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Background: Alport syndrome (AS) is a progressive renal disease with cochlear and ocular involvement. The majority of AS cases are X-linked (XLAS) and due to mutations in the COL4A5 gene. Although the disease may appear early in life and progress to end stage renal disease (ESRD) in young adults, in other families ESRD occurs in middle age. Few of the more than four hundred mutations described in COL4A5 are associated with adult type XLAS, but the families may be very large.Methods: We classified adult type AS mutation by prevalence in the US and we developed a molecular assay using a set of hybridization probes that identify the three most common adult type XLAS mutations; C1564S, L1649R, and R1677Q.Results: The test was validated on samples previously determined to contain one or none of these mutations. In the US, the test's clinical specificity and sensitivity are estimated to be higher than 99% and 75% respectively. Analytical specificity and sensitivity are above 99%.Conclusion: This test may be useful for presymptomatic and carrier testing in families with one of the mutations and in the diagnosis of unexplained hematuria or chronic kidney disease. [ABSTRACT FROM AUTHOR]

RASA1 mutations have been reported to be associated with hereditary capillary malformations (CM) with or without arteriovenous malformations (AVM), arteriovenous fistulas (AVF), or Parkes Weber syndrome. But the number of cases with RASA1 mutations reported to date is relatively small and the spectrum of phenotypes caused by mutations in this gene is not well defined. Mutation results and clinical findings in thirty-five unrelated consecutive cases sent for RASA1 molecular sequencing testing at ARUP Laboratories within the last two years were evaluated. Eight individuals had a pathogenic RASA1 mutation of which six were novel. These eight individuals all had CMs (seven had multifocal CMs; one had multiple CMs), and six also had a brain or facial AVM. Two individuals with multifocal CMs including one with a fast flow lesion had a variant of uncertain significance. All other individuals, including sixteen with CMs and one with a vein of Galen aneurysm, tested negative for a RASA1 mutation. Our data suggest that multifocal CM is the key clinical finding to suggest a RASA1 mutation. The clinical diagnostic mutation detection rate among all samples sent for RASA1 testing was 29% (10/35) which increases to approximately 39% (10/26) if patients without CMs are excluded., (Copyright © 2011 Elsevier Masson SAS. All rights reserved.)

Context: DNA sequencing is the method of choice for mutation detection in many genes., Objectives: To demonstrate the analytical accuracy and reliability of DNA sequencing assays developed in clinical laboratories. Only general guidelines exist for the validation of these tests. We provide examples of assay validation strategies for DNA sequencing tests., Design: We discuss important design and validation considerations., Results: The validation examples include an accuracy study to evaluate concordance between results obtained by the newly designed assay and analyzed by another method or laboratory. Precision (reproducibility) studies are performed to determine the robustness of the assay. To assess the quality of sequencing assays, several sequence quality measures are available. In addition, assessing the ability of primers to specifically and robustly amplify target regions before sequencing is important., Conclusion: Protocols for validation of laboratory-developed sequencing assays may vary between laboratories. An example summary of a validation is provided.

Deletions and duplications of single or multiple exons in specific genes are associated with human diseases. Multiplex ligation-dependant probe amplification (MLPA), a technique recently introduced to clinical laboratories, can detect deletions or duplications at the exon level. MLPA kits have a high multiplexing capability containing mixtures of exon-specific probes that target the gene of interest and control probes that hybridize to other genomic areas before PCR amplification. To verify each probe set, known positive samples with a single-exon deletion or duplication and normal samples are ideally used. Often, positive samples do not exist for each exon and normal samples are not suited to verify the identity of each probe set. We designed a straightforward approach using mixes of exon-specific PCR products as template to unequivocally verify each probe set in MLPA kits. This method can be used to verify the identity of MLPA probes for exons when positive samples are unavailable. Exon-specific probes from 15 MLPA kits were shown to hybridize to the targeted exons of interest. In one kit, this method identified probes that also bind a pseudogene, making them unreliable for clinical analysis. Incorporating this methodology in the analytical validation process will help ensure that MLPA results are interpreted correctly.

