required. Patients with multisystem autoimmunity/inflammation should be investigated for an underlying PID, and in those with PID early assessment of Tregs may help to assess the risk of autoimmunity/inflammation.

Clinical efficacy of a next-generation sequencing gene panel for primary immunodeficiency diagnostics

Primary immunodeficiencies (PIDs) are rare monogenic inborn errors of immunity that result in impairment of functions of the human immune system. PIDs have a broad phenotype with increased morbidity and mortality, and treatment choices are often complex. With increased accessibility of next‐generation sequencing (NGS), the rate of discovery of genetic causes for PID has increased exponentially. Identification of an underlying monogenic diagnosis provides important clinical benefits for patients with the potential to alter treatments, facilitate genetic counselling, and pre‐implantation diagnostics. We investigated a NGS PID panel of 242 genes within clinical care across a range of PID phenotypes. We also evaluated Phenomizer to predict causal genes from human phenotype ontology (HPO) terms. Twenty‐seven participants were recruited, and a total of 15 reportable variants were identified in 48% (13/27) of the participants. The panel results had implications for treatment in 37% (10/27) of participants. Phenomizer identified the genes harbouring variants from HPO terms in 33% (9/27) of participants. This study shows the clinical efficacy that genetic testing has in the care of PID. However, it also highlights some of the disadvantages of gene panels in the rapidly moving field of PID genomics and current challenges in HPO term assignment for PID.