Alport Syndrome is a progressive renal disease with cochlear and ocular involvement. The most common form ( approximately 80%) is inherited in an X-linked pattern. X-linked Alport Syndrome (XLAS) is caused by mutations in the type IV collagen alpha chain 5 (COL4A5). We have developed a curated disease-specific database containing reported sequence variants in COL4A5. Currently the database archives a total of 520 sequence variants, verified for their position within the COL4A5 gene and named following standard nomenclature. Sequence variants are reported with accompanying information on protein effect, classification of mutation vs. polymorphism, mutation type based on the first description in the literature, and links to pertinent publications. In addition, features of this database include disease information, relevant links for Alport syndrome literature, reference sequence information, and ability to query by various criteria. On-line submission for novel gene variants or updating information on existing database entries is also possible. This free online scientific resource was developed with the clinical laboratory in mind to serve as a reference and repository for COL4A5 variants.

Hereditary hemorrhagic telangiectasia is an autosomal dominant disease caused by mutations in the ACVRL1 and ENG genes characterized by arterio-venous malformations and telangiectases. Over 700 mutations have been described in these two genes, and missense mutations are common. We describe 10 cases in which more than one potentially pathogenic mutation was identified. We report that 8 novel missense mutations, as well as previously reported pathogenic missense mutations, were seen in combination with a second mutation, which raises questions with regards to their respective pathogenicity. Our data and discussion indicate the challenges of classifying missense mutations as pathogenic or benign and the value of co-segregation studies, as well as suggest that there may be hereditary hemorrhagic telangiectasia gene mutations that have only mild phenotypic effects. We present evidence to suggest that four missense mutations (ENG p.G331S, ENG p.L8P, ENG p.P452L and ACVRL1 p.C344R) are pathogenic, two novel mutations (ACVRL1 p.A311T and ENG p.S576G) are neutral, and two previously reported disease-causing mutations are benign or have suspected benign variants (ACVRL1 p.A482V and ENG p.V504M). We conclude that for the purpose of establishing a causative hereditary hemorrhagic telangiectasia mutation in a family proband, all exons and intron/exon borders of both genes should be sequenced and deletion/duplication analysis should be performed unless a mutation that is well-proven to be pathogenic is identified.

Clinical laboratories performing gene sequencing discover previously unreported and/or uncharacterized variants. Often these are missense or intronic mutations in which the contribution to disease cannot be predicted, and consequently these mutations are reported as variants of uncertain significance. Follow-up to assess family concordance is recommended by the American College of Medical Genetics to provide genetic evidence for clinical significance. Although family concordance studies show whether a variant segregates with disease in the family, the strength of evidence varies depending on the number and degree of relatedness of family members available for testing. We investigated a statistical model which accounts for the pedigree, inheritance patterns, and penetrance to determine the likelihood of a variant being a causative or deleterious mutation. We used hereditary hemorrhagic telangiectasia (HHT) as a model for an autosomal dominant disease. Pedigree data were transferred to MLINK, and a Bayesian analysis was calculated to determine the likelihood that a variant is causative of disease. In applying this analysis to HHT pedigrees we found Bayes Factors of variants showing odds in favor of causality ranging from approximately 4:1 to over 400:1. These numbers provide an objective measure of the strength of genetic evidence. Other parameters such as amino acid severity predictions, ortholog and paralog comparisons and functional assays can be included in the analysis to increase the evidence of causality.

Hereditary hemorrhagic telangiectasia is a vascular dysplasia with variable onset and expression. Through identification of a mutation in a proband, mutation testing can be offered to family members. Mutation carriers can receive medical surveillance and treatment before potentially fatal complications arise. In this study, we assessed the significance of clinical evaluations as part of hereditary hemorrhagic telangiectasia diagnostic testing to determine the clinical sensitivity of molecular testing and to report novel mutations. Based on reported clinical symptoms, we classified 142 consecutive cases as affected, suspected, or unlikely affected. We performed temperature gradient capillary electrophoresis and full gene sequencing of both ACVRL1 and ENG genes. We then compared the mutation detection rates between these groups, categorizing sequence variants as mutations, variants of uncertain significance (VUS), or known polymorphisms. Our mutation and VUS detection rate in affected individuals was 74% and 16% in the suspected/unlikely affected group. Sixty-one percent of the mutations and all VUS were novel. The mutation detection rate for temperature gradient capillary electrophoresis was 97%. Our results suggest that a careful clinical evaluation increases the mutation detection rate. We have confirmed the occurrence of de novo mutations in three patients. Our results also show that temperature gradient capillary electrophoresis is an efficient mutation screening method.

Hereditary hemorrhagic telangiectasia (HHT) is a genetically heterogeneous vascular dysplasia with multiple telangiectases and arteriovenous malformations and it is caused by mutations in endoglin gene (ENG) (HHT1) and activin A receptor type II-like 1 gene (ACVRL1) (HHT2). We evaluated 111 patients with HHT from 34 families by history, examination, screening for vascular malformations, and sequencing of both genes. We found mutations in 26 of the 34 kindreds (76%) analyzed-54% were in ENG and 46% were in ACVRL1. Mutations in ACVRL1 cluster largely in exons 7 and 8, but ENG mutations were widely distributed within that gene. We found that epistaxis had an earlier onset in patients with HHT1 than those with HHT2, but the severity by middle ages was similar. Pulmonary arteriovenous malformations were more frequent and on the average of larger size in HHT1. Hepatic vascular malformations were more common in patients with HHT2. Cerebral arteriovenous malformations were more common in patients with HHT1, but spinal arteriovenous malformations were seen only in patients with HHT2. Truncating mutations in ENG were associated with more affected organs and more severe hemorrhaging than were missense mutations. We conclude that HHT2 has a later onset than HHT1 and the former may disproportionately involve smaller vessels in tissues with more significant vascular remodeling.

Many inherited diseases involve large genes with many different mutations. Identifying a wide spectrum of mutations requires an efficient gene-scanning method. By differentiating thermodynamic stability and mobility of heteroduplexes from heterozygous samples, temperature gradient capillary electrophoresis (TGCE) was used to scan the entire coding region of the cystic fibrosis transmembrane conductance regulator gene. An initial panel (29 different mutations) showed 100% agreement between TGCE scanning and previously genotyped results for heterozygous samples. Different peak patterns were observed for single base substitutions and base insertions/deletions. Subsequently, 12 deidentified clinical samples genotyped as wild type for 32 mutations were scanned for the entire 27 exons. Results were 100% concordance with the bidirectional sequence analysis. Ten samples had nucleotide variations including a reported base insertion in intron 14b (2789 + 2insA) resulting in a possible mRNA splicing defect, and an unreported missense mutation in exon 20 (3991 G/A) with unknown clinical significance. This methodology does not require labeled primers or probes for detection and separation through a temperature gradient eliminates laborious temperature optimization required for other technologies. TGCE automation and high-throughput capability can be implemented in a clinical environment for mutation scanning with high sensitivity, thus reducing sequencing cost and effort.

Introduction: Cytochrome p450 (CYP) 2C9 and 2C19 metabolize a wide range of therapeutically important drugs. Genetic polymorphisms in the CYP2C9 and CYP2C19 genes result in variations in drug response. To correlate the dose required for therapeutic drug efficacy with genotype, accurate and reliable methods for detecting single nucleotide polymorphisms (SNPs) of CYP2C9 and CYP2C19 are required., Study Design: We evaluated two technologies for genotyping CYP2C9 (*2 and *3 alleles) and CYP2C19 (*2 and *3 alleles). We developed a multiplexed flow cytometric assay based on the Luminex xMAP system and oligonucleotide-tagged Universal Array microspheres. The Luminex assay was compared with the eSensor DNA detection system, provided by Motorola Life Sciences. Genotypes determined by the two methods were confirmed by sequence analysis., Results: Of the 101 whole-genome amplified DNA samples genotyped by the Luminex method, 15 (14.8%) were heterozygous and 1 was homozygous for the CYP2C9*2 polymorphism. For the CYP2C9*3 polymorphism, 13 (12.9%) were heterozygous and 1 was homozygous. Two samples had the CYP2C9*2/*3 genotype. For CYP2C19*2, 17 (16.8%) of the samples were heterozygous and one was homozygous. The CYP2C19*3 polymorphism was not found. Genotypes determined by the Luminex assay were in complete concordance with the eSensor SNP assay results. A dilution study showed that 1.5 ng of nucleic acid was adequate for PCR and subsequent detection of SNPs by the Luminex assay. The within run and between run coefficients of variance (CVs) for allelic ratios determined by the Luminex procedure were found to be